Citrus Sinensis ID: 048519

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-----
Protein Sequence
MSDLPPSLATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLNKTQNNPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHcHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHccccccccHHcHHHHHHHHHHccccccHHHHHHHccHHHHHHHHHHcccccccccccEEEEccccccccccccccccccccccccccccccEEEccccccccHHcHcccc
Coil and Loop (DISEMBL)
msdlppslatapialaAPRLLDLFVYDLLAStsntgknlpdaskielfngekfkcwqeKVFHVLHVYNLADYLQSSlleegtedYDKKLQTWNAESWgdyiktskhkkkqvSLKDAIIHIRIEEKNKIRDVFDKAKEfrsnanlientpqlnktqnnpndghsnnpkrliankkgncfvcGKIIHYANQCRHKAQ
Flexible Loop (DISEMBL)
msdlppslATAPIALAAPRLLDLFVYDLLASTsntgknlpdaSKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAeswgdyiktskhkkkqvslkDAIIhirieeknkirdVFDKAKEFRSnanlientpqlnktqnnpndghsNNPKRLIANKKGNCFVCGKIIHYAnqcrhkaq
Low Complexity Region (SEG)
MSDLPPSLATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLNKTQNNPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ
Disordered region (IsUnstruct)
**********APIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFD***********************************LIANKKGNCFVCGKIIHYANQC*****
Disordered Region (DISOPRED)
********ATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRI******************************************************CFVCGKIIHYANQCRH***
Disordered Region (DISEMBL)
MSDLPPSLATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKT*********LKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLNKTQNNPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ
Disordered Region (DISPRO)
***LPPSLATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRD*F***************************************NKKGNCFVCGKIIHYA*QC*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDLPPSLATAPIALAAPRLLDLFVYDLLASTSNTGKNLPDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLNKTQNNPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ
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	195
147838590	1046	hypothetical protein VITISV_025642 [Viti	0.507	0.094	0.481	1e-17
147780036	588	hypothetical protein VITISV_034115 [Viti	0.507	0.168	0.481	1e-16
147807877	663	hypothetical protein VITISV_012860 [Viti	0.441	0.129	0.473	9e-14
147791706	272	hypothetical protein VITISV_031523 [Viti	0.507	0.363	0.451	3e-13
147846834	965	hypothetical protein VITISV_005064 [Viti	0.728	0.147	0.330	3e-13
147826517	635	hypothetical protein VITISV_017997 [Viti	0.415	0.127	0.488	2e-12
38194910	1290	gag-pol polyprotein [Phaseolus vulgaris]	0.502	0.075	0.423	2e-10
147781792	1096	hypothetical protein VITISV_036207 [Viti	0.333	0.059	0.5	7e-09
359493505	1182	PREDICTED: wall-associated receptor kina	0.502	0.082	0.365	1e-07
359497847	478	PREDICTED: uncharacterized protein LOC10	0.492	0.200	0.37	5e-07

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

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/108 (48%), Positives = 70/108 (64%), Gaps = 9/108 (8%)

Query: 95  ESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQ---- 150
           +SW D     KHK+KQ+SL+D IIHIRIEE+N+ RD  +KAKE  S AN++E  P+    
Sbjct: 140 KSWKDXXXNMKHKRKQMSLEDVIIHIRIEEQNRNRDNVEKAKELSSKANVVEEKPKPKNN 199

Query: 151 LNKTQN---NPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ 195
            ++ QN    PN   SN  ++    K+GNCFVCGK  H+A QCRH+ +
Sbjct: 200 RSRKQNFRTKPN--ASNKVQQSTIKKRGNCFVCGKSRHHAAQCRHRKR 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780036|emb|CAN62301.1| hypothetical protein VITISV_034115 [Vitis vinifera]

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/108 (48%), Positives = 64/108 (59%), Gaps = 9/108 (8%)

Query: 95  ESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIE-------N 147
           ESW DY    KHK+KQ+ L+D IIHIRIEE+N  RD  +KAKE  S AN++E       N
Sbjct: 43  ESWKDYKNNMKHKRKQMFLEDVIIHIRIEEQNLNRDNIEKAKELSSKANVVEEKSKPKNN 102

Query: 148 TPQLNKTQNNPNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ 195
             +   +Q  PN   SN        K GNCFVCGK  H+A QCRH+ +
Sbjct: 103 RSRKQNSQTKPN--ASNKVHNSTIKKWGNCFVCGKSGHHAPQCRHRKR 148

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147807877|emb|CAN75361.1| hypothetical protein VITISV_012860 [Vitis vinifera]

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 59/95 (62%), Gaps = 9/95 (9%)

Query: 105 KHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIE-------NTPQLNKTQNN 157
           KHK+KQ+SL+D IIHIRIEE+N+ RD  +K KE  S AN++E       N  +   ++  
Sbjct: 158 KHKRKQISLEDVIIHIRIEEQNRNRDNVEKTKELSSKANVVEEKXKPKNNRSEKXNSRTK 217

Query: 158 PNDGHSNNPKRLIANKKGNCFVCGKIIHYANQCRH 192
           PN   SN  +     K+GNCFVCGK  H+A Q RH
Sbjct: 218 PNA--SNKVQNPTIKKRGNCFVCGKSGHHATQYRH 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147791706|emb|CAN64015.1| hypothetical protein VITISV_031523 [Vitis vinifera]

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 65/104 (62%), Gaps = 5/104 (4%)

Query: 95  ESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIE--NTPQLN 152
           ESW DY    KHKKKQ+SL+D IIHIRIEE+N+ +D  +KAKE  S AN++E  + P+ N
Sbjct: 67  ESWKDYKNNMKHKKKQMSLEDVIIHIRIEEQNRNKDNIEKAKELSSKANVVEEKSKPKNN 126

Query: 153 KTQNNPNDGHSNNPKRL---IANKKGNCFVCGKIIHYANQCRHK 193
           +++   +   SN   ++      K+GN  V GK  H A QC H+
Sbjct: 127 RSRKQNSRTKSNASNKVQNSTIKKRGNFCVYGKSRHCAVQCHHR 170

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147846834|emb|CAN80619.1| hypothetical protein VITISV_005064 [Vitis vinifera]

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/203 (33%), Positives = 85/203 (41%), Gaps = 61/203 (30%)

Query: 40  PDASKIELFNGEKFKCWQEKVFHVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNA----- 94
           P  SKI+ FN   FK WQE VF  + V NL   L     E+G E     L TW       
Sbjct: 10  PKTSKIDPFNRTLFKKWQEIVFSAIDVMNLGHILTDPKPEDGFES----LPTWEIGNKQV 65

Query: 95  -------------------------------------ESWGDYIKTSKHKKKQVSLKDAI 117
                                                ESW DY    KHK+KQ+      
Sbjct: 66  RHDILSIFSNELFDVYSIEDIKLPKPLVVGYLVETLLESWKDYKNNMKHKRKQM------ 119

Query: 118 IHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQ----LNKTQNNPND-GHSNNPKRLIAN 172
               IE++N+ RD  +KAKE  S AN+IE  P+     +K QN+      SN  +     
Sbjct: 120 ----IEKQNQNRDNVEKAKELSSKANVIEEKPKPKNNRSKKQNSRTKLNASNKVQNPTIK 175

Query: 173 KKGNCFVCGKIIHYANQCRHKAQ 195
           K+G+CFV GK  H+A QCRHK +
Sbjct: 176 KRGDCFVYGKFGHHAAQCRHKKR 198

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147826517|emb|CAN64075.1| hypothetical protein VITISV_017997 [Vitis vinifera]

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 58/90 (64%), Gaps = 9/90 (10%)

Query: 111 VSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIE--NTPQLNK-----TQNNPNDGHS 163
           +SLKD IIHIRIEE+N+ RD  +KAKE  S AN++E  + P+ N+     ++  PN   S
Sbjct: 1   MSLKDVIIHIRIEEQNRNRDNIEKAKELSSKANVVEEKSKPKNNRSRKQNSRTKPN--AS 58

Query: 164 NNPKRLIANKKGNCFVCGKIIHYANQCRHK 193
           N  +     K GNCFVCGK  H+A QCRH+
Sbjct: 59  NKVQNSTIKKXGNCFVCGKSGHHAAQCRHR 88

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/111 (42%), Positives = 63/111 (56%), Gaps = 13/111 (11%)

Query: 95  ESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLNKT 154
           +SW DY +  KH++KQ+SL D I HI IE+ N+      KAK   + AN+IE+ P   + 
Sbjct: 183 QSWTDYKQQLKHRQKQMSLSDLITHIIIEDTNRKECAAAKAKALSAKANVIEDKPAPKRY 242

Query: 155 Q------NNPNDGHS----NNPKRLIANKKGNCFVCGKIIHYANQCRHKAQ 195
           +        PN+  S     NP      KKGNCFVCGK  H+A QCRH+A+
Sbjct: 243 EKKFDHKKKPNNKFSRPSGTNP---TFKKKGNCFVCGKPGHHAPQCRHRAK 290

Source: Phaseolus vulgaris

Species: Phaseolus vulgaris

Genus: Phaseolus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 46/72 (63%), Gaps = 7/72 (9%)

Query: 95  ESWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIE-------N 147
           ESW DY    KHK KQ+SL+D IIHIRIEE+N+ RD  +KAKE  S AN++E       N
Sbjct: 160 ESWKDYKNNMKHKMKQMSLEDVIIHIRIEEQNRNRDNIEKAKELSSKANVVEEKSKPKNN 219

Query: 148 TPQLNKTQNNPN 159
             ++ KT +  N
Sbjct: 220 RKRIEKTSSKAN 231

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/104 (36%), Positives = 56/104 (53%), Gaps = 6/104 (5%)

Query: 96  SWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSN-ANLIE--NTPQLN 152
           SW  Y K   HK +  SL++   H+RIEE+ + RD   +     +N AN +   N P+  
Sbjct: 164 SWKGYRKRILHKSEDYSLEEIQKHLRIEEELRSRDKMAEESNGGTNKANAVSKANHPRGK 223

Query: 153 KTQNNPNDGHSNNPKR---LIANKKGNCFVCGKIIHYANQCRHK 193
              +  N G+  +PK+       KKG CFVCGK+ HYA +CR++
Sbjct: 224 NNNDKRNSGNYMSPKKNQEQFKGKKGPCFVCGKLGHYARECRYR 267

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497847|ref|XP_003635668.1| PREDICTED: uncharacterized protein LOC100854178, partial [Vitis vinifera]

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 53/100 (53%), Gaps = 4/100 (4%)

Query: 96  SWGDYIKTSKHKKKQVSLKDAIIHIRIEEKNKIRDVFDKAKEFRSNANLIENTPQLN-KT 154
           +W D+    KHK+K++S++D II +RIEE N+  +         + AN +E+    N KT
Sbjct: 195 AWKDFKNYLKHKRKEMSIEDLIIRLRIEEDNRRSEKKGAHTLNEAKANFVEHGQSSNAKT 254

Query: 155 QNNPNDGHSNNPKRLIANK---KGNCFVCGKIIHYANQCR 191
            NN   G    PK  I+ K   +G CF CGK  H +  CR
Sbjct: 255 NNNKGKGSKLGPKGGISKKPKFQGKCFNCGKQGHKSVDCR 294

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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)

No hits with e-value below 0.001 by BLAST

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	195
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	99.21
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	99.02
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.5
PF13696	32	zf-CCHC_2: Zinc knuckle	97.67
PF13917	42	zf-CCHC_3: Zinc knuckle	97.04
smart00343	26	ZnF_C2HC zinc finger.	96.75
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.23
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.79
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.19
PF14392	49	zf-CCHC_4: Zinc knuckle	95.07
PTZ00368	148	universal minicircle sequence binding protein (UMS	94.53
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	94.5
PF15288	40	zf-CCHC_6: Zinc knuckle	94.39
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.69
PF13961	27	DUF4219: Domain of unknown function (DUF4219)	92.66
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	92.61
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.48
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	91.13
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	83.04
KOG2044	931	consensus 5'-3' exonuclease HKE1/RAT1 [Replication	80.33

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

Probab=99.21  E-value=3.2e-11  Score=90.80  Aligned_cols=67  Identities=18%  Similarity=0.189  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHhhcCCCCCchhhHHHHHhhcccchHHHHHhhhcCC--cccCHHHHHHHHHHHHhhhh
Q 048519           62 HVLHVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKK--KQVSLKDAIIHIRIEEKNKI  128 (195)
Q Consensus        62 ~il~~~~L~~~L~~~~~~~~~~~~~~~IL~sLP~S~~~f~~~i~~~~--~~~sleeli~~L~~eE~~r~  128 (195)
                      ++.++..++.+|..+|.+++|++++..||.|||++|++|+++|.+..  +++++++|+++|..||..+.
T Consensus        44 hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~sy~~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~  112 (119)
T PF14227_consen   44 HINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPSYDSFVTALLYSKPEDELTLEEVKSKLLQEEERRK  112 (119)
T ss_pred             HHHHHHHHHHhhccccccchHHHHHHHHHHcCCHhHHHHHHHHHccCCCCCcCHHHHHHHHHHHHHHHH
Confidence            55556689999999999999999999999999999999999999875  89999999999999887443

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

Probab=99.02  E-value=5.9e-10  Score=83.89  Aligned_cols=70  Identities=17%  Similarity=0.158  Sum_probs=60.3

Q ss_pred             HhHHHHHHHH----HHHHHHhhcCCCCCchhhHHHHHhhcccchHHHHHhhhcCCcc--cCHHHHHHHHHHHHhhh
Q 048519           58 EKVFHVLHVY----NLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHKKKQ--VSLKDAIIHIRIEEKNK  127 (195)
Q Consensus        58 k~~~~il~~~----~L~~~L~~~~~~~~~~~~~~~IL~sLP~S~~~f~~~i~~~~~~--~sleeli~~L~~eE~~r  127 (195)
                      +...++.+|+    .|+++|+..|.+++|++++..||.+||++|+.|+++|....+.  +|++||+++|..+|...
T Consensus        38 ~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~  113 (119)
T PF14223_consen   38 KDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEMRL  113 (119)
T ss_pred             cccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHH
Confidence            4445555554    8899999999999999999999999999999999999987644  49999999999999733

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

Probab=98.50  E-value=3.4e-08  Score=51.09  Aligned_cols=17  Identities=41%  Similarity=0.968  Sum_probs=16.1

Q ss_pred             ceeecCCcceecccCCC
Q 048519          176 NCFVCGKIIHYANQCRH  192 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~  192 (195)
                      +||+||+.||++++||+
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            69999999999999985

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.67  E-value=1.6e-05  Score=46.80  Aligned_cols=19  Identities=26%  Similarity=0.670  Sum_probs=17.2

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      -.|++|+++|||.++||..
T Consensus         9 Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CEeecCCCCCccHhHCCCC
Confidence            4799999999999999873

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=97.04  E-value=0.00024  Score=44.45  Aligned_cols=19  Identities=26%  Similarity=0.749  Sum_probs=17.1

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      ...|+.|++.|||..+|+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4679999999999999993

>smart00343 ZnF_C2HC zinc finger

Probab=96.75  E-value=0.00052  Score=38.25  Aligned_cols=17  Identities=41%  Similarity=0.968  Sum_probs=15.5

Q ss_pred             ceeecCCcceecccCCC
Q 048519          176 NCFVCGKIIHYANQCRH  192 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~  192 (195)
                      .|+.||+.||++++|+.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            49999999999999983

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

Probab=96.23  E-value=0.0015  Score=39.31  Aligned_cols=20  Identities=50%  Similarity=1.032  Sum_probs=12.5

Q ss_pred             cceeecCCcceecccCCCcc
Q 048519          175 GNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~rK  194 (195)
                      .-|+.|||-.||+++|+.+.
T Consensus         3 ~~CprC~kg~Hwa~~C~sk~   22 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSKT   22 (36)
T ss_dssp             -C-TTTSSSCS-TTT---TC
T ss_pred             ccCcccCCCcchhhhhhhhh
Confidence            46999999999999998653

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

Probab=95.79  E-value=0.0036  Score=54.42  Aligned_cols=18  Identities=33%  Similarity=0.959  Sum_probs=16.5

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      -.||.|||.|||.++||.
T Consensus       161 ~~cyrcGkeghwskEcP~  178 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPV  178 (346)
T ss_pred             HHheeccccccccccCCc
Confidence            369999999999999986

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

Probab=95.19  E-value=0.0074  Score=49.44  Aligned_cols=18  Identities=33%  Similarity=0.792  Sum_probs=15.5

Q ss_pred             ccceeecCCcceecccCC
Q 048519          174 KGNCFVCGKIIHYANQCR  191 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~  191 (195)
                      ...||+||+.||.+++||
T Consensus        60 ~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccchhcccCcccccCC
Confidence            457999999999999998

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=95.07  E-value=0.0067  Score=38.92  Aligned_cols=18  Identities=39%  Similarity=0.929  Sum_probs=16.1

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      ..|++||..||..++|+.
T Consensus        32 ~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   32 RFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhhcCCCCcCcCHhHcCC
Confidence            369999999999999974

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

Probab=94.53  E-value=0.015  Score=45.35  Aligned_cols=19  Identities=32%  Similarity=0.891  Sum_probs=12.7

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      ..||+||..||++++||++
T Consensus       130 ~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        130 KTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             CccccCCCcCcccccCCCC
Confidence            4577777777777777653

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

Probab=94.50  E-value=0.014  Score=47.78  Aligned_cols=16  Identities=31%  Similarity=1.001  Sum_probs=15.3

Q ss_pred             cceeecCCcceecccC
Q 048519          175 GNCFVCGKIIHYANQC  190 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C  190 (195)
                      .+|++||..||++++|
T Consensus        98 ~~C~~Cg~~GH~~~dC  113 (190)
T COG5082          98 KKCYNCGETGHLSRDC  113 (190)
T ss_pred             cccccccccCcccccc
Confidence            5899999999999999

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=94.39  E-value=0.021  Score=35.33  Aligned_cols=20  Identities=30%  Similarity=0.594  Sum_probs=16.3

Q ss_pred             ccceeecCCcceec--ccCCCc
Q 048519          174 KGNCFVCGKIIHYA--NQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~a--r~C~~r  193 (195)
                      +.+|-.||..||.+  +.||-+
T Consensus         1 k~kC~~CG~~GH~~t~k~CP~~   22 (40)
T PF15288_consen    1 KVKCKNCGAFGHMRTNKRCPMY   22 (40)
T ss_pred             CccccccccccccccCccCCCC
Confidence            35799999999999  558754

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

Probab=93.69  E-value=0.028  Score=49.21  Aligned_cols=17  Identities=29%  Similarity=0.909  Sum_probs=15.9

Q ss_pred             ceeecCCcceecccCCC
Q 048519          176 NCFVCGKIIHYANQCRH  192 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~  192 (195)
                      .||.||..|||..+|+.
T Consensus       178 ~CyRCGqkgHwIqnCpT  194 (427)
T COG5222         178 VCYRCGQKGHWIQNCPT  194 (427)
T ss_pred             eEEecCCCCchhhcCCC
Confidence            69999999999999974

>PF13961 DUF4219: Domain of unknown function (DUF4219)

Probab=92.66  E-value=0.11  Score=29.31  Aligned_cols=24  Identities=21%  Similarity=0.519  Sum_probs=21.3

Q ss_pred             ccccchhhhhHhHHHHHHHHHHHH
Q 048519           48 FNGEKFKCWQEKVFHVLHVYNLAD   71 (195)
Q Consensus        48 f~g~~fk~Wqk~~~~il~~~~L~~   71 (195)
                      |||+||..|+.++..+|...+|-+
T Consensus         1 l~g~NY~~W~~~M~~~L~~~~lW~   24 (27)
T PF13961_consen    1 LDGTNYSTWKIRMKAYLESQDLWD   24 (27)
T ss_pred             CCccCHHHHHHHHHHHHHHcchhh
Confidence            899999999999999998877654

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

Probab=92.61  E-value=0.17  Score=39.51  Aligned_cols=54  Identities=11%  Similarity=0.027  Sum_probs=38.8

Q ss_pred             cccccccchhhhhHhHHHHHHHHHHHHHHhh-cCCCCC-ch----------hhHHHHHhhcccchH
Q 048519           45 IELFNGEKFKCWQEKVFHVLHVYNLADYLQS-SLLEEG-TE----------DYDKKLQTWNAESWG   98 (195)
Q Consensus        45 ~~~f~g~~fk~Wqk~~~~il~~~~L~~~L~~-~~~~~~-~~----------~~~~~IL~sLP~S~~   98 (195)
                      ..+|||+||..|+..+..+|...++...+.. ..+|.. +.          ....+|++++.++--
T Consensus        10 ~~kL~g~NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~~~~~~W~~~d~~v~swl~~sis~~i~   75 (152)
T PF14244_consen   10 SIKLNGSNYLSWSQQMEMALRGKGLWGFIDGTIPKPPETDPAYEKWERKDQLVLSWLLNSISPDIL   75 (152)
T ss_pred             ccCCCCccHHHHHHHHHHHHHhCCCcccccCccccccccchhhhhHHHhhhHHHHHHHHhhcHHHH
Confidence            4799999999999999999999988777764 222222 21          123577888877743

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

Probab=91.48  E-value=0.083  Score=41.20  Aligned_cols=20  Identities=25%  Similarity=0.743  Sum_probs=16.2

Q ss_pred             ccceeecCCcceecccCCCc
Q 048519          174 KGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ...||.|+..||++++|++.
T Consensus       103 ~~~C~~Cg~~gH~~~~C~~~  122 (148)
T PTZ00368        103 RRACYNCGGEGHISRDCPNA  122 (148)
T ss_pred             chhhcccCcCCcchhcCCCc
Confidence            34699999999999999763

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

Probab=91.13  E-value=0.085  Score=45.01  Aligned_cols=18  Identities=28%  Similarity=0.931  Sum_probs=16.6

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      ..||.||+.||+.++|+.
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            679999999999999985

>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes

Probab=83.04  E-value=0.64  Score=35.82  Aligned_cols=22  Identities=27%  Similarity=0.611  Sum_probs=18.3

Q ss_pred             CCCccceeecCCcceecccCCCc
Q 048519          171 ANKKGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       171 ~k~k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ......|.+|+ -.||...||.+
T Consensus       103 ~~~~v~CR~Ck-GdH~T~~CPyK  124 (128)
T PF12353_consen  103 GKSKVKCRICK-GDHWTSKCPYK  124 (128)
T ss_pred             CCceEEeCCCC-CCcccccCCcc
Confidence            34556899996 99999999976

Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.

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

Probab=80.33  E-value=0.71  Score=45.33  Aligned_cols=20  Identities=40%  Similarity=0.909  Sum_probs=17.3

Q ss_pred             ccceeecCCcceecccCCCc
Q 048519          174 KGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ...||.||..||.+.+|...
T Consensus       260 ~~~C~~cgq~gh~~~dc~g~  279 (931)
T KOG2044|consen  260 PRRCFLCGQTGHEAKDCEGK  279 (931)
T ss_pred             cccchhhcccCCcHhhcCCc
Confidence            34699999999999999754

---

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	195
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.69
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.58
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.53
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.47
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.03
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.52
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.46
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.46
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.39
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.38
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.37
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.36
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.34
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.31
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.3
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.3
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.24
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.15
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.12
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.11
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.11
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.99
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.67
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.55
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.93
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.07
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	90.2
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	86.69
3e2u_E	42	CAP-Gly domain-containing linker protein 1; struct	83.3
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	81.11

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=98.69  E-value=6.3e-09  Score=63.72  Aligned_cols=22  Identities=27%  Similarity=0.697  Sum_probs=19.3

Q ss_pred             CccceeecCCcceecccCCCcc
Q 048519          173 KKGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       173 ~k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      .+..||+||+.|||+++||+++
T Consensus         9 ~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            9 DRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCeeeECCCCCcchhhCcCCc
Confidence            3568999999999999999865

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

Probab=98.58  E-value=1.6e-08  Score=66.33  Aligned_cols=23  Identities=26%  Similarity=0.624  Sum_probs=19.9

Q ss_pred             CCccceeecCCcceecccCCCcc
Q 048519          172 NKKGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       172 k~k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ..+..||+||+.|||+++||+++
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCCcceeCCCCCcccccCcCCc
Confidence            34578999999999999999865

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=98.47  E-value=4.1e-08  Score=55.88  Aligned_cols=21  Identities=43%  Similarity=0.711  Sum_probs=18.2

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||+||+.||++++|+..+
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            367999999999999998654

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

Probab=98.03  E-value=1.3e-06  Score=56.94  Aligned_cols=20  Identities=40%  Similarity=0.861  Sum_probs=17.3

Q ss_pred             ccceeecCCcceecccCCCc
Q 048519          174 KGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ...||.||++|||+++|+..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            34799999999999999843

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

Probab=97.52  E-value=2.4e-05  Score=49.45  Aligned_cols=20  Identities=30%  Similarity=0.798  Sum_probs=17.9

Q ss_pred             cceeecCCcceecccCCCcc
Q 048519          175 GNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ..||.||+.||++++|+.++
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSSC
T ss_pred             CeeCcCCCcCCccCCCcCCC
Confidence            57999999999999999875

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

Probab=97.46  E-value=3.3e-05  Score=50.70  Aligned_cols=21  Identities=38%  Similarity=0.809  Sum_probs=18.4

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||.||+.||++++|+.+.
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CcceeECCCCCCccCcCCCcc
Confidence            457999999999999998754

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

Probab=97.46  E-value=2.8e-05  Score=46.74  Aligned_cols=16  Identities=38%  Similarity=0.870  Sum_probs=12.0

Q ss_pred             eeecCCcceecccCCC
Q 048519          177 CFVCGKIIHYANQCRH  192 (195)
Q Consensus       177 C~~CgK~GH~ar~C~~  192 (195)
                      ||.||+.||++++||+
T Consensus        24 C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           24 CWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CTTTCCSSSCTTTSCC
T ss_pred             cccCCCCCCccCcCcC
Confidence            7777777777777764

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

Probab=97.39  E-value=3.5e-05  Score=46.32  Aligned_cols=18  Identities=50%  Similarity=0.921  Sum_probs=16.1

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      +.||+||+.||++++|+.
T Consensus         1 i~C~~Cg~~GH~a~~C~~   18 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQ   18 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCS
T ss_pred             CeeeccCCCCcccccCCC
Confidence            369999999999999974

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

Probab=97.38  E-value=3.8e-05  Score=50.73  Aligned_cols=21  Identities=33%  Similarity=0.816  Sum_probs=18.4

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||+||+.||++++|+.++
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            357999999999999998764

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

Probab=97.37  E-value=5.5e-05  Score=47.76  Aligned_cols=19  Identities=47%  Similarity=0.826  Sum_probs=17.3

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      ..||+||+.||++++|+..
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCS
T ss_pred             CeeeecCCCCcChhhCcCC
Confidence            5799999999999999864

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

Probab=97.36  E-value=5.1e-05  Score=48.88  Aligned_cols=21  Identities=33%  Similarity=0.786  Sum_probs=17.8

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||.||+.||++++|+.++
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSSC
T ss_pred             CCEeCCCCCcCCccCCCcCcC
Confidence            357999999999999998764

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

Probab=97.34  E-value=4.8e-05  Score=50.60  Aligned_cols=21  Identities=33%  Similarity=0.691  Sum_probs=18.0

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||+||+.||++++|+.++
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            457999999999999998754

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

Probab=97.31  E-value=4.9e-05  Score=45.14  Aligned_cols=18  Identities=39%  Similarity=0.925  Sum_probs=16.1

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      ..||+||+.||++++|+.
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            579999999999999984

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

Probab=97.30  E-value=6.3e-05  Score=52.85  Aligned_cols=21  Identities=29%  Similarity=0.808  Sum_probs=18.5

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||+||+.||++++|++++
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSCC
T ss_pred             CCeecccCCCCcCcccCCccc
Confidence            467999999999999998764

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

Probab=97.30  E-value=7.8e-05  Score=49.17  Aligned_cols=20  Identities=45%  Similarity=1.072  Sum_probs=17.7

Q ss_pred             ccceeecCCcceecccCCCc
Q 048519          174 KGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ...||+||+.||++++|+..
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~   23 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKK   23 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTT
T ss_pred             CCcccccCCCCeehhhCcCC
Confidence            35799999999999999874

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

Probab=97.24  E-value=7.7e-05  Score=44.27  Aligned_cols=18  Identities=44%  Similarity=1.010  Sum_probs=16.4

Q ss_pred             ceeecCCcceecccCCCc
Q 048519          176 NCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~r  193 (195)
                      .||+||+.||++++|+..
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            599999999999999864

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

Probab=97.15  E-value=0.00016  Score=47.95  Aligned_cols=19  Identities=32%  Similarity=0.889  Sum_probs=17.1

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      ...||+||+.||++++|+.
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            3579999999999999985

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

Probab=97.12  E-value=7e-05  Score=49.08  Aligned_cols=18  Identities=44%  Similarity=1.119  Sum_probs=0.0

Q ss_pred             ceeecCCcceecccCCCc
Q 048519          176 NCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~r  193 (195)
                      .||.||+.||++++|+..
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            599999999999999864

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

Probab=97.11  E-value=0.00011  Score=50.57  Aligned_cols=21  Identities=33%  Similarity=0.691  Sum_probs=17.2

Q ss_pred             ccceeecCCcceecccCCCcc
Q 048519          174 KGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ...||+||+.||++++|+.++
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            357999999999999998754

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

Probab=97.11  E-value=0.00012  Score=47.11  Aligned_cols=19  Identities=47%  Similarity=0.910  Sum_probs=17.2

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      ..||.||+.||++++|+..
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSC
T ss_pred             cceeeeCCCCcChhhcCCC
Confidence            5799999999999999864

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

Probab=96.99  E-value=0.00025  Score=48.64  Aligned_cols=19  Identities=32%  Similarity=0.889  Sum_probs=17.0

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      ...||+||+.||++++|+.
T Consensus        24 ~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           24 GDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             TSCCTTTCCSSSCTTTCSS
T ss_pred             CCcccccCCcCcCcccCCC
Confidence            3579999999999999985

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

Probab=96.67  E-value=0.00043  Score=53.51  Aligned_cols=20  Identities=35%  Similarity=0.718  Sum_probs=15.7

Q ss_pred             cceeecCCcceecccCCCcc
Q 048519          175 GNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ..||.||+.||++++||++.
T Consensus       120 ~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A          120 KKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCTTTCCSSCCGGGCTTTT
T ss_pred             CcccccCCcCCEeccCcCCC
Confidence            46888888888888888653

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

Probab=96.55  E-value=0.00083  Score=51.86  Aligned_cols=19  Identities=32%  Similarity=0.889  Sum_probs=17.2

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      ...||+||+.||++++|+.
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCS
T ss_pred             CCcccEeCCccchhhhCCC
Confidence            3579999999999999987

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

Probab=95.93  E-value=0.0016  Score=48.42  Aligned_cols=19  Identities=26%  Similarity=0.847  Sum_probs=17.4

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      .+.||+||+.||++++||+
T Consensus       105 ~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          105 TIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCTTTTSSSCTTTTTSCC
T ss_pred             CCCcCCCCCCCcCcccCcC
Confidence            4689999999999999986

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

Probab=95.07  E-value=0.0071  Score=44.81  Aligned_cols=20  Identities=25%  Similarity=0.541  Sum_probs=17.1

Q ss_pred             ccceeecCCcceecccCCCc
Q 048519          174 KGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~r  193 (195)
                      ...||+||+.||++++||..
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCS
T ss_pred             CccCCCCCcCCcchhhCCCc
Confidence            35799999999999999864

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

Probab=90.20  E-value=0.058  Score=29.31  Aligned_cols=19  Identities=26%  Similarity=0.738  Sum_probs=16.2

Q ss_pred             ccceeecCCcceecccCCC
Q 048519          174 KGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       174 k~~C~~CgK~GH~ar~C~~  192 (195)
                      ++-|-+|...||+..+|..
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            4679999999999999964

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

Probab=83.30  E-value=0.24  Score=29.92  Aligned_cols=20  Identities=25%  Similarity=0.722  Sum_probs=17.1

Q ss_pred             CccceeecCCcceecccCCC
Q 048519          173 KKGNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       173 ~k~~C~~CgK~GH~ar~C~~  192 (195)
                      .++-|-+|-..|||..+|..
T Consensus        19 eRpYCe~CEVFGH~t~eC~d   38 (42)
T 3e2u_E           19 ERPYCEICEMFGHWATNCND   38 (42)
T ss_dssp             -CCEETTTTEESSCGGGCCT
T ss_pred             cCcccccceecccccccCCc
Confidence            35679999999999999964

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

Probab=81.11  E-value=0.33  Score=33.58  Aligned_cols=17  Identities=6%  Similarity=-0.140  Sum_probs=4.8

Q ss_pred             ceeecCCcceecccCCC
Q 048519          176 NCFVCGKIIHYANQCRH  192 (195)
Q Consensus       176 ~C~~CgK~GH~ar~C~~  192 (195)
                      .||+|+..||.+++|..
T Consensus        26 rcY~c~~~gh~~~~c~~   42 (83)
T 3nyb_B           26 RAYILVDDNEKAKPKVL   42 (83)
T ss_dssp             CCCCBC-----------
T ss_pred             cccccccCCcccccccC
Confidence            58888888888887754

---

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	195
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.66
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	98.15
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	98.0
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.92
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.68
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	93.86
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	93.85

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

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

Probab=98.66  E-value=3.1e-09  Score=57.79  Aligned_cols=21  Identities=48%  Similarity=0.771  Sum_probs=17.9

Q ss_pred             CccceeecCCcceecccCCCc
Q 048519          173 KKGNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       173 ~k~~C~~CgK~GH~ar~C~~r  193 (195)
                      +..+||+|||.||.+++|+-+
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSS
T ss_pred             ceeEeecCCccchhhhhccCc
Confidence            346899999999999999654

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

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

Probab=98.15  E-value=3.1e-07  Score=53.38  Aligned_cols=22  Identities=27%  Similarity=0.697  Sum_probs=19.3

Q ss_pred             CccceeecCCcceecccCCCcc
Q 048519          173 KKGNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       173 ~k~~C~~CgK~GH~ar~C~~rK  194 (195)
                      .+..|-+|.+.|||+++||++.
T Consensus         9 ~kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_           9 DRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSC
T ss_pred             cchhhHHHhhcCchhhhCccCC
Confidence            3568999999999999999864

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=98.00  E-value=6.4e-07  Score=46.57  Aligned_cols=18  Identities=39%  Similarity=0.936  Sum_probs=16.5

Q ss_pred             cceeecCCcceecccCCC
Q 048519          175 GNCFVCGKIIHYANQCRH  192 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~  192 (195)
                      +.||-|||.||.+++|..
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            679999999999999964

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

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

Probab=97.92  E-value=1.3e-06  Score=52.44  Aligned_cols=20  Identities=30%  Similarity=0.772  Sum_probs=18.1

Q ss_pred             cceeecCCcceecccCCCcc
Q 048519          175 GNCFVCGKIIHYANQCRHKA  194 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~rK  194 (195)
                      ..||.||+.||++++||+|+
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCCCeecccCCCCC
Confidence            46999999999999999875

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

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

Probab=97.68  E-value=4.8e-06  Score=49.79  Aligned_cols=19  Identities=47%  Similarity=0.880  Sum_probs=17.5

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      ++||+||+.||++++||.+
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            5799999999999999974

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=93.86  E-value=0.0082  Score=32.66  Aligned_cols=19  Identities=37%  Similarity=0.828  Sum_probs=16.9

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      +.|-.|+|--||+++|+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCS
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            4699999999999999865

>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=93.85  E-value=0.0086  Score=32.76  Aligned_cols=19  Identities=42%  Similarity=0.894  Sum_probs=16.9

Q ss_pred             cceeecCCcceecccCCCc
Q 048519          175 GNCFVCGKIIHYANQCRHK  193 (195)
Q Consensus       175 ~~C~~CgK~GH~ar~C~~r  193 (195)
                      +-|-.|+|--||+++|+.+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCCT
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            4699999999999999865