Citrus Sinensis ID: 048427

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-
Protein Sequence
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRKCHFCKKLGHKRELNAGDSKHGWKRK
Secondary Structure (PSIPRED)
ccEEEEEEccccccccccccHHHHHHHHHHHcHHccccEEEccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccc
Secondary Structure Prediction (SSPRO)
cccEEEEEccccccccccHHHHHHHHHHHEEEEHccHHHHcccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccEEEEEccccccccHHHHHHHHHHHHHHHHHcccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccc
Coil and Loop (DISEMBL)
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRdlalrvdepakptdkstavekaettrdnipacdKAKDYLAAVGRTFKKIDKAEKGNYLRLLANtqydgvsgVREHILKMTSYHKKLKemdvdlpddylvfqnleslppqfgnlrsqyntqrdtwNITELTAYVVQEEeslkkgksHTAIMAttqesgsvkkcsskgsnkffkkkkfgkktsrgnssttssstsesfKRKCHFckklghkrelnagdskhgwkrk
Flexible Loop (DISEMBL)
lvhsyivtgsLTYCVAIGENFEDRRDSILFYLSTLnrdlalrvdepakptdkstavekaettrdnipacdkAKDYLAAVGRTfkkidkaekgnyLRLLANtqydgvsgvREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEeslkkgkshTAIMattqesgsvkkcsskgsnkffkkkkfgkktsrgnssttssstsesfkrKCHFckklghkrelnagdskhgwkrk
Low Complexity Region (SEG)
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATTQEsgsvkkcsskgsnkffkkkkfgkktsrgnssttssstsesFKRKCHFCKKLGHKRELNAGDSKHGWKRK
Disordered region (IsUnstruct)
**HSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALR************************PACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVV******************************************************************HFC*********************
Disordered Region (DISOPRED)
*VHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEE*************************************************************CHFCKKLGHKRELNAGDSK******
Disordered Region (DISEMBL)
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEP***************TRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQE*********HTAIMATTQ**********KGSNKFFKKK***********************RKCHFCKKLGHKRELN***********
Disordered Region (DISPRO)
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATT*****************************************SFKRKCHFCKKLGHKRE*NA**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LVHSYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRKCHFCKKLGHKRELNAGDSKHGWKRK
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	261
147765339	1524	hypothetical protein VITISV_027663 [Viti	0.804	0.137	0.405	6e-37
147853374	1678	hypothetical protein VITISV_022424 [Viti	0.877	0.136	0.380	7e-34
147852962	900	hypothetical protein VITISV_007708 [Viti	0.877	0.254	0.357	7e-34
147836551	319	hypothetical protein VITISV_034019 [Viti	0.743	0.608	0.393	1e-33
147858651	1252	hypothetical protein VITISV_034340 [Viti	0.873	0.182	0.359	5e-32
147778061	999	hypothetical protein VITISV_038283 [Viti	0.754	0.197	0.355	3e-27
224077858	316	predicted protein [Populus trichocarpa]	0.862	0.712	0.321	4e-27
147780065	403	hypothetical protein VITISV_038796 [Viti	0.816	0.528	0.308	8e-26
147816553	1001	hypothetical protein VITISV_018026 [Viti	0.854	0.222	0.301	9e-26
147839923	1581	hypothetical protein VITISV_029441 [Viti	0.846	0.139	0.308	2e-25

>gi|147765339|emb|CAN69387.1| hypothetical protein VITISV_027663 [Vitis vinifera]

 Score =  160 bits (404), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/237 (40%), Positives = 138/237 (58%), Gaps = 27/237 (11%)

Query: 36  NRDLALRVDEPAKPT-----DKSTAVEKAE----------------TTRDNIPACDKAKD 74
           N DLALR+DEP+K T     DK +  EK E                + ++ +P   KAKD
Sbjct: 5   NLDLALRIDEPSKLTGVSFADKKSFYEKWEHSNRSCLMVMKYNMDKSIKECLPKTKKAKD 64

Query: 75  YLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDY 134
           +L  V   + KIDKAE   YL+LL  + YDGV GV +HI+K+  Y  K  EM V L + +
Sbjct: 65  FLEYVKANYNKIDKAEMATYLKLLTTSMYDGVGGVIDHIIKLKHYFNKANEMKVKLSEKF 124

Query: 135 LVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATTQESG 194
           L +  LESLP  F  ++  YN  ++ W + EL + VVQ E SLKK ++H+  + T Q S 
Sbjct: 125 LKWLILESLPTSFDAVKLTYNALKEEWTLEELMSIVVQHEVSLKKNETHSLALVTDQVSN 184

Query: 195 SVKKC---SSKGSNKFFKKKKFGKKTSRGNSSTTSSST-SESFKRKCHFCKKLGHKR 247
             KK    +S+GS++F +KK   ++ S  N+S +S++T +E FK KC+FC K+GHK+
Sbjct: 185 MKKKPPHKNSRGSSQFKRKKNLSQRVS--NASVSSNATKNEKFKGKCNFCHKIGHKQ 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147853374|emb|CAN82299.1| hypothetical protein VITISV_022424 [Vitis vinifera]

 Score =  150 bits (378), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 143/252 (56%), Gaps = 23/252 (9%)

Query: 20  NFEDRRDSILFYLSTLNRDLALRVDEPAKPTD-----KSTAVEKAE-------------- 60
           NFE+  +S   +++  N DLALRVDEP+KPTD     K +  E+ E              
Sbjct: 209 NFEEWYESFNVHMTLHNLDLALRVDEPSKPTDVSSTDKGSFYERWEHFNRSCLMVVKYTM 268

Query: 61  --TTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTS 118
               ++ +P  ++ KD+L  V   + KIDKAE   YL+LL  T YDGVSGVR+HI+K+  
Sbjct: 269 DKYIKECVPKKERVKDFLEYVKANYTKIDKAEMTTYLKLLTTTVYDGVSGVRDHIIKLKH 328

Query: 119 YHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLK 178
           Y  K  EM V+L + +L +  LESLP  F  ++  YN  ++ W + E  +  VQ E SLK
Sbjct: 329 YFNKANEMKVELSEKFLKWLILESLPASFDAVKLTYNALKEEWTLEEFMSIEVQHEVSLK 388

Query: 179 KGKSHTAIMATTQESGSVKKCSSK--GSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRK 236
           K ++H+  + T Q S   KK S K  G +K FK+K    +     S++++++ +E FK K
Sbjct: 389 KNETHSLALVTDQVSNMKKKPSHKNFGGSKQFKRKGNSSQGISNASASSNATKNERFKGK 448

Query: 237 CHFCKKLGHKRE 248
           C+FC K+ HK++
Sbjct: 449 CNFCHKISHKQD 460

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147852962|emb|CAN79076.1| hypothetical protein VITISV_007708 [Vitis vinifera]

 Score =  150 bits (378), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 138/252 (54%), Gaps = 23/252 (9%)

Query: 18  GENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKA------------------ 59
           G NFE+  +S   +++  N DLALRV E +KPTD S+  E +                  
Sbjct: 27  GNNFEEWFESFNVHMTLQNLDLALRVYEXSKPTDVSSXDEXSFYEXWEHSNRSCLMVMKY 86

Query: 60  ---ETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKM 116
              ++ ++ +P  ++AKD+L  V   + K+DKAE   +L+LL    YDGVSGV++HI+++
Sbjct: 87  TMDKSIKECMPKTERAKDFLEYVKANYTKVDKAEMATHLKLLTTIVYDGVSGVKDHIIRL 146

Query: 117 TSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEES 176
             Y  K  EM V+L   +L +  LESLP  F  ++  YN  ++ W + EL + VVQ E S
Sbjct: 147 RYYFNKANEMKVELGKKFLKWLILESLPVSFDAVKLTYNALKEEWTLEELMSIVVQHEVS 206

Query: 177 LKKGKSHTAIMATTQESGSVKKCSSK--GSNKFFKKKKFGKKTSRGNSSTTSSSTSESFK 234
           LKK ++H+  + T Q S   KK   K  G  K FK+K    + +     +++++ SE FK
Sbjct: 207 LKKNETHSLALVTDQVSNMKKKPPRKNFGGFKQFKRKGNSNQGTSNAFXSSNAAKSEKFK 266

Query: 235 RKCHFCKKLGHK 246
            KC+F  K+ HK
Sbjct: 267 GKCNFXHKIXHK 278

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147836551|emb|CAN77595.1| hypothetical protein VITISV_034019 [Vitis vinifera]

 Score =  149 bits (375), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 85/216 (39%), Positives = 121/216 (56%), Gaps = 22/216 (10%)

Query: 18  GENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKA------------------ 59
           G NFE+  +S   +++  N DLALRVDEP+KPTD S+A E++                  
Sbjct: 27  GNNFEEWYESFNVHMTLHNLDLALRVDEPSKPTDVSSABERSFYEIWEHSNRSCLMVMKY 86

Query: 60  ---ETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKM 116
              ++ ++ +P  ++AKD+L  V   + KIDK E  NYL+LL  T YDGVSGVR+HI+K+
Sbjct: 87  TMNKSIKECVPKMERAKDFLEYVKVKYTKIDKTEMTNYLKLLTTTMYDGVSGVRDHIIKL 146

Query: 117 TSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEES 176
             Y  K  EM ++L   +L +  LESLP  F  ++  YN  ++ W + EL + VVQ E S
Sbjct: 147 KHYFNKANEMKMELSXKFLKWLILESLPTSFDXVKLIYNALKEEWTLEELMSIVVQHEVS 206

Query: 177 LKKGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKK 212
           LKK ++H+  + T Q       C  K  N   KKKK
Sbjct: 207 LKKNETHSPALVTDQIGHKQTDC-FKFKNWLEKKKK 241

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147858651|emb|CAN81838.1| hypothetical protein VITISV_034340 [Vitis vinifera]

 Score =  144 bits (362), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 142/253 (56%), Gaps = 25/253 (9%)

Query: 20  NFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKA-------------------- 59
           NFE+  +S   +++  N DLALRVDEP+KPT+ S+  E++                    
Sbjct: 38  NFEEWFESFNVHMTLQNLDLALRVDEPSKPTNVSSVDERSFYERWEYSNRSCLMVMKYTM 97

Query: 60  -ETTRDNIPACDKAKDYLAAVGR-TFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMT 117
            ++ ++ +P  ++AKD    + R      DK E   +L+LL  T YD VSGVR+HI+K+ 
Sbjct: 98  DKSIKECVPKTERAKDXPWNMXRXNXTXXDKVEIETHLKLLTTTVYDRVSGVRDHIIKLK 157

Query: 118 SYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESL 177
            Y  K  EM V+L +++L +  LESLP  F  ++  YN  ++ W + EL + VVQ E SL
Sbjct: 158 HYFNKANEMKVELGENFLKWLILESLPVSFDAVKLTYNALKEEWTLEELMSIVVQHEVSL 217

Query: 178 KKGKSHTAIMATTQESGSVKKCSSK---GSNKFFKKKKFGKKTSRGNSSTTSSSTSESFK 234
           KK ++H+  + T Q S   KK   K   G  +F +K    + TS  ++S+++++ SE FK
Sbjct: 218 KKNETHSLALVTYQVSNMKKKPPHKNFGGFKQFKRKGNSNQGTSNASASSSNAAKSEKFK 277

Query: 235 RKCHFCKKLGHKR 247
             C+FC K+GHK+
Sbjct: 278 GNCNFCHKIGHKQ 290

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147778061|emb|CAN65284.1| hypothetical protein VITISV_038283 [Vitis vinifera]

 Score =  128 bits (321), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 127/239 (53%), Gaps = 42/239 (17%)

Query: 32  LSTLNRDLALRVDEPAKPTDKSTAVEKA---------------------ETTRDNIPACD 70
           ++  N DL LRV+EP+KPTD S+  E +                     ++ ++ +P  +
Sbjct: 1   MTLQNLDLVLRVNEPSKPTDMSSTDEISFYEIWEHSNRSCLMVMKYTMDKSIKECVPKTE 60

Query: 71  KAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDL 130
           +AKD+L  V   + KIDKAE   YL+LL  T YDGV GV++HI+K+  Y  K        
Sbjct: 61  RAKDFLEYVKANYTKIDKAEMTTYLKLLTTTMYDGVGGVKDHIIKLKHYFNK-------- 112

Query: 131 PDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHTAIMATT 190
                      SLP  F  ++  YN  ++ W + EL + VVQ E SLKK + H+  + T 
Sbjct: 113 -----------SLPTSFDAVKLTYNALKEEWTLEELMSIVVQHEVSLKKNEIHSFALVTD 161

Query: 191 QESGSVKKCSSK--GSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRKCHFCKKLGHKR 247
           Q S   KK S K  G +K FK+K    + +   S++++++ SE FK KC+FC K+GHK+
Sbjct: 162 QVSNMKKKPSHKNFGGSKQFKRKGNSSQGTSNASASSNATKSERFKGKCNFCHKIGHKQ 220

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077858|ref|XP_002305439.1| predicted protein [Populus trichocarpa] gi|222848403|gb|EEE85950.1| predicted protein [Populus trichocarpa]

 Score =  127 bits (320), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 133/271 (49%), Gaps = 46/271 (16%)

Query: 18  GENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTR-------------D 64
           G NF+  +D++L  L  ++ DLALR D P    D+ST+ EK +  R              
Sbjct: 20  GSNFKSCKDNLLIVLGVMDLDLALRTDSPPPFKDESTSDEKRDMERWEKSNRMCMMIMKR 79

Query: 65  NIPACDK---------AKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILK 115
            IP   +         AK++LA + + F K +KAE G  L  L + +Y G   VRE+IL+
Sbjct: 80  AIPEAFRGTMSDQITTAKEFLANIEKRFVKNEKAEIGTLLTSLISMKYKGKGNVREYILE 139

Query: 116 MTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEE 175
           M+    KLK + ++L +D LV   L SLP QF   +  YN Q++TW++ EL ++ VQEEE
Sbjct: 140 MSHLASKLKALQLELSEDLLVHLVLISLPTQFNQFKVSYNCQKETWSLNELISHCVQEEE 199

Query: 176 SLKKGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKKFGKKTSRGNSSTTS-----SSTS 230
            LK+ ++ +A +AT                  FK K   +K  +  + TT      + + 
Sbjct: 200 RLKQDRTESAHLATA-----------------FKDKGRKRKNFKDAAGTTPQKKQLTKSH 242

Query: 231 ESFKRKCHFCKKLGHKRELNAGDSKHGWKRK 261
           +S    C FC   GHK++     + H W+ K
Sbjct: 243 DSVGSSCFFCGAEGHKKK--QCTNYHAWRAK 271

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780065|emb|CAN60060.1| hypothetical protein VITISV_038796 [Vitis vinifera]

 Score =  123 bits (308), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 115/243 (47%), Gaps = 30/243 (12%)

Query: 12  TYCVAIGENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKAETTR-------- 63
           T  +  G N++  R  I F L  ++ D+ LR DEP  PT++ST   +A   +        
Sbjct: 149 TIEILSGSNYKRWRSDIEFVLGMMDLDMTLREDEPPNPTNESTEAMRAHYAKWEISNRLS 208

Query: 64  -------------DNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVR 110
                          IP  + AK++L  V   ++  D AE G+++  L N +YD + GVR
Sbjct: 209 LISIKRSIVDHLLGGIPESNNAKEFLVVVANRYQTSDNAEAGHFVDELMNMRYDDMKGVR 268

Query: 111 EHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYV 170
           E+ILKM     +LK +D+ +PD ++V Q L +LP  F  +++ YNT   +W + +L    
Sbjct: 269 EYILKMVHLQTRLKALDIPIPDKFIVHQALNTLPFSFSQIKAAYNTLNQSWGVNDLITKC 328

Query: 171 VQEEESLKKGK---SHTAIMATTQESGSVKKC-----SSKGSNKFFKKKKFGKKTSRGNS 222
           V EEE LK+     +H   +        V+K       S   NK FKK    +K   GN+
Sbjct: 329 VAEEEKLKRENNESTHLVALGKPNNQKRVEKARKPNFHSHKKNKNFKKSG-SEKQKNGNA 387

Query: 223 STT 225
             T
Sbjct: 388 KNT 390

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147816553|emb|CAN61880.1| hypothetical protein VITISV_018026 [Vitis vinifera]

 Score =  123 bits (308), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 125/252 (49%), Gaps = 29/252 (11%)

Query: 18  GENFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKA------------------ 59
           G NF+  ++ ++  L  ++ D ALR + P+  T  STA +++                  
Sbjct: 19  GTNFKKWKEHVIIVLGCMDLDFALRENRPSDLTSASTAEQRSTMEKWERSNRMSLMIMKH 78

Query: 60  ---ETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKM 116
              E  R  IP   +AK +L  +   F   +K E    L  L + +Y G   + E+I++M
Sbjct: 79  SIPEAIRGAIPEETQAKAFLDQIANRFAANEKVETNTILSKLVSMRYKGKENIMEYIMEM 138

Query: 117 TSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEES 176
           ++   +LK + ++L +D LV   L SLP QF   +  YNTQ++ W + EL A  VQEEE 
Sbjct: 139 SNLVTRLKALKLELSEDILVHLVLISLPTQFSPFKINYNTQKEKWTLNELIAQCVQEEER 198

Query: 177 LKKGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRK 236
           LK+ K  +A +A+T +          G+NK  K+   GK+T+   +S  +    +  +  
Sbjct: 199 LKQEKIKSAHLASTSQGF--------GTNKKRKRDNIGKQTAVSGTSKQNEQKKQDKEIT 250

Query: 237 CHFCKKLGHKRE 248
           C FCKK+GH ++
Sbjct: 251 CFFCKKVGHMKK 262

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839923|emb|CAN61695.1| hypothetical protein VITISV_029441 [Vitis vinifera]

 Score =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 122/250 (48%), Gaps = 29/250 (11%)

Query: 20  NFEDRRDSILFYLSTLNRDLALRVDEPAKPTDKSTAVEKA-------------------- 59
           NF+  ++ ++  L  ++ D ALR D P+  T  STA +++                    
Sbjct: 430 NFKKWKEHVIIVLGCMDLDFALREDRPSDLTSASTAEQRSTMEKWERSNRMSLMIMKHSI 489

Query: 60  -ETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTS 118
            E  R  IP   +AK +L  +   F    K E    L  L + +Y G   +RE+I++M++
Sbjct: 490 PEAIRGAIPEETQAKAFLDQIANRFAANXKVETSTILSKLVSMRYKGKXNIREYIMEMSN 549

Query: 119 YHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLK 178
              +LK + ++L +D LV   L SLP QF   +  YNTQ++ W + EL A  VQEEE LK
Sbjct: 550 LVTRLKALKLELSEDILVHLVLISLPTQFSPFKISYNTQKEKWTLNELIAQCVQEEERLK 609

Query: 179 KGKSHTAIMATTQESGSVKKCSSKGSNKFFKKKKFGKKTSRGNSSTTSSSTSESFKRKCH 238
           + K  +A +A+T +          G+NK  K+   GK+T+   +S       +  +  C 
Sbjct: 610 QEKIESAHLASTSQ--------GFGTNKKRKRDNKGKQTAVSGTSKQKEQKKQDKEITCF 661

Query: 239 FCKKLGHKRE 248
           FCKK GH ++
Sbjct: 662 FCKKAGHMKK 671

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	261
TAIR|locus:2164032	244	AT5G53670 "AT5G53670" [Arabido	0.528	0.565	0.253	0.00044

TAIR|locus:2164032 AT5G53670 "AT5G53670" [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 0.00044, P = 0.00044
 Identities = 39/154 (25%), Positives = 75/154 (48%)

Query:    18 GENFEDRRDSILFYLSTLNRDLALRVDEPAKPT-----DKSTAVE----KAETT---RDN 65
             G NF + ++ +L  L+ ++ DL+L  + P+ P      D+S  V     K       R  
Sbjct:    43 GSNFSEWKEHLLLVLALMDLDLSLMTERPSSPKELKHWDRSNRVSIMIMKIRIPQGFRGV 102

Query:    66 IPA-CDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLK 124
             +P     AKD+LA++   F K ++AE+       ++  Y     VRE I++M +   K K
Sbjct:   103 VPDDVTTAKDFLASLENFFAKNEEAERSRVQAESSSMSYIENENVRELIMRMKTLGAKRK 162

Query:   125 EMDVD--LPDDYLVFQ-NLESLPPQFGNLRSQYN 155
              + ++    +D ++    ++ LP Q+ +L++ Y+
Sbjct:   163 RLGINNIFSNDMMLAHCAVKMLPLQYISLKNVYS 196


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        0.316   0.132   0.385    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      261       221   0.00095  112 3  11 22  0.41    33
                                                     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:  1
  No. of states in DFA:  597 (63 KB)
  Total size of DFA:  179 KB (2104 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:  20.05u 0.16s 20.21t   Elapsed:  00:00:01
  Total cpu time:  20.05u 0.16s 20.21t   Elapsed:  00:00:01
  Start:  Sat May 11 02:30:13 2013   End:  Sat May 11 02:30:14 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00036719001 SubName- Full=Chromosome chr15 scaffold_82, whole genome shotgun sequence; (256 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	261
pfam14227	115	pfam14227, UBN2_2, gag-polypeptide of LTR copia-ty	2e-07
pfam14223	119	pfam14223, UBN2, gag-polypeptide of LTR copia-type	2e-07

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 23/116 (19%), Positives = 44/116 (37%), Gaps = 3/116 (2%)

Query: 69  CDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDV 128
              AK+    + + +       K    + L   +      V EH+ +      +L+ + V
Sbjct: 1   EKTAKELWDKLEKLYMTKSLTNKLYLKKKLYTLKMSEGKSVEEHLDEFNKLVNELESLGV 60

Query: 129 DLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAYVVQEEESLKKGKSHT 184
            + D+      L SLPP +        T RD   + ++ + ++ EE   KK K  +
Sbjct: 61  KIDDEDQAILLLSSLPPSYETFV---TTLRDELTLEDVKSALLSEELRRKKEKESS 113

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

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 98  LANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNLRSQYNTQ 157
             N +      + +++ +++    KL+ +   + D+ +V + L SLP ++  + +     
Sbjct: 32  FENLKMKDGESIDDYLDRLSEIVNKLRSLGEKISDEDVVEKILRSLPEKYEQIVTSIEES 91

Query: 158 RD--TWNITELTAYVVQEEESLKKGKS 182
           +D  T  + EL   +   EE LK+ K 
Sbjct: 92  KDLSTLTLEELVGRLKAHEERLKERKE 118

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	261
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	99.89
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	99.87
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	99.77
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.7
PF13961	27	DUF4219: Domain of unknown function (DUF4219)	98.54
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	98.25
PF13696	32	zf-CCHC_2: Zinc knuckle	97.94
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	97.78
PF13917	42	zf-CCHC_3: Zinc knuckle	97.19
smart00343	26	ZnF_C2HC zinc finger.	96.99
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.58
PF14392	49	zf-CCHC_4: Zinc knuckle	96.19
PF15288	40	zf-CCHC_6: Zinc knuckle	95.89
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.47
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.17
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.16
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.05
PTZ00368	148	universal minicircle sequence binding protein (UMS	94.95
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.97
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	89.58
PF02023	95	SCAN: SCAN domain; InterPro: IPR003309 A number of	88.31
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	86.69
KOG2044	931	consensus 5'-3' exonuclease HKE1/RAT1 [Replication	81.82
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	81.09

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

Probab=99.89  E-value=1.3e-22  Score=148.91  Aligned_cols=113  Identities=30%  Similarity=0.431  Sum_probs=106.8

Q ss_pred             cccHHHHHHHHHHhhccccHHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHhCCCchH
Q 048427           69 CDKAKDYLAAVGRTFKKIDKAEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFG  148 (261)
Q Consensus        69 ~~~a~~lW~~L~~~y~~~~~~~~~~l~~~l~~~~~~~~~~v~~~~~~l~~l~~~L~~~g~~~~d~~~~~~lL~~Lp~~~~  148 (261)
                      |++|+++|++|+..|+..+.+++..++++|+.+++.++.+|.+|+.+|+.++++|..+|.+++|++++.+||.+||++|+
T Consensus         1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~sy~   80 (119)
T PF14227_consen    1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPSYD   80 (119)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCHhHH
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCC--CCCCHHHHHHHHHHHHHHhhhCC
Q 048427          149 NLRSQYNTQR--DTWNITELTAYVVQEEESLKKGK  181 (261)
Q Consensus       149 ~~~~~~~~~~--~~~t~~~l~~~l~~~e~~~~~~~  181 (261)
                      +|+.++....  ..+++++|+++|..+|.+++...
T Consensus        81 ~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~~~  115 (119)
T PF14227_consen   81 SFVTALLYSKPEDELTLEEVKSKLLQEEERRKKSK  115 (119)
T ss_pred             HHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHhcc
Confidence            9999988754  78999999999999988876553

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

Probab=99.87  E-value=1.7e-21  Score=143.02  Aligned_cols=112  Identities=23%  Similarity=0.328  Sum_probs=106.0

Q ss_pred             ccHHHHHHHHHHhhccccH---HHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHhCCCc
Q 048427           70 DKAKDYLAAVGRTFKKIDK---AEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQ  146 (261)
Q Consensus        70 ~~a~~lW~~L~~~y~~~~~---~~~~~l~~~l~~~~~~~~~~v~~~~~~l~~l~~~L~~~g~~~~d~~~~~~lL~~Lp~~  146 (261)
                      +||+++|++|+..|.+.+.   +++..|..+|.++++.++.+|.+|+.+|..|+++|..+|.+++|.+++..||.|||++
T Consensus         1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~   80 (119)
T PF14223_consen    1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPS   80 (119)
T ss_pred             ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCch
Confidence            4899999999999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhcCCCCC--CHHHHHHHHHHHHHHhhhCC
Q 048427          147 FGNLRSQYNTQRDTW--NITELTAYVVQEEESLKKGK  181 (261)
Q Consensus       147 ~~~~~~~~~~~~~~~--t~~~l~~~l~~~e~~~~~~~  181 (261)
                      |++++..+....+..  |+++|+++|+.+|.+++...
T Consensus        81 y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~~~  117 (119)
T PF14223_consen   81 YDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKSKE  117 (119)
T ss_pred             hHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHcc
Confidence            999999999876655  99999999999999877553

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

Probab=99.77  E-value=2e-18  Score=131.95  Aligned_cols=122  Identities=16%  Similarity=0.113  Sum_probs=99.2

Q ss_pred             cccccCcccccccCCCChHHHHHHHHHHhhhcCc-ceeecc-CCCCCC----CCCChHHHHH---------hhccccCCC
Q 048427            4 SYIVTGSLTYCVAIGENFEDRRDSILFYLSTLNR-DLALRV-DEPAKP----TDKSTAVEKA---------ETTRDNIPA   68 (261)
Q Consensus         4 s~~~~~~~~i~kl~G~Ny~~Wk~~~~~~L~~~~~-~~~~~~-~~p~~~----~~~~~~~~~~---------~~i~~~i~~   68 (261)
                      |.+....+.+++|||+||..|+..|+.+|..+++ +++.+. +.|...    ..|...+.++         ++|+..|..
T Consensus         1 ~~~~~~~i~~~kL~g~NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~~~~~~W~~~d~~v~swl~~sis~~i~~~i~~   80 (152)
T PF14244_consen    1 SDNPSQPITSIKLNGSNYLSWSQQMEMALRGKGLWGFIDGTIPKPPETDPAYEKWERKDQLVLSWLLNSISPDILSTIIF   80 (152)
T ss_pred             CCCCCCcccccCCCCccHHHHHHHHHHHHHhCCCcccccCccccccccchhhhhHHHhhhHHHHHHHHhhcHHHHhhhHh
Confidence            4455666777999999999999999999999998 555553 233221    2455666555         778888899


Q ss_pred             cccHHHHHHHHHHhhcccc-HHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHH--HHHHhC
Q 048427           69 CDKAKDYLAAVGRTFKKID-KAEKGNYLRLLANTQYDGVSGVREHILKMTSYH--KKLKEM  126 (261)
Q Consensus        69 ~~~a~~lW~~L~~~y~~~~-~~~~~~l~~~l~~~~~~~~~~v~~~~~~l~~l~--~~L~~~  126 (261)
                      +++|+++|++|+++|...+ .++.+.|..+|..++.. +.+|.+|+.+|+.++  .+|...
T Consensus        81 ~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~-~~sv~ey~~~lk~l~~~~el~~~  140 (152)
T PF14244_consen   81 CETAKEIWDALKERFSQKSNASRVFQLRNELHSLKQG-DKSVTEYFNKLKSLWQEDELDEY  140 (152)
T ss_pred             hhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHhHHHHHhCc
Confidence            9999999999999999999 89999999999999954 677999999999999  556554

>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=98.70  E-value=6.4e-09  Score=48.93  Aligned_cols=18  Identities=33%  Similarity=0.541  Sum_probs=16.4

Q ss_pred             ccceeccccCcccccCCC
Q 048427          235 RKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~  252 (261)
                      ..||+||++||++++||+
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            369999999999999995

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 ....

>PF13961 DUF4219: Domain of unknown function (DUF4219)

Probab=98.54  E-value=5.4e-08  Score=50.97  Aligned_cols=24  Identities=17%  Similarity=0.120  Sum_probs=22.2

Q ss_pred             cCCCChHHHHHHHHHHhhhcCcce
Q 048427           16 AIGENFEDRRDSILFYLSTLNRDL   39 (261)
Q Consensus        16 l~G~Ny~~Wk~~~~~~L~~~~~~~   39 (261)
                      |||+||..|+.+|+++|+.+++.-
T Consensus         1 l~g~NY~~W~~~M~~~L~~~~lW~   24 (27)
T PF13961_consen    1 LDGTNYSTWKIRMKAYLESQDLWD   24 (27)
T ss_pred             CCccCHHHHHHHHHHHHHHcchhh
Confidence            799999999999999999999843

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

Probab=98.25  E-value=2.1e-05  Score=59.43  Aligned_cols=130  Identities=15%  Similarity=0.153  Sum_probs=86.5

Q ss_pred             cCCC--ChHHHHHHHHHHhhh-cCcceeeccCCCCCCCCCChHHHHHhhccccCCCcccHHHHHHHHHHhhccccHHHHH
Q 048427           16 AIGE--NFEDRRDSILFYLST-LNRDLALRVDEPAKPTDKSTAVEKAETTRDNIPACDKAKDYLAAVGRTFKKIDKAEKG   92 (261)
Q Consensus        16 l~G~--Ny~~Wk~~~~~~L~~-~~~~~~~~~~~p~~~~~~~~~~~~~~~i~~~i~~~~~a~~lW~~L~~~y~~~~~~~~~   92 (261)
                      |+|+  +|..|.......+.. ..+.-+.-..-    -.......-.+.|...-....+-..+|+.|+++|+.+... ..
T Consensus         1 F~G~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~----L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i-~~   75 (145)
T PF03564_consen    1 FDGDPSEWPEFIDQFDSLVHENPDLSDIEKLNY----LRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRI-IQ   75 (145)
T ss_pred             CCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHH----HHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHH-HH
Confidence            6887  788888888877766 33311000000    0000000000223333334566789999999999987653 34


Q ss_pred             HHHHHHHhcc---cCCCCCHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHhCCCchHHH
Q 048427           93 NYLRLLANTQ---YDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPPQFGNL  150 (261)
Q Consensus        93 ~l~~~l~~~~---~~~~~~v~~~~~~l~~l~~~L~~~g~~~~d~~~~~~lL~~Lp~~~~~~  150 (261)
                      .+..+|.++.   ..+...+..++.++..++..|..+|..+.+..++..|+..||+....-
T Consensus        76 ~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~~~~~l~~~i~~KLp~~~~~~  136 (145)
T PF03564_consen   76 ALLEELRNLPPISNDDPEALRSLVDKVNNCIRALKALGVNVDDPLLISIILSKLPPEIREK  136 (145)
T ss_pred             HHHHHHhccccccchhHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHCCHHHHHH
Confidence            5566666665   356677899999999999999999999999999999999999986543

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.94  E-value=6.9e-06  Score=44.13  Aligned_cols=23  Identities=22%  Similarity=0.286  Sum_probs=20.1

Q ss_pred             CCCCccceeccccCcccccCCCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      +-....|+.|+++|||..+||..
T Consensus         5 pP~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    5 PPPGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCCCEeecCCCCCccHhHCCCC
Confidence            45567899999999999999984

>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=97.78  E-value=4.7e-05  Score=52.90  Aligned_cols=66  Identities=18%  Similarity=0.234  Sum_probs=51.9

Q ss_pred             HHHHHHhhccccH--HHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHhCCC
Q 048427           76 LAAVGRTFKKIDK--AEKGNYLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVDLPDDYLVFQNLESLPP  145 (261)
Q Consensus        76 W~~L~~~y~~~~~--~~~~~l~~~l~~~~~~~~~~v~~~~~~l~~l~~~L~~~g~~~~d~~~~~~lL~~Lp~  145 (261)
                      |+.|+..|...-.  .....+..+|.++++ ++.+|.+|+.+|..++..+..   +++|+.++..|+.||.+
T Consensus        29 W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~---~~~e~~~v~~f~~GL~~   96 (96)
T PF03732_consen   29 WEEFKDAFRKRFFPPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP---PMDEEMLVERFIRGLRP   96 (96)
T ss_pred             HHHHHHHHHHHHhhhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC---CcCHHHHHHHHHHCCCC
Confidence            5555444443322  256678888999999 899999999999999998754   78999999999999965

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.

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=97.19  E-value=0.00016  Score=41.71  Aligned_cols=20  Identities=20%  Similarity=0.378  Sum_probs=17.5

Q ss_pred             CCccceeccccCcccccCCC
Q 048427          233 FKRKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~  252 (261)
                      ....|.+|++.|||..+|+.
T Consensus         3 ~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    3 ARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCcCcccCCCCcchhhCCC
Confidence            34679999999999999993

>smart00343 ZnF_C2HC zinc finger

Probab=96.99  E-value=0.00029  Score=36.45  Aligned_cols=18  Identities=33%  Similarity=0.453  Sum_probs=16.2

Q ss_pred             cceeccccCcccccCCCC
Q 048427          236 KCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       236 ~C~~C~~~GH~~~~C~~~  253 (261)
                      .|++|++.||++++|+..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999854

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

Probab=96.58  E-value=0.00087  Score=36.78  Aligned_cols=19  Identities=21%  Similarity=0.106  Sum_probs=12.3

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ..|+.|++-.||+.+|+.+
T Consensus         3 ~~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             -C-TTTSSSCS-TTT---T
T ss_pred             ccCcccCCCcchhhhhhhh
Confidence            4699999999999999877

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=96.19  E-value=0.0017  Score=39.27  Aligned_cols=21  Identities=24%  Similarity=0.604  Sum_probs=17.9

Q ss_pred             CCCccceeccccCcccccCCC
Q 048427          232 SFKRKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~  252 (261)
                      +-...|++||..||...+||+
T Consensus        29 ~lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   29 RLPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             CcChhhcCCCCcCcCHhHcCC
Confidence            344579999999999999985

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=95.89  E-value=0.0052  Score=34.87  Aligned_cols=20  Identities=30%  Similarity=0.491  Sum_probs=17.6

Q ss_pred             ccceeccccCccc--ccCCCCc
Q 048427          235 RKCHFCKKLGHKR--ELNAGDS  254 (261)
Q Consensus       235 ~~C~~C~~~GH~~--~~C~~~~  254 (261)
                      ++|..||..||.+  +.||-+.
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            5799999999999  7899873

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

Probab=95.47  E-value=0.0067  Score=47.05  Aligned_cols=17  Identities=29%  Similarity=0.530  Sum_probs=13.5

Q ss_pred             ccceeccccCcccccCC
Q 048427          235 RKCHFCKKLGHKRELNA  251 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~  251 (261)
                      .+|++||..||++++|.
T Consensus        98 ~~C~~Cg~~GH~~~dC~  114 (190)
T COG5082          98 KKCYNCGETGHLSRDCN  114 (190)
T ss_pred             cccccccccCccccccC
Confidence            67888888888888884

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

Probab=95.17  E-value=0.009  Score=46.37  Aligned_cols=21  Identities=24%  Similarity=0.354  Sum_probs=18.8

Q ss_pred             CCCCccceeccccCcccccCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNA  251 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~  251 (261)
                      ......||+||..||.++|||
T Consensus        57 ~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          57 REENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             cccccccchhcccCcccccCC
Confidence            456678999999999999999

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

Probab=95.16  E-value=0.019  Score=47.41  Aligned_cols=28  Identities=14%  Similarity=0.192  Sum_probs=22.9

Q ss_pred             CCCCccceeccccCcccccCCCCccccc
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGDSKHGW  258 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~~~~~~  258 (261)
                      +.....||.||..|||..+||.-+-+.|
T Consensus       173 pPpgY~CyRCGqkgHwIqnCpTN~Dpnf  200 (427)
T COG5222         173 PPPGYVCYRCGQKGHWIQNCPTNQDPNF  200 (427)
T ss_pred             CCCceeEEecCCCCchhhcCCCCCCCCc
Confidence            4556789999999999999998755544

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

Probab=95.05  E-value=0.0092  Score=49.15  Aligned_cols=23  Identities=26%  Similarity=0.266  Sum_probs=19.6

Q ss_pred             CCCCccceeccccCcccccCCCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      -...-.|+.||+.|||.++||..
T Consensus       157 mgDq~~cyrcGkeghwskEcP~~  179 (346)
T KOG0109|consen  157 MGDQSGCYRCGKEGHWSKECPVD  179 (346)
T ss_pred             CCCHHHheeccccccccccCCcc
Confidence            34455799999999999999987

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

Probab=94.95  E-value=0.014  Score=44.23  Aligned_cols=18  Identities=22%  Similarity=0.462  Sum_probs=10.2

Q ss_pred             ccceeccccCcccccCCC
Q 048427          235 RKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~  252 (261)
                      ..|++|+..||++++||+
T Consensus       130 ~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        130 KTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             CccccCCCcCcccccCCC
Confidence            455555555555555554

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

Probab=91.97  E-value=0.1  Score=39.48  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=16.2

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...|++|+..||++++||..
T Consensus        52 ~~~C~~Cg~~GH~~~~Cp~~   71 (148)
T PTZ00368         52 ERSCYNCGKTGHLSRECPEA   71 (148)
T ss_pred             CcccCCCCCcCcCcccCCCc
Confidence            45788888888888888876

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

Probab=89.58  E-value=0.16  Score=42.32  Aligned_cols=19  Identities=26%  Similarity=0.492  Sum_probs=17.5

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ..||.||..||+..+|+..
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             CccCCCCcCCcchhhCCCC
Confidence            7899999999999999954

>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=88.31  E-value=3.2  Score=28.80  Aligned_cols=73  Identities=21%  Similarity=0.293  Sum_probs=51.9

Q ss_pred             HHHHHHhcccCCCCCHHHHHHHHHHHHHHHHhCCC----CCChHHHHHHHHHhCCCchHHHHHHHhcCCCCCCHHHHHHH
Q 048427           94 YLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDV----DLPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAY  169 (261)
Q Consensus        94 l~~~l~~~~~~~~~~v~~~~~~l~~l~~~L~~~g~----~~~d~~~~~~lL~~Lp~~~~~~~~~~~~~~~~~t~~~l~~~  169 (261)
                      ...+|.++++.++.+..+++.+|..++.+=-....    .|-|-+++..||..||++....+..    ..+-|.+++...
T Consensus         5 ~r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~pe~~tkeqi~ellvlEQFL~~lP~e~~~wV~e----~~p~s~~ea~~L   80 (95)
T PF02023_consen    5 YRQRFRSFQYQEGEGPREFLSRLRELCDRWLQPEVHTKEQILELLVLEQFLNILPPEVQTWVRE----RKPESAEEAVAL   80 (95)
T ss_dssp             HHHHHHT--CCTTTSHHHHHHHHHHHHHHHH-TTTS-HHHHHHHHHHHHHHHHS-HHHHHHHHT----CS-SSHHHHHHH
T ss_pred             HHHHHhCCCCCCCCCHHHHHHHHHHHHHHhCccccCcHHHHHHHHHHHHHHHHCCHHHHHHHHh----cCCCCHHHHHHH
Confidence            45679999999999999999999999987644333    2446678889999999988776653    234477777776


Q ss_pred             H
Q 048427          170 V  170 (261)
Q Consensus       170 l  170 (261)
                      +
T Consensus        81 a   81 (95)
T PF02023_consen   81 A   81 (95)
T ss_dssp             H
T ss_pred             H
Confidence            6

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=86.69  E-value=0.31  Score=42.34  Aligned_cols=22  Identities=23%  Similarity=0.445  Sum_probs=19.3

Q ss_pred             CCCccceeccccCcccccCCCC
Q 048427          232 SFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      .....|.|||..||...+||+.
T Consensus       568 ~~~kGCayCgGLGHRItdCPKl  589 (610)
T KOG0341|consen  568 GGEKGCAYCGGLGHRITDCPKL  589 (610)
T ss_pred             CCccccccccCCCcccccCchh
Confidence            3445799999999999999998

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

Probab=81.82  E-value=0.71  Score=43.58  Aligned_cols=25  Identities=24%  Similarity=0.623  Sum_probs=20.6

Q ss_pred             CCCCccceeccccCcccccCCCCcc
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGDSK  255 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~~~  255 (261)
                      +.+..+|+.||..||.+++|.-+.+
T Consensus       257 P~~~~~C~~cgq~gh~~~dc~g~~~  281 (931)
T KOG2044|consen  257 PNKPRRCFLCGQTGHEAKDCEGKPR  281 (931)
T ss_pred             CCCcccchhhcccCCcHhhcCCcCC
Confidence            4556679999999999999987733

>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=81.09  E-value=0.84  Score=33.56  Aligned_cols=22  Identities=27%  Similarity=0.302  Sum_probs=19.3

Q ss_pred             CCCCccceeccccCcccccCCCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ....+.|.+|+ -.||...||-+
T Consensus       103 ~~~~v~CR~Ck-GdH~T~~CPyK  124 (128)
T PF12353_consen  103 GKSKVKCRICK-GDHWTSKCPYK  124 (128)
T ss_pred             CCceEEeCCCC-CCcccccCCcc
Confidence            56778999997 68999999976

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	261
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.65
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.64
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.62
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.48
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.07
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.55
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.54
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.49
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.47
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.46
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.41
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.39
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.34
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.33
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.3
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.3
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.24
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.21
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.17
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.14
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.0
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.99
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.74
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.7
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.5
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.11
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	95.19
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	94.43
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	89.15
3e2u_E	42	CAP-Gly domain-containing linker protein 1; struct	85.46

>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=98.65  E-value=1.3e-08  Score=57.47  Aligned_cols=24  Identities=21%  Similarity=0.454  Sum_probs=20.8

Q ss_pred             CCCCccceeccccCcccccCCCCc
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ......||+||+.|||+++||+..
T Consensus         7 ~~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            7 QLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCCCeeeECCCCCcchhhCcCCc
Confidence            445678999999999999999984

>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=98.64  E-value=2.8e-08  Score=60.56  Aligned_cols=25  Identities=20%  Similarity=0.472  Sum_probs=21.7

Q ss_pred             CCCCccceeccccCcccccCCCCcc
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGDSK  255 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~~~  255 (261)
                      ......||+||+.|||+++||++.+
T Consensus        20 ~~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           20 QLDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TCCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCCcceeCCCCCcccccCcCCcc
Confidence            5567789999999999999999844

>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=98.62  E-value=1.5e-08  Score=53.52  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=20.3

Q ss_pred             CCccceeccccCcccccCCCCccc
Q 048427          233 FKRKCHFCKKLGHKRELNAGDSKH  256 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~~~~~  256 (261)
                      +...||+||+.||++++|+...+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~prkk   28 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAPRRQ   28 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSSSC
T ss_pred             CCCEEEECCccccCHhHCcccccC
Confidence            457799999999999999987543

>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=98.48  E-value=4.3e-08  Score=50.24  Aligned_cols=19  Identities=26%  Similarity=0.485  Sum_probs=17.6

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ..||+||+.||++++||..
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            5699999999999999986

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

Probab=98.07  E-value=1.5e-06  Score=52.65  Aligned_cols=20  Identities=25%  Similarity=0.378  Sum_probs=17.6

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...||.||++|||+++||..
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            45799999999999999954

>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=97.55  E-value=3.1e-05  Score=46.02  Aligned_cols=21  Identities=24%  Similarity=0.438  Sum_probs=16.6

Q ss_pred             CccceeccccCcccccCCCCc
Q 048427          234 KRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ...||.||+.||++++||.+.
T Consensus        27 ~~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           27 RQGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CCSCSSSCCSSCCGGGCCSSC
T ss_pred             CCeeCcCCCcCCccCCCcCCC
Confidence            467888888888888888763

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

Probab=97.54  E-value=2.6e-05  Score=43.95  Aligned_cols=18  Identities=28%  Similarity=0.573  Sum_probs=11.7

Q ss_pred             cceeccccCcccccCCCC
Q 048427          236 KCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       236 ~C~~C~~~GH~~~~C~~~  253 (261)
                      .||+|++.||++++||..
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            466666666666666653

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

Probab=97.49  E-value=8.3e-05  Score=48.18  Aligned_cols=20  Identities=30%  Similarity=0.687  Sum_probs=14.5

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...||+|++.||++++||..
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCTTG
T ss_pred             CCccCCcCCcCCccCcCcCC
Confidence            45677777777777777765

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

Probab=97.47  E-value=3.7e-05  Score=43.32  Aligned_cols=19  Identities=16%  Similarity=0.305  Sum_probs=17.2

Q ss_pred             CccceeccccCcccccCCC
Q 048427          234 KRKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~  252 (261)
                      ...||.||+.||++++||+
T Consensus        21 ~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           21 QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CSSCTTTCCSSSCTTTSCC
T ss_pred             CCccccCCCCCCccCcCcC
Confidence            4679999999999999985

>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=97.46  E-value=4.8e-05  Score=45.19  Aligned_cols=22  Identities=23%  Similarity=0.332  Sum_probs=18.9

Q ss_pred             CCCccceeccccCcccccCCCC
Q 048427          232 SFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      +....||+||+.||++++|+..
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCCS
T ss_pred             CCcCeeeecCCCCcChhhCcCC
Confidence            3456799999999999999975

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

Probab=97.41  E-value=4.9e-05  Score=42.27  Aligned_cols=16  Identities=31%  Similarity=0.511  Sum_probs=9.7

Q ss_pred             ceeccccCcccccCCC
Q 048427          237 CHFCKKLGHKRELNAG  252 (261)
Q Consensus       237 C~~C~~~GH~~~~C~~  252 (261)
                      ||+|+++||++++||.
T Consensus         3 C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            3 CYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             BSSSCCSSCCTTTSSC
T ss_pred             ccccCCCCcchhhCcC
Confidence            6666666666666654

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

Probab=97.39  E-value=5.6e-05  Score=42.02  Aligned_cols=18  Identities=28%  Similarity=0.551  Sum_probs=16.7

Q ss_pred             ccceeccccCcccccCCC
Q 048427          235 RKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~  252 (261)
                      ..||.|+++||++++||.
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            679999999999999984

>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=97.34  E-value=6.1e-05  Score=45.95  Aligned_cols=20  Identities=30%  Similarity=0.506  Sum_probs=14.8

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...||.||+.||++++||..
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSS
T ss_pred             CCEeCCCCCcCCccCCCcCc
Confidence            45677777777777777765

>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=97.33  E-value=7.4e-05  Score=46.46  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=19.3

Q ss_pred             CCccceeccccCcccccCCCCc
Q 048427          233 FKRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ....||.|++.||++++|+...
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTT
T ss_pred             CCcceeECCCCCCccCcCCCcc
Confidence            3567999999999999999873

>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=8.9e-05  Score=45.20  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=19.0

Q ss_pred             CCCccceeccccCcccccCCCC
Q 048427          232 SFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      .....||+|++.||++++|+..
T Consensus        10 ~~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           10 RKTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GGTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCCcceeeeCCCCcChhhcCCC
Confidence            4456799999999999999975

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

Probab=97.30  E-value=8.1e-05  Score=46.43  Aligned_cols=21  Identities=19%  Similarity=0.692  Sum_probs=18.8

Q ss_pred             CccceeccccCcccccCCCCc
Q 048427          234 KRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ...||+|++.||++++||...
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            467999999999999999874

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

Probab=97.24  E-value=0.00012  Score=45.70  Aligned_cols=21  Identities=19%  Similarity=0.366  Sum_probs=18.5

Q ss_pred             CccceeccccCcccccCCCCc
Q 048427          234 KRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ...||+|++.||++++||...
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCcccccCCCCeehhhCcCCc
Confidence            356999999999999999863

>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=97.21  E-value=0.00011  Score=46.11  Aligned_cols=27  Identities=22%  Similarity=0.427  Sum_probs=20.9

Q ss_pred             CCccceeccccCcccccCCCCc-ccccc
Q 048427          233 FKRKCHFCKKLGHKRELNAGDS-KHGWK  259 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~~~-~~~~~  259 (261)
                      ....||+|++.||++++||... +-.|+
T Consensus        28 ~~~~C~~Cg~~GH~ar~Cp~~~~~~~~~   55 (63)
T 2cqf_A           28 QPKKCHFCQSISHMVASCPLKAQQGPSA   55 (63)
T ss_dssp             CSSCCTTTCCSSSCTTTCTGGGCSCCCC
T ss_pred             CCCccCCcCCcCCccCcCCCccccCCcc
Confidence            4578999999999999999863 33444

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

Probab=97.17  E-value=0.00014  Score=48.16  Aligned_cols=23  Identities=17%  Similarity=0.153  Sum_probs=19.7

Q ss_pred             CCCccceeccccCcccccCCCCc
Q 048427          232 SFKRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      .....|++||+.||+.++||+..
T Consensus        44 ~~~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B           44 FHTIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             -CCCBCSSSSCBSSCGGGCSSCC
T ss_pred             CCCCeecccCCCCcCcccCCccc
Confidence            34578999999999999999874

>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=97.14  E-value=0.00027  Score=44.30  Aligned_cols=20  Identities=20%  Similarity=0.302  Sum_probs=17.6

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...||+|++.||++++|+..
T Consensus         7 ~~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            7 GDRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             CCCCSSSCCSSSCTTTCCSC
T ss_pred             CCcccccCCCCcChhhCCCC
Confidence            35699999999999999963

>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=97.00  E-value=0.00011  Score=45.74  Aligned_cols=18  Identities=28%  Similarity=0.438  Sum_probs=0.0

Q ss_pred             cceeccccCcccccCCCC
Q 048427          236 KCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       236 ~C~~C~~~GH~~~~C~~~  253 (261)
                      .||+|+++||++++||..
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~   20 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEH   20 (60)
T ss_dssp             ------------------
T ss_pred             ccccCCCCCcCHhhCcCC
Confidence            599999999999999986

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

Probab=96.99  E-value=0.00025  Score=45.90  Aligned_cols=22  Identities=23%  Similarity=0.274  Sum_probs=19.0

Q ss_pred             CCCCccceeccccCcccccCCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNAG  252 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~  252 (261)
                      ......||+|++.||++++|+.
T Consensus        21 ~~r~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           21 RSKGDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             CSTTSCCTTTCCSSSCTTTCSS
T ss_pred             cCCCCcccccCCcCcCcccCCC
Confidence            3455679999999999999996

>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=96.74  E-value=0.00069  Score=50.17  Aligned_cols=21  Identities=29%  Similarity=0.672  Sum_probs=14.1

Q ss_pred             CccceeccccCcccccCCCCc
Q 048427          234 KRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ...||+|++.||++++||...
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTT
T ss_pred             CCcccccCCcCCEeccCcCCC
Confidence            456777777777777777653

>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=96.70  E-value=0.00061  Score=50.49  Aligned_cols=23  Identities=17%  Similarity=0.182  Sum_probs=19.6

Q ss_pred             CCCCccceeccccCcccccCCCC
Q 048427          231 ESFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       231 ~~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ++....||+|++.||++++|+..
T Consensus        94 p~~~~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           94 PKGGDRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             CCCSCCCTTTCCSSCCGGGCCSC
T ss_pred             cCCCCcccEeCCccchhhhCCCC
Confidence            34467899999999999999983

>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=0.00064  Score=44.97  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=16.3

Q ss_pred             CCccceeccccCcccccCCCC
Q 048427          233 FKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ++..|++|+..||++++||..
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGG
T ss_pred             ccCCCCCCCCCCCccccCCCc
Confidence            456799999999999999875

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

Probab=96.11  E-value=0.002  Score=46.24  Aligned_cols=22  Identities=18%  Similarity=0.163  Sum_probs=19.2

Q ss_pred             CCCccceeccccCcccccCCCC
Q 048427          232 SFKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...+.|++|++.||++++||+.
T Consensus       103 ~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A          103 FHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCCCCTTTTSSSCTTTTTSCCC
T ss_pred             CCCCCcCCCCCCCcCcccCcCC
Confidence            4567899999999999999973

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

Probab=95.19  E-value=0.0052  Score=30.28  Aligned_cols=20  Identities=25%  Similarity=0.567  Sum_probs=17.2

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ++-|-.|...||+..+|..-
T Consensus         3 RpYCe~CE~FGH~t~~C~d~   22 (26)
T 2hqh_E            3 RPYCEICEMFGHWATNCNDD   22 (26)
T ss_dssp             -CEETTTTEESSCGGGCCTT
T ss_pred             CccchHHHHhCcccccCCcc
Confidence            46799999999999999765

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

Probab=94.43  E-value=0.015  Score=41.54  Aligned_cols=20  Identities=30%  Similarity=0.547  Sum_probs=18.0

Q ss_pred             CccceeccccCcccccCCCC
Q 048427          234 KRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       234 ~~~C~~C~~~GH~~~~C~~~  253 (261)
                      ...|+.|+..||++++||..
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCS
T ss_pred             CccCCCCCcCCcchhhCCCc
Confidence            46899999999999999976

>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}

Probab=85.46  E-value=0.25  Score=27.35  Aligned_cols=21  Identities=24%  Similarity=0.479  Sum_probs=18.2

Q ss_pred             CCccceeccccCcccccCCCC
Q 048427          233 FKRKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       233 ~~~~C~~C~~~GH~~~~C~~~  253 (261)
                      .+.-|-.|-..|||..+|..-
T Consensus        19 eRpYCe~CEVFGH~t~eC~dd   39 (42)
T 3e2u_E           19 ERPYCEICEMFGHWATNCNDD   39 (42)
T ss_dssp             -CCEETTTTEESSCGGGCCTT
T ss_pred             cCcccccceecccccccCCcc
Confidence            467899999999999999865

---

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	261
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.92
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	98.32
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	98.31
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.95
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.81
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	95.76
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	95.64
d2fi2a1	92	Zinc finger protein 42 {Human (Homo sapiens) [TaxI	88.25

>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=98.92  E-value=2e-10  Score=56.22  Aligned_cols=26  Identities=23%  Similarity=0.413  Sum_probs=21.9

Q ss_pred             CCCccceeccccCcccccCCCCcccc
Q 048427          232 SFKRKCHFCKKLGHKRELNAGDSKHG  257 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~~~~~  257 (261)
                      ++.++||+||+.||++++|..+.+.|
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAPRkkg   29 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAPRRQG   29 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSSSSCC
T ss_pred             cceeEeecCCccchhhhhccCcccCC
Confidence            45688999999999999998875543

>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=98.32  E-value=1.7e-07  Score=49.27  Aligned_cols=23  Identities=22%  Similarity=0.449  Sum_probs=19.8

Q ss_pred             CCCccceeccccCcccccCCCCc
Q 048427          232 SFKRKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       232 ~~~~~C~~C~~~GH~~~~C~~~~  254 (261)
                      -....|-||++.|||+++||++.
T Consensus         8 L~kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_           8 LDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             ccchhhHHHhhcCchhhhCccCC
Confidence            34567999999999999999984

>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=98.31  E-value=9.5e-08  Score=44.47  Aligned_cols=19  Identities=26%  Similarity=0.485  Sum_probs=17.5

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      +.||-||+.||++++|...
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            5799999999999999875

>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=97.95  E-value=1.5e-06  Score=48.37  Aligned_cols=20  Identities=25%  Similarity=0.456  Sum_probs=17.9

Q ss_pred             ccceeccccCcccccCCCCc
Q 048427          235 RKCHFCKKLGHKRELNAGDS  254 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~~  254 (261)
                      ..|+.||+.||++++||+++
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCCCeecccCCCCC
Confidence            46999999999999999873

>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=97.81  E-value=2.9e-06  Score=47.21  Aligned_cols=19  Identities=32%  Similarity=0.478  Sum_probs=17.7

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ++||+||+.||++++||..
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSC
T ss_pred             CccccCCCcCcCcccCcCC
Confidence            6799999999999999985

>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=95.76  E-value=0.002  Score=31.88  Aligned_cols=19  Identities=26%  Similarity=0.263  Sum_probs=17.5

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ..|..|++--||+++|+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCS
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            4699999999999999987

>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=95.64  E-value=0.0024  Score=31.84  Aligned_cols=19  Identities=21%  Similarity=0.260  Sum_probs=17.5

Q ss_pred             ccceeccccCcccccCCCC
Q 048427          235 RKCHFCKKLGHKRELNAGD  253 (261)
Q Consensus       235 ~~C~~C~~~GH~~~~C~~~  253 (261)
                      ..|..|++--||+++|+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCCT
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            4699999999999999987

>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=88.25  E-value=1.5  Score=27.55  Aligned_cols=73  Identities=16%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             HHHHHHhcccCCCCCHHHHHHHHHHHHHHHHhCCCC----CChHHHHHHHHHhCCCchHHHHHHHhcCCCCCCHHHHHHH
Q 048427           94 YLRLLANTQYDGVSGVREHILKMTSYHKKLKEMDVD----LPDDYLVFQNLESLPPQFGNLRSQYNTQRDTWNITELTAY  169 (261)
Q Consensus        94 l~~~l~~~~~~~~~~v~~~~~~l~~l~~~L~~~g~~----~~d~~~~~~lL~~Lp~~~~~~~~~~~~~~~~~t~~~l~~~  169 (261)
                      ...+|..+++.++.+..+++.+++.++.+=-.....    |-|-++...||..||++....+..-.    +-|.+++...
T Consensus         7 ~rq~FR~f~y~e~~~p~e~l~rL~eLc~~WL~pe~~tkeqilelLVLEQFl~~lP~e~~~~V~e~~----p~s~~eav~L   82 (92)
T d2fi2a1           7 ARLRFRCFHYEEATGPQEALAQLRELCRQWLRPEVRSKEQMLELLVLEQFLGALPPEIQARVQGQR----PGSPEEAAAL   82 (92)
T ss_dssp             HHHHHHSCCCCTTTCHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHHHSCHHHHHHHHHHC----CCSHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHCCHHHHHHHHHhC----CCCHHHHHHH
Confidence            456799999999999999999999998876443322    33556788889999999776664333    3377777766


Q ss_pred             H
Q 048427          170 V  170 (261)
Q Consensus       170 l  170 (261)
                      +
T Consensus        83 ~   83 (92)
T d2fi2a1          83 V   83 (92)
T ss_dssp             H
T ss_pred             H
Confidence            5