Citrus Sinensis ID: 030604

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----

MASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cccccccccccccccccccccccccccccccccccEEEccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccc

masnchnegichscgktghrardcsthvqsggdlrlcnncykpghiaadctndkackncrktghiardcqnepvcnlcniaghvarqcpkgdslgerggggggerggggggdggggggryvGYHDVICRscnqmghmsrdcvgpliicrncggrghmayecpsgriadrgyrry

MASNCHNEGICHscgktghrarDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGhiardcqnepVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRghmayecpsgriadrgyrry

MASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLgerggggggerggggggdggggggrYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY

********GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVAR*********************************YVGYHDVICRSCNQMGHMSRDCVGPLIICRNC***********************

*A****NEGICHSCGKTGHRARDC******************P*************************CQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGG*YVGYHDVICRSCNQMGH***DCVGPLIICRNCGGRGHMAYECPS******GYRR*

MASNCHNEGICHSCG************VQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY

**********CH****T*HRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGD***ERGGGGGGERGGGGGGDGGG*******YHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECP************

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MASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		174	2.2.26 [Sep-21-2011]
P53849		153	Zinc finger protein GIS2	yes	no	0.844	0.960	0.349	4e-16
Q04832		271	DNA-binding protein HEXBP	yes	no	0.867	0.557	0.348	1e-11
P36627		179	Cellular nucleic acid-bin	yes	no	0.701	0.681	0.316	2e-10
O76743		1156	ATP-dependent RNA helicas	yes	no	0.540	0.081	0.304	4e-10
O42395		172	Cellular nucleic acid-bin	yes	no	0.787	0.796	0.325	3e-09
O65639		299	Cold shock protein 1 OS=A	no	no	0.747	0.434	0.287	8e-09
P53996		178	Cellular nucleic acid-bin	no	no	0.643	0.629	0.312	2e-08
P62634		177	Cellular nucleic acid-bin	yes	no	0.637	0.627	0.312	2e-08
Q5R5R5		177	Cellular nucleic acid-bin	yes	no	0.637	0.627	0.312	2e-08
P62633		177	Cellular nucleic acid-bin	yes	no	0.637	0.627	0.312	2e-08

>sp\|P53849\|GIS2_YEAST Zinc finger protein GIS2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GIS2 PE=1 SV=1	Back alignment and function desciption

 Score = 84.0 bits (206), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 57/163 (34%), Positives = 78/163 (47%), Gaps = 16/163 (9%)

Query: 7   NEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCT-----NDKACKNCRK 61
           ++  C+ CGK GH A DC +        RLC NC KPGH+  DCT       K C NC +
Sbjct: 2   SQKACYVCGKIGHLAEDCDSE-------RLCYNCNKPGHVQTDCTMPRTVEFKQCYNCGE 54

Query: 62  TGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYV 121
           TGH+  +C  +  C  CN  GH++R+CP+             +   GG         +  
Sbjct: 55  TGHVRSECTVQ-RCFNCNQTGHISRECPEPKKTSRFSKVSCYK--CGGPNHMAKDCMKED 111

Query: 122 GYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSG 164
           G   + C +C Q GHMSRDC     +C NC   GH++ +CP  
Sbjct: 112 GISGLKCYTCGQAGHMSRDCQNDR-LCYNCNETGHISKDCPKA 153

May act in the sexual differentiation pathway.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp\|Q04832\|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1	Back alignment and function description

>sp\|P36627\|BYR3_SCHPO Cellular nucleic acid-binding protein homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=byr3 PE=4 SV=1	Back alignment and function description

>sp\|O76743\|GLH4_CAEEL ATP-dependent RNA helicase glh-4 OS=Caenorhabditis elegans GN=glh-4 PE=2 SV=2	Back alignment and function description

>sp\|O42395\|CNBP_CHICK Cellular nucleic acid-binding protein OS=Gallus gallus GN=CNBP PE=2 SV=1	Back alignment and function description

>sp\|O65639\|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1	Back alignment and function description

>sp\|P53996\|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2	Back alignment and function description

>sp\|P62634\|CNBP_RAT Cellular nucleic acid-binding protein OS=Rattus norvegicus GN=Cnbp PE=2 SV=1	Back alignment and function description

>sp\|Q5R5R5\|CNBP_PONAB Cellular nucleic acid-binding protein OS=Pongo abelii GN=CNBP PE=2 SV=1	Back alignment and function description

>sp\|P62633\|CNBP_HUMAN Cellular nucleic acid-binding protein OS=Homo sapiens GN=CNBP PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		174
147835847		1850	hypothetical protein VITISV_044067 [Viti	0.890	0.083	0.680	1e-68
255538826		256	cellular nucleic acid binding protein, p	0.902	0.613	0.729	4e-65
225458095		254	PREDICTED: zinc finger protein GIS2-like	0.902	0.618	0.741	2e-64
225458097		157	PREDICTED: zinc finger protein GIS2-like	0.902	1.0	0.741	3e-64
302142593		272	unnamed protein product [Vitis vinifera]	0.867	0.555	0.744	1e-62
225427758		258	PREDICTED: zinc finger protein GIS2-like	0.902	0.608	0.678	4e-61
359475089		246	PREDICTED: zinc finger protein GIS2-like	0.902	0.638	0.678	8e-61
297744732		259	unnamed protein product [Vitis vinifera]	0.902	0.606	0.672	3e-60
224085782		239	predicted protein [Populus trichocarpa]	0.885	0.644	0.690	1e-59
449461615		260	PREDICTED: DNA-binding protein HEXBP-lik	0.959	0.642	0.689	9e-58

>gi\|147835847\|emb\|CAN70803.1\| hypothetical protein VITISV_044067 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  264 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 117/172 (68%), Positives = 132/172 (76%), Gaps = 17/172 (9%)

Query: 2    ASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRK 61
            ASNC NEGICH+CGKTGH ARDCS      GDLRLCNNCYK GHIAADCTNDKAC NCRK
Sbjct: 1631 ASNCPNEGICHTCGKTGHLARDCSAPPVPPGDLRLCNNCYKQGHIAADCTNDKACNNCRK 1690

Query: 62   TGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYV 121
            TGH+ARDC+N+PVCNLCN++GHVARQCPK + LG+R                 GGG R  
Sbjct: 1691 TGHLARDCRNDPVCNLCNVSGHVARQCPKANVLGDR-----------------GGGPRSS 1733

Query: 122  GYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRR 173
            G+ D++CR+C Q+GHMSRDC  PL+ICRNCGGRGHMA+ECPSGR  DR  RR
Sbjct: 1734 GFRDIVCRNCQQLGHMSRDCAAPLMICRNCGGRGHMAFECPSGRFMDRFPRR 1785

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255538826\|ref\|XP_002510478.1\| cellular nucleic acid binding protein, putative [Ricinus communis] gi\|223551179\|gb\|EEF52665.1\| cellular nucleic acid binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225458095\|ref\|XP_002279453.1\| PREDICTED: zinc finger protein GIS2-like isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225458097\|ref\|XP_002279470.1\| PREDICTED: zinc finger protein GIS2-like isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|302142593\|emb\|CBI19796.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225427758\|ref\|XP_002267480.1\| PREDICTED: zinc finger protein GIS2-like isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359475089\|ref\|XP_003631583.1\| PREDICTED: zinc finger protein GIS2-like isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297744732\|emb\|CBI37994.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224085782\|ref\|XP_002307695.1\| predicted protein [Populus trichocarpa] gi\|222857144\|gb\|EEE94691.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449461615\|ref\|XP_004148537.1\| PREDICTED: DNA-binding protein HEXBP-like [Cucumis sativus] gi\|449519884\|ref\|XP_004166964.1\| PREDICTED: DNA-binding protein HEXBP-like [Cucumis sativus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		174
TAIR\|locus:2005719		257	AT1G75560 [Arabidopsis thalian	0.534	0.361	0.784	2.6e-57
SGD\|S000005199		153	GIS2 "Translational activator	0.413	0.470	0.435	4.4e-25
UNIPROTKB\|B4DP17		160	CNBP "cDNA FLJ61146, highly si	0.5	0.543	0.387	1.7e-18
ZFIN\|ZDB-GENE-030131-7782		243	cnbpb "CCHC-type zinc finger,	0.448	0.320	0.411	1.2e-21
UNIPROTKB\|E2RPD7		179	CNBP "Uncharacterized protein"	0.442	0.430	0.431	1.6e-21
UNIPROTKB\|F8WFK2		179	Cnbp "Cellular nucleic acid-bi	0.442	0.430	0.431	1.6e-21
UNIPROTKB\|O42395		172	CNBP "Cellular nucleic acid-bi	0.436	0.441	0.420	1.1e-20
MGI\|MGI:88431		178	Cnbp "cellular nucleic acid bi	0.436	0.426	0.409	1.7e-20
POMBASE\|SPAC13D6.02c		179	byr3 "zinc finger protein Byr3	0.408	0.396	0.379	1.7e-20
UNIPROTKB\|F1N8C2		171	CNBP "Cellular nucleic acid-bi	0.5	0.508	0.387	1.7e-18

TAIR\|locus:2005719 AT1G75560 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 447 (162.4 bits), Expect = 2.6e-57, Sum P(2) = 2.6e-57
 Identities = 73/93 (78%), Positives = 83/93 (89%)

Query:     1 MASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCR 60
             +ASNC NEGICHSCGK+GHRARDCS      GDLRLCNNC+K GH+AADCTNDKACKNCR
Sbjct:   104 VASNCSNEGICHSCGKSGHRARDCSNSDSRAGDLRLCNNCFKQGHLAADCTNDKACKNCR 163

Query:    61 KTGHIARDCQNEPVCNLCNIAGHVARQCPKGDS 93
              +GHIARDC+N+PVCN+C+I+GHVAR CPKGDS
Sbjct:   164 TSGHIARDCRNDPVCNICSISGHVARHCPKGDS 196

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006457 "protein folding" evidence=RCA

GO:0009408 "response to heat" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

SGD\|S000005199 GIS2 "Translational activator for mRNAs with internal ribosome entry sites" [Saccharomyces cerevisiae (taxid:4932)]	Back alignment and assigned GO terms

UNIPROTKB\|B4DP17 CNBP "cDNA FLJ61146, highly similar to Cellular nucleic acid-binding protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-7782 cnbpb "CCHC-type zinc finger, nucleic acid binding protein b" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RPD7 CNBP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F8WFK2 Cnbp "Cellular nucleic acid-binding protein" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|O42395 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

MGI\|MGI:88431 Cnbp "cellular nucleic acid binding protein" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

POMBASE\|SPAC13D6.02c byr3 "zinc finger protein Byr3" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N8C2 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P53849	GIS2_YEAST	No assigned EC number	0.3496	0.8448	0.9607	yes	no

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	Alignment Graph	Length	Definition	E-value
Query		174
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	1e-16
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	4e-15
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	9e-08
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	3e-05
COG4907		595	COG4907, COG4907, Predicted membrane protein [Func	1e-04
PLN03138		796	PLN03138, PLN03138, Protein TOC75; Provisional	4e-04
PLN03138		796	PLN03138, PLN03138, Protein TOC75; Provisional	5e-04
PTZ00146		293	PTZ00146, PTZ00146, fibrillarin; Provisional	7e-04
PTZ00146		293	PTZ00146, PTZ00146, fibrillarin; Provisional	8e-04
PLN03138		796	PLN03138, PLN03138, Protein TOC75; Provisional	0.001
pfam05918		543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	0.002
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	0.003
PLN03138		796	PLN03138, PLN03138, Protein TOC75; Provisional	0.003
PTZ00146		293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.003
PTZ00146		293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.004

>gnl\|CDD\|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional	Back alignment and domain information

 Score = 72.5 bits (178), Expect = 1e-16
 Identities = 51/172 (29%), Positives = 75/172 (43%), Gaps = 46/172 (26%)

Query: 11  CHSCGKTGHRARDCSTHVQSG-GDLRLCNNCYKPGHIAADCTN------DKACKNCRKTG 63
           C+ CG  GH++R+C     +G    R C  C +PGH++ +C +      +++C NC KTG
Sbjct: 3   CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTG 62

Query: 64  HIARDCQNEP------VCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGG 117
           H++R+C   P       C  C   GH++R+CP                         GG 
Sbjct: 63  HLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAK---------------------GGA 101

Query: 118 GRYVGYHDVICRSCNQMGHMSRDCVGPLI------ICRNCGGRGHMAYECPS 163
            R   Y+      C   GH+SRDC            C NCG  GH++ +CP 
Sbjct: 102 ARRACYN------CGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147

Length = 148

>gnl\|CDD\|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]	Back alignment and domain information

>gnl\|CDD\|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]	Back alignment and domain information

>gnl\|CDD\|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]	Back alignment and domain information

>gnl\|CDD\|227244 COG4907, COG4907, Predicted membrane protein [Function unknown]	Back alignment and domain information

>gnl\|CDD\|215598 PLN03138, PLN03138, Protein TOC75; Provisional	Back alignment and domain information

>gnl\|CDD\|215598 PLN03138, PLN03138, Protein TOC75; Provisional	Back alignment and domain information

>gnl\|CDD\|240291 PTZ00146, PTZ00146, fibrillarin; Provisional	Back alignment and domain information

>gnl\|CDD\|240291 PTZ00146, PTZ00146, fibrillarin; Provisional	Back alignment and domain information

>gnl\|CDD\|215598 PLN03138, PLN03138, Protein TOC75; Provisional	Back alignment and domain information

>gnl\|CDD\|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)	Back alignment and domain information

>gnl\|CDD\|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional	Back alignment and domain information

>gnl\|CDD\|215598 PLN03138, PLN03138, Protein TOC75; Provisional	Back alignment and domain information

>gnl\|CDD\|240291 PTZ00146, PTZ00146, fibrillarin; Provisional	Back alignment and domain information

>gnl\|CDD\|240291 PTZ00146, PTZ00146, fibrillarin; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		174
PTZ00368		148	universal minicircle sequence binding protein (UMS	99.96
PTZ00368		148	universal minicircle sequence binding protein (UMS	99.92
COG5082		190	AIR1 Arginine methyltransferase-interacting protei	99.86
COG5082		190	AIR1 Arginine methyltransferase-interacting protei	99.83
KOG4400		261	consensus E3 ubiquitin ligase interacting with arg	99.63
KOG4400		261	consensus E3 ubiquitin ligase interacting with arg	99.55
PF00098		18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.3
PF00098		18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.2
PF13696		32	zf-CCHC_2: Zinc knuckle	97.04
PF13696		32	zf-CCHC_2: Zinc knuckle	96.68
PF13917		42	zf-CCHC_3: Zinc knuckle	96.54
smart00343		26	ZnF_C2HC zinc finger.	94.75
KOG0119		554	consensus Splicing factor 1/branch point binding p	94.57
smart00343		26	ZnF_C2HC zinc finger.	93.77
PF13917		42	zf-CCHC_3: Zinc knuckle	93.57
KOG0119		554	consensus Splicing factor 1/branch point binding p	93.54
PF15288		40	zf-CCHC_6: Zinc knuckle	90.87
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	89.78
PF14392		49	zf-CCHC_4: Zinc knuckle	89.64
COG5222		427	Uncharacterized conserved protein, contains RING Z	86.22
PF14787		36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	86.11
PF14392		49	zf-CCHC_4: Zinc knuckle	85.89
PF15288		40	zf-CCHC_6: Zinc knuckle	85.34
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	83.47
PF14787		36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	82.84
KOG0314		448	consensus Predicted E3 ubiquitin ligase [Posttrans	81.6

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional	Back alignment and domain information

Probab=99.96  E-value=7.5e-30  Score=194.21  Aligned_cols=128  Identities=38%  Similarity=0.972  Sum_probs=110.3

Q ss_pred             CCccCCCCCcCcCCCCCCccC-CCCcccccccCCCCCCCccccCc------ccccccccCCccccCCCCCc------ccc
Q 030604           10 ICHSCGKTGHRARDCSTHVQS-GGDLRLCNNCYKPGHIAADCTND------KACKNCRKTGHIARDCQNEP------VCN   76 (174)
Q Consensus        10 ~C~~Cg~~GH~~~~Cp~~~~~-~~~~~~C~~C~~~GH~~~~C~~~------~~C~~Cg~~GH~~~~Cp~~~------~C~   76 (174)
                      +||+|++.||++++||..... ......||+|++.||++.+||..      ..|++|++.||++++||+..      .|+
T Consensus         2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~   81 (148)
T PTZ00368          2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCY   81 (148)
T ss_pred             cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCCcccC
Confidence            799999999999999984321 23467999999999999999984      36999999999999999753      799


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCCC------Ccceec
Q 030604           77 LCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP------LIICRN  150 (174)
Q Consensus        77 ~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~------~~~C~~  150 (174)
                      +|++.||++++||+.....                           ...++||+|++.||+++|||+.      .++||+
T Consensus        82 ~Cg~~GH~~~~C~~~~~~~---------------------------~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~  134 (148)
T PTZ00368         82 NCGQTGHISRECPNRAKGG---------------------------AARRACYNCGGEGHISRDCPNAGKRPGGDKTCYN  134 (148)
T ss_pred             cCCCCCcccccCCCccccc---------------------------ccchhhcccCcCCcchhcCCCccccCCCCCcccc
Confidence            9999999999999966421                           1236899999999999999984      589999


Q ss_pred             cCCCCcCCCCCCCC
Q 030604          151 CGGRGHMAYECPSG  164 (174)
Q Consensus       151 Cg~~GH~a~~C~~~  164 (174)
                      |+++|||++|||+.
T Consensus       135 Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        135 CGQTGHLSRDCPDK  148 (148)
T ss_pred             CCCcCcccccCCCC
Confidence            99999999999974

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional	Back alignment and domain information

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

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

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PF13696 zf-CCHC_2: Zinc knuckle	Back alignment and domain information

>PF13696 zf-CCHC_2: Zinc knuckle	Back alignment and domain information

>PF13917 zf-CCHC_3: Zinc knuckle	Back alignment and domain information

>smart00343 ZnF_C2HC zinc finger	Back alignment and domain information

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

>smart00343 ZnF_C2HC zinc finger	Back alignment and domain information

>PF13917 zf-CCHC_3: Zinc knuckle	Back alignment and domain information

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

>PF15288 zf-CCHC_6: Zinc knuckle	Back alignment and domain information

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

>PF14392 zf-CCHC_4: Zinc knuckle	Back alignment and domain information

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A	Back alignment and domain information

>PF14392 zf-CCHC_4: Zinc knuckle	Back alignment and domain information

>PF15288 zf-CCHC_6: Zinc knuckle	Back alignment and domain information

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

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A	Back alignment and domain information

>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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 HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		174
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	99.95
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	99.95
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.68
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.53
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.53
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.45
2a51_A		39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.4
2ec7_A		49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.34
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.34
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.32
1a1t_A		55	Nucleocapsid protein; stem-loop RNA, viral protein	99.31
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.3
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	99.27
2a51_A		39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.26
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.2
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.19
2ec7_A		49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.17
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.11
1a1t_A		55	Nucleocapsid protein; stem-loop RNA, viral protein	99.07
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	99.04
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.96
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.76
1dsq_A		26	Nucleic acid binding protein P14; CCHC type zinc f	98.18
1a6b_B		40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.15
1dsq_A		26	Nucleic acid binding protein P14; CCHC type zinc f	98.0
1nc8_A		29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.95
1nc8_A		29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.8
1u6p_A		56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.79
1a6b_B		40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.76
2ysa_A		55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.43
1u6p_A		56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.39
2ysa_A		55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.08

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

Probab=99.95  E-value=3.2e-28  Score=179.18  Aligned_cols=116  Identities=24%  Similarity=0.635  Sum_probs=90.0

Q ss_pred             CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCC-CCCCccccCcccccccccCCccccCCCCC---ccccccccCCC
Q 030604            8 EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKP-GHIAADCTNDKACKNCRKTGHIARDCQNE---PVCNLCNIAGH   83 (174)
Q Consensus         8 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~-GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~~---~~C~~C~~~GH   83 (174)
                      ...||+|+++||++++||..        +||+|+++ ||++.+||..+.|++|++.||++++||+.   ..|++|++.||
T Consensus         4 ~~~C~~C~~~GH~~~~Cp~~--------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH   75 (124)
T 2lli_A            4 APKCNNCSQRGHLKKDCPHI--------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKH   75 (124)
T ss_dssp             SSCCSSCSSSSCCTTTTTSC--------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCC
T ss_pred             CCcccCCCCCCcCcccCcCC--------cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCc
Confidence            46899999999999999984        89999999 99999999988999999999999999975   68999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCC
Q 030604           84 VARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG  143 (174)
Q Consensus        84 ~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~  143 (174)
                      ++++||+.|..+........+            .....+...++||+|+++|||++|||+
T Consensus        76 ~~~~Cp~~~~~y~~~~~~~~~------------~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           76 SKERCPSIWRAYILVDDNEKA------------KPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CTTTCCCSTTSCCSSSCCCCC------------CCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             chhhCCCccccccccCccccc------------cccccCCCCCCcCCCCCCCcCcccCcC
Confidence            999999998754432210000            000011234567777777777776663

PyMOL of 2lli

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

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

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

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

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

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

>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	Back alignment and structure

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

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

>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	Back alignment and structure

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

>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	Back alignment and structure

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

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

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

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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*	Back alignment and structure

>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*	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		174
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	6e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.001
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002

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


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

 Score = 35.2 bits (81), Expect = 2e-04
 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 125 DVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECP 162
           +V C +C + GH +R+C  P    C  CG  GH   +C 
Sbjct: 1   NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

PyMOL of d2exfa1

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

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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		174
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	99.45
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	99.34
d1nc8a_		29	HIV nucleocapsid {Human immunodeficiency virus typ	97.92
d1nc8a_		29	HIV nucleocapsid {Human immunodeficiency virus typ	97.88
d1dsqa_		26	Nucleic acid binding protein p14 {Mouse mammary tu	96.62
d1a6bb_		40	Zinc finger protein ncp10 {Moloney murine leukemia	96.45
d1dsqa_		26	Nucleic acid binding protein p14 {Mouse mammary tu	96.17
d1a6bb_		40	Zinc finger protein ncp10 {Moloney murine leukemia	94.55

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

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=99.45  E-value=3e-14  Score=84.03  Aligned_cols=39  Identities=36%  Similarity=0.865  Sum_probs=36.3

Q ss_pred             cccccCCCCCCCCCCCCCC-CcceeccCCCCcCCCCCCCC
Q 030604          126 VICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSG  164 (174)
Q Consensus       126 ~~C~~Cg~~GH~~~dCp~~-~~~C~~Cg~~GH~a~~C~~~  164 (174)
                      ++||+|++.||+++|||.+ ...||+|++.||++++||+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCCCSSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCcCcCcccCcCCCcCccccCCCCCeecccCCCC
Confidence            6899999999999999986 46899999999999999975

PyMOL of d2exfa1

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

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}	Back information, alignment and structure

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}	Back information, alignment and structure

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

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

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

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