Citrus Sinensis ID: 045687

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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--
Protein Sequence
MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKANIVKNEAHPSKNQKPNKKFFKNKKTTFKKKKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccEEEEEEEEEccEEccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHEEEHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEccccccccccccccccccccccEEEEEccEEEEEEEEEEEEcccccccccc
Coil and Loop (DISEMBL)
mnlaefltepppdsdseNYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDagaqnfkmaedkevtsQIHGFHMLINDlkneniilpesfmTIDQLEKAKEITSkanivkneahpsknqkpnkkffknkkttfkkkkgncyvcgkpghfankcryrkgdhkppkanlvdgeDIIVAVVVTQENMVAAKGKKNG
Flexible Loop (DISEMBL)
mnlaefltepppdsdseNYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKanivkneahpsknqkpnkkffknkkttfkkkkgncyvcgkpghfANKCRYRKGDhkppkanlvdgeDIIVAVVVTQEnmvaakgkkng
Low Complexity Region (SEG)
MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKANIVKNEAHPSknqkpnkkffknkkttfkkkkGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG
Disordered region (IsUnstruct)
******************YEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQL************************************FKKKKGNCYVCGKPGHFANKCRYRKG*****KANLVDGEDIIVAVVVTQE***********
Disordered Region (DISOPRED)
*NLAEFLTEP**********VLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFH******************************************************************CYVCGKPGHFAN*********************IIVAVVVTQENMV*AK*****
Disordered Region (DISEMBL)
***************SENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKANIVKNEAHPSKNQKPNKKFFKNKKTTFKKKKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG
Disordered Region (DISPRO)
MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSK******************************KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVA*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKANIVKNEAHPSKNQKPNKKFFKNKKTTFKKKKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG
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	212
38194910	1290	gag-pol polyprotein [Phaseolus vulgaris]	0.943	0.155	0.380	1e-32
147781792	1096	hypothetical protein VITISV_036207 [Viti	0.636	0.123	0.391	6e-25
147838590	1046	hypothetical protein VITISV_025642 [Viti	0.867	0.175	0.346	4e-24
147805294	565	hypothetical protein VITISV_006704 [Viti	0.603	0.226	0.457	2e-23
147800584	1209	hypothetical protein VITISV_002698 [Viti	0.820	0.143	0.348	6e-20
147767180	1234	hypothetical protein VITISV_013138 [Viti	0.825	0.141	0.298	1e-18
147804859	1473	hypothetical protein VITISV_021427 [Viti	0.825	0.118	0.298	2e-18
147857754	804	hypothetical protein VITISV_032507 [Viti	0.825	0.217	0.298	5e-18
359493505	1182	PREDICTED: wall-associated receptor kina	0.825	0.148	0.306	6e-18
147782562	791	hypothetical protein VITISV_025981 [Viti	0.811	0.217	0.306	6e-18

>gi|38194910|gb|AAR13298.1| gag-pol polyprotein [Phaseolus vulgaris]

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 100/263 (38%), Positives = 139/263 (52%), Gaps = 63/263 (23%)

Query: 2   NLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQ 61
            +A  LT   PDS +   +V   +WI ANKVCR T+LS LSN+L+DVY+ +K A +IW  
Sbjct: 59  GVAHALTTAKPDSTTAAKQV--DDWIHANKVCRHTLLSVLSNDLFDVYASYKNAKDIWDS 116

Query: 62  LRKKYIIEDAGAQNF--------KMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTID 113
           L  KY  ED   Q F        +M + K++  QI+ +H LI D+K E+I LP+ F++  
Sbjct: 117 LILKYTAEDIVRQRFVIAKYYRWEMIKGKDIKIQINEYHKLIEDIKTESIKLPDEFVSEL 176

Query: 114 QLEKAKE---------------------IT---------------------SKANIVKNE 131
            +EK  +                     IT                     +KAN+++++
Sbjct: 177 LIEKLPQSWTDYKQQLKHRQKQMSLSDLITHIIIEDTNRKECAAAKAKALSAKANVIEDK 236

Query: 132 AHPSK-------NQKPNKKFFKNKKT--TFKKKKGNCYVCGKPGHFANKCRYRKGDHKPP 182
             P +        +KPN KF +   T  TF KKKGNC+VCGKPGH A +CR+R  +  PP
Sbjct: 237 PAPKRYEKKFDHKKKPNNKFSRPSGTNPTF-KKKGNCFVCGKPGHHAPQCRHRAKNDYPP 295

Query: 183 KANLVDGEDIIVAVVVTQENMVA 205
           KANL +GED IVA VV+Q N+V 
Sbjct: 296 KANLAEGEDTIVA-VVSQVNLVT 317

Source: Phaseolus vulgaris

Species: Phaseolus vulgaris

Genus: Phaseolus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147781792|emb|CAN72171.1| hypothetical protein VITISV_036207 [Vitis vinifera]

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 74/189 (39%), Positives = 95/189 (50%), Gaps = 54/189 (28%)

Query: 1   MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWA 60
           +NL   L +P P   S     LL  W   NK  R  I STLSNEL+D+Y Q K A EIW 
Sbjct: 37  VNLGHILIDPKPKDGSH----LLPTWETGNKQVRHAIPSTLSNELFDIYCQFKVAKEIWD 92

Query: 61  QLRKKYIIEDAGA--------QNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMT- 111
            + KKYI+EDAG         +NF+M EDK+V+SQIH +H+LINDL  E+I LPE FM  
Sbjct: 93  AMNKKYILEDAGTHKYVIGNFRNFQMTEDKDVSSQIHDYHLLINDLAIEDIKLPEPFMVG 152

Query: 112 -----------------------------------------IDQLEKAKEITSKANIVKN 130
                                                     D +EKAKE++SKAN+V+ 
Sbjct: 153 YLVETLPESWKDYKNNMKHKMKQMSLEDVIIHIRIEEQNRNRDNIEKAKELSSKANVVEE 212

Query: 131 EAHPSKNQK 139
           ++ P  N+K
Sbjct: 213 KSKPKNNRK 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147838590|emb|CAN76580.1| hypothetical protein VITISV_025642 [Vitis vinifera]

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 88/254 (34%), Positives = 117/254 (46%), Gaps = 70/254 (27%)

Query: 3   LAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQL 62
           L   LT+P  +  S     LL  W   NK  R  ILSTLS E++D+Y      Y I    
Sbjct: 39  LGHILTDPKLEDGSH----LLPTWETRNKQVRHAILSTLSXEIFDIYYVXTQKYAI---- 90

Query: 63  RKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTI---------- 112
                      +NF+M ED++V+SQIH +H+LINDL  E+I LP  FM            
Sbjct: 91  --------XNFRNFQMMEDRDVSSQIHDYHLLINDLAIEDIKLPGPFMASYLVETLLKSW 142

Query: 113 --------------------------------DQLEKAKEITSKANIVKNEAHPSKNQKP 140
                                           D +EKAKE++SKAN+V+ +  P KN + 
Sbjct: 143 KDXXXNMKHKRKQMSLEDVIIHIRIEEQNRNRDNVEKAKELSSKANVVEEKPKP-KNNRS 201

Query: 141 NKKFFKNK-------KTTFKKKKGNCYVCGKPGHFANKCRYRKGDHKP-PKANLVDGEDI 192
            K+ F+ K       + +  KK+GNC+VCGK  H A +CR+RK   K   KANLV  E I
Sbjct: 202 RKQNFRTKPNASNKVQQSTIKKRGNCFVCGKSRHHAAQCRHRKRTEKSNSKANLVXAEVI 261

Query: 193 IVAV---VVTQENM 203
              +   V T  NM
Sbjct: 262 TKVISFEVSTVTNM 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147805294|emb|CAN78262.1| hypothetical protein VITISV_006704 [Vitis vinifera]

 Score =  115 bits (287), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 65/142 (45%), Positives = 84/142 (59%), Gaps = 14/142 (9%)

Query: 1   MNLAEFLTEPPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWA 60
           +NL   LT+P P   S     LL  W   NK  R  ILSTLSNEL+D+Y Q K A EIW 
Sbjct: 37  VNLEHILTDPKPKDGSH----LLPTWETGNKQVRHAILSTLSNELFDIYCQFKVAKEIWD 92

Query: 61  QLRKKYIIEDAGAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFMTI 112
            + KKYI+EDA  Q        NF+M ED++V+SQIH +H+LINDL  E+I LPE F+  
Sbjct: 93  AMNKKYILEDAETQKYAIGNFRNFQMIEDRDVSSQIHDYHLLINDLAIEDIKLPEPFVVA 152

Query: 113 D--QLEKAKEITSKANIVKNEA 132
                ++ K+  SK N+ + E 
Sbjct: 153 QCRHKKRTKKTNSKENLAETEV 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147800584|emb|CAN72993.1| hypothetical protein VITISV_002698 [Vitis vinifera]

 Score =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 68/195 (34%), Positives = 95/195 (48%), Gaps = 21/195 (10%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+      EIW  L  KY  E+ G +        +FK   +K 
Sbjct: 19  ICRGHILNALSDRLYDLYTNTYSXREIWEALENKYKXEEEGTKKFLISQYIDFKFFXEKP 78

Query: 84  VTSQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITSKANIVKNEAHPSKNQKPNKK 143
              QIH   +++N LK   I   E+F     + K    + KAN V    HP      BK+
Sbjct: 79  XLPQIHELQVIVNKLKVLKIEXXEAFQVGAIVAKLPS-SWKANAVSKANHPRGKNNNBKR 137

Query: 144 ----FFKNKKTT--FKKKKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVV 197
               +   KK    FK KKG C+VCGKPGH+A +CRYRK D K    N +D E     ++
Sbjct: 138 NSGNYMSPKKNXEQFKGKKGXCFVCGKPGHYARECRYRK-DLKGAVVNAIDEE-----II 191

Query: 198 VTQENMVAAKGKKNG 212
            T  ++   +GK  G
Sbjct: 192 ATLSDVCVVQGKVQG 206

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147767180|emb|CAN66959.1| hypothetical protein VITISV_013138 [Vitis vinifera]

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 106/238 (44%), Gaps = 63/238 (26%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+    A EIW  L  KY  E+ G +        +FK  ++K 
Sbjct: 75  ICRGHILNALSDRLYDLYTNTNSAREIWEALENKYKAEEEGTKKFLISQYIDFKFFDEKP 134

Query: 84  VTSQIHGFHMLINDLKNENIILPESFM--------------------------TIDQLEK 117
           +  QIH   +++N LK   I LPE+F                           ++++++K
Sbjct: 135 LLPQIHELQVIVNKLKVLKIELPEAFQVGAIVAKLPSSWKGYRKRILHKSEDYSLEEIQK 194

Query: 118 AKEI-----------------TSKANIVKNEAHP------SKNQKPNKKFFKNKKTTFKK 154
              I                 T+KAN +    HP      +K    N    K  +  FK 
Sbjct: 195 HLRIEEESRSRDKMVEESNGGTNKANAISKANHPRGKNNNNKKNSGNYMSPKKNQEQFKG 254

Query: 155 KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG 212
           KKG C+VCGKPGH+A +CR+RK D K    N +D E     ++ T  ++   +GK  G
Sbjct: 255 KKGXCFVCGKPGHYARECRFRK-DQKGAVVNAIDEE-----IIATLSDVCVVQGKVQG 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147804859|emb|CAN66873.1| hypothetical protein VITISV_021427 [Vitis vinifera]

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 106/238 (44%), Gaps = 63/238 (26%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+    A EIW  L  KY  E+ G +        +FK  ++K 
Sbjct: 75  ICRGHILNALSDRLYDLYTNTXSAREIWEALENKYKAEEEGTKKFLISQYIDFKFFDEKP 134

Query: 84  VTSQIHGFHMLINDLKNENIILPESFM--------------------------TIDQLEK 117
           +  QIH   +++N LK   I LPE+F                           ++++++K
Sbjct: 135 LLPQIHELQVIVNKLKVLKIELPEAFQVGAIVAKLPSSWKGYRKRILHKSEDYSLEEIQK 194

Query: 118 AKEI-----------------TSKANIVKNEAHP------SKNQKPNKKFFKNKKTTFKK 154
              I                 T+KAN +    HP      +K    N    K  +  FK 
Sbjct: 195 HLRIEEESRSRDKMVEESNGGTNKANAISKANHPRGKNNNNKKNSGNYMSPKKNQEQFKG 254

Query: 155 KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG 212
           KKG C+VCGKPGH+A +CR+RK D K    N +D E     ++ T  ++   +GK  G
Sbjct: 255 KKGPCFVCGKPGHYARECRFRK-DQKGAVVNAIDEE-----IIATLSDVCVVQGKVQG 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147857754|emb|CAN78666.1| hypothetical protein VITISV_032507 [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 106/238 (44%), Gaps = 63/238 (26%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+    A EIW  L  KY  E+ G +        +FK  ++K 
Sbjct: 75  ICRGHILNALSDRLYDLYTNTNSAREIWEALENKYKAEEEGTKKFLISQYIDFKFFDEKP 134

Query: 84  VTSQIHGFHMLINDLKNENIILPESFM--------------------------TIDQLEK 117
           +  QIH   +++N LK   I LPE+F                           ++++++K
Sbjct: 135 LLPQIHELQVIVNKLKVLKIELPEAFQVGAIVAKLPSSWKGYRKRILHKSEDYSLEEIQK 194

Query: 118 AKEI-----------------TSKANIVKNEAHP------SKNQKPNKKFFKNKKTTFKK 154
              I                 T+KAN +    HP      +K    N    K  +  FK 
Sbjct: 195 HLRIKEESRSRDKMVEESNGGTNKANAISKANHPRGKNNNNKKNSGNYMSPKKNQEQFKG 254

Query: 155 KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG 212
           KKG C+VCGKPGH+A +CR+RK D K    N +D E     ++ T  ++   +GK  G
Sbjct: 255 KKGPCFVCGKPGHYARECRFRK-DQKGVVVNAIDEE-----IIATLSDVCVVQGKVQG 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493505|ref|XP_002263348.2| PREDICTED: wall-associated receptor kinase 2-like [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 107/238 (44%), Gaps = 63/238 (26%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+    A EIW  L  KY  E+ G +        +FK  ++K 
Sbjct: 67  ICRGHILNALSDRLYDLYTNTYSAREIWEALENKYKAEEEGTKKFLISQYIDFKFFDEKP 126

Query: 84  VTSQIHGFHMLINDLKNENIILPESFM--------------------------TIDQLEK 117
           +  QIH   +++N LK   I LPE+F                           ++++++K
Sbjct: 127 LLPQIHELQVIVNKLKVLKIELPEAFQVGAIVAKLPSSWKGYRKRILHKSEDYSLEEIQK 186

Query: 118 AKEI-----------------TSKANIVKNEAHP---SKNQKPNKKFF---KNKKTTFKK 154
              I                 T+KAN V    HP   + N K N   +   K  +  FK 
Sbjct: 187 HLRIEEELRSRDKMAEESNGGTNKANAVSKANHPRGKNNNDKRNSGNYMSPKKNQEQFKG 246

Query: 155 KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGKKNG 212
           KKG C+VCGK GH+A +CRYRK D K    N +D E     ++ T  ++   +GK  G
Sbjct: 247 KKGPCFVCGKLGHYARECRYRK-DLKGVVVNAIDEE-----IIATLSDVCVVQGKVQG 298

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782562|emb|CAN68340.1| hypothetical protein VITISV_025981 [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 105/235 (44%), Gaps = 63/235 (26%)

Query: 32  VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKE 83
           +CR  IL+ LS+ LYD+Y+    A EIW  L  KY  E+ G +        +FK  ++K 
Sbjct: 75  ICRGHILNALSDRLYDLYTNTNSAREIWEALENKYKAEEEGTKRFLISQYIDFKFVDEKP 134

Query: 84  VTSQIHGFHMLINDLKNENIILPESFM--------------------------TIDQLEK 117
           +  QIH   +++N LK   I LPE+F                           ++++++K
Sbjct: 135 LLPQIHKLQVIVNKLKVLKIELPEAFQVGAIVVKLPSSWKGYRKRILHKSEDYSLEEIQK 194

Query: 118 AKEI-----------------TSKANIVKNEAHPSKNQKPNKKFF------KNKKTTFKK 154
              I                 T+KAN V    HP      NKK        K  +  FK 
Sbjct: 195 HLRIEEESRSRDKMVEESNGGTNKANAVSKANHPKGKNNNNKKNSGNYMSPKKNQEQFKG 254

Query: 155 KKGNCYVCGKPGHFANKCRYRKGDHKPPKANLVDGEDIIVAVVVTQENMVAAKGK 209
           KKG C+VCGKPGH+A +CRYRK + K    N +D E     ++ T  ++   +GK
Sbjct: 255 KKGLCFVCGKPGHYARECRYRK-NQKGAVVNAIDEE-----IIATLSDVCVVQGK 303

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	212
TAIR|locus:2134618	488	AT4G00980 [Arabidopsis thalian	0.405	0.176	0.242	6.7e-06

TAIR|locus:2134618 AT4G00980 [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 6.7e-06, Sum P(2) = 6.7e-06
 Identities = 23/95 (24%), Positives = 54/95 (56%)

Query:    24 QNWIKANKVCRSTILSTLSNELYDVYSQH-KFAYEIWAQLRKKYIIEDAGAQN------- 75
             + W++ + +C + ++++LS+ LY  YSQ  K A E+W +L+  Y  +++ ++        
Sbjct:   251 KKWLRDDYLCYTHLMNSLSDHLYRRYSQKFKHAKELWDELKWVYQCDESKSKRSQVRKYI 310

Query:    76 -FKMAEDKEVTSQIHGFHMLINDLKNENIILPESF 109
              F+M E++ +  Q+  F+ + + + +  + L E+F
Sbjct:   311 EFRMVEERPILEQVQVFNKIADSIVSAGMFLDEAF 345

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

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	212
pfam14227	115	pfam14227, UBN2_2, gag-polypeptide of LTR copia-ty	1e-05
smart00343	17	smart00343, ZnF_C2HC, zinc finger	7e-04
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	0.001

>gnl|CDD|222609 pfam14227, UBN2_2, gag-polypeptide of LTR copia-type

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 52  HKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENI 103
            K A E+W +L K Y+ +    +          KM+E K V   +  F+ L+N+L++  +
Sbjct: 1   EKTAKELWDKLEKLYMTKSLTNKLYLKKKLYTLKMSEGKSVEEHLDEFNKLVNELESLGV 60

Query: 104 ILPESF 109
            + +  
Sbjct: 61  KIDDED 66

This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type. Length = 115

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 35.5 bits (83), Expect = 7e-04
 Identities = 9/15 (60%), Positives = 9/15 (60%)

Query: 159 CYVCGKPGHFANKCR 173
           CY CGK GH A  C 
Sbjct: 2   CYNCGKEGHIARDCP 16

Length = 17

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 34.7 bits (81), Expect = 0.001
 Identities = 9/15 (60%), Positives = 9/15 (60%)

Query: 159 CYVCGKPGHFANKCR 173
           CY CGK GH A  C 
Sbjct: 3   CYNCGKEGHLARDCP 17

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	212
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	99.57
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	98.97
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	98.92
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.67
PF13696	32	zf-CCHC_2: Zinc knuckle	97.88
smart00343	26	ZnF_C2HC zinc finger.	96.95
PF13917	42	zf-CCHC_3: Zinc knuckle	96.87
PF15288	40	zf-CCHC_6: Zinc knuckle	96.6
PF14392	49	zf-CCHC_4: Zinc knuckle	96.49
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.43
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.81
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.55
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.29
PTZ00368	148	universal minicircle sequence binding protein (UMS	95.26
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.53
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	92.73
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.72
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	91.46
KOG2560	529	consensus RNA splicing factor - Slu7p [RNA process	87.95
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	85.78
KOG2044	931	consensus 5'-3' exonuclease HKE1/RAT1 [Replication	84.03
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	83.61
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	83.54
KOG0119	554	consensus Splicing factor 1/branch point binding p	83.5
COG5179	968	TAF1 Transcription initiation factor TFIID, subuni	81.57

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

Probab=99.57  E-value=7.2e-15  Score=111.03  Aligned_cols=95  Identities=19%  Similarity=0.348  Sum_probs=77.2

Q ss_pred             cccccc-CCCCCCCcchHHHHHHHHHHHHHHHHHHHhhccHHHHHhhcccccHHHHHHHHHHHHhhcccccccc------
Q 045687            4 AEFLTE-PPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNF------   76 (212)
Q Consensus         4 ~~vl~e-~~P~~~~~~~~~~~~~W~~~d~~a~~~I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~~~~~~~~~~------   76 (212)
                      +||.++ ++|.+.++    +++.|.+.|.++++||+++|+++++..|..++||+++|++|+++|+..++..+.+      
T Consensus        36 ~~i~g~~~~P~~~~~----~~~~W~~~d~~v~swl~~sis~~i~~~i~~~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l  111 (152)
T PF14244_consen   36 GFIDGTIPKPPETDP----AYEKWERKDQLVLSWLLNSISPDILSTIIFCETAKEIWDALKERFSQKSNASRVFQLRNEL  111 (152)
T ss_pred             ccccCccccccccch----hhhhHHHhhhHHHHHHHHhhcHHHHhhhHhhhhHHHHHHHHHHHhhcccHHHHHHHHHHHH
Confidence            344443 45544444    7999999999999999999999999999999999999999999999777455521      


Q ss_pred             --eecCCccHHHHHHHHHHHH--HHHHhCC
Q 045687           77 --KMAEDKEVTSQIHGFHMLI--NDLKNEN  102 (212)
Q Consensus        77 --~~~~~~sv~~~i~~~~~l~--~~L~~~~  102 (212)
                        ..+++++|.+|+.+|+.|+  .+|....
T Consensus       112 ~~~kq~~~sv~ey~~~lk~l~~~~el~~~~  141 (152)
T PF14244_consen  112 HSLKQGDKSVTEYFNKLKSLWQEDELDEYR  141 (152)
T ss_pred             HHHhhCCCcHHHHHHHHHHHhHHHHHhCcC
Confidence              1278999999999999999  5565543

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

Probab=98.97  E-value=6.2e-10  Score=80.48  Aligned_cols=59  Identities=31%  Similarity=0.477  Sum_probs=55.4

Q ss_pred             cccHHHHHHHHHHHHhhcccccc--------cceecCCccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687           52 HKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFM  110 (212)
Q Consensus        52 ~~tA~~lW~~L~~~y~~~~~~~~--------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~~l~d~~~  110 (212)
                      |+||++||++|+..|+..+...+        .++|.++.+|.+||.+|..|+++|..+|.+|+|+++
T Consensus         1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~   67 (119)
T PF14227_consen    1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDK   67 (119)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHH
Confidence            68999999999999998887765        788999999999999999999999999999999988

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

Probab=98.92  E-value=1.6e-09  Score=78.36  Aligned_cols=58  Identities=22%  Similarity=0.393  Sum_probs=53.1

Q ss_pred             ccHHHHHHHHHHHHhhccc---ccc--------cceecCCccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687           53 KFAYEIWAQLRKKYIIEDA---GAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFM  110 (212)
Q Consensus        53 ~tA~~lW~~L~~~y~~~~~---~~~--------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~~l~d~~~  110 (212)
                      +||+++|++|+..|++.+.   ...        .++|.++.+|.+|+.+|..|+++|..+|.+++|..+
T Consensus         1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~   69 (119)
T PF14223_consen    1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDL   69 (119)
T ss_pred             ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhH
Confidence            5899999999999998887   332        788899999999999999999999999999999988

>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=98.67  E-value=6.3e-09  Score=49.47  Aligned_cols=18  Identities=44%  Similarity=1.228  Sum_probs=16.4

Q ss_pred             cceeecCCCccccccCcC
Q 045687          157 GNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~  174 (212)
                      +.||+||+.||++++||+
T Consensus         1 ~~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    1 RKCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             SBCTTTSCSSSCGCTSSS
T ss_pred             CcCcCCCCcCcccccCcc
Confidence            369999999999999985

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 ....

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.88  E-value=4.5e-06  Score=45.24  Aligned_cols=19  Identities=32%  Similarity=0.777  Sum_probs=17.6

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      .-.|+.|++.||++++||.
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CCEeecCCCCCccHhHCCC
Confidence            3679999999999999998

>smart00343 ZnF_C2HC zinc finger

Probab=96.95  E-value=0.00033  Score=36.39  Aligned_cols=19  Identities=47%  Similarity=1.104  Sum_probs=16.4

Q ss_pred             ceeecCCCccccccCcCcc
Q 045687          158 NCYVCGKPGHFANKCRYRK  176 (212)
Q Consensus       158 ~C~~Cgk~GH~~~~C~~~~  176 (212)
                      .|++||+.||++++||...
T Consensus         1 ~C~~CG~~GH~~~~C~~~~   19 (26)
T smart00343        1 KCYNCGKEGHIARDCPKXX   19 (26)
T ss_pred             CCccCCCCCcchhhCCccc
Confidence            4999999999999998443

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.87  E-value=0.00044  Score=40.14  Aligned_cols=19  Identities=32%  Similarity=0.922  Sum_probs=17.5

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      ...|..|++.||+..+|+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4789999999999999996

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=96.60  E-value=0.002  Score=36.74  Aligned_cols=22  Identities=27%  Similarity=0.576  Sum_probs=19.0

Q ss_pred             cceeecCCCcccc--ccCcCccCC
Q 045687          157 GNCYVCGKPGHFA--NKCRYRKGD  178 (212)
Q Consensus       157 ~~C~~Cgk~GH~~--~~C~~~~~~  178 (212)
                      ++|..||..||.+  +.||-+...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~~~   25 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYCWS   25 (40)
T ss_pred             ccccccccccccccCccCCCCCCC
Confidence            6799999999998  779987763

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=96.49  E-value=0.00079  Score=40.64  Aligned_cols=19  Identities=32%  Similarity=0.844  Sum_probs=17.3

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      ...|++||..||...+||+
T Consensus        31 p~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ChhhcCCCCcCcCHhHcCC
Confidence            4779999999999999985

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

Probab=96.43  E-value=0.0011  Score=36.75  Aligned_cols=21  Identities=43%  Similarity=0.885  Sum_probs=14.1

Q ss_pred             cceeecCCCccccccCcCccC
Q 045687          157 GNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ..|+.|+|..|++.+|+.+.+
T Consensus         3 ~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             -C-TTTSSSCS-TTT---TCC
T ss_pred             ccCcccCCCcchhhhhhhhhc
Confidence            579999999999999998877

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

Probab=95.81  E-value=0.0036  Score=48.32  Aligned_cols=19  Identities=32%  Similarity=0.994  Sum_probs=14.7

Q ss_pred             CCcceeecCCCccccccCc
Q 045687          155 KKGNCYVCGKPGHFANKCR  173 (212)
Q Consensus       155 ~~~~C~~Cgk~GH~~~~C~  173 (212)
                      ....||+||+.||.++|||
T Consensus        59 ~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          59 ENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             cccccchhcccCcccccCC
Confidence            3467888888888888887

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

Probab=95.55  E-value=0.0054  Score=47.34  Aligned_cols=21  Identities=33%  Similarity=1.009  Sum_probs=17.5

Q ss_pred             cceeecCCCccccccC-cCccC
Q 045687          157 GNCYVCGKPGHFANKC-RYRKG  177 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C-~~~~~  177 (212)
                      .+|++||..||++++| |.+.+
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~~~  119 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSKDQ  119 (190)
T ss_pred             cccccccccCccccccCccccc
Confidence            6899999999999999 44333

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

Probab=95.29  E-value=0.0099  Score=48.73  Aligned_cols=22  Identities=36%  Similarity=1.067  Sum_probs=19.8

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      .-.|+-|||.|||.++||....
T Consensus       160 q~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHHheeccccccccccCCccCC
Confidence            4569999999999999998877

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

Probab=95.26  E-value=0.0084  Score=44.85  Aligned_cols=17  Identities=41%  Similarity=1.136  Sum_probs=8.6

Q ss_pred             ceeecCCCccccccCcC
Q 045687          158 NCYVCGKPGHFANKCRY  174 (212)
Q Consensus       158 ~C~~Cgk~GH~~~~C~~  174 (212)
                      .||.|+..||+.++||.
T Consensus       105 ~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368        105 ACYNCGGEGHISRDCPN  121 (148)
T ss_pred             hhcccCcCCcchhcCCC
Confidence            45555555555555544

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

Probab=94.53  E-value=0.069  Score=44.05  Aligned_cols=22  Identities=32%  Similarity=0.856  Sum_probs=19.4

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      .-.||.||..|||...||.-.+
T Consensus       176 gY~CyRCGqkgHwIqnCpTN~D  197 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTNQD  197 (427)
T ss_pred             ceeEEecCCCCchhhcCCCCCC
Confidence            3679999999999999997666

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

Probab=92.73  E-value=0.47  Score=34.98  Aligned_cols=79  Identities=15%  Similarity=0.110  Sum_probs=61.4

Q ss_pred             HHHHHHHHHhhccHHHHHhhcccc----cHHHHHHHHHHHHhhcccccc-----c-----ceecCCccHHHHHHHHHHHH
Q 045687           30 NKVCRSTILSTLSNELYDVYSQHK----FAYEIWAQLRKKYIIEDAGAQ-----N-----FKMAEDKEVTSQIHGFHMLI   95 (212)
Q Consensus        30 d~~a~~~I~~sl~~~i~~~i~~~~----tA~~lW~~L~~~y~~~~~~~~-----~-----~~~~~~~sv~~~i~~~~~l~   95 (212)
                      +..=+.+|.+.|..+....|.++.    +=..+|+.|+++|+......+     .     +...+...+...+..+..++
T Consensus        27 d~~K~~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i  106 (145)
T PF03564_consen   27 DIEKLNYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEELRNLPPISNDDPEALRSLVDKVNNCI  106 (145)
T ss_pred             HHHHHHHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHH
Confidence            455567899999999999888763    238899999999997665443     2     22345667889999999999


Q ss_pred             HHHHhCCCCCCcc
Q 045687           96 NDLKNENIILPES  108 (212)
Q Consensus        96 ~~L~~~~~~l~d~  108 (212)
                      ..|..+|..+++.
T Consensus       107 ~~L~~lg~~~~~~  119 (145)
T PF03564_consen  107 RALKALGVNVDDP  119 (145)
T ss_pred             HHHHHcCCCCCCH
Confidence            9999999888843

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

Probab=91.72  E-value=0.077  Score=39.62  Aligned_cols=19  Identities=37%  Similarity=1.078  Sum_probs=14.3

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      ...|+.|++.||+.++|+.
T Consensus        77 ~~~C~~Cg~~GH~~~~C~~   95 (148)
T PTZ00368         77 PRSCYNCGQTGHISRECPN   95 (148)
T ss_pred             CcccCcCCCCCcccccCCC
Confidence            3568888888888888864

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

Probab=91.46  E-value=0.078  Score=43.49  Aligned_cols=19  Identities=37%  Similarity=1.127  Sum_probs=17.3

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..||.||+.||+..+|+..
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             CccCCCCcCCcchhhCCCC
Confidence            6799999999999999965

>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]

Probab=87.95  E-value=0.15  Score=44.40  Aligned_cols=25  Identities=32%  Similarity=0.610  Sum_probs=21.9

Q ss_pred             cCCcceeecCCCccccccCcCccCC
Q 045687          154 KKKGNCYVCGKPGHFANKCRYRKGD  178 (212)
Q Consensus       154 ~~~~~C~~Cgk~GH~~~~C~~~~~~  178 (212)
                      -+.+-|.+||-.||..++|..++++
T Consensus       110 yRKGACeNCGAmtHk~KDCmERPRK  134 (529)
T KOG2560|consen  110 YRKGACENCGAMTHKVKDCMERPRK  134 (529)
T ss_pred             HhhhhhhhhhhhhcchHHHhhcchh
Confidence            3468899999999999999988884

>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=85.78  E-value=0.37  Score=35.20  Aligned_cols=22  Identities=36%  Similarity=0.933  Sum_probs=18.4

Q ss_pred             cCCcceeecCCCccccccCcCcc
Q 045687          154 KKKGNCYVCGKPGHFANKCRYRK  176 (212)
Q Consensus       154 ~~~~~C~~Cgk~GH~~~~C~~~~  176 (212)
                      ...+.|.+|+ ..||...||.+-
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            3458899996 999999999763

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.

>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]

Probab=84.03  E-value=0.44  Score=44.43  Aligned_cols=29  Identities=21%  Similarity=0.295  Sum_probs=22.2

Q ss_pred             ccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687           82 KEVTSQIHGFHMLINDLKNENIILPESFM  110 (212)
Q Consensus        82 ~sv~~~i~~~~~l~~~L~~~~~~l~d~~~  110 (212)
                      ...++--.+..++..++...|..|++...
T Consensus       123 Keaae~~~e~e~~ree~~~~G~~lpp~~~  151 (931)
T KOG2044|consen  123 KEAAEKEAEIERLREEFEAEGKFLPPKVK  151 (931)
T ss_pred             hHHHHHHHHHHHHHHHHHhcCCcCCchhh
Confidence            33456667778888999999999988755

>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=83.61  E-value=2.3  Score=28.30  Aligned_cols=44  Identities=18%  Similarity=0.287  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHhhcccccc------cceecCCccHHHHHHHHHHHHHHHHh
Q 045687           56 YEIWAQLRKKYIIEDAGAQ------NFKMAEDKEVTSQIHGFHMLINDLKN  100 (212)
Q Consensus        56 ~~lW~~L~~~y~~~~~~~~------~~~~~~~~sv~~~i~~~~~l~~~L~~  100 (212)
                      .++=..|...|........      .++. ++++|.+|+.+|..|+..+..
T Consensus        30 ~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~   79 (96)
T PF03732_consen   30 EEFKDAFRKRFFPPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP   79 (96)
T ss_pred             HHHHHHHHHHHhhhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC
Confidence            3444445555554333222      3444 799999999999999998764

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.

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

Probab=83.54  E-value=0.46  Score=41.10  Aligned_cols=22  Identities=27%  Similarity=0.622  Sum_probs=19.9

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ..-|.|||-.||...+||++..
T Consensus       570 ~kGCayCgGLGHRItdCPKle~  591 (610)
T KOG0341|consen  570 EKGCAYCGGLGHRITDCPKLEA  591 (610)
T ss_pred             ccccccccCCCcccccCchhhh
Confidence            3569999999999999999877

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

Probab=83.50  E-value=0.59  Score=41.28  Aligned_cols=19  Identities=32%  Similarity=0.906  Sum_probs=17.6

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..|++||-.||+..+|+..
T Consensus       286 n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  286 NVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             ccccccCCcccccccCCCc
Confidence            4899999999999999877

>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=81.57  E-value=0.89  Score=41.45  Aligned_cols=23  Identities=26%  Similarity=0.621  Sum_probs=19.6

Q ss_pred             CCcceeecCCCcccc--ccCcCccC
Q 045687          155 KKGNCYVCGKPGHFA--NKCRYRKG  177 (212)
Q Consensus       155 ~~~~C~~Cgk~GH~~--~~C~~~~~  177 (212)
                      ...+|-+||..||++  +.||....
T Consensus       936 Ttr~C~nCGQvGHmkTNK~CP~f~s  960 (968)
T COG5179         936 TTRTCGNCGQVGHMKTNKACPKFSS  960 (968)
T ss_pred             cceecccccccccccccccCccccC
Confidence            357899999999987  56998887

---

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	212
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	6e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	2e-04
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-04
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	6e-04
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	8e-04
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	9e-04

>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 = 6e-05
 Identities = 12/28 (42%), Positives = 16/28 (57%)

Query: 157 GNCYVCGKPGHFANKCRYRKGDHKPPKA 184
           G+C+ CGK GHFA  C     ++  PK 
Sbjct: 2   GSCFKCGKKGHFAKNCHEHAHNNAEPKV 29

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

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 3/40 (7%)

Query: 146 KNKKTTFKKKKGNCYVCGKPGHFANKCRYRK---GDHKPP 182
                   K  G C  C +  H+AN+C+ +    G+  PP
Sbjct: 20  HAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQGNPIPP 59

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

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 154 KKKGNCYVCGKPGHFANKCR 173
           + +G CY CG PGH+  +C 
Sbjct: 2   RARGLCYTCGSPGHYQAQCP 21

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

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 12/48 (25%), Positives = 15/48 (31%), Gaps = 10/48 (20%)

Query: 131 EAHPSKN-QKPNKKFFKNKKTTFKKKKGNCYVCGKPGHFANKCRYRKG 177
             H      K  K             +  C +C   GH A +CR R G
Sbjct: 13  PGHYQAQCPKKRKS---------GNSRERCQLCNGMGHNAKQCRKRDG 51

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 36.2 bits (83), Expect = 8e-04
 Identities = 11/38 (28%), Positives = 16/38 (42%)

Query: 146 KNKKTTFKKKKGNCYVCGKPGHFANKCRYRKGDHKPPK 183
           K K          CY CG  GHF + C+ ++    P +
Sbjct: 36  KAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSRVPNE 73

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

 Score = 34.9 bits (80), Expect = 9e-04
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 159 CYVCGKPGHFANKCRYRKGDHK 180
           CY CGKPGH +++CR  K   K
Sbjct: 3   CYNCGKPGHLSSQCRAPKVCFK 24

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	212
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.77
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.74
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.55
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.46
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.92
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.5
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.49
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.47
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.45
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.4
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.38
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.37
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.36
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.34
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.34
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.3
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.23
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.23
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.15
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.04
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.01
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.01
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.75
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.55
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.5
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.19
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.16
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	91.82
3alr_A	106	Nanos protein; zinc-finger, translational repressi	81.09

>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=98.77  E-value=9.2e-09  Score=62.89  Aligned_cols=26  Identities=23%  Similarity=0.698  Sum_probs=22.2

Q ss_pred             CCcceeecCCCccccccCcCccCCCC
Q 045687          155 KKGNCYVCGKPGHFANKCRYRKGDHK  180 (212)
Q Consensus       155 ~~~~C~~Cgk~GH~~~~C~~~~~~~k  180 (212)
                      ....||+||+.|||+++||++..+..
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~~~~~~   47 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKKPRGPR   47 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTCCCSSC
T ss_pred             CCCcceeCCCCCcccccCcCCccccC
Confidence            34789999999999999999887544

>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=98.74  E-value=5.5e-09  Score=59.36  Aligned_cols=25  Identities=24%  Similarity=0.719  Sum_probs=21.9

Q ss_pred             CcceeecCCCccccccCcCccCCCC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKGDHK  180 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~~~k  180 (212)
                      ...||+||+.|||+++||+...+.+
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~~~r   34 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPRGPR   34 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCTT
T ss_pred             CCeeeECCCCCcchhhCcCCcccCC
Confidence            4789999999999999999887544

>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=98.55  E-value=1.9e-08  Score=53.33  Aligned_cols=22  Identities=41%  Similarity=0.865  Sum_probs=19.5

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+||+.||++++|+.+.+
T Consensus         6 ~~~C~nCgk~GH~ar~C~~prk   27 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             CCEEEECCccccCHhHCccccc
Confidence            4779999999999999998765

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

Probab=97.92  E-value=2.6e-06  Score=51.74  Aligned_cols=22  Identities=36%  Similarity=0.990  Sum_probs=18.8

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||.||++||++++||...+
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~~~   28 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTNGD   28 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGGGC
T ss_pred             CCccccCCCcCcccccCCCCCC
Confidence            3579999999999999996554

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

Probab=97.50  E-value=2.2e-05  Score=44.25  Aligned_cols=18  Identities=56%  Similarity=1.278  Sum_probs=15.1

Q ss_pred             ceeecCCCccccccCcCc
Q 045687          158 NCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       158 ~C~~Cgk~GH~~~~C~~~  175 (212)
                      .||+||+.||++++||.+
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            588888888888888865

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

Probab=97.49  E-value=2.7e-05  Score=43.91  Aligned_cols=18  Identities=28%  Similarity=0.741  Sum_probs=16.8

Q ss_pred             cceeecCCCccccccCcC
Q 045687          157 GNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~  174 (212)
                      ..||.||+.||++++||+
T Consensus        22 ~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SSCTTTCCSSSCTTTSCC
T ss_pred             CccccCCCCCCccCcCcC
Confidence            679999999999999985

>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=97.47  E-value=3e-05  Score=46.03  Aligned_cols=18  Identities=44%  Similarity=1.064  Sum_probs=9.0

Q ss_pred             cceeecCCCccccccCcC
Q 045687          157 GNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~  174 (212)
                      ..||.||+.||++++||.
T Consensus        28 ~~C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCS
T ss_pred             CeeCcCCCcCCccCCCcC
Confidence            345555555555555544

>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=97.45  E-value=4.3e-05  Score=45.34  Aligned_cols=22  Identities=41%  Similarity=0.865  Sum_probs=19.3

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+||+.||++++||....
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~~~   27 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAPRR   27 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCSSC
T ss_pred             cCeeeecCCCCcChhhCcCCCC
Confidence            4679999999999999998653

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

Probab=97.40  E-value=4.7e-05  Score=42.38  Aligned_cols=17  Identities=47%  Similarity=1.376  Sum_probs=11.6

Q ss_pred             cceeecCCCccccccCc
Q 045687          157 GNCYVCGKPGHFANKCR  173 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~  173 (212)
                      ..||.||+.||++++||
T Consensus        20 ~~C~~Cg~~GH~a~~C~   36 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCR   36 (37)
T ss_dssp             TTCSSCCCTTGGGGTTC
T ss_pred             CeEccCCCcCCccCcCc
Confidence            66666666666666665

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

Probab=97.38  E-value=4.7e-05  Score=42.36  Aligned_cols=17  Identities=59%  Similarity=1.538  Sum_probs=15.8

Q ss_pred             ceeecCCCccccccCcC
Q 045687          158 NCYVCGKPGHFANKCRY  174 (212)
Q Consensus       158 ~C~~Cgk~GH~~~~C~~  174 (212)
                      .||+||+.||++++||.
T Consensus         2 ~C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             CBSSSCCSSCCTTTSSC
T ss_pred             cccccCCCCcchhhCcC
Confidence            59999999999999985

>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=97.37  E-value=5.6e-05  Score=46.85  Aligned_cols=22  Identities=32%  Similarity=0.788  Sum_probs=19.7

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||.||+.||++++|+....
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CcceeECCCCCCccCcCCCccc
Confidence            4789999999999999998765

>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=97.36  E-value=5e-05  Score=46.19  Aligned_cols=19  Identities=47%  Similarity=1.111  Sum_probs=10.0

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..||+||+.||++++||..
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSC
T ss_pred             cceeeeCCCCcChhhcCCC
Confidence            3455555555555555543

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

Probab=97.34  E-value=5.6e-05  Score=49.97  Aligned_cols=22  Identities=36%  Similarity=1.026  Sum_probs=19.6

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+||+.||+.++||....
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCeecccCCCCcCcccCCcccc
Confidence            4789999999999999998664

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

Probab=97.34  E-value=5.2e-05  Score=47.18  Aligned_cols=22  Identities=41%  Similarity=0.943  Sum_probs=18.4

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||.|++.||++++||....
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC-
T ss_pred             CCeeCCCCCCCCCcCCCcCCCc
Confidence            3679999999999999997765

>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=97.30  E-value=6.7e-05  Score=45.62  Aligned_cols=22  Identities=41%  Similarity=0.955  Sum_probs=19.0

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||.||+.||++++||....
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~~~   54 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTERQA   54 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSSCC
T ss_pred             CCEeCCCCCcCCccCCCcCcCC
Confidence            3679999999999999997653

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

Probab=97.23  E-value=0.00016  Score=45.21  Aligned_cols=22  Identities=18%  Similarity=0.551  Sum_probs=18.3

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+|++.||++++||....
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~~~   50 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLKAQ   50 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGGGC
T ss_pred             CCccCCcCCcCCccCcCCCccc
Confidence            4679999999999999987654

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

Probab=97.23  E-value=9.9e-05  Score=45.87  Aligned_cols=22  Identities=41%  Similarity=1.254  Sum_probs=19.1

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+|++.||++++||....
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~   25 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRK   25 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTS
T ss_pred             CCcccccCCCCeehhhCcCCcC
Confidence            3679999999999999998654

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

Probab=97.15  E-value=0.00016  Score=46.67  Aligned_cols=19  Identities=21%  Similarity=0.672  Sum_probs=9.6

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..||.||+.||++++||..
T Consensus        47 ~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           47 KKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             CCCTTTCCTTSCGGGCTTG
T ss_pred             CccCCcCCcCCccCcCcCC
Confidence            3455555555555555443

>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=97.04  E-value=9.3e-05  Score=45.81  Aligned_cols=20  Identities=50%  Similarity=1.270  Sum_probs=0.0

Q ss_pred             cceeecCCCccccccCcCcc
Q 045687          157 GNCYVCGKPGHFANKCRYRK  176 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~  176 (212)
                      ..||.|++.||++++||...
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             --------------------
T ss_pred             CccccCCCCCcCHhhCcCCC
Confidence            35999999999999999864

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

Probab=97.01  E-value=0.0002  Score=44.80  Aligned_cols=19  Identities=37%  Similarity=0.980  Sum_probs=17.4

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..||+|++.||++++|+..
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            6799999999999999964

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

Probab=97.01  E-value=0.00018  Score=46.43  Aligned_cols=22  Identities=36%  Similarity=0.869  Sum_probs=18.9

Q ss_pred             CCcceeecCCCccccccCcCcc
Q 045687          155 KKGNCYVCGKPGHFANKCRYRK  176 (212)
Q Consensus       155 ~~~~C~~Cgk~GH~~~~C~~~~  176 (212)
                      ....||+||+.||++++|+...
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~~   44 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLPP   44 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSCC
T ss_pred             CCCcccccCCcCcCcccCCCCC
Confidence            3477999999999999999644

>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=96.75  E-value=0.00054  Score=50.34  Aligned_cols=20  Identities=20%  Similarity=0.632  Sum_probs=10.4

Q ss_pred             cceeecCCCccccccCcCcc
Q 045687          157 GNCYVCGKPGHFANKCRYRK  176 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~  176 (212)
                      ..||.||+.||++++||...
T Consensus       120 ~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A          120 KKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCTTTCCSSCCGGGCTTTT
T ss_pred             CcccccCCcCCEeccCcCCC
Confidence            34555555555555555443

>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=96.55  E-value=0.00062  Score=49.99  Aligned_cols=22  Identities=32%  Similarity=0.806  Sum_probs=18.9

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...||+||+.||++++|+...+
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~~  118 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPPQ  118 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCCC
T ss_pred             CCcccEeCCccchhhhCCCCCC
Confidence            4679999999999999998443

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

Probab=96.50  E-value=0.00067  Score=44.75  Aligned_cols=22  Identities=23%  Similarity=0.441  Sum_probs=17.8

Q ss_pred             CcceeecCCCccccccCcCccC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ...|+.|+..||++++||...+
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~~r   26 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSIWR   26 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGGTC
T ss_pred             cCCCCCCCCCCCccccCCCccc
Confidence            4789999999999999997643

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

Probab=96.19  E-value=0.0011  Score=47.09  Aligned_cols=19  Identities=42%  Similarity=1.086  Sum_probs=17.7

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      .+.||+||+.||++++||+
T Consensus       105 ~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          105 TIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCTTTTSSSCTTTTTSCC
T ss_pred             CCCcCCCCCCCcCcccCcC
Confidence            5789999999999999986

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

Probab=95.16  E-value=0.0066  Score=42.98  Aligned_cols=17  Identities=29%  Similarity=0.886  Sum_probs=8.1

Q ss_pred             ceeecCCC-ccccccCcC
Q 045687          158 NCYVCGKP-GHFANKCRY  174 (212)
Q Consensus       158 ~C~~Cgk~-GH~~~~C~~  174 (212)
                      .||+||+. ||++++||.
T Consensus        24 ~C~~Cg~~~gH~~~~C~~   41 (124)
T 2lli_A           24 ICSYCGATDDHYSRHCPK   41 (124)
T ss_dssp             CCTTTCCTTTCCTTTGGG
T ss_pred             cCcCCCCcCCccCcccCC
Confidence            45555544 444444443

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

Probab=91.82  E-value=0.028  Score=27.96  Aligned_cols=19  Identities=32%  Similarity=0.807  Sum_probs=16.5

Q ss_pred             CcceeecCCCccccccCcC
Q 045687          156 KGNCYVCGKPGHFANKCRY  174 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~  174 (212)
                      ++.|-+|.-.||+..+|..
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            4789999999999999964

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

Probab=81.09  E-value=0.44  Score=32.11  Aligned_cols=22  Identities=27%  Similarity=0.623  Sum_probs=18.7

Q ss_pred             CcceeecCCCc---cccccCcCccC
Q 045687          156 KGNCYVCGKPG---HFANKCRYRKG  177 (212)
Q Consensus       156 ~~~C~~Cgk~G---H~~~~C~~~~~  177 (212)
                      .-.|-.||-.|   |+.+.||...+
T Consensus        71 ~Y~CpiCGATGd~AHT~kYCP~~~~   95 (106)
T 3alr_A           71 QYKCPLCGATGAKAHTKRFCPMVDK   95 (106)
T ss_dssp             GCCCTTTCCCGGGCCCGGGCTTCGG
T ss_pred             cccCCCCCCcCCcccceecCCCCCC
Confidence            36799999999   99999997665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	212
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.84
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	98.4
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	98.33
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.89
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.8
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	95.2
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	94.63

>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=98.84  E-value=3.9e-10  Score=55.95  Aligned_cols=23  Identities=43%  Similarity=0.873  Sum_probs=20.7

Q ss_pred             CCcceeecCCCccccccCcCccC
Q 045687          155 KKGNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       155 ~~~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ..++||+|||.||++++|..+.+
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSSS
T ss_pred             ceeEeecCCccchhhhhccCccc
Confidence            46889999999999999998876

>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=98.40  E-value=3e-08  Score=46.96  Aligned_cols=19  Identities=37%  Similarity=1.036  Sum_probs=17.0

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      +.||-|||.||++++|..-
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            6899999999999999643

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

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

Probab=98.33  E-value=1.3e-07  Score=50.36  Aligned_cols=25  Identities=24%  Similarity=0.719  Sum_probs=21.5

Q ss_pred             CcceeecCCCccccccCcCccCCCC
Q 045687          156 KGNCYVCGKPGHFANKCRYRKGDHK  180 (212)
Q Consensus       156 ~~~C~~Cgk~GH~~~~C~~~~~~~k  180 (212)
                      ...|-||.+.|||+++||++.+..+
T Consensus        10 kDQCAyCke~GHW~~dCPkkprg~k   34 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKKPRGPR   34 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCTT
T ss_pred             chhhHHHhhcCchhhhCccCCCCCC
Confidence            4779999999999999998887443

>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=97.89  E-value=2e-06  Score=47.99  Aligned_cols=19  Identities=42%  Similarity=1.015  Sum_probs=15.0

Q ss_pred             cceeecCCCccccccCcCc
Q 045687          157 GNCYVCGKPGHFANKCRYR  175 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~  175 (212)
                      ..||.||+.||++++||++
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCCCeecccCCCC
Confidence            4688888888888888765

>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=97.80  E-value=2.8e-06  Score=47.41  Aligned_cols=21  Identities=43%  Similarity=0.972  Sum_probs=18.7

Q ss_pred             cceeecCCCccccccCcCccC
Q 045687          157 GNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ++||+||+.||++++||.+..
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~~   22 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPRK   22 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCCC
T ss_pred             CccccCCCcCcCcccCcCCCc
Confidence            679999999999999998644

>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=95.20  E-value=0.0036  Score=31.43  Aligned_cols=21  Identities=33%  Similarity=0.835  Sum_probs=19.3

Q ss_pred             cceeecCCCccccccCcCccC
Q 045687          157 GNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ..|..|+|.-||+++|..+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk~~   23 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKSKTD   23 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCCTTS
T ss_pred             ccCccccCcchHHHHhhhhhc
Confidence            579999999999999998877

>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=94.63  E-value=0.0051  Score=30.72  Aligned_cols=21  Identities=29%  Similarity=0.653  Sum_probs=18.9

Q ss_pred             cceeecCCCccccccCcCccC
Q 045687          157 GNCYVCGKPGHFANKCRYRKG  177 (212)
Q Consensus       157 ~~C~~Cgk~GH~~~~C~~~~~  177 (212)
                      ..|-.|+|.-||+++|..+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk~~   23 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSKFD   23 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCSEE
T ss_pred             ccCccccCcchHHHHhhhhhc
Confidence            579999999999999997766