Citrus Sinensis ID: 024873

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-------180-------190-------200-------210-------220-------230-------240-------250-------260-

MSSVSRSRSRSRSRSPLDRKIRSDRFSYRDAPYRRGSRRGYSQSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFLDRYSRRY

ccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cccccccccccccccccHHHHccccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccc

mssvsrsrsrsrsrspldrkirsdrfsyrdapyrrgsrrgysqsnlcknckrpghfarecpnvaichncglpghiasecttkalcwncrepghmagncpnegichtcgkaghrardctapplppgdlrlcnncykqghfaadctndkacnncrktghlardcpndpicnlcnvsghvarhcpksgglgdrysggsgargsggsgargggyrdivcrncqqlghmsrdcmgplmvchncggrghlayecpsgrfldrysrry

mssvsrsrsrsrsrspldrkirsdrfsyrdapyrrgsrrgysqsnlckNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGhlardcpndPICNLCNVSGHVARHCPKSGGLGDRYSGGSGARGsggsgargggyrDIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGhlayecpsgrfldrysrry

MssvsrsrsrsrsrsPLDRKIRSDRFSYRDAPyrrgsrrgysQSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKsgglgdrysggsgargsggsgargggyrdIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFLDRYSRRY

*********************************************LCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNC**************ICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHC****************************YRDIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFL*******

*********************************************LCKNCKRPGHFARECPNVAICHN*GLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGH*******************NCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKSGGL************SGGSGARGGGYRDIVCRNCQQ*GHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFL**YSRRY

******************RKIRSDRFSYRDAPYRRGSRRGYSQSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKSGGLGDRYS**************GGGYRDIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFLDRYSRRY

****************************RDA***********QSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPP****DLRLCNNC*KQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVS*HV***C******************************DIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGR*L*******

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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		261	2.2.26 [Sep-21-2011]
Q04832		271	DNA-binding protein HEXBP	yes	no	0.708	0.682	0.312	2e-21
P53849		153	Zinc finger protein GIS2	yes	no	0.517	0.882	0.350	1e-17
O76743		1156	ATP-dependent RNA helicas	yes	no	0.375	0.084	0.396	2e-17
Q3T0Q6		170	Cellular nucleic acid-bin	yes	no	0.509	0.782	0.366	3e-15
O65639		299	Cold shock protein 1 OS=A	no	no	0.597	0.521	0.331	3e-15
O42395		172	Cellular nucleic acid-bin	yes	no	0.509	0.773	0.362	4e-15
P36627		179	Cellular nucleic acid-bin	yes	no	0.517	0.754	0.383	8e-15
P62634		177	Cellular nucleic acid-bin	yes	no	0.509	0.751	0.352	1e-14
Q5R5R5		177	Cellular nucleic acid-bin	yes	no	0.509	0.751	0.352	1e-14
P62633		177	Cellular nucleic acid-bin	yes	no	0.509	0.751	0.352	1e-14

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

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/278 (31%), Positives = 113/278 (40%), Gaps = 93/278 (33%)

Query: 44  SNLCKNCKRPGHFARECPNV--------AICHNCGLPGHIASECTTKA--------LCWN 87
           S  C+NC + GH+ARECP            C  CG  GH++ EC  +A         C+ 
Sbjct: 15  STSCRNCGKEGHYARECPEADSKGDERSTTCFRCGEEGHMSRECPNEARSGAAGAMTCFR 74

Query: 88  CREPGHMAGNCPNEGI--------CHTCGKAGHRARDCT------------------APP 121
           C E GHM+ +CPN           C+ CG+ GH +RDC                   A  
Sbjct: 75  CGEAGHMSRDCPNSAKPGAAKGFECYKCGQEGHLSRDCPSSQGGSRGGYGQKRGRSGAQG 134

Query: 122 LPPGDLRLCNNCYKQGHFAADCTN---------DKACNNCRKTGHLARDCPN-------- 164
              GD R C  C   GH + DC N         D+ C  C   GH++RDCPN        
Sbjct: 135 GYSGD-RTCYKCGDAGHISRDCPNGQGGYSGAGDRTCYKCGDAGHISRDCPNGQGGYSGA 193

Query: 165 -DPICNLCNVSGHVARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGH 223
            D  C  C  SGH++R CP +G      S GSG               D  C  C + GH
Sbjct: 194 GDRKCYKCGESGHMSRECPSAG------STGSG---------------DRACYKCGKPGH 232

Query: 224 MSRDCMGPLM-----------VCHNCGGRGHLAYECPS 250
           +SR+C                 C+ CG  GH++ +CPS
Sbjct: 233 ISRECPEAGGSYGGSRGGGDRTCYKCGEAGHISRDCPS 270

Binds to single-stranded DNA located in the 5' hexanucleotide repeat region of the L.major leishmanolysin (GP63) gene.
Leishmania major (taxid: 5664)

>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 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\|Q3T0Q6\|CNBP_BOVIN Cellular nucleic acid-binding protein OS=Bos taurus 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\|O42395\|CNBP_CHICK Cellular nucleic acid-binding protein OS=Gallus gallus GN=CNBP PE=2 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\|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		261
449461615		260	PREDICTED: DNA-binding protein HEXBP-lik	0.938	0.942	0.869	1e-117
356516892		259	PREDICTED: zinc finger protein GIS2-like	0.934	0.942	0.857	1e-115
356508208		254	PREDICTED: zinc finger protein GIS2-like	0.923	0.948	0.849	1e-115
224080454		242	predicted protein [Populus trichocarpa]	0.915	0.987	0.814	1e-114
225427758		258	PREDICTED: zinc finger protein GIS2-like	0.957	0.968	0.770	1e-114
255648279		254	unknown [Glycine max]	0.923	0.948	0.845	1e-114
359475089		246	PREDICTED: zinc finger protein GIS2-like	0.900	0.955	0.792	1e-111
297744732		259	unnamed protein product [Vitis vinifera]	0.900	0.907	0.788	1e-110
255543853		252	cellular nucleic acid binding protein, p	0.885	0.916	0.805	1e-110
289540929		256	zinc knuckle (ccHc-type) family protein	0.919	0.937	0.797	1e-108

>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

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 214/246 (86%), Positives = 225/246 (91%), Gaps = 1/246 (0%)

Query: 16  PLDRKIRSDRFSYRDAPYRRGSRRGYSQSNLCKNCKRPGHFARECPNVAICHNCGLPGHI 75
           PLDRKIRSDRFSYRDAPYRR SRRG+S+ NLCKNCKRPGHFARECPNVAICHNCGLPGHI
Sbjct: 16  PLDRKIRSDRFSYRDAPYRRESRRGFSRDNLCKNCKRPGHFARECPNVAICHNCGLPGHI 75

Query: 76  ASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYK 135
           ASECTTK+LCWNCREPGHMA +CPNEGICHTCGKAGHRARDCTAPP+PPGDLRLCNNCYK
Sbjct: 76  ASECTTKSLCWNCREPGHMASSCPNEGICHTCGKAGHRARDCTAPPMPPGDLRLCNNCYK 135

Query: 136 QGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKSGGLGDRYSGGS 195
           QGH AADCTN+KACNNCRKTGHLARDCPNDPICNLCNVSGHVAR CPKS  LGDR   G 
Sbjct: 136 QGHIAADCTNEKACNNCRKTGHLARDCPNDPICNLCNVSGHVARQCPKSNVLGDRGDRGI 195

Query: 196 GARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPSGRFLD 255
            + G G     G GYRD+VCRNCQQLGHMSRDCMGPLM+CHNCGGRGHLAYECPSGRF+D
Sbjct: 196 SS-GGGSGRGSGSGYRDVVCRNCQQLGHMSRDCMGPLMICHNCGGRGHLAYECPSGRFMD 254

Query: 256 RYSRRY 261
           R+ RRY
Sbjct: 255 RFPRRY 260

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356516892\|ref\|XP_003527126.1\| PREDICTED: zinc finger protein GIS2-like [Glycine max]	Back alignment and taxonomy information

>gi\|356508208\|ref\|XP_003522851.1\| PREDICTED: zinc finger protein GIS2-like [Glycine max]	Back alignment and taxonomy information

>gi\|224080454\|ref\|XP_002306137.1\| predicted protein [Populus trichocarpa] gi\|222849101\|gb\|EEE86648.1\| predicted protein [Populus trichocarpa]	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\|255648279\|gb\|ACU24592.1\| unknown [Glycine max]	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\|255543853\|ref\|XP_002512989.1\| cellular nucleic acid binding protein, putative [Ricinus communis] gi\|223548000\|gb\|EEF49492.1\| cellular nucleic acid binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|289540929\|gb\|ADD09600.1\| zinc knuckle (ccHc-type) family protein [Trifolium repens]	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		261
TAIR\|locus:2005719		257	AT1G75560 [Arabidopsis thalian	0.881	0.894	0.576	6.6e-81
ASPGD\|ASPL0000028407		171	AN5111 [Emericella nidulans (t	0.482	0.736	0.357	9.2e-20
POMBASE\|SPAC13D6.02c		179	byr3 "zinc finger protein Byr3	0.478	0.698	0.390	1.9e-24
SGD\|S000005199		153	GIS2 "Translational activator	0.509	0.869	0.364	5.2e-26
ASPGD\|ASPL0000040986		233	AN9093 [Emericella nidulans (t	0.521	0.583	0.370	7.2e-20
UNIPROTKB\|B4DP17		160	CNBP "cDNA FLJ61146, highly si	0.505	0.825	0.398	1.6e-24
CGD\|CAL0002417		175	GIS2 [Candida albicans (taxid:	0.494	0.737	0.333	2.5e-17
UNIPROTKB\|Q59YJ9		175	GIS2 "Putative uncharacterized	0.494	0.737	0.333	2.5e-17
TAIR\|locus:2135139		299	CSDP1 "cold shock domain prote	0.409	0.357	0.359	9.8e-16
ZFIN\|ZDB-GENE-030131-7782		243	cnbpb "CCHC-type zinc finger,	0.505	0.543	0.364	1.6e-22

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

 Score = 812 (290.9 bits), Expect = 6.6e-81, P = 6.6e-81
 Identities = 144/250 (57%), Positives = 168/250 (67%)

Query:    16 PLDRKIRSDRFSYRDAPXXXXXX--XXXXQSNLCKNCKRPGHFARECPNVAICHNCGLPG 73
             P DR++RS+R SY DAP            Q NLC NCKRPGHFAR+C NV++C+NCGLPG
Sbjct:    24 PRDRRMRSERVSYHDAPSRREREPRRAFSQGNLCNNCKRPGHFARDCSNVSVCNNCGLPG 83

Query:    74 HIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTAPPLPPGDLRLCNNC 133
             HIA+ECT ++ CWNCREPGH+A NC NEGICH+CGK+GHRARDC+      GDLRLCNNC
Sbjct:    84 HIAAECTAESRCWNCREPGHVASNCSNEGICHSCGKSGHRARDCSNSDSRAGDLRLCNNC 143

Query:   134 YKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPKXXXXXXXXXX 193
             +KQGH AADCTNDKAC NCR +GH+ARDC NDP+CN+C++SGHVARHCPK          
Sbjct:   144 FKQGHLAADCTNDKACKNCRTSGHIARDCRNDPVCNICSISGHVARHCPKGDSNYSDRGS 203

Query:   194 XXXXXXXXXXXXXXXXXXXIVCRNCQQLGHMSRDCMG--PLMVCHNCGGRGHLAYECPSG 251
                                        L  MSRD  G   +++CHNCGGRGH AYECPS 
Sbjct:   204 RVRDGGMQRGG----------------LSRMSRDREGVSAMIICHNCGGRGHRAYECPSA 247

Query:   252 RFLDRYSRRY 261
             R  DR  RRY
Sbjct:   248 RVADRGFRRY 257

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

ASPGD\|ASPL0000028407 AN5111 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

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

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

ASPGD\|ASPL0000040986 AN9093 [Emericella nidulans (taxid:162425)]	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

CGD\|CAL0002417 GIS2 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|Q59YJ9 GIS2 "Putative uncharacterized protein GIS2" [Candida albicans SC5314 (taxid:237561)]	Back alignment and assigned GO terms

TAIR\|locus:2135139 CSDP1 "cold shock domain protein 1" [Arabidopsis thaliana (taxid:3702)]	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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.IV.762.1	SubName- Full=Putative uncharacterized protein; (242 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		261
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	5e-21
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	6e-20
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	4e-19
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	2e-13
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	2e-12
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	3e-11
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	5e-10
COG5082		190	COG5082, AIR1, Arginine methyltransferase-interact	4e-08
PTZ00368		148	PTZ00368, PTZ00368, universal minicircle sequence	3e-06
COG1198		730	COG1198, PriA, Primosomal protein N' (replication	0.001

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

 Score = 86.0 bits (213), Expect = 5e-21
 Identities = 54/146 (36%), Positives = 72/146 (49%), Gaps = 27/146 (18%)

Query: 45  NLCKNCKRPGHFARECPNVAI--------CHNCGLPGHIASECTTKAL------CWNCRE 90
            +C  C   GH +RECPN A         C+ CG PGH++ EC +         C+NC +
Sbjct: 1   MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGK 60

Query: 91  PGHMAGNCPNEG------ICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCT 144
            GH++  CP          C+ CG+ GH +R+C          R C NC  +GH + DC 
Sbjct: 61  TGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP 120

Query: 145 N-------DKACNNCRKTGHLARDCP 163
           N       DK C NC +TGHL+RDCP
Sbjct: 121 NAGKRPGGDKTCYNCGQTGHLSRDCP 146

Length = 148

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

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

>gnl\|CDD\|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		261
PTZ00368		148	universal minicircle sequence binding protein (UMS	99.94
PTZ00368		148	universal minicircle sequence binding protein (UMS	99.94
COG5082		190	AIR1 Arginine methyltransferase-interacting protei	99.82
COG5082		190	AIR1 Arginine methyltransferase-interacting protei	99.79
KOG4400		261	consensus E3 ubiquitin ligase interacting with arg	99.73
KOG4400		261	consensus E3 ubiquitin ligase interacting with arg	99.62
PF00098		18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.08
PF00098		18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.03
PF13696		32	zf-CCHC_2: Zinc knuckle	96.07
PF13696		32	zf-CCHC_2: Zinc knuckle	95.69
PF13917		42	zf-CCHC_3: Zinc knuckle	95.3
PF13917		42	zf-CCHC_3: Zinc knuckle	93.35
smart00343		26	ZnF_C2HC zinc finger.	93.34
PF14392		49	zf-CCHC_4: Zinc knuckle	93.2
smart00343		26	ZnF_C2HC zinc finger.	92.51
KOG0119		554	consensus Splicing factor 1/branch point binding p	92.15
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	92.14
KOG0119		554	consensus Splicing factor 1/branch point binding p	92.02
PF15288		40	zf-CCHC_6: Zinc knuckle	86.81
PF15288		40	zf-CCHC_6: Zinc knuckle	85.53
PF14392		49	zf-CCHC_4: Zinc knuckle	82.44

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

Probab=99.94  E-value=3.4e-27  Score=194.93  Aligned_cols=133  Identities=38%  Similarity=0.883  Sum_probs=87.3

Q ss_pred             hcccCCCCCCCCCCCCC--------CCccccCCCCCcCCCCCCCCCCCCCCCcccccccCCCCcccccCCCcccCCCCCC
Q 024873           84 LCWNCREPGHMAGNCPN--------EGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKT  155 (261)
Q Consensus        84 ~C~~C~~~GH~~~~Cp~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~C~~Cg~~  155 (261)
                      +||+|++.||++++||+        ...||+|++.||++++||..... .....|++|++.||++.+||+...       
T Consensus         2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~Cg~~GH~~~~Cp~~~~-------   73 (148)
T PTZ00368          2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGG-RGERSCYNCGKTGHLSRECPEAPP-------   73 (148)
T ss_pred             cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCC-CCCcccCCCCCcCcCcccCCCccc-------
Confidence            34444444444444443        24788888888888888765321 112345555555555555544210       


Q ss_pred             CcccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCCC----
Q 024873          156 GHLARDCPNDPICNLCNVSGHVARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGP----  231 (261)
Q Consensus       156 GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~~----  231 (261)
                      +      .....|++|++.||++++||+.+..                     ....++||+|++.||++++||..    
T Consensus        74 ~------~~~~~C~~Cg~~GH~~~~C~~~~~~---------------------~~~~~~C~~Cg~~gH~~~~C~~~~~~~  126 (148)
T PTZ00368         74 G------SGPRSCYNCGQTGHISRECPNRAKG---------------------GAARRACYNCGGEGHISRDCPNAGKRP  126 (148)
T ss_pred             C------CCCcccCcCCCCCcccccCCCcccc---------------------cccchhhcccCcCCcchhcCCCccccC
Confidence            0      0124799999999999999986421                     01246899999999999999874    


Q ss_pred             --CceeeccCCCCcccCCCCCC
Q 024873          232 --LMVCHNCGGRGHLAYECPSG  251 (261)
Q Consensus       232 --~~~C~~Cg~~GH~~~~C~~~  251 (261)
                        .+.||+|++.|||++|||+.
T Consensus       127 ~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        127 GGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             CCCCccccCCCcCcccccCCCC
Confidence              57999999999999999973

>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

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

>smart00343 ZnF_C2HC zinc finger	Back alignment and domain information

>PF14392 zf-CCHC_4: 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

>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

>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

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		261
2lli_A		124	Low Resolution Structure Of Rna-Binding Subunit Of		7e-05
2bl6_A		37	Solution Structure Of The Zn Complex Of Eiav Ncp11(		1e-04

>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The Tramp Complex Length = 124

Back alignment and structure

Iteration: 1

Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust. Identities = 34/118 (28%), Positives = 44/118 (37%), Gaps = 20/118 (16%) Query: 47 CKNCKRPGHFARECPNVAICHNCG-LPGHIASECTTKALCWNCREPGHMAGNCPNEG--- 102 C NC + GH ++CP++ IC CG H + C C C E GH CP++ Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKV 65 Query: 103 ICHTCGKAGHRARDC---------------TAPPLPPGDLRLCNNCYKQGHFAADCTN 145 C C H C P + P C NC +GHF DC Sbjct: 66 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 123

PyMOL of 2lli

>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58) Peptide, Including Two Cchc Zn-Binding Motifs Length = 37

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		261
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	6e-19
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-14
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	2e-11
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	2e-04
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	1e-07
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	4e-06
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	6e-06
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	3e-05
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	6e-05
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	1e-04
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	8e-07
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	1e-04
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-04
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	3e-05
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	7e-05
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	7e-05
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	8e-04
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	4e-05
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	1e-04
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	5e-04
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	5e-04
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	6e-04
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	5e-05
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	8e-05
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	5e-04
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	5e-04
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	1e-04
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	1e-04
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	2e-04
3gv2_A		342	Ca, fusion protein consisting of capsid protein P2	5e-04

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124	Back alignment and structure

 Score = 79.4 bits (195), Expect = 6e-19
 Identities = 27/125 (21%), Positives = 42/125 (33%), Gaps = 7/125 (5%)

Query: 42  SQSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNE 101
             +  C NC + GH  ++CP++   +      H +  C     C  C E GH    CP++
Sbjct: 2   EAAPKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHK 61

Query: 102 G---ICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHL 158
                C  C    H    C +            +  ++        +   C NC   GH 
Sbjct: 62  WKKVQCTLCKSKKHSKERCPSIWRAYI----LVDDNEKAKPKVLPFHTIYCYNCGGKGHF 117

Query: 159 ARDCP 163
             DC 
Sbjct: 118 GDDCK 122

PyMOL of 2lli

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124	Back alignment and structure

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124	Back alignment and structure

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124	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* Length = 148	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* Length = 148	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* Length = 148	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* Length = 148	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* Length = 148	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* Length = 148	Back alignment and structure

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61	Back alignment and structure

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61	Back alignment and structure

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61	Back alignment and structure

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74	Back alignment and structure

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74	Back alignment and structure

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74	Back alignment and structure

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74	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} Length = 63	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} Length = 63	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} Length = 63	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} Length = 63	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} Length = 63	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 Length = 60	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 Length = 60	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 Length = 60	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 Length = 60	Back alignment and structure

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37	Back alignment and structure

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37	Back alignment and structure

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37	Back alignment and structure

>3gv2_A Ca, fusion protein consisting of capsid protein P24, linker and carbon dioxide-concentrating...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1} Length = 342	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		261
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	99.93
2lli_A		124	Protein AIR2; RNA surveillance, RNA degradation, R	99.93
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.61
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.52
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.47
2a51_A		39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.31
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.27
2ec7_A		49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.27
1a1t_A		55	Nucleocapsid protein; stem-loop RNA, viral protein	99.23
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.23
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.18
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.14
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	99.12
2bl6_A		37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.12
2a51_A		39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.09
1a1t_A		55	Nucleocapsid protein; stem-loop RNA, viral protein	99.06
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.06
2ec7_A		49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	98.98
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	98.95
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	98.85
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.84
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.61
1dsq_A		26	Nucleic acid binding protein P14; CCHC type zinc f	97.86
1dsq_A		26	Nucleic acid binding protein P14; CCHC type zinc f	97.83
1nc8_A		29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.8
1a6b_B		40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.78
1a6b_B		40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.64
1nc8_A		29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.61
1u6p_A		56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.38
1u6p_A		56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.32
2ysa_A		55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.02
2ysa_A		55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.46
2hqh_E		26	Restin; beta/BETA structure, zinc finger motif, st	81.24

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

Probab=99.93  E-value=1.7e-25  Score=178.41  Aligned_cols=115  Identities=27%  Similarity=0.668  Sum_probs=77.0

Q ss_pred             CccccCCCCCcCCCCCCCCCCCCCCCcccccccCC-CCcccccCCCcccCCCCCCCcccCCCCCC---CCCCCCCcCCCC
Q 024873          102 GICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQ-GHFAADCTNDKACNNCRKTGHLARDCPND---PICNLCNVSGHV  177 (261)
Q Consensus       102 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~-GH~a~dCp~~~~C~~Cg~~GH~~~~Cp~~---~~C~~C~~~GH~  177 (261)
                      ..||+|++.||++++||+.        .||+|++. ||++.+||+...|++|++.||++++||+.   +.||+|++.||+
T Consensus         5 ~~C~~C~~~GH~~~~Cp~~--------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~   76 (124)
T 2lli_A            5 PKCNNCSQRGHLKKDCPHI--------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHS   76 (124)
T ss_dssp             SCCSSCSSSSCCTTTTTSC--------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCC
T ss_pred             CcccCCCCCCcCcccCcCC--------cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcc
Confidence            3566666666666666652        47777776 77777777767788888888888888864   689999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCC
Q 024873          178 ARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMG  230 (261)
Q Consensus       178 a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~  230 (261)
                      +++||+.|...........+     .. ...+...++||+|+++|||++|||+
T Consensus        77 ~~~Cp~~~~~y~~~~~~~~~-----~~-~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           77 KERCPSIWRAYILVDDNEKA-----KP-KVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             TTTCCCSTTSCCSSSCCCCC-----CC-SCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             hhhCCCccccccccCccccc-----cc-cccCCCCCCcCCCCCCCcCcccCcC
Confidence            99999988632211100000     00 0111345678888888888877774

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

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

>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

>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

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

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

>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

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

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

>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

>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

>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

>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

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1	Back alignment and structure

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} 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

>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

>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

>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

>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

>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

>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {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		261
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-04
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	4e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	7e-04
d2exfa1		42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.001

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42	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 = 36.8 bits (85), Expect = 1e-04
 Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)

Query: 130 CNNCYKQGHFAADCTN--DKACNNCRKTGHLARDCPN 164
           C NC K+GH A +C     K C  C K GH  +DC  
Sbjct: 4   CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40

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

>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		261
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	99.38
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	99.11
d1nc8a_		29	HIV nucleocapsid {Human immunodeficiency virus typ	97.85
d1nc8a_		29	HIV nucleocapsid {Human immunodeficiency virus typ	97.74
d1dsqa_		26	Nucleic acid binding protein p14 {Mouse mammary tu	96.21
d1dsqa_		26	Nucleic acid binding protein p14 {Mouse mammary tu	95.75
d1a6bb_		40	Zinc finger protein ncp10 {Moloney murine leukemia	94.83
d1a6bb_		40	Zinc finger protein ncp10 {Moloney murine leukemia	93.75

>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=99.38  E-value=1e-13  Score=88.17  Aligned_cols=41  Identities=34%  Similarity=0.878  Sum_probs=37.4

Q ss_pred             ccccccCcCCCcccccCCCC-CceeeccCCCCcccCCCCCCC
Q 024873          212 DIVCRNCQQLGHMSRDCMGP-LMVCHNCGGRGHLAYECPSGR  252 (261)
Q Consensus       212 ~~~C~~C~~~GH~~~dC~~~-~~~C~~Cg~~GH~~~~C~~~~  252 (261)
                      +|.||+|++.||+++|||.+ .+.||+||+.||++++||+.+
T Consensus         1 ni~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1           1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             CCCCTTTCCSSSCTTTCSSCCCSSCSSSCCSSSCTTTCCSSC
T ss_pred             CCccccCCCcCcCcccCcCCCcCccccCCCCCeecccCCCCC
Confidence            47899999999999999986 468999999999999999864

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

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