Citrus Sinensis ID: 040998

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
Protein Sequence
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGKKT
Secondary Structure (PSIPRED)
ccccccEEEEEEEEcccccccccccHHHHHHHccccEEEEEEccccccHHHHHHHHHHHHcccccEEEEEEEccEEEEEEccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHccEEEEEEEEcccccHcccHHHHHHHHHHcccEEEEEccccccccccEEEEEEEEEccccccEEEEEcccEEEEEEcccccHHHccccccccccccccccccccccHcccccc
Coil and Loop (DISEMBL)
TSDKIDSMVAWIKlsnmphyyyhkkvlpMVGQVMGEVIhidfntrsasRRKFVRIAVKIALDKPLCLQFLldgriqkveyeslpincfncgkyghvsigcpengdgeepqdengkkt
Flexible Loop (DISEMBL)
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIdfntrsasrrKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCpengdgeepqdengkkt
Low Complexity Region (SEG)
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGKKT
Disordered region (IsUnstruct)
******SMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGC*****************
Disordered Region (DISOPRED)
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGC*****************
Disordered Region (DISEMBL)
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPEN**************
Disordered Region (DISPRO)
*SDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSI*C*****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGKKT
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	117
332322109	678	hypothetical protein [Beta vulgaris subs	0.820	0.141	0.375	6e-14
87116463	1898	unnamed protein product [Ipomoea batatas	0.837	0.051	0.367	2e-13
255555973	87	hypothetical protein RCOM_0935160 [Ricin	0.743	1.0	0.425	3e-13
15226168	515	zinc ion binding / nucleic acid binding	0.863	0.196	0.356	4e-13
158828302	496	gag non-LTR retrotransposase [Arabidopsi	0.854	0.201	0.35	2e-12
87116458	532	unnamed protein product [Ipomoea batatas	0.837	0.184	0.346	2e-12
357477937	484	hypothetical protein MTR_4g113700 [Medic	0.974	0.235	0.333	3e-12
357445233	504	hypothetical protein MTR_2g005460 [Medic	0.940	0.218	0.336	4e-12
3327393	409	putative Ta11-like non-LTR retroelement	0.888	0.254	0.307	5e-12
356562050	470	PREDICTED: uncharacterized protein LOC10	0.837	0.208	0.377	7e-12

>gi|332322109|emb|CCA66008.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 81.6 bits (200), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 58/96 (60%)

Query: 5   IDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKP 64
           I  + AW+++ ++   Y+ K+ L  +G  +G+VI ID NT S  R ++VR  +++ L KP
Sbjct: 220 IKKLTAWVRIPHLSVEYFDKQFLHSIGSKIGKVIKIDRNTESMDRGQYVRFCIEVDLSKP 279

Query: 65  LCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGC 100
           L  +F L+G++  V+YE L + CF CG  GH    C
Sbjct: 280 LLSKFRLNGKVWIVQYEGLRLICFKCGHLGHKEDTC 315

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116463|dbj|BAE79384.1| unnamed protein product [Ipomoea batatas]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/98 (36%), Positives = 54/98 (55%)

Query: 4   KIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDK 63
           K   M  W++LS +   Y+    +  + + +G+ + +D  T +  R +F R AV+I LDK
Sbjct: 183 KFQKMAVWVRLSELSMEYFRDDTIKAILENIGKPLGLDRTTMARERGRFARAAVEIDLDK 242

Query: 64  PLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCP 101
           PL  +  + G +QKVEYE L + CF CG  GH    CP
Sbjct: 243 PLVSEIWVMGDVQKVEYEGLHVVCFGCGVVGHREQACP 280

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555973|ref|XP_002519021.1| hypothetical protein RCOM_0935160 [Ricinus communis] gi|223541684|gb|EEF43232.1| hypothetical protein RCOM_0935160 [Ricinus communis]

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 54/87 (62%)

Query: 5  IDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKP 64
          + ++VAW++   MP  YYH+ +L  + +V+   + +D NT+ A+R KF R+AVK+ L  P
Sbjct: 1  MKTVVAWVRFLRMPVKYYHENILQAIDKVVRTTVKVDMNTQLANRGKFTRVAVKLNLVNP 60

Query: 65 LCLQFLLDGRIQKVEYESLPINCFNCG 91
          L  +  LDG  Q VEYE LP   F CG
Sbjct: 61 LVTKIHLDGFNQHVEYEGLPKIFFTCG 87

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226168|ref|NP_178215.1| zinc ion binding / nucleic acid binding [Arabidopsis thaliana] gi|6598620|gb|AAF18653.1| hypothetical protein [Arabidopsis thaliana] gi|330250297|gb|AEC05391.1| zinc ion binding / nucleic acid binding protein [Arabidopsis thaliana]

 Score = 78.6 bits (192), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 59/101 (58%)

Query: 3   DKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALD 62
           D I +   W++LSN+P+ YYH+ +L  + + +G  + +D NT +  + +F R+ +++ L 
Sbjct: 159 DDIVTTPVWVRLSNIPYNYYHRCLLMEIARGLGRPLKVDMNTINFDKGRFARVCIEVNLA 218

Query: 63  KPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPEN 103
           KPL    L++G    V YE L   C +CG YGH+   CP N
Sbjct: 219 KPLKGTVLINGDRYFVAYEGLSKICSSCGIYGHLVHSCPRN 259

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|158828302|gb|ABW81177.1| gag non-LTR retrotransposase [Arabidopsis cebennensis]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 56/100 (56%)

Query: 3   DKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALD 62
           D+I +   WI+LSN+P  +YHK +L  + + +G  + +D  T    R +F R+ V++ L 
Sbjct: 152 DEITTTPVWIRLSNLPVTFYHKTILMGIAKGLGHPVKVDLITIRFDRGRFARVCVEVNLK 211

Query: 63  KPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPE 102
           +PL    +++GR   V YE L   C  CG YGH+   C +
Sbjct: 212 RPLKGTVMVNGRRYYVSYEGLNAICSKCGMYGHLVHTCSQ 251

Source: Arabidopsis cebennensis

Species: Arabidopsis cebennensis

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116458|dbj|BAE79381.1| unnamed protein product [Ipomoea batatas]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/98 (34%), Positives = 53/98 (54%)

Query: 4   KIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDK 63
           K   M  W++L  +   Y+    +  + + +G+ + +D  T +  + +F R AV+I LDK
Sbjct: 183 KFQKMAVWVRLPELSMEYFRDDTIKAILENIGKPLRLDRTTMAREKGRFARAAVEIDLDK 242

Query: 64  PLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCP 101
           PL  +  + G +QKVEYE L + CF CG  GH    CP
Sbjct: 243 PLVSEIWVMGDVQKVEYEGLHVVCFGCGVVGHREQACP 280

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357477937|ref|XP_003609254.1| hypothetical protein MTR_4g113700 [Medicago truncatula] gi|355510309|gb|AES91451.1| hypothetical protein MTR_4g113700 [Medicago truncatula]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 58/114 (50%)

Query: 4   KIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDK 63
           K+D  V W++   +   YY + +L  +   +G+ I +D NT    R KF R+ V+I L  
Sbjct: 170 KVDRTVVWVRFPGLNLVYYDESLLLAMATTLGQPIKVDTNTLKVERGKFARVCVEIDLTV 229

Query: 64  PLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGKKT 117
           P+  +  ++G   KV+Y+ L + C NCG YGH+   C       EP   N  KT
Sbjct: 230 PVVGKIWVNGHWYKVQYKGLHLICTNCGCYGHLGRNCCSKPPAAEPVTLNHLKT 283

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445233|ref|XP_003592894.1| hypothetical protein MTR_2g005460 [Medicago truncatula] gi|92893902|gb|ABE91952.1| Zinc finger, CCHC-type [Medicago truncatula] gi|355481942|gb|AES63145.1| hypothetical protein MTR_2g005460 [Medicago truncatula]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 37/110 (33%), Positives = 56/110 (50%)

Query: 4   KIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDK 63
           K+D  V W++   +   YY +  L  +   +G  I +D NT    R KF R+ V+I L  
Sbjct: 170 KVDRTVVWVRFPGLNLVYYDESFLLAMASALGRPIKVDTNTLKVERGKFARVCVEIDLTV 229

Query: 64  PLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDEN 113
           P+  +  ++G   KV+YE L + C NCG YGH+   C E     +P+  N
Sbjct: 230 PVVGKIWVNGHWYKVQYEGLHLICTNCGCYGHLGRNCMEKPSTFDPRSPN 279

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3327393|gb|AAC26675.1| putative Ta11-like non-LTR retroelement protein [Arabidopsis thaliana]

 Score = 75.1 bits (183), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 58/104 (55%)

Query: 3   DKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALD 62
           D+I + + W+++SN+P  YYH+ +L  + + +G+ I ++       R  F R+ VK+ L 
Sbjct: 111 DEIVTTLVWVRISNLPVNYYHETILTAIVEGLGKPIKVNLTILRKERAHFARVCVKVNLK 170

Query: 63  KPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPENGDG 106
           +PL    +++G      YE L + C  CG +GH++  CP+   G
Sbjct: 171 QPLKGTVVVNGECYYASYEGLNVICSLCGVFGHLAGACPKRSPG 214

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562050|ref|XP_003549288.1| PREDICTED: uncharacterized protein LOC100791212 [Glycine max]

 Score = 74.3 bits (181), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 55/98 (56%)

Query: 4   KIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDK 63
           KID  + W++  ++   YY + +L  + + +G  I +D NT    R  F RI V+I L+K
Sbjct: 173 KIDKTMVWVRFPSLNLIYYDENILLALARAIGTPIKVDSNTLDVRRGHFARICVQIDLNK 232

Query: 64  PLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCP 101
           P+  +  L G   KVEYE L   C +CG YGH++  CP
Sbjct: 233 PVVGKVGLKGYWYKVEYEGLHRICSSCGCYGHLARECP 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	117
TAIR|locus:2045756	515	AT2G01050 [Arabidopsis thalian	0.863	0.196	0.356	2e-14
TAIR|locus:1009023409	361	AT5G36228 [Arabidopsis thalian	0.957	0.310	0.273	5.3e-08
TAIR|locus:2099826	336	AT3G31430 "AT3G31430" [Arabido	0.880	0.306	0.259	1.6e-06
TAIR|locus:1006230619	367	AT5G18636 "AT5G18636" [Arabido	0.777	0.247	0.239	4.8e-05
TAIR|locus:2146990	367	AT5G25200 "AT5G25200" [Arabido	0.777	0.247	0.239	4.8e-05
TAIR|locus:2827815	307	AT2G17920 [Arabidopsis thalian	0.777	0.296	0.218	5.8e-05
TAIR|locus:4515102790	403	AT2G02103 "AT2G02103" [Arabido	0.777	0.225	0.229	0.00019
TAIR|locus:2076106	262	AT3G24070 [Arabidopsis thalian	0.760	0.339	0.247	0.00042
UNIPROTKB|F8VXY6	133	ZCRB1 "Zinc finger CCHC-type a	0.572	0.503	0.324	0.00045
TAIR|locus:2062652	367	AT2G41590 "AT2G41590" [Arabido	0.777	0.247	0.218	0.00045

TAIR|locus:2045756 AT2G01050 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 2.0e-14, P = 2.0e-14
 Identities = 36/101 (35%), Positives = 59/101 (58%)

Query:     3 DKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALD 62
             D I +   W++LSN+P+ YYH+ +L  + + +G  + +D NT +  + +F R+ +++ L 
Sbjct:   159 DDIVTTPVWVRLSNIPYNYYHRCLLMEIARGLGRPLKVDMNTINFDKGRFARVCIEVNLA 218

Query:    63 KPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCPEN 103
             KPL    L++G    V YE L   C +CG YGH+   CP N
Sbjct:   219 KPLKGTVLINGDRYFVAYEGLSKICSSCGIYGHLVHSCPRN 259

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:1009023409 AT5G36228 [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 32/117 (27%), Positives = 56/117 (47%)

Query:     1 TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIA 60
             T D +  +  W+ +  +P  Y  ++ + ++   +GEV+ +DFN  + S+  F+R+ V++ 
Sbjct:   114 TEDFLTFIDVWVHIRGIPLPYVSERTVEIIASTLGEVVAMDFNEETTSQITFIRVKVRMD 173

Query:    61 LDKPLC----LQFLLDGRIQ-KVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDE 112
               +PL     ++F    R     EYE L   C NC +  H    CP     EE  +E
Sbjct:   174 FTEPLRFFRRVRFASRERAMIGFEYEKLQRVCTNCCRVNHQVSHCPYVVHQEEMDNE 230

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2099826 AT3G31430 "AT3G31430" [Arabidopsis thaliana (taxid:3702)]

 Score = 117 (46.2 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 28/108 (25%), Positives = 49/108 (45%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQ-- 68
             W+++  +P  + ++ V+  +G+ +G+V+  DFN    +R  F R+ +   +  PL  Q  
Sbjct:   217 WVQIRGIPFQFLNRGVVEHIGRALGQVLDTDFNVEVVARMDFARVLLHWDITHPLRFQRH 276

Query:    69 FLLDGRIQ---KVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDEN 113
             F     +    +  YE L   C  CG   H    C     GEE  D++
Sbjct:   277 FQFTAGVNTLLRFRYERLRGFCEVCGMLTHDFGACLIQNGGEEQADDD 324

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:1006230619 AT5G18636 "AT5G18636" [Arabidopsis thaliana (taxid:3702)]

 Score = 104 (41.7 bits), Expect = 4.8e-05, P = 4.8e-05
 Identities = 23/96 (23%), Positives = 50/96 (52%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIAL-DKPLCLQF 69
             W+++  +P  Y  ++ +  + Q +GE+I +DF+  ++ +  F+R+ V+  + D+    Q 
Sbjct:   124 WVQIRGIPLPYVSEETVLEIAQDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRFFQR 183

Query:    70 LL--DGRIQKV--EYESLPINCFNCGKYGHVSIGCP 101
             ++   G    +  +YE L   C +C ++ H    CP
Sbjct:   184 IIFDSGETATIRFQYERLRRLCSSCFRFTHNRAYCP 219

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2146990 AT5G25200 "AT5G25200" [Arabidopsis thaliana (taxid:3702)]

 Score = 104 (41.7 bits), Expect = 4.8e-05, P = 4.8e-05
 Identities = 23/96 (23%), Positives = 50/96 (52%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIAL-DKPLCLQF 69
             W+++  +P  Y  ++ +  + Q +GE+I +DF+  ++ +  F+R+ V+  + D+    Q 
Sbjct:   124 WVQIRGIPLPYVSEETVLEIAQDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRFFQR 183

Query:    70 LL--DGRIQKV--EYESLPINCFNCGKYGHVSIGCP 101
             ++   G    +  +YE L   C +C ++ H    CP
Sbjct:   184 IIFDSGETATIRFQYERLRRLCSSCFRFTHNRAYCP 219

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2827815 AT2G17920 [Arabidopsis thaliana (taxid:3702)]

 Score = 102 (41.0 bits), Expect = 5.8e-05, P = 5.8e-05
 Identities = 21/96 (21%), Positives = 49/96 (51%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPL-CLQF 69
             W+++  +P  Y  ++    + Q +G +I +DF+  ++++  ++R+ V++ +   L   Q 
Sbjct:   124 WVQMRGIPFLYVSEETALEIAQEIGAIISLDFHDTTSTQIAYIRVRVRVGITDSLRFFQR 183

Query:    70 LL----DGRIQKVEYESLPINCFNCGKYGHVSIGCP 101
             +     +  + + +YE L   C NC ++ H    CP
Sbjct:   184 ITFESGESALIRFQYERLRRICSNCFRFTHNRNYCP 219

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:4515102790 AT2G02103 "AT2G02103" [Arabidopsis thaliana (taxid:3702)]

 Score = 99 (39.9 bits), Expect = 0.00019, P = 0.00019
 Identities = 22/96 (22%), Positives = 49/96 (51%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIAL-DKPLCLQF 69
             W+++  +P  Y  ++ +  +   +GE+I +DF+  ++ +  F+R+ V+  + D+    Q 
Sbjct:   124 WVQIRGIPLPYVSEETVMEIAHDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRFFQR 183

Query:    70 LL--DGRIQKV--EYESLPINCFNCGKYGHVSIGCP 101
             ++   G    +  +YE L   C +C ++ H    CP
Sbjct:   184 VIFDSGETATIRFQYERLRRLCSSCFRFTHNRAYCP 219

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2076106 AT3G24070 [Arabidopsis thaliana (taxid:3702)]

 Score = 93 (37.8 bits), Expect = 0.00042, P = 0.00042
 Identities = 25/101 (24%), Positives = 45/101 (44%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIALDKPLCLQFL 70
             W+K+  +P  Y     +  +   MGEV+ ++ +         VR  V + +D  LC + +
Sbjct:     2 WLKIRGIPIQYLCDGTVREIASSMGEVMEVELDDGMVDLSS-VRARVNVCVDTRLCFKKV 60

Query:    71 L---DGRIQKVE--YESLPIN------CFNCGKYGHVSIGC 100
                  G ++ V   YE + ++      CFNCG   H++  C
Sbjct:    61 ARFDSGEVKIVSFRYEDIGMSKARFKFCFNCGDMNHLARNC 101

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F8VXY6 ZCRB1 "Zinc finger CCHC-type and RNA-binding motif-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 25/77 (32%), Positives = 40/77 (51%)

Query:    44 TRSASRRK-FVR-IAVKIALDKPLCLQFLLDGRIQKVEYESLPINCFNCGKYGHVSIGCP 101
             TR+ + ++ F R I   IA+D     +F     I++  Y      C+ CG+ GH+S  CP
Sbjct:    27 TRAINNKQLFGRVIKASIAIDNGRAAEF-----IRRRNYFDKS-KCYECGESGHLSYACP 80

Query:   102 EN--GDGEEPQDENGKK 116
             +N  G+ E P+ +  KK
Sbjct:    81 KNMLGEREPPKKKEKKK 97

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2062652 AT2G41590 "AT2G41590" [Arabidopsis thaliana (taxid:3702)]

 Score = 95 (38.5 bits), Expect = 0.00045, P = 0.00045
 Identities = 21/96 (21%), Positives = 50/96 (52%)

Query:    11 WIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVKIAL-DKPLCLQF 69
             W+++  +P  Y  ++ +  + Q +GEV+ +D++  ++ +  ++R+ V+  + D+    Q 
Sbjct:   124 WVQIRGIPLPYVSEETVMEIAQDLGEVLMLDYHDTTSIQIAYIRVRVRFGITDRLRFFQR 183

Query:    70 LL--DGRIQKV--EYESLPINCFNCGKYGHVSIGCP 101
             ++   G    +  +YE L   C +C ++ H    CP
Sbjct:   184 IVFDSGETATIRFQYERLRRICSSCFRFTHNRAYCP 219

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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: AT3G45253 transposable element gene; non-LTR retrotransposon family (LINE), has a 3.0e-48 P-value blast match to GB-AAA67727 reverse transcriptase (LINE-element) (Mus musculus) (1751 aa) (Arabidopsis thaliana)

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	117
pfam14111	153	pfam14111, DUF4283, Domain of unknown function (DU	4e-11
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	3e-06
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	0.004

>gnl|CDD|222549 pfam14111, DUF4283, Domain of unknown function (DUF4283)

 Score = 56.1 bits (136), Expect = 4e-11
 Identities = 13/58 (22%), Positives = 32/58 (55%)

Query: 1   TSDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVK 58
           + +++  +  W+++  +P + + +++L  +G   G  + +D +T    R +F RI VK
Sbjct: 96  SEEELKRIPVWVRIYGLPLHLWSEEILKRIGSACGGFVAVDEDTEGRERLQFARILVK 153

This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues. Length = 153

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

 Score = 41.1 bits (97), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 5/46 (10%)

Query: 61  LDKPLCLQFLLDGR-----IQKVEYESLPINCFNCGKYGHVSIGCP 101
           + KPL  +  +        + KV YE LP  CF+CG+ GH    CP
Sbjct: 3   VSKPLRFEVNVKFPSGEEAVVKVRYERLPNFCFHCGRLGHSDKECP 48

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins. Length = 49

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

 Score = 32.4 bits (75), Expect = 0.004
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 85  INCFNCGKYGHVSIGCPE 102
             C+NCGK GH++  CPE
Sbjct: 1   RKCYNCGKEGHLARDCPE 18

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	117
PF14392	49	zf-CCHC_4: Zinc knuckle	99.63
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	99.58
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.54
PF13696	32	zf-CCHC_2: Zinc knuckle	96.57
smart00343	26	ZnF_C2HC zinc finger.	94.65
PF15288	40	zf-CCHC_6: Zinc knuckle	94.15
PF13917	42	zf-CCHC_3: Zinc knuckle	92.67
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	90.51
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	89.94
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	89.7
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	89.62
PTZ00368	148	universal minicircle sequence binding protein (UMS	88.39
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	87.86
KOG2044	931	consensus 5'-3' exonuclease HKE1/RAT1 [Replication	84.5
COG5222	427	Uncharacterized conserved protein, contains RING Z	83.77

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=99.63  E-value=1.8e-16  Score=91.83  Aligned_cols=44  Identities=43%  Similarity=0.889  Sum_probs=40.0

Q ss_pred             EccCCCceeEEEEe---ce--EEEEeeccCCcccccccccccCCCCCCC
Q 040998           59 IALDKPLCLQFLLD---GR--IQKVEYESLPINCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        59 idl~kPL~~~v~v~---g~--~~~v~YE~lp~~C~~Cg~~GH~~~~C~~  102 (117)
                      +|+++||...+.+.   |.  ++.|+|||||.||++||.+||..++|++
T Consensus         1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen    1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcCC
Confidence            58999999998885   43  6899999999999999999999999985

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=99.58  E-value=6.2e-16  Score=107.01  Aligned_cols=57  Identities=26%  Similarity=0.579  Sum_probs=54.3

Q ss_pred             ccccceEeEEEEecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEEE
Q 040998            2 SDKIDSMVAWIKLSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVK   58 (117)
Q Consensus         2 ~~~l~~~~~WVri~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V~   58 (117)
                      ++.++++++||||+|||++||+++++++||+.+|+|+++|.++.+..+++|+||+|+
T Consensus        97 ~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv~V~  153 (153)
T PF14111_consen   97 EVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARVRVE  153 (153)
T ss_pred             ccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEEEEC
Confidence            467889999999999999999999999999999999999999999999999999985

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.54  E-value=5.1e-05  Score=34.92  Aligned_cols=17  Identities=53%  Similarity=1.450  Sum_probs=15.8

Q ss_pred             ccccccccccCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~  102 (117)
                      .|+.||..||...+||.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999984

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=96.57  E-value=0.0013  Score=34.62  Aligned_cols=24  Identities=38%  Similarity=0.769  Sum_probs=20.5

Q ss_pred             cccccccccccCCCCCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENGDGEE  108 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~~~~~  108 (117)
                      ..|..|+.-||...+||...+.+|
T Consensus         9 Y~C~~C~~~GH~i~dCP~~~Pk~e   32 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTNKPKGE   32 (32)
T ss_pred             CEeecCCCCCccHhHCCCCCCCCC
Confidence            689999999999999999665543

>smart00343 ZnF_C2HC zinc finger

Probab=94.65  E-value=0.015  Score=28.63  Aligned_cols=19  Identities=47%  Similarity=1.288  Sum_probs=16.3

Q ss_pred             ccccccccccCCCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~~~  104 (117)
                      .|+.||..||...+|+...
T Consensus         1 ~C~~CG~~GH~~~~C~~~~   19 (26)
T smart00343        1 KCYNCGKEGHIARDCPKXX   19 (26)
T ss_pred             CCccCCCCCcchhhCCccc
Confidence            4999999999999998443

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=94.15  E-value=0.045  Score=30.12  Aligned_cols=23  Identities=35%  Similarity=0.836  Sum_probs=19.0

Q ss_pred             cccccccccccCC--CCCCCCCCCC
Q 040998           85 INCFNCGKYGHVS--IGCPENGDGE  107 (117)
Q Consensus        85 ~~C~~Cg~~GH~~--~~C~~~~~~~  107 (117)
                      ..|..||-+||..  +.||......
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~~~~   26 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYCWSG   26 (40)
T ss_pred             ccccccccccccccCccCCCCCCCC
Confidence            3699999999987  7899987653

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=92.67  E-value=0.063  Score=29.86  Aligned_cols=20  Identities=35%  Similarity=0.974  Sum_probs=17.8

Q ss_pred             CCcccccccccccCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~  102 (117)
                      -...|..|+..||..-+|+.
T Consensus         3 ~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    3 ARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCcCcccCCCCcchhhCCC
Confidence            34689999999999999995

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

Probab=90.51  E-value=0.12  Score=37.65  Aligned_cols=23  Identities=39%  Similarity=0.911  Sum_probs=19.6

Q ss_pred             eeccCCcccccccccccCCCCCC
Q 040998           79 EYESLPINCFNCGKYGHVSIGCP  101 (117)
Q Consensus        79 ~YE~lp~~C~~Cg~~GH~~~~C~  101 (117)
                      .+-.-..+|+.||..||...+||
T Consensus        55 ~~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          55 AIREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             cccccccccchhcccCcccccCC
Confidence            44445689999999999999999

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

Probab=89.94  E-value=0.16  Score=37.05  Aligned_cols=17  Identities=47%  Similarity=1.202  Sum_probs=15.3

Q ss_pred             cccccccccccCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCP  101 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~  101 (117)
                      ..|++||..||...+|+
T Consensus        98 ~~C~~Cg~~GH~~~dC~  114 (190)
T COG5082          98 KKCYNCGETGHLSRDCN  114 (190)
T ss_pred             cccccccccCccccccC
Confidence            68999999999999994

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

Probab=89.70  E-value=0.18  Score=39.20  Aligned_cols=21  Identities=43%  Similarity=0.980  Sum_probs=18.9

Q ss_pred             cccccccccccCCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      .-|+.||+-||.+++||....
T Consensus       161 ~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHheeccccccccccCCccCC
Confidence            579999999999999998754

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

Probab=89.62  E-value=0.3  Score=26.22  Aligned_cols=22  Identities=36%  Similarity=0.566  Sum_probs=13.6

Q ss_pred             CcccccccccccCCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      |..|+.|++-.|...+|....+
T Consensus         2 ~~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    2 PGLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             --C-TTTSSSCS-TTT---TCC
T ss_pred             CccCcccCCCcchhhhhhhhhc
Confidence            5689999999999999988764

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

Probab=88.39  E-value=0.28  Score=33.82  Aligned_cols=19  Identities=47%  Similarity=1.260  Sum_probs=11.9

Q ss_pred             CcccccccccccCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~  102 (117)
                      +..|+.|+..||...+||.
T Consensus       129 ~~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        129 DKTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             CCccccCCCcCcccccCCC
Confidence            3566666666666666664

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

Probab=87.86  E-value=0.27  Score=37.06  Aligned_cols=25  Identities=44%  Similarity=1.002  Sum_probs=19.0

Q ss_pred             EeeccCCcccccccccccCCCCCCCC
Q 040998           78 VEYESLPINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        78 v~YE~lp~~C~~Cg~~GH~~~~C~~~  103 (117)
                      +.+.+- .+||.||..||...+|+..
T Consensus       138 ~~~~~~-~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  138 VDGPKP-AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             ccCCCC-CccCCCCcCCcchhhCCCC
Confidence            344444 6799999999999999854

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

Probab=84.50  E-value=0.7  Score=40.40  Aligned_cols=29  Identities=28%  Similarity=0.649  Sum_probs=25.4

Q ss_pred             EEeeccCCcccccccccccCCCCCCCCCC
Q 040998           77 KVEYESLPINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        77 ~v~YE~lp~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      .+.+...|.-|+.||..||..++|.-...
T Consensus       253 E~~~P~~~~~C~~cgq~gh~~~dc~g~~~  281 (931)
T KOG2044|consen  253 EEFFPNKPRRCFLCGQTGHEAKDCEGKPR  281 (931)
T ss_pred             eeecCCCcccchhhcccCCcHhhcCCcCC
Confidence            45569999999999999999999998855

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

Probab=83.77  E-value=0.58  Score=36.71  Aligned_cols=22  Identities=41%  Similarity=0.955  Sum_probs=19.7

Q ss_pred             cccccccccccCCCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      ..||.||.-||...+|+.....
T Consensus       177 Y~CyRCGqkgHwIqnCpTN~Dp  198 (427)
T COG5222         177 YVCYRCGQKGHWIQNCPTNQDP  198 (427)
T ss_pred             eeEEecCCCCchhhcCCCCCCC
Confidence            6899999999999999987653

---

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	117
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.32
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.21
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	96.93
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.89
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.61
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.06
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	95.96
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	95.82
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	95.73
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	95.55
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	95.55
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	95.54
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.54
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.5
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	95.43
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	95.41
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	95.22
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	94.95
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	94.9
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	94.46
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	94.36
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	94.15
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	93.49
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.99
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	92.84
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	92.08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	91.97
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	90.41
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	88.19
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	81.41

>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=97.21  E-value=0.00018  Score=38.93  Aligned_cols=23  Identities=30%  Similarity=0.699  Sum_probs=20.3

Q ss_pred             CcccccccccccCCCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      ...||.||..||...+||.+..+
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~~   32 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPRG   32 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCC
T ss_pred             CCeeeECCCCCcchhhCcCCccc
Confidence            46899999999999999998654

>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=96.93  E-value=0.00046  Score=34.56  Aligned_cols=21  Identities=43%  Similarity=0.920  Sum_probs=18.3

Q ss_pred             CcccccccccccCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      +..||.||+.||...+|+.+.
T Consensus         6 ~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCEEEECCccccCHhHCcccc
Confidence            467999999999999998653

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=96.89  E-value=0.00044  Score=40.06  Aligned_cols=25  Identities=28%  Similarity=0.562  Sum_probs=21.2

Q ss_pred             cCCcccccccccccCCCCCCCCCCC
Q 040998           82 SLPINCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        82 ~lp~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      .-..-|+.||..||...+||.....
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~~~   45 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKPRG   45 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCCCS
T ss_pred             CCCCcceeCCCCCcccccCcCCccc
Confidence            3457799999999999999998654

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

Probab=96.61  E-value=0.0009  Score=38.59  Aligned_cols=20  Identities=55%  Similarity=1.235  Sum_probs=17.5

Q ss_pred             cccccccccccCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      ..|+.||..||..++|+...
T Consensus         8 ~~C~kCGk~GH~~k~Cp~~~   27 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPTNG   27 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSGGG
T ss_pred             CccccCCCcCcccccCCCCC
Confidence            57999999999999999543

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

Probab=96.06  E-value=0.0028  Score=35.34  Aligned_cols=18  Identities=50%  Similarity=1.141  Sum_probs=9.4

Q ss_pred             cccccccccccCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~  102 (117)
                      ..||.||..||...+|+.
T Consensus         7 ~~C~~Cg~~GH~a~~C~~   24 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRA   24 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCC
T ss_pred             CeeeecCCCCcChhhCcC
Confidence            445555555555555544

>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=95.96  E-value=0.0042  Score=34.58  Aligned_cols=22  Identities=45%  Similarity=1.019  Sum_probs=19.2

Q ss_pred             CcccccccccccCCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      ...|+.||..||...+|+....
T Consensus        27 ~~~C~~Cg~~GH~~~~C~~~~~   48 (49)
T 2ec7_A           27 RQGCWKCGKTGHVMAKCPERQA   48 (49)
T ss_dssp             CCSCSSSCCSSCCGGGCCSSCC
T ss_pred             CCeeCcCCCcCCccCCCcCCCC
Confidence            3579999999999999998764

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

Probab=95.82  E-value=0.0036  Score=36.42  Aligned_cols=20  Identities=25%  Similarity=0.625  Sum_probs=10.7

Q ss_pred             ccccccccccCCCCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      .|+.||..||...+|+....
T Consensus        32 ~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           32 RCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             BCTTTCCBSSCGGGCCCCC-
T ss_pred             eeCCCCCCCCCcCCCcCCCc
Confidence            45555555555555555443

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

Probab=95.73  E-value=0.0057  Score=37.95  Aligned_cols=23  Identities=39%  Similarity=0.907  Sum_probs=20.3

Q ss_pred             CcccccccccccCCCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      ..+|+.||.-||..++|+.....
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~r~s   68 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEKRSS   68 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSCCSC
T ss_pred             CCeecccCCCCcCcccCCccccC
Confidence            47999999999999999988643

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=95.55  E-value=0.005  Score=34.94  Aligned_cols=18  Identities=44%  Similarity=1.075  Sum_probs=9.5

Q ss_pred             ccccccccccCCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~~  103 (117)
                      .|+.||..||...+|+..
T Consensus        35 ~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           35 GCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             BCTTTCCBSSCGGGCSSS
T ss_pred             EeCCCCCcCCccCCCcCc
Confidence            455555555555555543

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

Probab=95.55  E-value=0.0053  Score=35.68  Aligned_cols=22  Identities=32%  Similarity=0.797  Sum_probs=19.7

Q ss_pred             CCcccccccccccCCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      -+..||.|+..||...+|+...
T Consensus         3 ~~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            3 ARGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             CTTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCCcccccCCCCeehhhCcCCc
Confidence            4678999999999999999864

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

Probab=95.54  E-value=0.0056  Score=32.01  Aligned_cols=17  Identities=53%  Similarity=1.243  Sum_probs=11.7

Q ss_pred             ccccccccccCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~  102 (117)
                      .||.||..||...+|+.
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            46777777777777765

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

Probab=95.54  E-value=0.0063  Score=32.19  Aligned_cols=18  Identities=39%  Similarity=0.955  Sum_probs=12.8

Q ss_pred             cccccccccccCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~  102 (117)
                      ..|+.||..||...+|+.
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            467777777777777763

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

Probab=95.50  E-value=0.0063  Score=32.18  Aligned_cols=18  Identities=50%  Similarity=1.113  Sum_probs=16.6

Q ss_pred             ccccccccccCCCCCCCC
Q 040998           86 NCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        86 ~C~~Cg~~GH~~~~C~~~  103 (117)
                      .||.||..||...+|+..
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999975

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

Probab=95.43  E-value=0.011  Score=34.13  Aligned_cols=23  Identities=26%  Similarity=0.498  Sum_probs=20.0

Q ss_pred             CCcccccccccccCCCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      ....|+.||..||...+|+....
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CCcceeECCCCCCccCcCCCccc
Confidence            45789999999999999998764

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

Probab=95.41  E-value=0.0051  Score=32.19  Aligned_cols=19  Identities=42%  Similarity=0.946  Sum_probs=17.0

Q ss_pred             CcccccccccccCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~  102 (117)
                      +..|+.||..||..++|+.
T Consensus        19 ~~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           19 PKVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             BTTCSSCCCTTGGGGTTCC
T ss_pred             cCeEccCCCcCCccCcCcC
Confidence            4689999999999999974

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=95.22  E-value=0.0076  Score=34.16  Aligned_cols=22  Identities=41%  Similarity=1.020  Sum_probs=19.2

Q ss_pred             cCCcccccccccccCCCCCCCC
Q 040998           82 SLPINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        82 ~lp~~C~~Cg~~GH~~~~C~~~  103 (117)
                      +-+..||.||..||...+|+..
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            4467899999999999999875

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

Probab=94.95  E-value=0.013  Score=34.23  Aligned_cols=19  Identities=32%  Similarity=0.749  Sum_probs=11.0

Q ss_pred             CcccccccccccCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~  102 (117)
                      +..||.|+..||...+|+.
T Consensus         7 ~~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            7 GDRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCCSSSCCSSSCTTTCCS
T ss_pred             CCcccccCCCCcChhhCCC
Confidence            3456666666666666653

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

Probab=94.90  E-value=0.0087  Score=29.09  Aligned_cols=20  Identities=25%  Similarity=0.679  Sum_probs=17.3

Q ss_pred             CcccccccccccCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~  103 (117)
                      .++|-+|..+||...+|+..
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            47899999999999999754

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

Probab=94.46  E-value=0.018  Score=34.91  Aligned_cols=21  Identities=29%  Similarity=0.631  Sum_probs=16.9

Q ss_pred             CCcccccccccccCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~  103 (117)
                      .+..||.||..||...+|+..
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSC
T ss_pred             CCCcccccCCcCcCcccCCCC
Confidence            556789999999998888853

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

Probab=94.36  E-value=0.023  Score=33.18  Aligned_cols=21  Identities=29%  Similarity=0.773  Sum_probs=19.0

Q ss_pred             CcccccccccccCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      +..|+.||..||...+|+...
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCccCCcCCcCCccCcCCCcc
Confidence            578999999999999999764

>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=94.15  E-value=0.0086  Score=34.53  Aligned_cols=20  Identities=45%  Similarity=1.044  Sum_probs=0.0

Q ss_pred             cccccccccccCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      ..||.|+..||...+|+...
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            36999999999999999864

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

Probab=93.49  E-value=0.019  Score=35.57  Aligned_cols=22  Identities=23%  Similarity=0.445  Sum_probs=16.8

Q ss_pred             cCCcccccccccccCCCCCCCC
Q 040998           82 SLPINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        82 ~lp~~C~~Cg~~GH~~~~C~~~  103 (117)
                      |-...|+.|+..||..++||..
T Consensus         3 ~k~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            3 WKKVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             ----CCSSSCCSSSCGGGCGGG
T ss_pred             cccCCCCCCCCCCCccccCCCc
Confidence            4567899999999999999874

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

Probab=92.99  E-value=0.038  Score=37.56  Aligned_cols=18  Identities=33%  Similarity=0.820  Sum_probs=12.9

Q ss_pred             cccccccccccCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPE  102 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~  102 (117)
                      ..||+||..||...+|+.
T Consensus        98 ~~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCS
T ss_pred             CcccEeCCccchhhhCCC
Confidence            357777777777777776

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

Probab=92.84  E-value=0.034  Score=33.63  Aligned_cols=22  Identities=27%  Similarity=0.714  Sum_probs=19.4

Q ss_pred             CCcccccccccccCCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPENG  104 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~~  104 (117)
                      .+..|+.||..||...+|+...
T Consensus        45 ~~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           45 QPKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCCCCTTTCCTTSCGGGCTTGG
T ss_pred             CCCccCCcCCcCCccCcCcCCc
Confidence            3578999999999999999865

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

Probab=92.08  E-value=0.077  Score=34.61  Aligned_cols=21  Identities=43%  Similarity=0.964  Sum_probs=18.6

Q ss_pred             CCcccccccccccCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~  103 (117)
                      -...|++||..||...+||..
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCCC
T ss_pred             CCCCcCCCCCCCcCcccCcCC
Confidence            458999999999999999863

>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=91.97  E-value=0.052  Score=36.88  Aligned_cols=22  Identities=23%  Similarity=0.622  Sum_probs=18.8

Q ss_pred             cccccccccccCCCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      ..|+.||..||...+||.....
T Consensus       120 ~~C~~Cg~~GH~~r~Cp~~~~~  141 (148)
T 3ts2_A          120 KKCHFCQSINHMVASCPLKAQQ  141 (148)
T ss_dssp             CCCTTTCCSSCCGGGCTTTTC-
T ss_pred             CcccccCCcCCEeccCcCCCCC
Confidence            4699999999999999987554

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

Probab=90.41  E-value=0.27  Score=31.97  Aligned_cols=22  Identities=23%  Similarity=0.462  Sum_probs=18.2

Q ss_pred             CcccccccccccCCCCCCCCCC
Q 040998           84 PINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        84 p~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      ...|+.||..||..++|+....
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~~   85 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIWR   85 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCSTT
T ss_pred             CccCCCCCcCCcchhhCCCccc
Confidence            3679999999999999997643

>4ayb_H DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_H 2y0s_H 2waq_H 4b1o_H 4b1p_Z 2pmz_H 3hkz_H

Probab=81.41  E-value=1.2  Score=27.35  Aligned_cols=44  Identities=14%  Similarity=0.125  Sum_probs=36.1

Q ss_pred             ecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEE
Q 040998           14 LSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAV   57 (117)
Q Consensus        14 i~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V   57 (117)
                      ...||.-+.+..+++.+|-.-|.++++...+......-|-|+.|
T Consensus        39 ~~qLP~I~~~DPva~~~g~k~GdVvkI~R~S~tag~~~~YR~vv   82 (84)
T 4ayb_H           39 PEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYGEVVSYRYVI   82 (84)
T ss_dssp             GGGSCCEESSSHHHHHHTCCTTCEEEEEEEETTTEEEEEEEEEE
T ss_pred             HhHCCeecccCHhHHhhCCCCCCEEEEEEcCCCCCccEEEEEEe
Confidence            35789999999999999999999999999876554455657765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	117
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.001

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

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 32.1 bits (73), Expect = 0.001
 Identities = 9/18 (50%), Positives = 11/18 (61%)

Query: 85  INCFNCGKYGHVSIGCPE 102
           + CFNCGK GH +  C  
Sbjct: 2   VKCFNCGKEGHTARNCRA 19

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	117
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.42
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.38
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	96.67
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	96.09
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	93.97
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	91.23
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	89.78
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	88.89
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	86.05

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

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.42  E-value=3.4e-05  Score=37.09  Aligned_cols=24  Identities=38%  Similarity=0.769  Sum_probs=19.9

Q ss_pred             cCCcccccccccccCCCCCCCCCC
Q 040998           82 SLPINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        82 ~lp~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      +-+..||+||+.||..++|.-+..
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSSSS
T ss_pred             cceeEeecCCccchhhhhccCccc
Confidence            345789999999999999986643

>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=96.67  E-value=0.00043  Score=36.39  Aligned_cols=19  Identities=42%  Similarity=0.982  Sum_probs=12.9

Q ss_pred             cccccccccccCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~  103 (117)
                      ..|+.||..||...+||.+
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            3577777777777777654

>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=96.09  E-value=0.0012  Score=34.65  Aligned_cols=19  Identities=47%  Similarity=1.160  Sum_probs=17.3

Q ss_pred             cccccccccccCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPEN  103 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~  103 (117)
                      ..||.||..||...+||.+
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            4699999999999999975

>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=93.97  E-value=0.02  Score=29.06  Aligned_cols=22  Identities=32%  Similarity=0.744  Sum_probs=19.3

Q ss_pred             cccccccccccCCCCCCCCCCC
Q 040998           85 INCFNCGKYGHVSIGCPENGDG  106 (117)
Q Consensus        85 ~~C~~Cg~~GH~~~~C~~~~~~  106 (117)
                      .-|..|..-||..++||.+..+
T Consensus        11 DQCAyCke~GHW~~dCPkkprg   32 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKPRG   32 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSCCC
T ss_pred             hhhHHHhhcCchhhhCccCCCC
Confidence            4699999999999999988654

>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.23  E-value=0.15  Score=28.88  Aligned_cols=45  Identities=20%  Similarity=0.398  Sum_probs=38.2

Q ss_pred             ecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEEE
Q 040998           14 LSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAVK   58 (117)
Q Consensus        14 i~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V~   58 (117)
                      ...||.-+++..+++.+|-.-|.++++...+......-|-|+.|+
T Consensus        22 ~~qLP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~i~YR~vv~   66 (68)
T d1hmja_          22 IQQLPKIYEDDPVIQEIGAKEGDVVRVIRKSPTAGVSIAYRLVIK   66 (68)
T ss_pred             HHHCCcccccCHHHHHhCCCCCcEEEEEEcCCCCCCceEEEEEEE
Confidence            457999999999999999999999999998766555667788775

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.78  E-value=0.16  Score=28.96  Aligned_cols=44  Identities=25%  Similarity=0.293  Sum_probs=37.4

Q ss_pred             ecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEE
Q 040998           14 LSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAV   57 (117)
Q Consensus        14 i~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V   57 (117)
                      ...||.-+++..+++.+|-.-|.++++...+......-|-|++|
T Consensus        29 ~~qLP~I~~~DPva~~~g~~~GdvikI~R~s~tag~~~~YR~~V   72 (72)
T d1dzfa2          29 ESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM   72 (72)
T ss_dssp             GGGSCEECTTCHHHHHHTCCTTCEEEEECTTCSSSTTCEEEEEC
T ss_pred             HhHCCeecccCHhhhhcCCCCCCEEEEEEcCCCCCceeEEEEeC
Confidence            35799999999999999999999999999876665666778765

>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=88.89  E-value=0.18  Score=24.26  Aligned_cols=23  Identities=26%  Similarity=0.498  Sum_probs=20.6

Q ss_pred             CCcccccccccccCCCCCCCCCC
Q 040998           83 LPINCFNCGKYGHVSIGCPENGD  105 (117)
Q Consensus        83 lp~~C~~Cg~~GH~~~~C~~~~~  105 (117)
                      +|..|-.|++=-|...+|.....
T Consensus         1 ~P~lCPrC~kG~HWa~~Crsk~~   23 (32)
T d1cl4a_           1 VPGLCPRCKRGKHWANECKSKTD   23 (32)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CCccCccccCcchHHHHhhhhhc
Confidence            58899999999999999987754

>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.05  E-value=0.18  Score=29.19  Aligned_cols=44  Identities=16%  Similarity=0.217  Sum_probs=35.6

Q ss_pred             ecCCCccccccchhhhhhhccccEEEEeccCCCccccceEEEEE
Q 040998           14 LSNMPHYYYHKKVLPMVGQVMGEVIHIDFNTRSASRRKFVRIAV   57 (117)
Q Consensus        14 i~~lP~~~~~~~~~~~I~~~iG~~l~vD~~~~~~~~~~y~Rv~V   57 (117)
                      ...||.-+++..+++.+|-.-|.++++...+......-|-|+.|
T Consensus        33 ~~qLP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~~~YR~vv   76 (77)
T d1eika_          33 PEQLPKIKTTDPVAKAIGAKRGDIVKIIRKSPTAEEFVTYRLVQ   76 (77)
T ss_dssp             TTTSCCCBTTSHHHHGGGCCTTCEEEEEEEETTTEEEEEEEECB
T ss_pred             HHHCCeecccCHhhhhhCCcCCcEEEEEEcCCCCCCceEEEEEe
Confidence            35799999999999999999999999999876544445556654