Citrus Sinensis ID: 037799

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLDDSHEKRQKI
Secondary Structure (PSIPRED)
cEEEEEccEEEEEEEccccccccccccEEEEEEEEccccHHccHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHccccccEEEEEEcccEEEEEEEccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEcccEEEEEEcccccccccccccEEEEEEEEccccHHHccHHHHHHHHHHcccEEEEcccccccccccEEEEEEEEEcccccccEEEEEcEEEEEEEcccccHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mhfltlnnyltvqpwtpsfdvnktdmeQVNVWIRLPGLAVHLYNRKILQKLGELVGIviridphtassaRGRFARIAVRLSldkplvsqfvldgkvqkveyeglpvicftcgryghtfwtlddshekrqki
Flexible Loop (DISEMBL)
MHFLTLnnyltvqpwtpsfDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDphtassargRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTfwtlddshekrqki
Low Complexity Region (SEG)
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLDDSHEKRQKI
Disordered region (IsUnstruct)
**FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTL**********
Disordered Region (DISOPRED)
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLDD********
Disordered Region (DISEMBL)
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLD*********
Disordered Region (DISPRO)
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTL**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLDDSHEKRQKI
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	131
87116458	532	unnamed protein product [Ipomoea batatas	0.847	0.208	0.441	4e-22
87116461	532	unnamed protein product [Ipomoea batatas	0.847	0.208	0.432	2e-21
332322109	678	hypothetical protein [Beta vulgaris subs	0.870	0.168	0.403	2e-21
87116463	1898	unnamed protein product [Ipomoea batatas	0.847	0.058	0.432	9e-20
356562050	470	PREDICTED: uncharacterized protein LOC10	0.870	0.242	0.421	1e-19
342365825	1613	RNA-directed DNA polymerase [Arachis hyp	0.870	0.070	0.333	2e-16
332322101	744	hypothetical protein [Beta vulgaris subs	0.870	0.153	0.385	2e-16
158828302	496	gag non-LTR retrotransposase [Arabidopsi	0.916	0.241	0.366	3e-16
2244916	655	hypothetical protein [Arabidopsis thalia	0.854	0.170	0.401	6e-16
357445233	504	hypothetical protein MTR_2g005460 [Medic	0.870	0.226	0.368	7e-16

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

 Score =  109 bits (272), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/111 (44%), Positives = 70/111 (63%)

Query: 6   LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
            +NYL  Q W P+F       +++ VW+RLP L++  +    ++ + E +G  +R+D  T
Sbjct: 164 FDNYLITQRWVPNFKPRTAKFQKMAVWVRLPELSMEYFRDDTIKAILENIGKPLRLDRTT 223

Query: 66  ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +  +GRFAR AV + LDKPLVS+  + G VQKVEYEGL V+CF CG  GH
Sbjct: 224 MAREKGRFARAAVEIDLDKPLVSEIWVMGDVQKVEYEGLHVVCFGCGVVGH 274

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116461|dbj|BAE79383.1| unnamed protein product [Ipomoea batatas]

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/111 (43%), Positives = 70/111 (63%)

Query: 6   LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
            +NYL  Q W P+F+      +++ VW+RLP L++  +    ++ + E +G  +R+D  T
Sbjct: 164 FDNYLITQRWVPNFEPRTAKFQKMAVWVRLPELSMEYFRDDTIKAILENIGKPLRLDRTT 223

Query: 66  ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +  +GRFAR AV + L KPLVS+  + G VQKVEYEGL V+CF CG  GH
Sbjct: 224 MAREKGRFARAAVEIDLGKPLVSEIWVMGDVQKVEYEGLHVVCFGCGVVGH 274

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/114 (40%), Positives = 78/114 (68%)

Query: 3   FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRID 62
           +L  ++YLT++ W P+F  ++  ++++  W+R+P L+V  ++++ L  +G  +G VI+ID
Sbjct: 197 WLIGDSYLTIRKWVPNFVSDQEPIKKLTAWVRIPHLSVEYFDKQFLHSIGSKIGKVIKID 256

Query: 63  PHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +T S  RG++ R  + + L KPL+S+F L+GKV  V+YEGL +ICF CG  GH
Sbjct: 257 RNTESMDRGQYVRFCIEVDLSKPLLSKFRLNGKVWIVQYEGLRLICFKCGHLGH 310

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 =  101 bits (252), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/111 (43%), Positives = 67/111 (60%)

Query: 6   LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
            +NYL  Q W P F       +++ VW+RL  L++  +    ++ + E +G  + +D  T
Sbjct: 164 FDNYLITQRWVPDFKPRTAKFQKMAVWVRLSELSMEYFRDDTIKAILENIGKPLGLDRTT 223

Query: 66  ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +  RGRFAR AV + LDKPLVS+  + G VQKVEYEGL V+CF CG  GH
Sbjct: 224 MARERGRFARAAVEIDLDKPLVSEIWVMGDVQKVEYEGLHVVCFGCGVVGH 274

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/114 (42%), Positives = 69/114 (60%)

Query: 3   FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRID 62
           ++  ++YLT+Q WTP F      +++  VW+R P L +  Y+  IL  L   +G  I++D
Sbjct: 151 WMIFDHYLTIQTWTPDFISPTAKIDKTMVWVRFPSLNLIYYDENILLALARAIGTPIKVD 210

Query: 63  PHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +T    RG FARI V++ L+KP+V +  L G   KVEYEGL  IC +CG YGH
Sbjct: 211 SNTLDVRRGHFARICVQIDLNKPVVGKVGLKGYWYKVEYEGLHRICSSCGCYGH 264

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|342365825|gb|AEL30359.1| RNA-directed DNA polymerase [Arachis hypogaea]

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 68/114 (59%)

Query: 3   FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRID 62
           +L   +Y+ V+PW   F   +       VWI++ GL +  Y  + + ++   +GI +++D
Sbjct: 151 WLIDGHYVAVKPWDVDFRPCEKSFGSTLVWIQVSGLPIWCYQEQAMLRIASAIGIPVKVD 210

Query: 63  PHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
             T  + RG++AR  V+++L+ P++   +++G   +VEYE LP+IC TC RYGH
Sbjct: 211 LATKLAERGKYARACVQINLELPVIKHIIVEGVTYEVEYESLPLICATCARYGH 264

Source: Arachis hypogaea

Species: Arachis hypogaea

Genus: Arachis

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|332322101|emb|CCA65996.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 44/114 (38%), Positives = 68/114 (59%)

Query: 3   FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRID 62
           +  LN+YL +  W P F  +++  +++ VWIR P L +  Y+++ L  +   VG  I++D
Sbjct: 183 WFILNHYLMLTRWKPDFRPSQSVFDKIMVWIRFPELPLEYYDKEALFAIAGKVGKPIKVD 242

Query: 63  PHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
             T   ARGR+AR+ + L L K LVS+  +    Q VEYE L ++CF CG+ GH
Sbjct: 243 YATDHMARGRYARVCIELDLAKALVSKVWVARAWQNVEYENLSLVCFLCGKIGH 296

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 89.7 bits (221), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 44/120 (36%), Positives = 67/120 (55%)

Query: 6   LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
             +YL +Q W P FD  + ++    VWIRL  L V  Y++ IL  + + +G  +++D  T
Sbjct: 134 FGSYLLLQAWDPDFDPLRDEITTTPVWIRLSNLPVTFYHKTILMGIAKGLGHPVKVDLIT 193

Query: 66  ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHTFWTLDDSH 125
               RGRFAR+ V ++L +PL    +++G+   V YEGL  IC  CG YGH   T   ++
Sbjct: 194 IRFDRGRFARVCVEVNLKRPLKGTVMVNGRRYYVSYEGLNAICSKCGMYGHLVHTCSQAN 253

Source: Arabidopsis cebennensis

Species: Arabidopsis cebennensis

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2244916|emb|CAB10338.1| hypothetical protein [Arabidopsis thaliana] gi|7268308|emb|CAB78602.1| hypothetical protein [Arabidopsis thaliana]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 45/112 (40%), Positives = 64/112 (57%)

Query: 6   LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
           L + L VQ W+P F+  +  +E   VW+R+  L V  Y+ +IL  +   +G  I++D  T
Sbjct: 156 LGSILMVQAWSPEFNPLRDVIETTPVWVRVANLPVTFYHNEILLGIAAGLGKPIKVDLTT 215

Query: 66  ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGHT 117
               RGRFAR+ V ++L  PL    V++G+   V YEGL  IC  CG YGHT
Sbjct: 216 LRKERGRFARVCVEVNLKNPLKGTLVVNGERYFVSYEGLQTICSLCGIYGHT 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 = 88.6 bits (218), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 42/114 (36%), Positives = 65/114 (57%)

Query: 3   FLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRID 62
           +L  ++ L V  WTP F      +++  VW+R PGL +  Y+   L  +   +G  I++D
Sbjct: 148 WLIFDHCLAVTHWTPEFASPNAKVDRTVVWVRFPGLNLVYYDESFLLAMASALGRPIKVD 207

Query: 63  PHTASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
            +T    RG+FAR+ V + L  P+V +  ++G   KV+YEGL +IC  CG YGH
Sbjct: 208 TNTLKVERGKFARVCVEIDLTVPVVGKIWVNGHWYKVQYEGLHLICTNCGCYGH 261

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	131
TAIR|locus:2045756	515	AT2G01050 [Arabidopsis thalian	0.847	0.215	0.378	1.1e-17
TAIR|locus:2099826	336	AT3G31430 "AT3G31430" [Arabido	0.801	0.312	0.254	8.7e-05
TAIR|locus:2827815	307	AT2G17920 [Arabidopsis thalian	0.824	0.351	0.224	9.6e-05
TAIR|locus:1006230619	367	AT5G18636 "AT5G18636" [Arabido	0.671	0.239	0.236	0.00013
TAIR|locus:2146990	367	AT5G25200 "AT5G25200" [Arabido	0.671	0.239	0.236	0.00013
TAIR|locus:4515102790	403	AT2G02103 "AT2G02103" [Arabido	0.671	0.218	0.236	0.00019
TAIR|locus:2062652	367	AT2G41590 "AT2G41590" [Arabido	0.671	0.239	0.236	0.00021

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

 Score = 223 (83.6 bits), Expect = 1.1e-17, P = 1.1e-17
 Identities = 42/111 (37%), Positives = 67/111 (60%)

Query:     6 LNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
             L NYL VQ W+  FD  + D+    VW+RL  +  + Y+R +L ++   +G  +++D +T
Sbjct:   141 LGNYLLVQDWSSRFDPLRDDIVTTPVWVRLSNIPYNYYHRCLLMEIARGLGRPLKVDMNT 200

Query:    66 ASSARGRFARIAVRLSLDKPLVSQFVLDGKVQKVEYEGLPVICFTCGRYGH 116
              +  +GRFAR+ + ++L KPL    +++G    V YEGL  IC +CG YGH
Sbjct:   201 INFDKGRFARVCIEVNLAKPLKGTVLINGDRYFVAYEGLSKICSSCGIYGH 251

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 = 101 (40.6 bits), Expect = 8.7e-05, P = 8.7e-05
 Identities = 29/114 (25%), Positives = 48/114 (42%)

Query:    10 LTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSA 69
             + +Q W P   +       +  W+++ G+     NR +++ +G  +G V+  D +    A
Sbjct:   199 ILLQRWEPQIPL----FPFIPFWVQIRGIPFQFLNRGVVEHIGRALGQVLDTDFNVEVVA 254

Query:    70 RGRFARIAVRLSLDKPLVSQ--FVLDGKVQ---KVEYEGLPVICFTCGRYGHTF 118
             R  FAR+ +   +  PL  Q  F     V    +  YE L   C  CG   H F
Sbjct:   255 RMDFARVLLHWDITHPLRFQRHFQFTAGVNTLLRFRYERLRGFCEVCGMLTHDF 308

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 100 (40.3 bits), Expect = 9.6e-05, P = 9.6e-05
 Identities = 26/116 (22%), Positives = 57/116 (49%)

Query:     7 NNYLTV-QPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHT 65
             NN+    Q W P+  +N   +  +++W+++ G+     + +   ++ + +G +I +D H 
Sbjct:   100 NNWFVASQRWQPAPALNF--VTTIDLWVQMRGIPFLYVSEETALEIAQEIGAIISLDFHD 157

Query:    66 ASSARGRFARIAVRLSLDKPL-VSQFVL----DGKVQKVEYEGLPVICFTCGRYGH 116
              +S +  + R+ VR+ +   L   Q +     +  + + +YE L  IC  C R+ H
Sbjct:   158 TTSTQIAYIRVRVRVGITDSLRFFQRITFESGESALIRFQYERLRRICSNCFRFTH 213

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

 Score = 100 (40.3 bits), Expect = 0.00013, P = 0.00013
 Identities = 22/93 (23%), Positives = 51/93 (54%)

Query:    29 VNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPL-- 86
             +++W+++ G+ +   + + + ++ + +G +I +D H A+S +  F R+ VR  +   L  
Sbjct:   121 IDLWVQIRGIPLPYVSEETVLEIAQDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRF 180

Query:    87 VSQFVLD-GKVQKV--EYEGLPVICFTCGRYGH 116
               + + D G+   +  +YE L  +C +C R+ H
Sbjct:   181 FQRIIFDSGETATIRFQYERLRRLCSSCFRFTH 213

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 = 100 (40.3 bits), Expect = 0.00013, P = 0.00013
 Identities = 22/93 (23%), Positives = 51/93 (54%)

Query:    29 VNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPL-- 86
             +++W+++ G+ +   + + + ++ + +G +I +D H A+S +  F R+ VR  +   L  
Sbjct:   121 IDLWVQIRGIPLPYVSEETVLEIAQDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRF 180

Query:    87 VSQFVLD-GKVQKV--EYEGLPVICFTCGRYGH 116
               + + D G+   +  +YE L  +C +C R+ H
Sbjct:   181 FQRIIFDSGETATIRFQYERLRRLCSSCFRFTH 213

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 99 (39.9 bits), Expect = 0.00019, P = 0.00019
 Identities = 22/93 (23%), Positives = 50/93 (53%)

Query:    29 VNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPL-- 86
             +++W+++ G+ +   + + + ++   +G +I +D H A+S +  F R+ VR  +   L  
Sbjct:   121 IDLWVQIRGIPLPYVSEETVMEIAHDLGEIISLDFHEATSPQIAFIRVRVRFGITDRLRF 180

Query:    87 VSQFVLD-GKVQKV--EYEGLPVICFTCGRYGH 116
               + + D G+   +  +YE L  +C +C R+ H
Sbjct:   181 FQRVIFDSGETATIRFQYERLRRLCSSCFRFTH 213

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 98 (39.6 bits), Expect = 0.00021, P = 0.00021
 Identities = 22/93 (23%), Positives = 50/93 (53%)

Query:    29 VNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVRLSLDKPL-- 86
             +++W+++ G+ +   + + + ++ + +G V+ +D H  +S +  + R+ VR  +   L  
Sbjct:   121 IDLWVQIRGIPLPYVSEETVMEIAQDLGEVLMLDYHDTTSIQIAYIRVRVRFGITDRLRF 180

Query:    87 VSQFVLD-GKVQKV--EYEGLPVICFTCGRYGH 116
               + V D G+   +  +YE L  IC +C R+ H
Sbjct:   181 FQRIVFDSGETATIRFQYERLRRICSSCFRFTH 213


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        0.325   0.140   0.440    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      131       131   0.00091  102 3  11 22  0.50    30
                                                     29  0.42    33


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:  7
  No. of states in DFA:  594 (63 KB)
  Total size of DFA:  141 KB (2087 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:  14.02u 0.20s 14.22t   Elapsed:  00:00:01
  Total cpu time:  14.02u 0.20s 14.22t   Elapsed:  00:00:01
  Start:  Fri May 10 00:30:39 2013   End:  Fri May 10 00:30:40 2013

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	131
pfam14111	153	pfam14111, DUF4283, Domain of unknown function (DU	3e-18
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	1e-09

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

 Score = 75.3 bits (186), Expect = 3e-18
 Identities = 22/73 (30%), Positives = 45/73 (61%)

Query: 7   NNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTA 66
              L ++ W+P    ++ +++++ VW+R+ GL +HL++ +IL+++G   G  + +D  T 
Sbjct: 81  GWALILERWSPEVGCSEEELKRIPVWVRIYGLPLHLWSEEILKRIGSACGGFVAVDEDTE 140

Query: 67  SSARGRFARIAVR 79
              R +FARI V+
Sbjct: 141 GRERLQFARILVK 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 = 50.3 bits (121), Expect = 1e-09
 Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 5/43 (11%)

Query: 80  LSLDKPLVSQFVLDGK-----VQKVEYEGLPVICFTCGRYGHT 117
           L + KPL  +  +        V KV YE LP  CF CGR GH+
Sbjct: 1   LDVSKPLRFEVNVKFPSGEEAVVKVRYERLPNFCFHCGRLGHS 43

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	99.86
PF14392	49	zf-CCHC_4: Zinc knuckle	99.65
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.37
smart00343	26	ZnF_C2HC zinc finger.	94.19
PF13696	32	zf-CCHC_2: Zinc knuckle	93.51
PF15288	40	zf-CCHC_6: Zinc knuckle	93.03
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	90.99
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	88.61
PF13917	42	zf-CCHC_3: Zinc knuckle	88.4
KOG2560	529	consensus RNA splicing factor - Slu7p [RNA process	83.11
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	80.99

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=99.86  E-value=2.5e-23  Score=147.81  Aligned_cols=79  Identities=32%  Similarity=0.668  Sum_probs=76.8

Q ss_pred             CCeeeeCceEEEEeecCCCCCCccCcceeeeeeecCCCchhhhhHHHHHHHHhhcceEEEEecCCCccchhHHHHHHHH
Q 037799            1 MHFLTLNNYLTVQPWTPSFDVNKTDMEQVNVWIRLPGLAVHLYNRKILQKLGELVGIVIRIDPHTASSARGRFARIAVR   79 (131)
Q Consensus         1 ~PW~f~~~~l~l~~w~~~~~~~~~~~~~~~vWVri~~lP~~~~~~~~~~~i~~~iG~~l~vD~~t~~~~~~~~~RV~V~   79 (131)
                      .||+|+|+.+++++|+|++++++..++++++|||++|||++||+++++++||+.+|+++++|.+|.+..+++||||||+
T Consensus        75 ~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv~V~  153 (153)
T PF14111_consen   75 GPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARVRVE  153 (153)
T ss_pred             ccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEEEEC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999999985

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=99.65  E-value=8.4e-17  Score=95.16  Aligned_cols=44  Identities=39%  Similarity=0.747  Sum_probs=39.7

Q ss_pred             hhcCCCceEEEEEc---Ce--EeEEEEccCccccccccccccCcCcCCC
Q 037799           80 LSLDKPLVSQFVLD---GK--VQKVEYEGLPVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus        80 id~~kpL~~~v~i~---g~--~~~v~YE~lp~~C~~Cg~~GH~~~~C~~  123 (131)
                      +|+++||++++.++   |+  .+.|+|||||.||++||.+||+.++|++
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            68999999998773   54  5899999999999999999999999985

>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=97.37  E-value=9e-05  Score=34.73  Aligned_cols=17  Identities=35%  Similarity=0.759  Sum_probs=15.7

Q ss_pred             ccccccccccCcCcCCC
Q 037799          107 ICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~  123 (131)
                      .|++||..||...+|++
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            59999999999999984

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 ....

>smart00343 ZnF_C2HC zinc finger

Probab=94.19  E-value=0.02  Score=28.81  Aligned_cols=17  Identities=29%  Similarity=0.774  Sum_probs=15.4

Q ss_pred             ccccccccccCcCcCCC
Q 037799          107 ICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~  123 (131)
                      .|+.||..||...+|+.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            49999999999999983

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=93.51  E-value=0.028  Score=30.08  Aligned_cols=21  Identities=24%  Similarity=0.586  Sum_probs=18.2

Q ss_pred             cccccccccccCcCcCCCchh
Q 037799          106 VICFTCGRYGHTFWTLDDSHE  126 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~~~  126 (131)
                      ..|..|+.-||..+.|+.-.+
T Consensus         9 Y~C~~C~~~GH~i~dCP~~~P   29 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTNKP   29 (32)
T ss_pred             CEeecCCCCCccHhHCCCCCC
Confidence            489999999999999997443

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=93.03  E-value=0.043  Score=30.79  Aligned_cols=17  Identities=29%  Similarity=0.571  Sum_probs=14.5

Q ss_pred             ccccccccccCc--CcCCC
Q 037799          107 ICFTCGRYGHTF--WTLDD  123 (131)
Q Consensus       107 ~C~~Cg~~GH~~--~~C~~  123 (131)
                      .|..||-+||..  +.||.
T Consensus         3 kC~~CG~~GH~~t~k~CP~   21 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCPM   21 (40)
T ss_pred             cccccccccccccCccCCC
Confidence            699999999987  67874

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

Probab=90.99  E-value=0.1  Score=38.91  Aligned_cols=17  Identities=29%  Similarity=0.735  Sum_probs=9.6

Q ss_pred             cccccccccccCcCcCC
Q 037799          106 VICFTCGRYGHTFWTLD  122 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~  122 (131)
                      ..|++||..||....|+
T Consensus        98 ~~C~~Cg~~GH~~~dC~  114 (190)
T COG5082          98 KKCYNCGETGHLSRDCN  114 (190)
T ss_pred             cccccccccCccccccC
Confidence            45555555555555553

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

Probab=88.61  E-value=0.19  Score=37.48  Aligned_cols=22  Identities=27%  Similarity=0.576  Sum_probs=18.7

Q ss_pred             EccCccccccccccccCcCcCC
Q 037799          101 YEGLPVICFTCGRYGHTFWTLD  122 (131)
Q Consensus       101 YE~lp~~C~~Cg~~GH~~~~C~  122 (131)
                      +-.--.+|++||..||..+.|+
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3344579999999999999999

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=88.40  E-value=0.24  Score=28.09  Aligned_cols=19  Identities=32%  Similarity=0.658  Sum_probs=17.1

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      -..|..|+..||-..+|+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4589999999999999994

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

Probab=83.11  E-value=0.3  Score=40.95  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=23.1

Q ss_pred             cccccccccccCcCcCCCchhhhcC
Q 037799          106 VICFTCGRYGHTFWTLDDSHEKRQK  130 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~~~~~~~  130 (131)
                      .+|-+||-+||..+.|-.-+.|+|+
T Consensus       113 GACeNCGAmtHk~KDCmERPRK~gA  137 (529)
T KOG2560|consen  113 GACENCGAMTHKVKDCMERPRKVGA  137 (529)
T ss_pred             hhhhhhhhhhcchHHHhhcchhhcc
Confidence            5999999999999999999998875

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

Probab=80.99  E-value=0.62  Score=38.92  Aligned_cols=20  Identities=25%  Similarity=0.413  Sum_probs=18.2

Q ss_pred             cccccccccccCcCcCCCch
Q 037799          106 VICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      .-|.+||-+||-...||++-
T Consensus       571 kGCayCgGLGHRItdCPKle  590 (610)
T KOG0341|consen  571 KGCAYCGGLGHRITDCPKLE  590 (610)
T ss_pred             cccccccCCCcccccCchhh
Confidence            57999999999999999874

---

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	131
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	96.65
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.64
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.41
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.11
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	95.19
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	94.94
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	94.83
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	94.5
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.43
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	94.39
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.3
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	94.18
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	94.07
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	93.67
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	93.35
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	92.99
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	92.95
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	92.9
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	92.65
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	92.47
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	92.05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	91.88
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	91.32
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	90.01
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	89.5
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	87.87
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	86.49
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	86.31
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	83.48

>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=96.65  E-value=0.00051  Score=35.09  Aligned_cols=20  Identities=25%  Similarity=0.685  Sum_probs=17.6

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ...||+||..||..++|+.+
T Consensus         6 ~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             CCEEEECCccccCHhHCccc
Confidence            35699999999999999865

>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=96.64  E-value=0.00086  Score=33.39  Aligned_cols=19  Identities=32%  Similarity=0.863  Sum_probs=17.2

Q ss_pred             cccccccccccCcCcCCCc
Q 037799          106 VICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ..||.||..||..+.|+..
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            5699999999999999864

>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=96.41  E-value=0.0011  Score=36.56  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=18.9

Q ss_pred             ccccccccccccCcCcCCCchh
Q 037799          105 PVICFTCGRYGHTFWTLDDSHE  126 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~~~  126 (131)
                      ..-|++||..||-...|+....
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCeeeECCCCCcchhhCcCCcc
Confidence            3589999999999999997643

>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=96.11  E-value=0.0017  Score=38.38  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=19.6

Q ss_pred             ccccccccccccCcCcCCCchhh
Q 037799          105 PVICFTCGRYGHTFWTLDDSHEK  127 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~~~~  127 (131)
                      ..-|++||..||-...|+....+
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~~~   45 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKPRG   45 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCCCS
T ss_pred             CCcceeCCCCCcccccCcCCccc
Confidence            45799999999999999976544

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

Probab=95.19  E-value=0.0061  Score=30.18  Aligned_cols=19  Identities=26%  Similarity=0.473  Sum_probs=16.8

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      .++|-.|..+||...+|+.
T Consensus         3 RpYCe~CE~FGH~t~~C~d   21 (26)
T 2hqh_E            3 RPYCEICEMFGHWATNCND   21 (26)
T ss_dssp             -CEETTTTEESSCGGGCCT
T ss_pred             CccchHHHHhCcccccCCc
Confidence            4689999999999999975

>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=94.94  E-value=0.011  Score=33.49  Aligned_cols=20  Identities=25%  Similarity=0.685  Sum_probs=14.1

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      +..|+.||..||...+|+..
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCS
T ss_pred             cCeeeecCCCCcChhhCcCC
Confidence            45677777777777777653

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

Probab=94.83  E-value=0.0076  Score=35.36  Aligned_cols=18  Identities=33%  Similarity=0.755  Sum_probs=16.4

Q ss_pred             cccccccccccCcCcCCC
Q 037799          106 VICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~  123 (131)
                      ..|+.||..||-.++|+.
T Consensus         8 ~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSG
T ss_pred             CccccCCCcCcccccCCC
Confidence            479999999999999984

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

Probab=94.50  E-value=0.015  Score=34.52  Aligned_cols=19  Identities=32%  Similarity=0.620  Sum_probs=10.0

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      +..||.||..||....|+.
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~   22 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPK   22 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTT
T ss_pred             CCcccccCCCCeehhhCcC
Confidence            3445555555555555543

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

Probab=94.43  E-value=0.015  Score=31.30  Aligned_cols=18  Identities=39%  Similarity=0.855  Sum_probs=15.5

Q ss_pred             ccccccccccCcCcCCCc
Q 037799          107 ICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~~  124 (131)
                      .|++||..||...+|+..
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            589999999999999854

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

Probab=94.39  E-value=0.015  Score=30.90  Aligned_cols=17  Identities=29%  Similarity=0.731  Sum_probs=14.1

Q ss_pred             ccccccccccCcCcCCC
Q 037799          107 ICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~  123 (131)
                      .|++||..||...+|+.
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            58888888888888875

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

Probab=94.30  E-value=0.016  Score=31.24  Aligned_cols=18  Identities=28%  Similarity=0.587  Sum_probs=16.5

Q ss_pred             cccccccccccCcCcCCC
Q 037799          106 VICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~  123 (131)
                      ..|+.||..||..+.|+.
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            589999999999999974

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

Probab=94.18  E-value=0.015  Score=30.93  Aligned_cols=19  Identities=32%  Similarity=0.688  Sum_probs=16.8

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      +..|+.||..||..+.|+.
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            4689999999999999973

>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=94.07  E-value=0.019  Score=33.19  Aligned_cols=19  Identities=37%  Similarity=0.756  Sum_probs=13.3

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      +..|+.||..||....|+.
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~   30 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRA   30 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSS
T ss_pred             CcceeeeCCCCcChhhcCC
Confidence            4567777777777777764

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

Probab=93.67  E-value=0.023  Score=35.97  Aligned_cols=20  Identities=25%  Similarity=0.607  Sum_probs=17.9

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ..+|++||.-||..++|+..
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSC
T ss_pred             CCeecccCCCCcCcccCCcc
Confidence            37999999999999999954

>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=93.35  E-value=0.029  Score=33.44  Aligned_cols=19  Identities=21%  Similarity=0.391  Sum_probs=12.9

Q ss_pred             ccccccccccccCcCcCCC
Q 037799          105 PVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~  123 (131)
                      +..||+||..||...+|+.
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            3467777777777777763

>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=92.99  E-value=0.03  Score=31.67  Aligned_cols=18  Identities=28%  Similarity=0.728  Sum_probs=16.6

Q ss_pred             cccccccccccCcCcCCC
Q 037799          106 VICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~  123 (131)
                      ..|+.||..||....|+.
T Consensus        28 ~~C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCS
T ss_pred             CeeCcCCCcCCccCCCcC
Confidence            579999999999999985

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

Probab=92.95  E-value=0.023  Score=35.93  Aligned_cols=20  Identities=20%  Similarity=0.204  Sum_probs=16.7

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ...|+.||..||..+.|+.+
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGG
T ss_pred             cCCCCCCCCCCCccccCCCc
Confidence            45799999999999999865

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

Probab=92.90  E-value=0.035  Score=34.28  Aligned_cols=20  Identities=20%  Similarity=0.336  Sum_probs=16.4

Q ss_pred             CccccccccccccCcCcCCC
Q 037799          104 LPVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       104 lp~~C~~Cg~~GH~~~~C~~  123 (131)
                      .+..||+||..||....|+.
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSS
T ss_pred             CCCcccccCCcCcCcccCCC
Confidence            45679999999999999974

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

Probab=92.65  E-value=0.043  Score=32.41  Aligned_cols=20  Identities=20%  Similarity=0.317  Sum_probs=17.6

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ...|+.||..||....|+..
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCC
Confidence            35799999999999999864

>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=92.47  E-value=0.023  Score=33.38  Aligned_cols=18  Identities=33%  Similarity=0.778  Sum_probs=0.0

Q ss_pred             ccccccccccCcCcCCCc
Q 037799          107 ICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~~  124 (131)
                      .||.||..||...+|+..
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            477777777777777643

>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=92.05  E-value=0.047  Score=31.44  Aligned_cols=18  Identities=28%  Similarity=0.722  Sum_probs=16.6

Q ss_pred             cccccccccccCcCcCCC
Q 037799          106 VICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~  123 (131)
                      ..|+.||..||....|+.
T Consensus        34 ~~C~~Cg~~GH~~~~C~~   51 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCTE   51 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSS
T ss_pred             CEeCCCCCcCCccCCCcC
Confidence            579999999999999985

>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=91.88  E-value=0.059  Score=31.57  Aligned_cols=22  Identities=23%  Similarity=0.338  Sum_probs=19.0

Q ss_pred             CccccccccccccCcCcCCCch
Q 037799          104 LPVICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       104 lp~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      ....|+.||..||..+.|+...
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            3568999999999999999654

>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=91.32  E-value=0.073  Score=31.64  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=18.4

Q ss_pred             ccccccccccccCcCcCCCch
Q 037799          105 PVICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      +..|+.||..||....|+...
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            568999999999999998643

>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=90.01  E-value=0.088  Score=36.59  Aligned_cols=19  Identities=21%  Similarity=0.426  Sum_probs=16.8

Q ss_pred             cccccccccccCcCcCCCc
Q 037799          106 VICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ..|++||..||...+|+..
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSC
T ss_pred             CcccEeCCccchhhhCCCC
Confidence            3699999999999999863

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

Probab=89.50  E-value=0.12  Score=31.78  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=18.4

Q ss_pred             ccccccccccccCcCcCCCch
Q 037799          105 PVICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      +..|+.||..||....|+...
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCTTGG
T ss_pred             CCccCCcCCcCCccCcCcCCc
Confidence            468999999999999998653

>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=87.87  E-value=0.17  Score=35.12  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=18.5

Q ss_pred             ccccccccccccCcCcCCCch
Q 037799          105 PVICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      +..|+.||..||....|+...
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            568999999999999999653

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

Probab=86.49  E-value=0.26  Score=32.75  Aligned_cols=20  Identities=25%  Similarity=0.574  Sum_probs=17.8

Q ss_pred             CccccccccccccCcCcCCC
Q 037799          104 LPVICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       104 lp~~C~~Cg~~GH~~~~C~~  123 (131)
                      -...|++||..||..+.|+.
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCC
T ss_pred             CCCCcCCCCCCCcCcccCcC
Confidence            35799999999999999985

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

Probab=83.48  E-value=0.43  Score=31.71  Aligned_cols=20  Identities=20%  Similarity=0.200  Sum_probs=17.4

Q ss_pred             cccccccccccCcCcCCCch
Q 037799          106 VICFTCGRYGHTFWTLDDSH  125 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~~  125 (131)
                      ..|+.||..||..+.|+...
T Consensus        65 ~~C~~Cg~~GH~~~~Cp~~~   84 (124)
T 2lli_A           65 VQCTLCKSKKHSKERCPSIW   84 (124)
T ss_dssp             CSSSSSCSSCCCTTTCCCST
T ss_pred             ccCCCCCcCCcchhhCCCcc
Confidence            57999999999999999764

---

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	131
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.39
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.85
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.24
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.1
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	88.46

>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=97.39  E-value=2e-05  Score=38.60  Aligned_cols=20  Identities=25%  Similarity=0.685  Sum_probs=17.8

Q ss_pred             ccccccccccccCcCcCCCc
Q 037799          105 PVICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       105 p~~C~~Cg~~GH~~~~C~~~  124 (131)
                      ..-||+||+.||..++|.-+
T Consensus         6 ~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             eeEeecCCccchhhhhccCc
Confidence            45799999999999999865

>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=96.85  E-value=0.00019  Score=33.62  Aligned_cols=19  Identities=32%  Similarity=0.863  Sum_probs=16.9

Q ss_pred             cccccccccccCcCcCCCc
Q 037799          106 VICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~  124 (131)
                      +.||.||+-||..+.|..-
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            5799999999999999853

>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=95.24  E-value=0.003  Score=33.68  Aligned_cols=18  Identities=39%  Similarity=0.833  Sum_probs=15.4

Q ss_pred             ccccccccccCcCcCCCc
Q 037799          107 ICFTCGRYGHTFWTLDDS  124 (131)
Q Consensus       107 ~C~~Cg~~GH~~~~C~~~  124 (131)
                      .|++||..||...+|+..
T Consensus         3 ~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCTTTCCSSSCTTTCSSC
T ss_pred             ccccCCCcCcCcccCcCC
Confidence            589999999999999864

>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=95.10  E-value=0.0039  Score=33.17  Aligned_cols=18  Identities=28%  Similarity=0.722  Sum_probs=16.5

Q ss_pred             cccccccccccCcCcCCC
Q 037799          106 VICFTCGRYGHTFWTLDD  123 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~  123 (131)
                      ..|+.||..||....|+.
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCCCeecccCCC
Confidence            479999999999999985

>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=88.46  E-value=0.088  Score=27.07  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=18.6

Q ss_pred             cccccccccccCcCcCCCchh
Q 037799          106 VICFTCGRYGHTFWTLDDSHE  126 (131)
Q Consensus       106 ~~C~~Cg~~GH~~~~C~~~~~  126 (131)
                      .-|.+|..-||-.++|++...
T Consensus        11 DQCAyCke~GHW~~dCPkkpr   31 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSCC
T ss_pred             hhhHHHhhcCchhhhCccCCC
Confidence            479999999999999997754