Citrus Sinensis ID: 045690

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220
Protein Sequence
MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
Secondary Structure (PSIPRED)
ccEEcccccHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHEHccccHHHHHHHcccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEc
Coil and Loop (DISEMBL)
mtwimgsvdqslvlnlkpyKTAKDMWEYLKKVynqdntakCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSnlmnrdlspslDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHgkskgrdmrqvqcfsCKEYRHIIVNCAKKFcnyckkpghiikecptrpqncqasqavvas
Flexible Loop (DISEMBL)
mtwimgsvdqslvLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAArsnlmnrdlspSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAhgkskgrdMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGhiikecptrpqNCQASQAVVAS
Low Complexity Region (SEG)
MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
Disordered region (IsUnstruct)
**WIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGV*******************************SLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGK**GRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKEC****************
Disordered Region (DISOPRED)
MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELL***********************************************************NYCKKPGHIIKEC****************
Disordered Region (DISEMBL)
MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAA**********QVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECPTR*************
Disordered Region (DISPRO)
*TWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREEQRLATQ**********************************************KKFCN*CKKPGHIIKECPTRP************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQASQAVVAS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

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	0.968	0.252	0.537	1e-65
359484000	1689	PREDICTED: uncharacterized protein LOC10	0.968	0.126	0.537	1e-64
147793835	1303	hypothetical protein VITISV_031057 [Viti	0.968	0.163	0.534	3e-64
147780419	1308	hypothetical protein VITISV_015686 [Viti	0.968	0.162	0.532	5e-64
147806416	1162	hypothetical protein VITISV_031906 [Viti	0.940	0.178	0.524	8e-64
147866201	1157	hypothetical protein VITISV_037079 [Viti	0.9	0.171	0.518	5e-59
147839099	369	hypothetical protein VITISV_007963 [Viti	0.890	0.531	0.497	8e-58
147770281	1652	hypothetical protein VITISV_021584 [Viti	0.954	0.127	0.506	2e-55
147802545	958	hypothetical protein VITISV_007221 [Viti	0.85	0.195	0.513	3e-55
147846218	2116	hypothetical protein VITISV_033373 [Viti	0.854	0.088	0.483	7e-53

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

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 115/214 (53%), Positives = 152/214 (71%), Gaps = 1/214 (0%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++GSV+  +V +L+P+++A+ MW YLKKVY+QDN A+ F LE+ IA +  G LSIQ+
Sbjct: 66  MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 125

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y S    LW +Y D++   VPI +L+ +Q +H  ++RDQFLMKLRPEY++ RS+L+NR  
Sbjct: 126 YYSAFLTLWHEYADLVTADVPIAALSTIQXIHATTRRDQFLMKLRPEYESVRSSLLNRSP 185

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYA-AAHGKSKGRDMRQVQCFSCKEY 179
            PSLD+CF ELLREEQRL+TQ IL+Q+         A AA G+      + +QCF CKEY
Sbjct: 186 VPSLDICFGELLREEQRLSTQAILEQSHGSSGTTTVAYAAQGRGPPMHSKNLQCFCCKEY 245

Query: 180 RHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
            HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 246 GHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 279

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 =  251 bits (642), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 115/214 (53%), Positives = 152/214 (71%), Gaps = 1/214 (0%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++GSV+  +V +L+P+++A+ MW YLKKVY+QDN A+ F LE+ IA +  G LSIQ+
Sbjct: 66  MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 125

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

Query: 121 SPSLDVCFKELLREEQRLATQTILQQN-KMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEY 179
            PSLD+CF ELLREEQRL+TQ IL+Q+      AI   AA G+      + +QCF CKEY
Sbjct: 186 VPSLDICFGELLREEQRLSTQAILEQSHGSSGTAIVAYAAQGRGPPMHSKNLQCFCCKEY 245

Query: 180 RHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
            HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 246 GHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 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 =  250 bits (639), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 115/215 (53%), Positives = 152/215 (70%), Gaps = 2/215 (0%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++GSV+  +V +L+P+++A+ MW YLKKVY+QDN A+ F LE+ IA +  G LSIQ+
Sbjct: 208 MSWLLGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 267

Query: 61  YLSGIQNLWAKYVDMIYVQVP-IESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRD 119
           Y S    LW +Y D++   VP I +L+ +Q +H  ++RDQFLMKLRPEY++ RS+L+NR 
Sbjct: 268 YYSAFLTLWHEYADLVTADVPIIATLSTIQTIHATTRRDQFLMKLRPEYESVRSSLLNRS 327

Query: 120 LSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYA-AAHGKSKGRDMRQVQCFSCKE 178
             PSLD+CF ELLREEQRL+TQ IL+Q+         A AA G+      + +QCF CKE
Sbjct: 328 PVPSLDICFGELLREEQRLSTQAILEQSHGSSGTTTVAYAAQGRGPPMHSKNLQCFCCKE 387

Query: 179 YRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           Y HI   C KKFC+YCKK GHIIKEC  RPQN QA
Sbjct: 388 YGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQA 422

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 =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 114/214 (53%), Positives = 151/214 (70%), Gaps = 1/214 (0%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++GSV+  +V +L+P+++A+ MW YLKKVY+QDN A+ F LE+ IA +  G LSIQ+
Sbjct: 55  MSWLIGSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQHGSLSIQD 114

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y S    LW +Y D++   VPI +L+ +Q +H  ++RDQFLMKL PEY++ RS+L+NR  
Sbjct: 115 YYSAFLTLWHEYADLVTTDVPIAALSTIQTIHVTTRRDQFLMKLCPEYESVRSSLLNRSP 174

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

Query: 180 RHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 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 =  248 bits (634), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 109/208 (52%), Positives = 153/208 (73%), Gaps = 1/208 (0%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           ++W++GS+   +V NL+ + TAK+MWEYL+++YNQDN A CF LE EIA ++QG+LSI+ 
Sbjct: 36  VSWLLGSIKPHMVNNLRSFSTAKEMWEYLRRIYNQDNNACCFQLELEIAYFTQGNLSIEQ 95

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

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEYR 180
            P+LD+C  ELLREEQRLATQ  + Q ++H   +  A A  + +GR+  Q+QC+SCKE+ 
Sbjct: 156 VPTLDICLGELLREEQRLATQAEMGQERLHSEIVNVAYA-TQGRGREKGQIQCYSCKEFG 214

Query: 181 HIIVNCAKKFCNYCKKPGHIIKECPTRP 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 =  233 bits (593), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 112/216 (51%), Positives = 139/216 (64%), Gaps = 18/216 (8%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           MTWI+ SV+   VLNL+PYKT   MW YL  VYNQDN+A+ F LEYE+A ++QG LSI+ 
Sbjct: 73  MTWILSSVEPHFVLNLRPYKTVATMWNYLHTVYNQDNSARRFQLEYEMANFTQGSLSIEE 132

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y SG Q LW  Y D++Y  VP  +L+ VQ VH  SKRDQFLMKLRP+++ ARSNLMNR L
Sbjct: 133 YFSGFQTLWIDYSDIVYANVPAAALSVVQAVHATSKRDQFLMKLRPDFEIARSNLMNRHL 192

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

Query: 179 YRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQAS 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 (583), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 106/213 (49%), Positives = 141/213 (66%), Gaps = 17/213 (7%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++ SV+  +V +L+P+++A+ MW YLKKVY+QDN A+ F LE+ I  +  G LSIQ+
Sbjct: 1   MSWLLSSVEPHIVTHLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIVMFQHGSLSIQD 60

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y S     W +Y D++   VPI++L+ +Q +H  + RDQFLMKLRPEY++ RS+L+NR  
Sbjct: 61  YYSAFLTFWHEYADLVTADVPIDALSTIQTIHATTLRDQFLMKLRPEYESVRSSLLNRSH 120

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQCFSCKEYR 180
            PSLD+CF ELLREEQ L+TQ I++Q            +HG S         CF  KEY 
Sbjct: 121 VPSLDICFGELLREEQHLSTQAIMEQ------------SHGSSG-----TATCFCYKEYE 163

Query: 181 HIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 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 =  221 bits (563), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 110/217 (50%), Positives = 151/217 (69%), Gaps = 7/217 (3%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           M+W++GSV+  +V +L+P+ +A+ MW YLKKVY+QDN A+ F L++ IA +  G LSIQ+
Sbjct: 160 MSWLLGSVEPHIVTHLRPHCSAQSMWAYLKKVYHQDNDARRFQLDHAIAMFQHGSLSIQD 219

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y S    LW +Y D++   VPI +L+ +Q +H  ++RDQFLMKLR +Y++  S+L+N+  
Sbjct: 220 YYSTFLTLWHEYADLVTADVPIAALSTIQTIHTTTQRDQFLMKLRSKYESVCSSLLNKSH 279

Query: 121 SPSLDVCFKELLREEQRLATQTILQQNKMHDN----AIAYAAAHGKSKGRDMRQVQCFSC 176
            PSLD+ F ELLR+EQRL+TQ IL+Q+  H N     +AY AA G+      + +QCF C
Sbjct: 280 VPSLDIFFGELLRKEQRLSTQAILEQS--HGNYGTTTVAY-AAQGRGPRMHSKNLQCFCC 336

Query: 177 KEYRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQA 213
           KEY HI   C KKFC+YCKK GHIIKEC  RPQN Q 
Sbjct: 337 KEYGHIAATCPKKFCSYCKKKGHIIKECRIRPQNRQT 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 =  220 bits (561), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 111/216 (51%), Positives = 137/216 (63%), Gaps = 29/216 (13%)

Query: 1   MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
           MTWI+ SV+  LVLN +PYKT   MW YL  VYNQDN+A+ F LE E A ++QG LSI+ 
Sbjct: 63  MTWILSSVEPHLVLNQRPYKTVAVMWNYLHTVYNQDNSARRFQLECEKANFTQGSLSIEE 122

Query: 61  YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
           Y   +                          H  SKRDQFLMKLRP+++ ARSN+MNR  
Sbjct: 123 YFFAM--------------------------HATSKRDQFLMKLRPDFEIARSNMMNRHH 156

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

Query: 179 YRHIIVNCAKKFCNYCKKPGHIIKECPTRPQNCQAS 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 =  212 bits (540), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 102/211 (48%), Positives = 135/211 (63%), Gaps = 23/211 (10%)

Query: 1    MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
            M+W++GSV   +V  L+P+++A+ MW YLKKVY+QDN A+ F LE+ IA +         
Sbjct: 885  MSWLLGSVKPHIVTYLRPHRSAQSMWAYLKKVYHQDNDARRFQLEHAIAMFQH------- 937

Query: 61   YLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDL 120
                           +   VPI +L+ +Q +H  ++RDQFLMKLR EY++ RS+L+NR  
Sbjct: 938  ---------------VTADVPIAALSTIQTIHATTRRDQFLMKLRSEYESVRSSLLNRSH 982

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

Query: 180  RHIIVNCAKKFCNYCKKPGHIIKECPTRPQN 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	0.260	4.2e-06
DICTYBASE|DDB_G0293328	131	DDB_G0293328 "Cellular nucleic	0.195	0.328	0.367	6.1e-05
UNIPROTKB|P69730	486	gag "Gag polyprotein" [Equine	0.677	0.306	0.25	0.00068

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

 Score = 125 (49.1 bits), Expect = 4.2e-06, P = 4.2e-06
 Identities = 36/138 (26%), Positives = 63/138 (45%)

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

Query:    61 YLSGIQNLWAKYVDMIYVQVP--------IESLADVQGVHEQSKRDQFLM--KLRPEYKA 110
             Y   +  +W +  +  Y  +P         E     +   E+ +R +FLM  KL   ++A
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

DICTYBASE|DDB_G0293328 DDB_G0293328 "Cellular nucleic acid-binding protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 99 (39.9 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query:   167 DMRQVQCFSCKEYRHIIVNCAK------KFCNYCKKPGHIIKECPTRPQ 209
             ++++  C+ CKE  HI  NC K      + C  C   GH+ +ECP  PQ
Sbjct:     3 EIKEKSCYKCKEVGHISRNCPKNPEAGDRACYVCNVVGHLSRECPQNPQ 51

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 112 (44.5 bits), Expect = 0.00068, P = 0.00068
 Identities = 40/160 (25%), Positives = 70/160 (43%)

Query:    54 GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARS 113
             G    QN   G +  + ++VD +  Q  I+S    Q + +       +     E + A  
Sbjct:   270 GKPKAQNIRQGAKEPYPEFVDRLLSQ--IKSEGHPQEISKFLTDTLTIQNANEECRNAMR 327

Query:   114 NLMNRD-LSPSLDVCFKELLREEQRLATQTILQQNKMHDNAIAYAAAHGKSKGRDMRQVQ 172
             +L   D L   +  C +++   +Q++    +L   K     +A     G  KG  ++  Q
Sbjct:   328 HLRPEDTLEEKMYAC-RDIGTTKQKMM---LLA--KALQTGLAGPFKGGALKGGPLKAAQ 381

Query:   173 -CFSCKEYRHIIVNC-AKKFCNYCKKPGHIIKECPTRPQN 210
              C++C +  H+   C A K C  CK+PGH  K+C + P+N
Sbjct:   382 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKN 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   0.132   0.402    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:  3
  No. of states in DFA:  615 (65 KB)
  Total size of DFA:  205 KB (2115 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:  22.52u 0.11s 22.63t   Elapsed:  00:00:01
  Total cpu time:  22.52u 0.11s 22.63t   Elapsed:  00:00:01
  Start:  Fri May 10 00:27:06 2013   End:  Fri May 10 00:27:07 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	1e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	2e-04
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	0.002

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

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 21/49 (42%), Positives = 35/49 (71%)

Query: 21  TAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLW 69
           TAK++W+ LK+ ++  NT++ F L+ EIAR  QG LS+  Y + +++LW
Sbjct: 69  TAKEVWDALKERFSDGNTSRVFELKREIARLKQGGLSVTEYYNKLKSLW 117

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 = 21/49 (42%), Gaps = 7/49 (14%)

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

Length = 148

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

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 2/46 (4%)

Query: 168 MRQVQCFSCKEYRHIIVNCAKKFCNYCKKPGHIIKECPTRPQ--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	99.84
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	99.8
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	99.43
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.69
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	98.52
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.12
PF13696	32	zf-CCHC_2: Zinc knuckle	97.93
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.66
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	97.36
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	97.33
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.3
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	97.02
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.98
smart00343	26	ZnF_C2HC zinc finger.	96.92
PF13917	42	zf-CCHC_3: Zinc knuckle	96.88
PF15288	40	zf-CCHC_6: Zinc knuckle	96.59
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	96.33
PF14392	49	zf-CCHC_4: Zinc knuckle	96.08
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.31
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	95.22
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	93.62
PF14893	331	PNMA: PNMA	92.71
PF02023	95	SCAN: SCAN domain; InterPro: IPR003309 A number of	90.75
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	85.69
KOG0314	448	consensus Predicted E3 ubiquitin ligase [Posttrans	85.67
TIGR03823	168	FliZ flagellar regulatory protein FliZ. FliZ is in	82.55
PRK11582	169	flagella biosynthesis protein FliZ; Provisional	82.38
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	81.62

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

Probab=99.84  E-value=5.2e-20  Score=129.27  Aligned_cols=109  Identities=25%  Similarity=0.407  Sum_probs=99.2

Q ss_pred             ccHHHHHHHHHHHhccCCc---hhHhhHHHHHHHhh-cCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHH
Q 045690           20 KTAKDMWEYLKKVYNQDNT---AKCFHLEYEIARYS-QGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQS   95 (220)
Q Consensus        20 ~ta~~~W~~L~~~f~~~~~---~~~~~l~~~~~~~~-~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~   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            5899999999999999988   99999999999998 58999999999999999999977 776655           66


Q ss_pred             HHHHHHhhcchhHHHHHHhhhcCCCCC--CHHHHHHHHHHHHHHHHH
Q 045690           96 KRDQFLMKLRPEYKAARSNLMNRDLSP--SLDVCFKELLREEQRLAT  140 (220)
Q Consensus        96 ~~~~~l~gLp~~~~~~~~~~~~~~~~~--t~~e~~~~l~~~e~r~~~  140 (220)
                      .+.++|+|||++|+.++..+....+.+  |++++++.|..+|.+...
T Consensus        69 ~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~  115 (119)
T PF14223_consen   69 LVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKS  115 (119)
T ss_pred             HHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence            677799999999999999999987777  999999999999988774

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

Probab=99.80  E-value=1e-18  Score=122.71  Aligned_cols=110  Identities=25%  Similarity=0.317  Sum_probs=93.3

Q ss_pred             CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHH
Q 045690           19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKR   97 (220)
Q Consensus        19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~   97 (220)
                      ++||+++|+.|+..|...+.+....+.+.|...+. ++.+|.+|+.+|..++++|.++ |..+++           +.++
T Consensus         1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~-g~~i~d-----------~~~~   68 (119)
T PF14227_consen    1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSL-GVPIDD-----------EDKV   68 (119)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccc-cccchH-----------HHHH
Confidence            57999999999999997776666666666666655 6899999999999999999977 887766           4555


Q ss_pred             HHHHhhcchhHHHHHHhhhcCC--CCCCHHHHHHHHHHHHHHHHH
Q 045690           98 DQFLMKLRPEYKAARSNLMNRD--LSPSLDVCFKELLREEQRLAT  140 (220)
Q Consensus        98 ~~~l~gLp~~~~~~~~~~~~~~--~~~t~~e~~~~l~~~e~r~~~  140 (220)
                      ..+|.+||++|++|+.++....  ..++++++...|..+|.++..
T Consensus        69 ~~lL~sLP~sy~~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~  113 (119)
T PF14227_consen   69 IILLSSLPPSYDSFVTALLYSKPEDELTLEEVKSKLLQEEERRKK  113 (119)
T ss_pred             HHHHHcCCHhHHHHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHh
Confidence            5599999999999999988865  889999999999999987764

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

Probab=99.43  E-value=1.7e-13  Score=100.21  Aligned_cols=75  Identities=25%  Similarity=0.660  Sum_probs=70.6

Q ss_pred             CceecccccHHHHhccCCCccHHHHHHHHHHHhccCC-chhHhhHHHHHHHhhcCCCcHHHHHHHHHHHH--HHHhcc
Q 045690            1 MTWIMGSVDQSLVLNLKPYKTAKDMWEYLKKVYNQDN-TAKCFHLEYEIARYSQGDLSIQNYLSGIQNLW--AKYVDM   75 (220)
Q Consensus         1 ~~~i~~sl~~~~~~~i~~~~ta~~~W~~L~~~f~~~~-~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~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            4799999999999999999999999999999999777 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=98.69  E-value=9.1e-09  Score=46.61  Aligned_cols=17  Identities=47%  Similarity=1.239  Sum_probs=16.0

Q ss_pred             cccccccccccccCCCC
Q 045690          190 FCNYCKKPGHIIKECPT  206 (220)
Q Consensus       190 ~C~~C~k~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            69999999999999995

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=98.52  E-value=2.7e-07  Score=61.65  Aligned_cols=71  Identities=20%  Similarity=0.372  Sum_probs=58.8

Q ss_pred             CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHH
Q 045690           19 YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRD   98 (220)
Q Consensus        19 ~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~   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            4578888888888888643  46688899999999999999999999999998872      12         6688888


Q ss_pred             HHHhhcch
Q 045690           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=98.12  E-value=1.9e-06  Score=63.67  Aligned_cols=42  Identities=29%  Similarity=0.824  Sum_probs=34.2

Q ss_pred             CCCCCccccccCCCccccccccC-------------------ccccccccccccccCC-CCC
Q 045690          166 RDMRQVQCFSCKEYRHIIVNCAK-------------------KFCNYCKKPGHIIKEC-PTR  207 (220)
Q Consensus       166 ~~~~~~~~~~~~~~g~~~~~~~~-------------------~~C~~C~k~GH~~~~C-~~~  207 (220)
                      .....+.|+.|+..||.+++|+.                   .+|+.||..||++++| |.+
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             ccccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCccc
Confidence            34455679999999999999981                   1899999999999999 443

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.93  E-value=3.9e-06  Score=43.38  Aligned_cols=21  Identities=38%  Similarity=0.942  Sum_probs=18.3

Q ss_pred             CccccccccccccccCCCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~~~  208 (220)
                      .-.|+.|++.||++++||...
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~~   28 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTNK   28 (32)
T ss_pred             CCEeecCCCCCccHhHCCCCC
Confidence            347999999999999999843

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

Probab=97.66  E-value=2.6e-05  Score=56.66  Aligned_cols=37  Identities=32%  Similarity=0.916  Sum_probs=25.6

Q ss_pred             ccccccCCCccccccccCc--------cccccccccccccCCCCC
Q 045690          171 VQCFSCKEYRHIIVNCAKK--------FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~~--------~C~~C~k~GH~~~~C~~~  207 (220)
                      ..|+.|+..||.+..|+..        .||.|+..||++++||..
T Consensus        78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~  122 (148)
T PTZ00368         78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA  122 (148)
T ss_pred             cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence            3577777777777766552        477777777777777764

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

Probab=97.36  E-value=0.00013  Score=58.16  Aligned_cols=42  Identities=33%  Similarity=0.790  Sum_probs=37.4

Q ss_pred             ccccccCCCcccccccc---CccccccccccccccCCCCCCCCCc
Q 045690          171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQNCQ  212 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~---~~~C~~C~k~GH~~~~C~~~~~~~~  212 (220)
                      ..||+|+..||....|+   ...||.|++.||..++||.......
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~~  188 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSKS  188 (261)
T ss_pred             CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccccc
Confidence            35999999999999999   7899999999999999998876543

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

Probab=97.33  E-value=0.00069  Score=48.90  Aligned_cols=95  Identities=15%  Similarity=0.187  Sum_probs=67.5

Q ss_pred             eecccccHHHHhccCC----CccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc----CCCcHHHHHHHHHHHHHHHhc
Q 045690            3 WIMGSVDQSLVLNLKP----YKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ----GDLSIQNYLSGIQNLWAKYVD   74 (220)
Q Consensus         3 ~i~~sl~~~~~~~i~~----~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~----~~~sv~ey~~~~~~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 YLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPR-RIIQALLEELRNLPPISNDDPEALRSLVDKVNNCIRALKA  111 (145)
T ss_pred             HHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCch-HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555544    4678999999999999654 134566666666653    468899999999999999997


Q ss_pred             ccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHH
Q 045690           75 MIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKA  110 (220)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~  110 (220)
                      + |..+.+           ...+..|+..||++...
T Consensus       112 l-g~~~~~-----------~~l~~~i~~KLp~~~~~  135 (145)
T PF03564_consen  112 L-GVNVDD-----------PLLISIILSKLPPEIRE  135 (145)
T ss_pred             c-CCCCCC-----------HHHHHHHHHHCCHHHHH
Confidence            6 665433           44555699999988443

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

Probab=97.30  E-value=0.00023  Score=51.63  Aligned_cols=37  Identities=35%  Similarity=0.977  Sum_probs=24.4

Q ss_pred             cccccCCCccccccccCc-------cccccccccccccCCCCCC
Q 045690          172 QCFSCKEYRHIIVNCAKK-------FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~~-------~C~~C~k~GH~~~~C~~~~  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            466666667666666554       4777777777777776644

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

Probab=97.02  E-value=0.00041  Score=36.62  Aligned_cols=21  Identities=29%  Similarity=0.608  Sum_probs=14.0

Q ss_pred             cccccccccccccCCCCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~~~  210 (220)
                      -|+.|++-.||+++|+.+...
T Consensus         4 ~CprC~kg~Hwa~~C~sk~d~   24 (36)
T PF14787_consen    4 LCPRCGKGFHWASECRSKTDV   24 (36)
T ss_dssp             C-TTTSSSCS-TTT---TCCC
T ss_pred             cCcccCCCcchhhhhhhhhcc
Confidence            599999999999999988754

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

Probab=96.98  E-value=0.0022  Score=54.04  Aligned_cols=47  Identities=26%  Similarity=0.542  Sum_probs=39.4

Q ss_pred             CCCCCCCCCCccccccCCCccccccccCc------cccccccccccccCCCCC
Q 045690          161 GKSKGRDMRQVQCFSCKEYRHIIVNCAKK------FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~------~C~~C~k~GH~~~~C~~~  207 (220)
                      ..+..+......|..|+..||++-.|+..      .|++|+-.||+..+|+..
T Consensus       252 lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  252 LNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             hCCCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence            34444444556799999999999999877      899999999999999987

>smart00343 ZnF_C2HC zinc finger

Probab=96.92  E-value=0.00036  Score=34.68  Aligned_cols=18  Identities=44%  Similarity=1.084  Sum_probs=16.0

Q ss_pred             cccccccccccccCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~  207 (220)
                      .|+.|++.||++++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999844

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.88  E-value=0.00064  Score=37.73  Aligned_cols=19  Identities=37%  Similarity=0.885  Sum_probs=17.0

Q ss_pred             CccccccccccccccCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~  206 (220)
                      ...|.+|+..|||..+||.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            3569999999999999995

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=96.59  E-value=0.002  Score=35.12  Aligned_cols=22  Identities=32%  Similarity=0.609  Sum_probs=18.9

Q ss_pred             ccccccccccccc--cCCCCCCCC
Q 045690          189 KFCNYCKKPGHII--KECPTRPQN  210 (220)
Q Consensus       189 ~~C~~C~k~GH~~--~~C~~~~~~  210 (220)
                      .+|..||..||+.  +.||.+.+.
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~~~   25 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYCWS   25 (40)
T ss_pred             ccccccccccccccCccCCCCCCC
Confidence            4699999999999  789998754

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

Probab=96.33  E-value=0.0022  Score=47.64  Aligned_cols=38  Identities=29%  Similarity=0.736  Sum_probs=31.9

Q ss_pred             ccccccCCCcccccccc-Cc----cccccccccccccCCCCCC
Q 045690          171 VQCFSCKEYRHIIVNCA-KK----FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~-~~----~C~~C~k~GH~~~~C~~~~  208 (220)
                      ..|+.|+..||.+..|. .+    .|+.|+..+|++++||...
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~~  140 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIW  140 (190)
T ss_pred             cccccccccCccccccCcccccCcceeccCCCccccccCcccc
Confidence            57999999999999993 32    7999999999999998644

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=96.08  E-value=0.002  Score=37.36  Aligned_cols=18  Identities=50%  Similarity=1.099  Sum_probs=16.5

Q ss_pred             ccccccccccccccCCCC
Q 045690          189 KFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~  206 (220)
                      ..|++||..||..++||+
T Consensus        32 ~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   32 RFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhhcCCCCcCcCHhHcCC
Confidence            379999999999999985

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

Probab=95.40  E-value=0.0095  Score=47.19  Aligned_cols=24  Identities=33%  Similarity=0.718  Sum_probs=19.9

Q ss_pred             cccCccccccccccccccCCCCCC
Q 045690          185 NCAKKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       185 ~~~~~~C~~C~k~GH~~~~C~~~~  208 (220)
                      .-+.-.||.||..|||..+||...
T Consensus       173 pPpgY~CyRCGqkgHwIqnCpTN~  196 (427)
T COG5222         173 PPPGYVCYRCGQKGHWIQNCPTNQ  196 (427)
T ss_pred             CCCceeEEecCCCCchhhcCCCCC
Confidence            334458999999999999999765

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

Probab=95.31  E-value=0.0065  Score=47.99  Aligned_cols=19  Identities=47%  Similarity=0.875  Sum_probs=17.3

Q ss_pred             cccccccccccccCCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~  208 (220)
                      .|+.||+.|||.++||...
T Consensus       162 ~cyrcGkeghwskEcP~~~  180 (346)
T KOG0109|consen  162 GCYRCGKEGHWSKECPVDR  180 (346)
T ss_pred             HheeccccccccccCCccC
Confidence            7999999999999999753

>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=95.22  E-value=0.016  Score=25.98  Aligned_cols=17  Identities=47%  Similarity=1.081  Sum_probs=15.2

Q ss_pred             cccccCCCccccccccC
Q 045690          172 QCFSCKEYRHIIVNCAK  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            59999999999999874

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 ....

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

Probab=93.62  E-value=0.054  Score=43.13  Aligned_cols=43  Identities=30%  Similarity=0.738  Sum_probs=35.2

Q ss_pred             CCccccccCCCcccccccc--CccccccccccccccCCCCCCCCC
Q 045690          169 RQVQCFSCKEYRHIIVNCA--KKFCNYCKKPGHIIKECPTRPQNC  211 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~--~~~C~~C~k~GH~~~~C~~~~~~~  211 (220)
                      ....|+.|+..|+....|.  ...|+.|+..||++++||......
T Consensus        71 ~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~  115 (261)
T KOG4400|consen   71 PEVSCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEG  115 (261)
T ss_pred             CCceeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcc
Confidence            3446889999998888777  459999999999999999876544

>PF14893 PNMA: PNMA

Probab=92.71  E-value=2  Score=35.45  Aligned_cols=54  Identities=24%  Similarity=0.303  Sum_probs=44.8

Q ss_pred             CCccHHHHHHHHHHHhccCCchhHhhHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHh
Q 045690           18 PYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYV   73 (220)
Q Consensus        18 ~~~ta~~~W~~L~~~f~~~~~~~~~~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~   73 (220)
                      .-.|+.+..+.|+..|....  ....++..|.++.| .+|+|.+|+.++..+..+.-
T Consensus       228 P~~t~~~~l~aL~~~Fg~~e--s~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav  282 (331)
T PF14893_consen  228 PKQTAQDCLKALGQVFGSSE--SRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAV  282 (331)
T ss_pred             CCCCHHHHHHHHHHhcCCcc--cHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHH
Confidence            45689999999999999543  25677888877766 69999999999999999964

>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=90.75  E-value=3.5  Score=27.40  Aligned_cols=79  Identities=14%  Similarity=0.114  Sum_probs=50.5

Q ss_pred             HHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHHHHHhhhcCCCCC
Q 045690           44 LEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSP  122 (220)
Q Consensus        44 l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~~~~~~~~~~~~~  122 (220)
                      .++.|..... ++++..+++.++..|+.+=-.  +...+.      .++-|-..+++||..||++....+.    ....-
T Consensus         5 ~r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~--pe~~tk------eqi~ellvlEQFL~~lP~e~~~wV~----e~~p~   72 (95)
T PF02023_consen    5 YRQRFRSFQYQEGEGPREFLSRLRELCDRWLQ--PEVHTK------EQILELLVLEQFLNILPPEVQTWVR----ERKPE   72 (95)
T ss_dssp             HHHHHHT--CCTTTSHHHHHHHHHHHHHHHH---TTTS-H------HHHHHHHHHHHHHHHS-HHHHHHHH----TCS-S
T ss_pred             HHHHHhCCCCCCCCCHHHHHHHHHHHHHHhCc--cccCcH------HHHHHHHHHHHHHHHCCHHHHHHHH----hcCCC
Confidence            4667777765 599999999999999866531  211121      2236677788999999999777654    23344


Q ss_pred             CHHHHHHHHHHH
Q 045690          123 SLDVCFKELLRE  134 (220)
Q Consensus       123 t~~e~~~~l~~~  134 (220)
                      +.+++...+...
T Consensus        73 s~~ea~~Lae~~   84 (95)
T PF02023_consen   73 SAEEAVALAEDY   84 (95)
T ss_dssp             SHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            677777665544

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.

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

Probab=85.69  E-value=0.36  Score=40.35  Aligned_cols=27  Identities=33%  Similarity=0.707  Sum_probs=22.0

Q ss_pred             CccccccccccccccCCCCCCCCCccc
Q 045690          188 KKFCNYCKKPGHIIKECPTRPQNCQAS  214 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~~~~~~~~~  214 (220)
                      .+.|.|||..||-..+||+....++..
T Consensus       570 ~kGCayCgGLGHRItdCPKle~~~~k~  596 (610)
T KOG0341|consen  570 EKGCAYCGGLGHRITDCPKLEAQQNKQ  596 (610)
T ss_pred             ccccccccCCCcccccCchhhhhcchh
Confidence            347999999999999999987654443

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

Probab=85.67  E-value=0.9  Score=38.75  Aligned_cols=38  Identities=37%  Similarity=0.830  Sum_probs=29.4

Q ss_pred             cccccCCCccccccccCc-------cccccccccccccCCCCCCC
Q 045690          172 QCFSCKEYRHIIVNCAKK-------FCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~~-------~C~~C~k~GH~~~~C~~~~~  209 (220)
                      .|-.|...+|+...+...       .|+.|+..|||.+.||.-..
T Consensus       135 ~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~~  179 (448)
T KOG0314|consen  135 VCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVSG  179 (448)
T ss_pred             eeeecccCccccccccccCCCCCCcceecCCCCCccceeccccCC
Confidence            466677777777655433       99999999999999987553

>TIGR03823 FliZ flagellar regulatory protein FliZ

Probab=82.55  E-value=6.4  Score=28.48  Aligned_cols=57  Identities=14%  Similarity=0.176  Sum_probs=37.0

Q ss_pred             HhhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchh-HHHHHHhh
Q 045690           50 RYSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPE-YKAARSNL  115 (220)
Q Consensus        50 ~~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~-~~~~~~~~  115 (220)
                      .......||.||+-+++.|=.-|.   ...+|.+.+      .+...-..+...||.. +.+.+.++
T Consensus        99 QTeMshStvrEYVVRLRRLd~lL~---~~n~p~~~~------~~~~~~~~~~~~Lp~~~~nNyriAL  156 (168)
T TIGR03823        99 QTEMSHSTVREYVVRLRRLDELLV---AQNYPAEQF------QDGFLQERLADWLPSTATNNYRIAL  156 (168)
T ss_pred             hhccccccHHHHHHHHHHHHHHHh---hccCCHHHh------ccchHHHHHHhhCchhhhhHHHHHH
Confidence            334456799999999999987776   345555333      4445556678888865 55554443

FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex.

>PRK11582 flagella biosynthesis protein FliZ; Provisional

Probab=82.38  E-value=7.2  Score=28.25  Aligned_cols=56  Identities=13%  Similarity=0.176  Sum_probs=36.6

Q ss_pred             hhcCCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchh-HHHHHHhh
Q 045690           51 YSQGDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPE-YKAARSNL  115 (220)
Q Consensus        51 ~~~~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~-~~~~~~~~  115 (220)
                      ......||.||+-+++.|=.-|.   ...+|.+.+      .+...-..+...||.. +.+.+.++
T Consensus       100 TeMshSTvrEYVVRLRRLd~lL~---~~n~p~~~~------~~~~~~~~~~~~Lp~~~~nNyriAL  156 (169)
T PRK11582        100 TEMSHSTVREYVVRLRRLDEHLH---EQNIPLDLL------QDGFLDERLAPWLPDTSTNNYRIAL  156 (169)
T ss_pred             cccccccHHHHHHHHHHHHHHHh---hccCCHHHh------cchhHHHHHHhhcchhhhhHHHHHH
Confidence            34456799999999999987776   345565333      4444555678888865 55554443

>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=81.62  E-value=0.75  Score=32.41  Aligned_cols=22  Identities=32%  Similarity=0.680  Sum_probs=17.8

Q ss_pred             ccCccccccccccccccCCCCCC
Q 045690          186 CAKKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       186 ~~~~~C~~C~k~GH~~~~C~~~~  208 (220)
                      .....|..|+ -.||...||.+-
T Consensus       104 ~~~v~CR~Ck-GdH~T~~CPyKd  125 (128)
T PF12353_consen  104 KSKVKCRICK-GDHWTSKCPYKD  125 (128)
T ss_pred             CceEEeCCCC-CCcccccCCccc
Confidence            3445899996 789999999863

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.

---

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	3e-08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	3e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	1e-05
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	2e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	7e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-04
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	2e-04
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	3e-04
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	4e-04
3gv2_A	342	Ca, fusion protein consisting of capsid protein P2	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 = 26/58 (44%), Gaps = 4/58 (6%)

Query: 162 KSKGRDMRQVQCFSCKEYRHIIVNC----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 = 48.0 bits (114), Expect = 3e-08
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 161 GKSKGRDMRQVQCFSCKEYRHIIVNC----AKKFCNYCKKPGHIIKECPTRPQNCQASQ 215
           G S     R   C++C    H    C      K C++C+   H++  CP + Q   ++Q
Sbjct: 1   GSSGSSGDR---CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQ 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 = 44.6 bits (105), Expect = 3e-06
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 163 SKGRDMRQVQCFSCKEYRHIIVNCAK----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 = 40.6 bits (95), Expect = 1e-05
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 8/46 (17%)

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

>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 = 39.5 bits (92), Expect = 2e-05
 Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

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

>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 = 38.8 bits (90), Expect = 7e-05
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 11/49 (22%)

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

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

 Score = 39.8 bits (92), Expect = 1e-04
 Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 170 QVQCFSCKEYRHIIVNCAKKFCNYC-KKPGHIIKECPTR 207
             +C +C +  H+  +C    C+YC     H  + CP  
Sbjct: 4   APKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKA 42

>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 Length = 55

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 169 RQVQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
           + V+CF+C +  HI  NC    KK C  C K GH +K+C  R  N
Sbjct: 11  KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 55

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

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

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

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

 Score = 36.1 bits (83), Expect = 4e-04
 Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

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

>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 = 8e-04
 Identities = 4/48 (8%), Positives = 11/48 (22%), Gaps = 1/48 (2%)

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

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	99.02
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	98.92
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	98.91
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	98.9
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	98.89
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.88
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	98.88
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	98.88
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.81
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.64
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	98.55
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.53
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.48
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.44
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.09
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	98.02
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	97.87
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.62
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.55
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.48
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.42
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.39
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.06
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.01
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.83
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.77
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.25
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	95.16
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	94.76
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	94.49
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	93.33
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	91.81
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	90.79
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	85.71

>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=99.02  E-value=2.5e-10  Score=65.78  Aligned_cols=41  Identities=29%  Similarity=0.799  Sum_probs=36.3

Q ss_pred             CCccccccCCCccccccccCc---cccccccccccccCCCCCCC
Q 045690          169 RQVQCFSCKEYRHIIVNCAKK---FCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~~---~C~~C~k~GH~~~~C~~~~~  209 (220)
                      ....||.|+..||.++.|+.+   .||.|++.||++++||.++.
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~   48 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA   48 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCCSSCC
T ss_pred             CcCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCcCCCC
Confidence            345799999999999999874   79999999999999998764

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

Probab=98.92  E-value=6.6e-10  Score=60.07  Aligned_cols=35  Identities=37%  Similarity=0.993  Sum_probs=32.3

Q ss_pred             cccccCCCccccccccC-ccccccccccccccCCCC
Q 045690          172 QCFSCKEYRHIIVNCAK-KFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~-~~C~~C~k~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 489999999999999985

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

Probab=98.91  E-value=8e-10  Score=66.76  Aligned_cols=41  Identities=34%  Similarity=0.754  Sum_probs=35.3

Q ss_pred             CccccccCCCccccccccCc--------cccccccccccccCCCCCCCC
Q 045690          170 QVQCFSCKEYRHIIVNCAKK--------FCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~~--------~C~~C~k~GH~~~~C~~~~~~  210 (220)
                      ...||.|+..||.++.|+..        .||.|++.||++++||.++..
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~   52 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGN   52 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC--
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCCcC
Confidence            34699999999999999873        699999999999999998754

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

Probab=98.90  E-value=8.6e-10  Score=60.36  Aligned_cols=35  Identities=29%  Similarity=0.728  Sum_probs=32.3

Q ss_pred             cccccCCCccccccccC---ccccccccccccccCCCC
Q 045690          172 QCFSCKEYRHIIVNCAK---KFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~---~~C~~C~k~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

>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=98.89  E-value=9.3e-10  Score=65.13  Aligned_cols=40  Identities=43%  Similarity=0.881  Sum_probs=35.7

Q ss_pred             CccccccCCCccccccccC---ccccccccccccccCCCCCCC
Q 045690          170 QVQCFSCKEYRHIIVNCAK---KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~---~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      ...||.|+..||.++.|+.   ..||.|++.||++++||.++.
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~   54 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA   54 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCSSSCC
T ss_pred             CcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCcCcCC
Confidence            4579999999999999976   489999999999999998754

>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=98.88  E-value=1.4e-09  Score=77.59  Aligned_cols=45  Identities=24%  Similarity=0.724  Sum_probs=37.3

Q ss_pred             CCccccccCCCccccccccC----ccccccccccccccCCCCCCCCCcc
Q 045690          169 RQVQCFSCKEYRHIIVNCAK----KFCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~----~~C~~C~k~GH~~~~C~~~~~~~~~  213 (220)
                      +...||+|+..||.++.|+.    ..||.|++.||++++||.+.+....
T Consensus        96 ~~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~~~~~  144 (148)
T 3ts2_A           96 GGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQGPS  144 (148)
T ss_dssp             CSCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC----
T ss_pred             CCCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCCCCCc
Confidence            34579999999999999987    5899999999999999998765433

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

Probab=98.88  E-value=1.7e-09  Score=67.71  Aligned_cols=41  Identities=27%  Similarity=0.827  Sum_probs=36.3

Q ss_pred             CCccccccCCCccccccccC----ccccccccccccccCCCCCCC
Q 045690          169 RQVQCFSCKEYRHIIVNCAK----KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~----~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      ....||.|+..||.+++|+.    ..||.|++.||++++||.+..
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~   67 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ   67 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTTGGG
T ss_pred             CCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcCCcC
Confidence            44579999999999999984    589999999999999998764

>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=98.88  E-value=1.8e-09  Score=65.57  Aligned_cols=40  Identities=28%  Similarity=0.838  Sum_probs=35.5

Q ss_pred             CccccccCCCcccccccc----CccccccccccccccCCCCCCC
Q 045690          170 QVQCFSCKEYRHIIVNCA----KKFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~----~~~C~~C~k~GH~~~~C~~~~~  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            356999999999999998    4589999999999999998754

>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=98.81  E-value=1.8e-09  Score=65.05  Aligned_cols=38  Identities=32%  Similarity=0.840  Sum_probs=19.0

Q ss_pred             cccccCCCccccccccC-----------ccccccccccccccCCCCCCC
Q 045690          172 QCFSCKEYRHIIVNCAK-----------KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       172 ~~~~~~~~g~~~~~~~~-----------~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      .||.|+..||.+++|+.           ..||.|++.||++++||.+..
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             --------------------------CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             ccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCccc
Confidence            59999999999998865           479999999999999998864

>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=98.64  E-value=1.9e-08  Score=54.65  Aligned_cols=27  Identities=37%  Similarity=0.997  Sum_probs=22.0

Q ss_pred             cCccccccccccccccCCCCCCCCCcc
Q 045690          187 AKKFCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       187 ~~~~C~~C~k~GH~~~~C~~~~~~~~~  213 (220)
                      ....||+||+.|||+++||.+......
T Consensus         9 ~~~~C~~Cgk~GH~ardCP~~~~~~r~   35 (40)
T 1a6b_B            9 DRDQCAYCKEKGHWAKDCPKKPRGPRG   35 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSCCCTTC
T ss_pred             CCCeeeECCCCCcchhhCcCCcccCCC
Confidence            345799999999999999998765443

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

Probab=98.55  E-value=5.3e-08  Score=62.12  Aligned_cols=37  Identities=14%  Similarity=0.329  Sum_probs=21.0

Q ss_pred             ccccCCCccccccccC----ccccccccccccccCCCCCCC
Q 045690          173 CFSCKEYRHIIVNCAK----KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       173 ~~~~~~~g~~~~~~~~----~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      |+.|+..||.++.|..    ..||+||+.||+.++||....
T Consensus        27 cY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           27 AYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CCCBC-------------CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             ccccccCCcccccccCCCCCCeecccCCCCcCcccCCcccc
Confidence            4445555544443322    379999999999999998764

>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=98.53  E-value=5.1e-08  Score=57.06  Aligned_cols=27  Identities=37%  Similarity=0.972  Sum_probs=22.0

Q ss_pred             ccCccccccccccccccCCCCCCCCCc
Q 045690          186 CAKKFCNYCKKPGHIIKECPTRPQNCQ  212 (220)
Q Consensus       186 ~~~~~C~~C~k~GH~~~~C~~~~~~~~  212 (220)
                      .....||+||+.|||+++||.+.....
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~~~~~   47 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKPRGPR   47 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCCCSSC
T ss_pred             CCCCcceeCCCCCcccccCcCCccccC
Confidence            344589999999999999999876543

>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=98.44  E-value=1.1e-07  Score=48.09  Aligned_cols=21  Identities=29%  Similarity=0.629  Sum_probs=18.3

Q ss_pred             ccccccccccccccCCCCCCC
Q 045690          189 KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      ..||+|++.||++++||...+
T Consensus         7 ~~C~nCgk~GH~ar~C~~prk   27 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSSSS
T ss_pred             CEEEECCccccCHhHCccccc
Confidence            579999999999999987643

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

Probab=98.09  E-value=9.6e-07  Score=51.42  Aligned_cols=20  Identities=55%  Similarity=1.070  Sum_probs=17.4

Q ss_pred             CccccccccccccccCCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~~  207 (220)
                      ...||.||+.|||+++||..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            34799999999999999954

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

Probab=98.02  E-value=2.5e-06  Score=59.05  Aligned_cols=36  Identities=31%  Similarity=0.762  Sum_probs=23.0

Q ss_pred             cccccCCC-ccccccccCc-cccccccccccccCCCCC
Q 045690          172 QCFSCKEY-RHIIVNCAKK-FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       172 ~~~~~~~~-g~~~~~~~~~-~C~~C~k~GH~~~~C~~~  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 6666666553 566666677777777654

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

Probab=97.87  E-value=8.8e-06  Score=56.28  Aligned_cols=38  Identities=32%  Similarity=0.709  Sum_probs=34.4

Q ss_pred             ccccccCCCccccccccC----ccccccccccccccCCCCCC
Q 045690          171 VQCFSCKEYRHIIVNCAK----KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~----~~C~~C~k~GH~~~~C~~~~  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            479999999999999987    48999999999999999864

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

Probab=97.62  E-value=1.6e-05  Score=49.49  Aligned_cols=21  Identities=29%  Similarity=0.479  Sum_probs=18.0

Q ss_pred             cCccccccccccccccCCCCC
Q 045690          187 AKKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       187 ~~~~C~~C~k~GH~~~~C~~~  207 (220)
                      +...||+|++.||++++|+..
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSC
T ss_pred             CCCcccccCCcCcCcccCCCC
Confidence            335799999999999999963

>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=97.55  E-value=3.8e-05  Score=44.98  Aligned_cols=24  Identities=33%  Similarity=0.574  Sum_probs=19.8

Q ss_pred             ccccCccccccccccccccCCCCC
Q 045690          184 VNCAKKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       184 ~~~~~~~C~~C~k~GH~~~~C~~~  207 (220)
                      ...+...||.|++.||++++||..
T Consensus         8 g~~~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A            8 NQRKTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GGGGTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCCCCcceeeeCCCCcChhhcCCC
Confidence            334456899999999999999875

>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=97.48  E-value=5.2e-05  Score=43.22  Aligned_cols=20  Identities=30%  Similarity=0.622  Sum_probs=18.0

Q ss_pred             CccccccccccccccCCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~~  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            45799999999999999985

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

Probab=97.42  E-value=5e-05  Score=41.05  Aligned_cols=18  Identities=39%  Similarity=0.881  Sum_probs=16.7

Q ss_pred             cccccccccccccCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~  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

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

Probab=97.39  E-value=5.8e-05  Score=40.29  Aligned_cols=18  Identities=39%  Similarity=0.988  Sum_probs=16.6

Q ss_pred             cccccccccccccCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~  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            599999999999999974

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

Probab=97.06  E-value=0.0002  Score=42.74  Aligned_cols=21  Identities=33%  Similarity=0.967  Sum_probs=18.4

Q ss_pred             ccccccccccccccCCCCCCC
Q 045690          189 KFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~~~~  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=97.01  E-value=0.0001  Score=43.89  Aligned_cols=19  Identities=37%  Similarity=0.782  Sum_probs=0.0

Q ss_pred             cccccccccccccCCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~  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=96.83  E-value=0.00036  Score=41.93  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=17.2

Q ss_pred             ccccccccccccccCCCCC
Q 045690          189 KFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~~  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            5799999999999999964

>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=96.77  E-value=0.00076  Score=47.83  Aligned_cols=21  Identities=33%  Similarity=0.605  Sum_probs=18.3

Q ss_pred             CccccccccccccccCCCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       188 ~~~C~~C~k~GH~~~~C~~~~  208 (220)
                      ...||+|++.||++++||..+
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~  117 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPP  117 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCC
T ss_pred             CCcccEeCCccchhhhCCCCC
Confidence            457999999999999999743

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

Probab=96.25  E-value=0.0011  Score=42.09  Aligned_cols=38  Identities=21%  Similarity=0.232  Sum_probs=22.9

Q ss_pred             CccccccCCCccccccccCc-cccccccccccccCCCCC
Q 045690          170 QVQCFSCKEYRHIIVNCAKK-FCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~~-~C~~C~k~GH~~~~C~~~  207 (220)
                      ...|+.|+..||.++.|+.. .||.|+..||++++|+..
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p   43 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLP   43 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGGTCCCCBC------------
T ss_pred             cCCCCCCCCCCCccccCCCcccccccccCCcccccccCC
Confidence            45799999999999999987 899999999999999754

>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=95.16  E-value=0.014  Score=31.30  Aligned_cols=24  Identities=38%  Similarity=0.682  Sum_probs=19.9

Q ss_pred             CCCCCccccccCCCccccccccCc
Q 045690          166 RDMRQVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       166 ~~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      .......||.|+..||++++|+.+
T Consensus         6 ~~~~~~~C~~Cgk~GH~ardCP~~   29 (40)
T 1a6b_B            6 SQLDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred             CCCCCCeeeECCCCCcchhhCcCC
Confidence            444566899999999999999875

>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=94.76  E-value=0.015  Score=28.01  Aligned_cols=19  Identities=37%  Similarity=0.837  Sum_probs=16.7

Q ss_pred             ccccccCCCccccccccCc
Q 045690          171 VQCFSCKEYRHIIVNCAKK  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            4699999999999998764

>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=94.49  E-value=0.027  Score=32.61  Aligned_cols=24  Identities=38%  Similarity=0.682  Sum_probs=19.7

Q ss_pred             CCCCCccccccCCCccccccccCc
Q 045690          166 RDMRQVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       166 ~~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      .......||.|+..||++++|+.+
T Consensus        19 ~~~~~~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           19 SQLDRDQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             TTCCTTBCSSSCCBSSCGGGCTTC
T ss_pred             CCCCCCcceeCCCCCcccccCcCC
Confidence            344456799999999999999875

>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=93.33  E-value=0.061  Score=26.54  Aligned_cols=20  Identities=20%  Similarity=0.650  Sum_probs=17.0

Q ss_pred             CccccccCCCccccccccCc
Q 045690          170 QVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~~  189 (220)
                      ...||.|+..||.+++|+.+
T Consensus         6 ~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             CCEEEECCccccCHhHCccc
Confidence            45799999999999988754

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

Probab=91.81  E-value=0.051  Score=25.72  Aligned_cols=19  Identities=26%  Similarity=0.842  Sum_probs=16.0

Q ss_pred             CccccccccccccccCCCC
Q 045690          188 KKFCNYCKKPGHIIKECPT  206 (220)
Q Consensus       188 ~~~C~~C~k~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            3469999999999999965

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

Probab=90.79  E-value=0.15  Score=29.36  Aligned_cols=20  Identities=35%  Similarity=0.796  Sum_probs=17.1

Q ss_pred             CccccccCCCccccccccCc
Q 045690          170 QVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~~  189 (220)
                      ...||+|++.||+.+.|+..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            44799999999999999843

---

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	4e-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 = 43.3 bits (102), Expect = 4e-07
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 3/40 (7%)

Query: 171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTR 207
           V+CF+C +  H   NC    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 = 32.7 bits (74), 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	99.2
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.72
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	98.5
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	98.23
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.75
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	96.39
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	96.37
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	95.37
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	94.68
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	85.63
d2fi2a1	92	Zinc finger protein 42 {Human (Homo sapiens) [TaxI	82.49

>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=99.20  E-value=4.7e-12  Score=68.85  Aligned_cols=38  Identities=39%  Similarity=0.853  Sum_probs=34.9

Q ss_pred             ccccccCCCccccccccCc---cccccccccccccCCCCCC
Q 045690          171 VQCFSCKEYRHIIVNCAKK---FCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       171 ~~~~~~~~~g~~~~~~~~~---~C~~C~k~GH~~~~C~~~~  208 (220)
                      ..||+|+..||.+.+|+.+   .||.||+.||++++||.++
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCCCSSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCcCcCcccCcCCCcCccccCCCCCeecccCCCCC
Confidence            4699999999999999875   7999999999999999874

>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=98.72  E-value=3.3e-09  Score=49.95  Aligned_cols=23  Identities=26%  Similarity=0.544  Sum_probs=19.3

Q ss_pred             cCccccccccccccccCCCCCCC
Q 045690          187 AKKFCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       187 ~~~~C~~C~k~GH~~~~C~~~~~  209 (220)
                      ...+||+||+.||++++|+...+
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSSS
T ss_pred             ceeEeecCCccchhhhhccCccc
Confidence            34589999999999999987654

>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=98.50  E-value=2.8e-08  Score=50.42  Aligned_cols=24  Identities=42%  Similarity=1.081  Sum_probs=20.8

Q ss_pred             cccccccccccccCCCCCCCCCcc
Q 045690          190 FCNYCKKPGHIIKECPTRPQNCQA  213 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~~~~~~  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            699999999999999998865444

>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=98.23  E-value=2.1e-07  Score=41.71  Aligned_cols=19  Identities=37%  Similarity=0.891  Sum_probs=16.9

Q ss_pred             ccccccccccccccCCCCC
Q 045690          189 KFCNYCKKPGHIIKECPTR  207 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~~  207 (220)
                      +.||-||+.||+.++|...
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            5699999999999999764

>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=97.75  E-value=6.3e-06  Score=43.98  Aligned_cols=20  Identities=30%  Similarity=0.655  Sum_probs=17.8

Q ss_pred             ccccccccccccccCCCCCC
Q 045690          189 KFCNYCKKPGHIIKECPTRP  208 (220)
Q Consensus       189 ~~C~~C~k~GH~~~~C~~~~  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=96.39  E-value=0.00069  Score=32.56  Aligned_cols=21  Identities=33%  Similarity=0.844  Sum_probs=18.4

Q ss_pred             cccccccccccccCCCCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTRPQN  210 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~~~  210 (220)
                      .|..|++--||+++|+++...
T Consensus         4 lCPrC~kG~HWa~~Crsk~~~   24 (32)
T d1cl4a_           4 LCPRCKRGKHWANECKSKTDN   24 (32)
T ss_dssp             SCSSCSSCSSCSTTCCCTTSS
T ss_pred             cCccccCcchHHHHhhhhhcc
Confidence            599999999999999988653

>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=96.37  E-value=0.00072  Score=32.31  Aligned_cols=20  Identities=35%  Similarity=0.685  Sum_probs=17.9

Q ss_pred             cccccccccccccCCCCCCC
Q 045690          190 FCNYCKKPGHIIKECPTRPQ  209 (220)
Q Consensus       190 ~C~~C~k~GH~~~~C~~~~~  209 (220)
                      .|..|++--||+++|+++..
T Consensus         4 lCPrC~kG~HWa~~Crsk~~   23 (31)
T d1dsva_           4 LCPRCKKGYHWKSECKSKFD   23 (31)
T ss_dssp             BCTTTCSSBSCTTTCCCSEE
T ss_pred             cCccccCcchHHHHhhhhhc
Confidence            59999999999999998754

>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=95.37  E-value=0.006  Score=28.21  Aligned_cols=21  Identities=19%  Similarity=0.662  Sum_probs=17.6

Q ss_pred             CCccccccCCCccccccccCc
Q 045690          169 RQVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       169 ~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      ....||.|++.||.++.|..+
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSS
T ss_pred             ceeEeecCCccchhhhhccCc
Confidence            456899999999999988654

>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=94.68  E-value=0.0083  Score=26.40  Aligned_cols=19  Identities=37%  Similarity=0.798  Sum_probs=16.1

Q ss_pred             CccccccCCCccccccccC
Q 045690          170 QVQCFSCKEYRHIIVNCAK  188 (220)
Q Consensus       170 ~~~~~~~~~~g~~~~~~~~  188 (220)
                      ++-||+|++.||.+++|..
T Consensus         2 gpvcfscgktghikkdck~   20 (26)
T d1dsqa_           2 GPVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTTC
T ss_pred             CCEEEecCCcccchhhhhh
Confidence            3469999999999998864

>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=85.63  E-value=0.33  Score=23.96  Aligned_cols=23  Identities=39%  Similarity=0.715  Sum_probs=18.8

Q ss_pred             CCCCccccccCCCccccccccCc
Q 045690          167 DMRQVQCFSCKEYRHIIVNCAKK  189 (220)
Q Consensus       167 ~~~~~~~~~~~~~g~~~~~~~~~  189 (220)
                      .-..-+|--|...||++++|+++
T Consensus         7 ~L~kDQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_           7 QLDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSSS
T ss_pred             cccchhhHHHhhcCchhhhCccC
Confidence            33455899999999999999865

>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=82.49  E-value=3.4  Score=24.78  Aligned_cols=78  Identities=15%  Similarity=0.086  Sum_probs=52.1

Q ss_pred             hHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHhcccccCCCcccHHHHHHHHHHHHHHHHHhhcchhHHHHHHhhhcCCCC
Q 045690           43 HLEYEIARYSQ-GDLSIQNYLSGIQNLWAKYVDMIYVQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLS  121 (220)
Q Consensus        43 ~l~~~~~~~~~-~~~sv~ey~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~gLp~~~~~~~~~~~~~~~~  121 (220)
                      ..+..|..... ++.+..+++.++..|+..=-.  +...+.      .++.|-..+++||+.||++....+.    ....
T Consensus         6 ~~rq~FR~f~y~e~~~p~e~l~rL~eLc~~WL~--pe~~tk------eqilelLVLEQFl~~lP~e~~~~V~----e~~p   73 (92)
T d2fi2a1           6 AARLRFRCFHYEEATGPQEALAQLRELCRQWLR--PEVRSK------EQMLELLVLEQFLGALPPEIQARVQ----GQRP   73 (92)
T ss_dssp             HHHHHHHSCCCCTTTCHHHHHHHHHHHHHHHHC--TTTCCH------HHHHHHHHHHHHHHHSCHHHHHHHH----HHCC
T ss_pred             HHHHHHhcCCCcccCCHHHHHHHHHHHHHHHcC--CcccCH------HHHHHHHHHHHHHHHCCHHHHHHHH----HhCC
Confidence            45666777755 699999999999999877641  221121      2336677778899999999666543    2334


Q ss_pred             CCHHHHHHHHH
Q 045690          122 PSLDVCFKELL  132 (220)
Q Consensus       122 ~t~~e~~~~l~  132 (220)
                      -+.++++..+.
T Consensus        74 ~s~~eav~L~E   84 (92)
T d2fi2a1          74 GSPEEAAALVD   84 (92)
T ss_dssp             CSHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            56677765544