Citrus Sinensis ID: 030923

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
Protein Sequence
MREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
Secondary Structure (PSIPRED)
ccccccHHHHHHcccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHccccccccHHHHHHHHcccccccccccccccccccHHHHHHccccccccccccccccHHHccc
Secondary Structure Prediction (SSPRO)
ccccccEEHEEEccccccccccccccHHHHHcccccccccccccccccccccccccccccccHcccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccHHHccccc
Coil and Loop (DISEMBL)
mreergvcrafqrgectrgdgckfshneqraantgggpqdrssrwghekfegfswgkndsssratgsgrvalegnpnqsdrreekrsirhdhrekpredhgrredkrsrrhsdnnefearsredhyrrdekrpkrhesesylredqdrrggdksstgrgdssshrhrer
Flexible Loop (DISEMBL)
mreergvcrafqrgectrgdgckfshneqraantgggpqdrssrWGHEKFEgfswgkndsssratgsgrvalegnpnqsdrreekrsirhdhrekpredhgrredkrsrrhsdnnefearsredhyrrdekrpkrhesesylredqdrrggdksstgrgdssshrhrer
Low Complexity Region (SEG)
MREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
Disordered region (IsUnstruct)
*************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*****GV*RAFQRGECTRGDGCK**************************************************************************************************************************************************
Disordered Region (DISEMBL)
MREERGVCRAFQRGECTRGDGCKFSHNE****************WGHEKFEGFSWG**********SGRVALE************************************************************************************************
Disordered Region (DISPRO)
****RGVCRAFQRGECTRGDGCKFS******A*****************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
Positional Conservation
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	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	169	2.2.26 [Sep-21-2011]
Q9SD61	352	Zinc finger CCCH domain-c	yes	no	0.284	0.136	0.775	9e-15
Q10B98	312	Zinc finger CCCH domain-c	yes	no	0.928	0.503	0.352	8e-07

>sp|Q9SD61|C3H42_ARATH Zinc finger CCCH domain-containing protein 42 OS=Arabidopsis thaliana GN=At3g47120 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 38/49 (77%), Positives = 43/49 (87%), Gaps = 1/49 (2%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEK 49
           RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSS+W H+K
Sbjct: 130 REARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSKWDHDK 178

Arabidopsis thaliana (taxid: 3702)

>sp|Q10B98|C3H25_ORYSJ Zinc finger CCCH domain-containing protein 25 OS=Oryza sativa subsp. japonica GN=Os03g0826400 PE=2 SV=1

 Score = 53.1 bits (126), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 67/190 (35%), Positives = 91/190 (47%), Gaps = 33/190 (17%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRS-SRW----------GHEKF 50
           RE RGVC AFQ+GEC RG  C++SH+EQR ANTG G ++ S +RW           H+KF
Sbjct: 130 REARGVCYAFQKGECNRGASCRYSHDEQRNANTGWGSKEESKARWEHDRHHEPPMSHKKF 189

Query: 51  EGFSWGKNDSSSRATGSGRVALEGNPNQSDRRE--EKRSIRHDHREKPREDHGR----RE 104
              S G+     RA    +    G   QS R E  + R  R  H ++  +DH R    R 
Sbjct: 190 PS-SAGEQRFPDRAKEENKST--GREGQSSRSEAYKDRDSRLRHSDRGSKDHDRYRHDRS 246

Query: 105 DKRSR--RHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTG----R 158
            +RSR  R  +N+ +          RDEK  +      +   DQ R   D  S+G    R
Sbjct: 247 PERSRGDRQRNNDRYAQG-------RDEKSERYRSEVKHDEGDQKRSRRDTDSSGHYERR 299

Query: 159 GDSSSHRHRE 168
           G+  S R+R+
Sbjct: 300 GNEDSERYRK 309

Oryza sativa subsp. japonica (taxid: 39947)

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	169
224104290	243	predicted protein [Populus trichocarpa]	0.633	0.440	0.594	1e-25
356551855	354	PREDICTED: zinc finger CCCH domain-conta	0.863	0.412	0.405	2e-18
357490653	393	RNA binding domain protein [Medicago tru	0.757	0.325	0.493	9e-18
449460375	395	PREDICTED: zinc finger CCCH domain-conta	0.798	0.341	0.398	1e-17
297745915	375	unnamed protein product [Vitis vinifera]	0.852	0.384	0.441	4e-17
225434618	429	PREDICTED: uncharacterized protein LOC10	0.396	0.156	0.637	8e-17
297819328	316	hypothetical protein ARALYDRAFT_905943 [	0.668	0.357	0.474	1e-15
356498939	235	PREDICTED: zinc finger CCCH domain-conta	0.497	0.357	0.53	8e-15
147840589	737	hypothetical protein VITISV_032469 [Viti	0.846	0.194	0.397	7e-14
15232729	352	RNA-binding motif protein, X-linked 2 [A	0.284	0.136	0.775	4e-13

>gi|224104290|ref|XP_002313385.1| predicted protein [Populus trichocarpa] gi|222849793|gb|EEE87340.1| predicted protein [Populus trichocarpa]

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/116 (59%), Positives = 79/116 (68%), Gaps = 9/116 (7%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSS 61
           RE RGVC AFQRGEC RG GC+FSH+EQRAANTG G QD+SSRWGHE F+G         
Sbjct: 130 REARGVCHAFQRGECNRGAGCRFSHDEQRAANTGWGAQDKSSRWGHEMFDG------PKK 183

Query: 62  SRATGSGRVALEGNPNQSDRREEKRSIRHDHRE---KPREDHGRREDKRSRRHSDN 114
           S    S  +  E +P Q+DRREEKRS  HD  E   KPRED+ RREDK+ RR  D+
Sbjct: 184 SEERSSYNMPSESHPKQNDRREEKRSRWHDDNEIVQKPREDYNRREDKKLRRLEDD 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356551855|ref|XP_003544288.1| PREDICTED: zinc finger CCCH domain-containing protein 42-like [Glycine max]

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/202 (40%), Positives = 105/202 (51%), Gaps = 56/202 (27%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS----WGK 57
           RE RGVCRAFQRGECTRG  CKFSH+EQRAANTG G ++   +WGH+KF+G       G 
Sbjct: 130 REARGVCRAFQRGECTRGASCKFSHDEQRAANTGWGREEDKPKWGHDKFDGPKKERRSGN 189

Query: 58  N-----------DSSSRATGSGRVALEGNPNQSDR------------------------- 81
           N           DS SRA  +    L+  P +SDR                         
Sbjct: 190 NQSNHIAETRDRDSFSRARNND-AELDNQPKRSDRKEMTKREYRYKREEKGSRRDDYDGM 248

Query: 82  ---------REEKRSIRHDHRE-KPRE-DHGRREDKRSRRHSDNNEFEARSREDHYRRDE 130
                    REEKRSI+ D  E +P+  D   REDKRSRR  DN++  ++SRE H   ++
Sbjct: 249 KLEPKDHHLREEKRSIKPDDVEVEPKSRDSDIREDKRSRRR-DNDDIVSKSREPHGYSED 307

Query: 131 KRPKRH---ESESYLREDQDRR 149
           ++ ++H   ES    RED DR+
Sbjct: 308 RKSRKHSEGESAPKPREDYDRK 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357490653|ref|XP_003615614.1| RNA binding domain protein [Medicago truncatula] gi|355516949|gb|AES98572.1| RNA binding domain protein [Medicago truncatula]

 Score = 95.1 bits (235), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/148 (49%), Positives = 92/148 (62%), Gaps = 20/148 (13%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS----WGK 57
           RE RGVCRAFQRGECTRG GCKFSH+EQRAANTG G  +  ++  ++K++G      +G 
Sbjct: 130 REARGVCRAFQRGECTRGAGCKFSHDEQRAANTGWG-DNGIAKGDNDKYDGPKKERRYGN 188

Query: 58  N-----------DSSSRATGSGRVALEGNPNQSDRREEKRSIRH--DHREKPREDHGRRE 104
           N           DS SRA G+G + L+    +SDRREEK   R   D     RE+  RRE
Sbjct: 189 NQPDRIPETRDRDSRSRAHGNG-MELDNPSKRSDRREEKMLRRQDGDGNFVGRENTSRRE 247

Query: 105 DKRSRRHSDNNEFEARSREDHYRRDEKR 132
           +KR R + D +EFE   RED +RR+EKR
Sbjct: 248 EKRPRDYKD-DEFEQWPREDRHRREEKR 274

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460375|ref|XP_004147921.1| PREDICTED: zinc finger CCCH domain-containing protein 25-like [Cucumis sativus]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/173 (39%), Positives = 95/173 (54%), Gaps = 38/173 (21%)

Query: 5   RGVCRAFQRGECTRGDGCKFSHNEQRAANTG-GGPQDRSSRWGHEKFEGFSWGKNDSSSR 63
           RGVCRAFQRGECTRG GCKFSH+EQRAA+TG G  +D SS+WGH+KF+  S   +D    
Sbjct: 133 RGVCRAFQRGECTRGAGCKFSHDEQRAADTGWGAAEDASSKWGHDKFD--SRKNHDKELH 190

Query: 64  ATG--------------SGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSR 109
           A G              SG +  E  P   D  +E          K REDHG +++KRSR
Sbjct: 191 AKGRKTSDNLGRHPRETSGSLRQENRPRGWDDSKESEL-------KSREDHGGKDEKRSR 243

Query: 110 RHSDNNEFEARSREDHY--------------RRDEKRPKRHESESYLREDQDR 148
           R+  +   + +S +D Y              R+DEKR ++H+++  ++ + DR
Sbjct: 244 RYDLDGNSDPKSGDDQYKGEEKRSSRNHDDNRKDEKRSRKHDNDDEMKLEDDR 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745915|emb|CBI15971.3| unnamed protein product [Vitis vinifera]

 Score = 92.8 bits (229), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/163 (44%), Positives = 94/163 (57%), Gaps = 19/163 (11%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSS 61
           RE RGVCRAFQRGEC RG GCKFSH+EQRA+NTG G +D+SSRWGH+KF+G +  K+D  
Sbjct: 130 REARGVCRAFQRGECNRGAGCKFSHDEQRASNTGWGSEDKSSRWGHDKFQGST--KSDGR 187

Query: 62  SRATGSGRVALEGNPNQSDR--REEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEA 119
             +  + RV  E    +  R   ++ RS R    E  RE H RR              E 
Sbjct: 188 PNSIPTNRVH-EPTVGEGHRFGNKDARSSRTKGSEGGRESHHRRS-------------EL 233

Query: 120 RSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSS 162
             R+   R  E++ ++ E E   +EDQDRR  ++ S GR DS+
Sbjct: 234 DIRDQDGRGLERQMEQKEKELNYKEDQDRRTTERRS-GRPDSN 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434618|ref|XP_002279321.1| PREDICTED: uncharacterized protein LOC100246760 [Vitis vinifera]

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 44/69 (63%), Positives = 54/69 (78%), Gaps = 2/69 (2%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSS 61
           RE RGVCRAFQRGEC RG GCKFSH+EQRA+NTG G +D+SSRWGH+KF+G +  K+D  
Sbjct: 130 REARGVCRAFQRGECNRGAGCKFSHDEQRASNTGWGSEDKSSRWGHDKFQGST--KSDGR 187

Query: 62  SRATGSGRV 70
             +  + RV
Sbjct: 188 PNSIPTNRV 196

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819328|ref|XP_002877547.1| hypothetical protein ARALYDRAFT_905943 [Arabidopsis lyrata subsp. lyrata] gi|297323385|gb|EFH53806.1| hypothetical protein ARALYDRAFT_905943 [Arabidopsis lyrata subsp. lyrata]

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/135 (47%), Positives = 77/135 (57%), Gaps = 22/135 (16%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEKFEG-------- 52
           RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSSRW H+KF G        
Sbjct: 130 REARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSRWDHDKFNGAKKGGTSF 189

Query: 53  -----FSWGKNDSSSRATGSGRVALEGNPNQSDRRE-EKRSIR----HDHREKPREDHGR 102
                F     + S R  G G  A  G P + +R E E    R    +D RE+ R   G 
Sbjct: 190 GHRGDFKSDAEEKSYRGKGDGD-AWYGRPKERERVEREDMGPRSRDAYDMREQKRS--GP 246

Query: 103 REDKRSRRHSDNNEF 117
            +D RSR H+  N++
Sbjct: 247 YDDSRSRSHNAGNDY 261

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498939|ref|XP_003518303.1| PREDICTED: zinc finger CCCH domain-containing protein 42-like [Glycine max]

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 53/100 (53%), Positives = 61/100 (61%), Gaps = 16/100 (16%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS----WGK 57
           RE RGVCRAFQRGECTRG  CKFSH+EQRAANTG G ++   +WGH+KFEG       G 
Sbjct: 130 REARGVCRAFQRGECTRGASCKFSHDEQRAANTGWGREEDKPKWGHDKFEGPKKERRSGN 189

Query: 58  N-----------DSSSRATGSGRVALEGNPNQSDRREEKR 86
           N           DS +RA       L+  P +SDRRE KR
Sbjct: 190 NQSNHIPETRDRDSRTRARNFD-AELDNQPKKSDRRETKR 228

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147840589|emb|CAN72715.1| hypothetical protein VITISV_032469 [Vitis vinifera]

 Score = 82.0 bits (201), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 72/181 (39%), Positives = 96/181 (53%), Gaps = 38/181 (20%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQ-------------------RAANTGGGPQDRS 42
           RE RGVCRAFQRGEC RG GCKFSH+EQ                   RA+NTG G +D+S
Sbjct: 130 REARGVCRAFQRGECNRGAGCKFSHDEQDLTFSWLSKSWRLVLQGLERASNTGWGSEDKS 189

Query: 43  SRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDR--REEKRSIRHDHREKPREDH 100
           SRWGH+KF+G +  K+D    +  + RV  E    +  R   ++ RS R    E  RE H
Sbjct: 190 SRWGHDKFQGST--KSDGRPNSIPTNRVH-EPTVGEGHRFGNKDARSSRTKGSEGGRESH 246

Query: 101 GRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGD 160
            RR           +E + R ++   R  E++ ++ E E   +EDQDRR  ++ S GR D
Sbjct: 247 HRR-----------SELDIRDQDG--RGLERQMEQKEKELNYKEDQDRRTTERRS-GRPD 292

Query: 161 S 161
           S
Sbjct: 293 S 293

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232729|ref|NP_190296.1| RNA-binding motif protein, X-linked 2 [Arabidopsis thaliana] gi|75337070|sp|Q9SD61.1|C3H42_ARATH RecName: Full=Zinc finger CCCH domain-containing protein 42; Short=AtC3H42 gi|6522593|emb|CAB61958.1| putative RNA binding protein [Arabidopsis thaliana] gi|27311733|gb|AAO00832.1| putative RNA-binding protein [Arabidopsis thaliana] gi|34098859|gb|AAQ56812.1| At3g47120 [Arabidopsis thaliana] gi|332644724|gb|AEE78245.1| RNA-binding motif protein, X-linked 2 [Arabidopsis thaliana]

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 38/49 (77%), Positives = 43/49 (87%), Gaps = 1/49 (2%)

Query: 2   REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEK 49
           RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSS+W H+K
Sbjct: 130 REARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSKWDHDK 178

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	169
TAIR|locus:2075676	352	AT3G47120 [Arabidopsis thalian	0.893	0.428	0.421	2.1e-22
DICTYBASE|DDB_G0288797	560	fip1l1 "cleavage and polyadeny	0.686	0.207	0.330	4e-10
WB|WBGene00018926	419	F56A11.6 [Caenorhabditis elega	0.840	0.338	0.304	9.5e-09
ZFIN|ZDB-GENE-030131-1495	635	zrsr2 "zinc finger (CCCH type)	0.917	0.244	0.291	3.9e-08
UNIPROTKB|E1C591	747	PPIG "Uncharacterized protein"	0.869	0.196	0.306	7.9e-08
MGI|MGI:1919414	326	Rbmx2 "RNA binding motif prote	0.710	0.368	0.298	1.5e-07
ZFIN|ZDB-GENE-040426-2822	687	ppig "peptidyl-prolyl isomeras	0.609	0.149	0.321	2.4e-07
FB|FBgn0031273	826	CG2839 [Drosophila melanogaste	0.609	0.124	0.301	5e-07
ZFIN|ZDB-GENE-040426-1619	1759	zc3h13 "zinc finger CCCH-type	0.917	0.088	0.294	2e-06
TAIR|locus:2132358	422	AT4G02720 "AT4G02720" [Arabido	0.804	0.322	0.270	2e-06

TAIR|locus:2075676 AT3G47120 [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 75/178 (42%), Positives = 99/178 (55%)

Query:     2 REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEKFEGF-----SW 55
             RE RGVCRAFQRGECTRGD CKFSH+E+RAA TG G  +DRSS+W  +K  G      S+
Sbjct:   180 REGRGVCRAFQRGECTRGDSCKFSHDEKRAATTGWGHEEDRSSKWDQDKLNGAKKGGTSF 239

Query:    56 GKN--------DSSSRATGSGRVALEGNPNQSDR--REEK--RSI-RHDHREKPREDHGR 102
             G          + S R  G G  +  G P + +R  RE+   RS   +D +E+ R   GR
Sbjct:   240 GNRGDFKPDVEEKSYRGRGDGDASY-GRPKERERVDREDMGPRSRDAYDMKEQKRS--GR 296

Query:   103 REDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGD 160
              ++  SRRH+D  ++    RED   R +   KR ++ES  R+  DR   D+ S  R D
Sbjct:   297 YDNAYSRRHNDEIDYV---REDKGSRAQDWEKR-KAESR-RDRNDREEKDRDSLRRED 349

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

DICTYBASE|DDB_G0288797 fip1l1 "cleavage and polyadenylation specificity factor FIP1" [Dictyostelium discoideum (taxid:44689)]

 Score = 137 (53.3 bits), Expect = 4.0e-10, Sum P(2) = 4.0e-10
 Identities = 40/121 (33%), Positives = 57/121 (47%)

Query:    49 KFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRS 108
             ++E  S   N+ S    GS R   E + + S R +  R  R   RE+ R+D  R E +RS
Sbjct:   356 QYEDDSNNNNNGSGSGGGSDRRRNESS-SSSSRGDSDRGERE--RERDRDDRDRSERERS 412

Query:   109 RRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRE 168
              R  D +E E   R +  R D  R +R  S+   R D+D+     SS+    SSS R  +
Sbjct:   413 DR--DRSERERSDRSERERSDRDRSERERSDRSERSDRDKTSSSSSSSNNNSSSSTRGSD 470

Query:   169 R 169
             R
Sbjct:   471 R 471

GO:0003723 "RNA binding" evidence=ISS

GO:0006379 "mRNA cleavage" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISS

WB|WBGene00018926 F56A11.6 [Caenorhabditis elegans (taxid:6239)]

 Score = 139 (54.0 bits), Expect = 9.5e-09, P = 9.5e-09
 Identities = 46/151 (30%), Positives = 63/151 (41%)

Query:    25 SHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKND---SSSRATGSGRVALEGNPNQSDR 81
             S  ++    + GG + RS R  H+K       ++D   S SR     R       ++ DR
Sbjct:   248 SRQDRERDRSRGGEKSRSPRKSHQKSVDRDKTRSDKDRSRSRKDREDRDRERSRKDREDR 307

Query:    82 -REEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESES 140
              RE  R  R D   K RED  R   ++ R      + E RSR+D   RD  R +    + 
Sbjct:   308 DRERSRKEREDRSRKDREDRERERSRKEREDRSRKDRE-RSRQDREDRDRDRDRDRSRKD 366

Query:   141 YLREDQD--RRGGDKSSTGRGDSSSHRHRER 169
               R+D+   RR  D  S  R D  S   RER
Sbjct:   367 --RDDKSCSRRSRDDRSEERKDRKSRDDRER 395

GO:0016021 "integral to membrane" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

ZFIN|ZDB-GENE-030131-1495 zrsr2 "zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2" [Danio rerio (taxid:7955)]

 Score = 136 (52.9 bits), Expect = 3.9e-08, P = 3.9e-08
 Identities = 49/168 (29%), Positives = 74/168 (44%)

Query:     2 REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSS 61
             R +  +C  F R +C +G  C F H  +   N      DR      ++  GFS      S
Sbjct:   319 RWKTAICGLFDRRKCPKGKHCNFLHVFRNPDNEFW-EADRDLHMSPDRGGGFS--ARHMS 375

Query:    62 SRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARS 121
              R    G  +  GN   S+R + +R+ R  H  +     GRR   R RR S + E  +RS
Sbjct:   376 GR---DGMWSQRGN--SSERFQRRRTDRRSHSRERYSYRGRRSRSRERR-SRSRERRSRS 429

Query:   122 REDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER 169
             RE   R  E++ +  E +S  R  + R+   ++S  R  S+S R + R
Sbjct:   430 RERRSRSRERQNRNRERQSRSRSREKRKS--ENSIRR--STSQREQSR 473

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E1C591 PPIG "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 134 (52.2 bits), Expect = 7.9e-08, P = 7.9e-08
 Identities = 49/160 (30%), Positives = 72/160 (45%)

Query:    17 TRGDGCKFSHNEQRAANTGGGPQDRSSRWG--HEKFEGFSW------GKNDSSSRATGSG 68
             +RG   + S +++R+   G    +R  R     EK +  S       GK+ SSSR     
Sbjct:   502 SRGRDKERSRSKERSRRAGSRSNERDHRKSKDREKHKSRSREREHARGKHSSSSRTRERS 561

Query:    69 RVALEGNPNQSDRREEKRSIRHDH-REKPREDHGRREDKRSRRHSDNNEFEARSREDHYR 127
             +    G   +S  R+  RS   ++ R + RE   RR   R RR + +     R RE+  R
Sbjct:   562 KSRDRGRRGRSRSRDRDRSRSKEYSRNRDRESRRRRSRSRERRGTPDRY---RGRENRRR 618

Query:   128 RDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHR 167
             R+ +  +R ES+S  RE    R   +SS  R DS S R R
Sbjct:   619 RNSRSSEREESQSRNRERYSNRES-RSSYKRNDSESQRKR 657

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

MGI|MGI:1919414 Rbmx2 "RNA binding motif protein, X-linked 2" [Mus musculus (taxid:10090)]

 Score = 126 (49.4 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 37/124 (29%), Positives = 58/124 (46%)

Query:    48 EKFEGFSWGKNDSSSR-ATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDK 106
             EK EG +  +  S SR AT   +     +   S +  E R+ + +HRE  ++ H    D 
Sbjct:   173 EKTEGQAQAEQPSCSRSATVKEKKDERASRKHSSKTSE-RAQKSEHRES-KKSHSGSPDG 230

Query:   107 RSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLRE-DQDRRGGDKSSTGRGDSSSHR 165
             RS  H+   + E ++R++  + + K   R E+E   RE ++ R  G  S   RG S    
Sbjct:   231 RSSYHARAEDPECKARKEKPKHEHKSASRREAEEKSRERERGRSSGTHSGRHRGHSDGRS 290

Query:   166 HRER 169
             HR R
Sbjct:   291 HRSR 294

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-040426-2822 ppig "peptidyl-prolyl isomerase G (cyclophilin G)" [Danio rerio (taxid:7955)]

 Score = 129 (50.5 bits), Expect = 2.4e-07, P = 2.4e-07
 Identities = 35/109 (32%), Positives = 49/109 (44%)

Query:    62 SRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHS-DNNEFEAR 120
             SR+ G G+     +  +  R    R  +  HR + RE   R  D   RR S DN   E R
Sbjct:   550 SRSRGRGQRGQSRDRGRDRRHSSSRERKTSHRSRSRE-RARGRDAEDRRKSADNKSRETR 608

Query:   121 SREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER 169
              R+    R  K     +  S  RED+ +R  DKS TG  DS + + ++R
Sbjct:   609 GRD----RSSKERSSQKQRSREREDRQKRRKDKSDTGSSDSDNDKRKKR 653

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

FB|FBgn0031273 CG2839 [Drosophila melanogaster (taxid:7227)]

 Score = 127 (49.8 bits), Expect = 5.0e-07, P = 5.0e-07
 Identities = 32/106 (30%), Positives = 49/106 (46%)

Query:    63 RATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSR 122
             R    G+   E    +  RREE++    + REK R D  RR ++  RR  +    E R R
Sbjct:   522 RRREEGKRKEEERREKERRREEEKRKEEERREKERRDEERRREEERRREEERRREEERRR 581

Query:   123 EDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRE 168
             E+  RR+E+R +  E +   RE++ RR  ++           R RE
Sbjct:   582 EEERRREEERRREEERK---REEERRREEERRREEERRREEERRRE 624

GO:0030246 "carbohydrate binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1619 zc3h13 "zinc finger CCCH-type containing 13" [Danio rerio (taxid:7955)]

 Score = 125 (49.1 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 51/173 (29%), Positives = 77/173 (44%)

Query:     2 REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSS 61
             +EER   R   R E  R D    + NE R   TG G    S     EK  G    + D+S
Sbjct:   622 QEERSYGRGHGR-EDMRNDARTDNRNESRVERTGRGRGHGSDVT--EKARGSRASQADNS 678

Query:    62 SRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARS 121
             S    SG  + E   ++S    E+ + R+  R++  +D  R E  R  R   +NE   R 
Sbjct:   679 S---ASGHDSWE---SRSSGLRERSTERNTDRDR-YDDRPRGEQPRDERRGAHNE---RD 728

Query:   122 REDHYRRDEKRP----KRHESESYLREDQ-DRRGGDKSSTGRGDSSSHRHRER 169
             R D+  R+++ P    +++  E   RE++ D R  D+    R D +  R +ER
Sbjct:   729 RRDNREREQRAPSPVRQQNRGEDLEREERRDDRRNDRGDDRRDDRTREREKER 781

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2132358 AT4G02720 "AT4G02720" [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 39/144 (27%), Positives = 64/144 (44%)

Query:    27 NEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKR 86
             N     +  GG +D +S+ G E+      GK+DS S + G      +   ++S RR  KR
Sbjct:    77 NADEIQDKNGGERDDNSK-GKERK-----GKSDSESESDGLRSRKRKSKSSRSKRRR-KR 129

Query:    87 SIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQ 146
             S   D   +  E     ED+R RR S +   ++RS     ++   R K   S+S    D+
Sbjct:   130 SYDSDSESEGSESDSEEEDRRRRRKSSSKRKKSRSSRSFRKKRSHRRKTKYSDSDESSDE 189

Query:   147 DRRGG-DKSSTGRGDSSSHRHRER 169
             D +     SS+G  + +  + + R
Sbjct:   190 DSKAEISASSSGEEEDTKSKSKRR 213

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_IX3799	hypothetical protein (243 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.VIII.2127.1	hypothetical protein (133 aa)			•						0.458
	gw1.XV.2574.1	hypothetical protein (203 aa)			•						0.454
	eugene3.00050125	hypothetical protein (218 aa)			•						0.445
	estExt_fgenesh4_pg.C_LG_VII0461	hypothetical protein (218 aa)			•						0.440
	gw1.232.53.1	hypothetical protein (203 aa)			•						0.437

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	169
smart00356	27	smart00356, ZnF_C3H1, zinc finger	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002

>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 12/22 (54%), Positives = 16/22 (72%)

Query: 7  VCRAFQRGECTRGDGCKFSHNE 28
          +C+ F+RG C RGD CKF+H  
Sbjct: 6  LCKFFKRGYCPRGDRCKFAHPL 27

Length = 27

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 79  SDRREEKRSIRHDHREKPRE--DHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRH 136
           S+R   +   R   R++ R   +   RED R R     +    RS      R  +   R 
Sbjct: 21  SERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80

Query: 137 ESESYLREDQDRRGGDKSSTGRGDSSSHRHR 167
            S S    +Q RR     S         + R
Sbjct: 81  RSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 30/96 (31%), Positives = 36/96 (37%), Gaps = 7/96 (7%)

Query: 81  RREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDE----KRPKRH 136
           R EE    R   R + R+    R  +RSR  S   +   RSRE  YR D     +R    
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 137 ESESYLREDQDRRGGD---KSSTGRGDSSSHRHRER 169
            S   LR    RR  D   + S        HR R R
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLR 96

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 9/83 (10%)

Query: 70  VALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRD 129
              E    +++ + E++  R   R+  R D   R D R  R           RE    R+
Sbjct: 587 KPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRT---------RREGRENRE 637

Query: 130 EKRPKRHESESYLREDQDRRGGD 152
           E R  R +++    E ++ +  +
Sbjct: 638 ENRRNRRQAQQQTAETRESQQAE 660

Length = 1068

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
smart00356	27	ZnF_C3H1 zinc finger.	97.77
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	97.39
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	95.62
KOG1763	343	consensus Uncharacterized conserved protein, conta	92.87
COG5152	259	Uncharacterized conserved protein, contains RING a	91.3
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	89.68
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	89.15
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	84.92
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	84.72
KOG2185	486	consensus Predicted RNA-processing protein, contai	84.43
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	83.16
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	81.14

>smart00356 ZnF_C3H1 zinc finger

Probab=97.77  E-value=1.1e-05  Score=45.66  Aligned_cols=24  Identities=46%  Similarity=1.041  Sum_probs=21.6

Q ss_pred             cccchhhhcccccCCCCcccccch
Q 030923            5 RGVCRAFQRGECTRGDGCKFSHNE   28 (169)
Q Consensus         5 ~~vc~afq~gec~rg~~crfshd~   28 (169)
                      .-+|..|++|+|..|++|+|+|+.
T Consensus         4 ~~~C~~~~~g~C~~g~~C~~~H~~   27 (27)
T smart00356        4 TELCKFFKRGYCPYGDRCKFAHPL   27 (27)
T ss_pred             CCcCcCccCCCCCCCCCcCCCCcC
Confidence            348999999999999999999974

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.39  E-value=5.2e-05  Score=44.78  Aligned_cols=24  Identities=50%  Similarity=1.144  Sum_probs=18.5

Q ss_pred             cccchhhhc-ccccCCCCcccccch
Q 030923            5 RGVCRAFQR-GECTRGDGCKFSHNE   28 (169)
Q Consensus         5 ~~vc~afq~-gec~rg~~crfshd~   28 (169)
                      ..+|..|++ |.|.+|+.|+|+|++
T Consensus         3 ~~~C~~f~~~g~C~~G~~C~f~H~~   27 (27)
T PF00642_consen    3 TKLCRFFMRTGTCPFGDKCRFAHGE   27 (27)
T ss_dssp             SSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred             cccChhhccCCccCCCCCcCccCCC
Confidence            458998888 999999999999985

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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. 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: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=95.62  E-value=0.004  Score=56.22  Aligned_cols=25  Identities=52%  Similarity=1.117  Sum_probs=22.3

Q ss_pred             cccchhhhcccccCCCC-cccccchh
Q 030923            5 RGVCRAFQRGECTRGDG-CKFSHNEQ   29 (169)
Q Consensus         5 ~~vc~afq~gec~rg~~-crfshd~~   29 (169)
                      +-||.+||+|-|+||+- |+|-|-+.
T Consensus        37 ~eVCReF~rn~C~R~d~~CkfaHP~~   62 (331)
T KOG2494|consen   37 LEVCREFLRNTCSRGDRECKFAHPPK   62 (331)
T ss_pred             HHHHHHHHhccccCCCccccccCCCC
Confidence            45999999999999999 99999775

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]

Probab=92.87  E-value=0.04  Score=50.00  Aligned_cols=49  Identities=39%  Similarity=0.733  Sum_probs=35.6

Q ss_pred             cchhhhcccccCCCCcccccchhccccCCCC----C-CCCCCccccccccCCCCCC
Q 030923            7 VCRAFQRGECTRGDGCKFSHNEQRAANTGGG----P-QDRSSRWGHEKFEGFSWGK   57 (169)
Q Consensus         7 vc~afq~gec~rg~~crfshd~~~~a~~g~g----~-~~~~~~w~~d~~~~~~k~~   57 (169)
                      ||--|..|.|+-|+-|+||||.+..--.---    + .+-|  |..++..+..-++
T Consensus        94 vCafFk~g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdem--WD~~kl~~vv~~K  147 (343)
T KOG1763|consen   94 VCAFFKQGTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEM--WDEEKLEEVVLKK  147 (343)
T ss_pred             HHHHHhccCCCCCCcccccchHHHhhhccchhccccchhhh--hhHHHHHHHHHhh
Confidence            7999999999999999999999865433211    1 2335  9988887665433

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=91.30  E-value=0.076  Score=46.46  Aligned_cols=46  Identities=33%  Similarity=0.630  Sum_probs=31.4

Q ss_pred             ccchhh-hcccccCCCCcccccchhccccCCCCCCCCCCccccccccCCCC
Q 030923            6 GVCRAF-QRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSW   55 (169)
Q Consensus         6 ~vc~af-q~gec~rg~~crfshd~~~~a~~g~g~~~~~~~w~~d~~~~~~k   55 (169)
                      -||-.| |+|-|.+|++|+|.|+-. .--|||--   ..-|..+.-.++.+
T Consensus       142 dVCKdyk~TGYCGYGDsCKflH~R~-D~KtGWkL---n~EWnA~~Ee~~v~  188 (259)
T COG5152         142 DVCKDYKETGYCGYGDSCKFLHDRS-DFKTGWKL---NQEWNAEYEEAPVI  188 (259)
T ss_pred             ccccchhhcccccCCchhhhhhhhh-hhhccccc---chhhcchhhhcccc
Confidence            477666 799999999999999854 34678863   23465544444443

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=89.68  E-value=0.15  Score=48.75  Aligned_cols=22  Identities=41%  Similarity=1.192  Sum_probs=20.5

Q ss_pred             ccchhhhcccccCCCCcccccc
Q 030923            6 GVCRAFQRGECTRGDGCKFSHN   27 (169)
Q Consensus         6 ~vc~afq~gec~rg~~crfshd   27 (169)
                      -+|++|-+|-|.+||+|-|.|.
T Consensus       237 tpCPefrkG~C~rGD~CEyaHg  258 (528)
T KOG1595|consen  237 TPCPEFRKGSCERGDSCEYAHG  258 (528)
T ss_pred             ccCcccccCCCCCCCccccccc
Confidence            3799999999999999999996

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=89.15  E-value=0.15  Score=46.25  Aligned_cols=24  Identities=38%  Similarity=0.768  Sum_probs=21.5

Q ss_pred             cccchhhhcccccCCCCcccccchh
Q 030923            5 RGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         5 ~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      ...||+||+|+|+|-. |||-|-++
T Consensus        71 v~aC~Ds~kgrCsR~n-CkylHpp~   94 (331)
T KOG2494|consen   71 VIACFDSQKGRCSREN-CKYLHPPQ   94 (331)
T ss_pred             EEEEeccccCccCccc-ceecCCCh
Confidence            4569999999999988 99999886

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]

Probab=84.92  E-value=0.32  Score=43.44  Aligned_cols=22  Identities=45%  Similarity=1.061  Sum_probs=20.9

Q ss_pred             ccchhhhcccccCCCCcccccc
Q 030923            6 GVCRAFQRGECTRGDGCKFSHN   27 (169)
Q Consensus         6 ~vc~afq~gec~rg~~crfshd   27 (169)
                      -||--|..+.|+-|+.|.|+|+
T Consensus        86 ~vcalF~~~~c~kg~~ckF~h~  107 (299)
T COG5252          86 VVCALFLNKTCAKGDACKFAHG  107 (299)
T ss_pred             HHHHHhccCccccCchhhhhcc
Confidence            3899999999999999999999

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=84.72  E-value=0.35  Score=43.77  Aligned_cols=18  Identities=44%  Similarity=0.936  Sum_probs=16.3

Q ss_pred             hhcccccCCCCcccccch
Q 030923           11 FQRGECTRGDGCKFSHNE   28 (169)
Q Consensus        11 fq~gec~rg~~crfshd~   28 (169)
                      =++|.|..|+||+|.|+-
T Consensus       193 keTgycg~gdSckFlh~r  210 (313)
T KOG1813|consen  193 KETGYCGYGDSCKFLHDR  210 (313)
T ss_pred             HhhCcccccchhhhhhhh
Confidence            379999999999999984

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]

Probab=84.43  E-value=0.47  Score=44.92  Aligned_cols=26  Identities=35%  Similarity=0.846  Sum_probs=22.7

Q ss_pred             ccccchhhhcccccCCCCcccccchh
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      +.-.|.-|+-|+|--+.+|||||.-.
T Consensus       139 sMkpC~ffLeg~CRF~enCRfSHG~~  164 (486)
T KOG2185|consen  139 SMKPCKFFLEGRCRFGENCRFSHGLD  164 (486)
T ss_pred             hhccchHhhccccccCcccccccCcc
Confidence            44579999999999999999999753

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=83.16  E-value=0.45  Score=43.02  Aligned_cols=25  Identities=36%  Similarity=0.923  Sum_probs=23.6

Q ss_pred             ccchhhhcccccCCCCcccccchhc
Q 030923            6 GVCRAFQRGECTRGDGCKFSHNEQR   30 (169)
Q Consensus         6 ~vc~afq~gec~rg~~crfshd~~~   30 (169)
                      -||--||+|.|..|+-|||+|+...
T Consensus         9 tic~~~~~g~c~~g~~cr~~h~~~~   33 (344)
T KOG1039|consen    9 TICKYYQKGNCKFGDLCRLSHSLPD   33 (344)
T ss_pred             hhhhhcccccccccceeeeeccCch
Confidence            7999999999999999999999874

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=81.14  E-value=0.74  Score=38.99  Aligned_cols=24  Identities=42%  Similarity=1.002  Sum_probs=21.6

Q ss_pred             ccchhhhc-ccccCCCCcccccchh
Q 030923            6 GVCRAFQR-GECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq~-gec~rg~~crfshd~~   29 (169)
                      -.|--|++ |-|.+|+-|+|-|-..
T Consensus       178 ~lC~~f~~tG~C~yG~rC~F~H~~~  202 (332)
T KOG1677|consen  178 KLCPKFQKTGLCKYGSRCRFIHGEP  202 (332)
T ss_pred             cCCCccccCCCCCCCCcCeecCCCc
Confidence            36888998 9999999999999876

---

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

ID	Length	Definition	E-value
Query	169
2rhk_C	72	Cleavage and polyadenylation specificity factor su	4e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	9e-04

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens} Length = 72

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 7  VCRAFQRGECTRGDGCKFSHN 27
          VC+ + RG C +GD C+F H 
Sbjct: 18 VCKHWLRGLCKKGDQCEFLHE 38

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 35.6 bits (82), Expect = 9e-04
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 7  VCRAFQRGECTRGDGCKFSH 26
          VC+ + RG C +GD C+F H
Sbjct: 12 VCKHWLRGLCKKGDQCEFLH 31

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	97.76
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	97.76
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	97.68
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	97.37
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	97.17
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	97.16
2rhk_C	72	Cleavage and polyadenylation specificity factor su	97.02
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	96.94
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	96.8
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	96.78
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	96.46
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	96.42
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	95.59
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	94.85
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	94.57
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	94.51
2rhk_C	72	Cleavage and polyadenylation specificity factor su	93.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	92.01

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=97.76  E-value=7.5e-06  Score=55.94  Aligned_cols=26  Identities=46%  Similarity=1.174  Sum_probs=23.4

Q ss_pred             ccccchhhhcccccCCCC-cccccchh
Q 030923            4 ERGVCRAFQRGECTRGDG-CKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~-crfshd~~   29 (169)
                      ...||..||+|.|++|++ |+|+|+..
T Consensus         5 k~~vC~~f~~G~C~rg~~~C~f~H~~~   31 (70)
T 3d2q_A            5 RLEVCREYQRGNCNRGENDCRFAHPAD   31 (70)
T ss_dssp             EEEBCHHHHTTCCSSCTTTCSSBCCCT
T ss_pred             cchhCHHHhcCCCCCCCCCCCCccCcc
Confidence            457999999999999996 99999875

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=97.76  E-value=8.3e-06  Score=58.32  Aligned_cols=27  Identities=52%  Similarity=1.070  Sum_probs=24.1

Q ss_pred             ccccchhhhcccccCCC-Ccccccchhc
Q 030923            4 ERGVCRAFQRGECTRGD-GCKFSHNEQR   30 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~-~crfshd~~~   30 (169)
                      .+.||..||+|.|++|+ .|+|+|.+..
T Consensus         8 ~~~VCr~FlrG~C~r~d~~C~f~H~~~~   35 (83)
T 3d2n_A            8 TLEVCREFQRGTCSRPDTECKFAHPSKS   35 (83)
T ss_dssp             EEEBCTTGGGTCCCSCTTTCSSBCCCTT
T ss_pred             cchhcHHHhcCCCCCCCCCCCCcCCCcc
Confidence            35799999999999997 9999999863

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=97.68  E-value=1.1e-05  Score=58.61  Aligned_cols=27  Identities=52%  Similarity=1.084  Sum_probs=24.5

Q ss_pred             ccccchhhhcccccCCC-Ccccccchhc
Q 030923            4 ERGVCRAFQRGECTRGD-GCKFSHNEQR   30 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~-~crfshd~~~   30 (169)
                      ...||..||+|.|++|+ .|+|+|.+..
T Consensus        16 ~~~VCrdFlrG~C~r~d~~CrfsH~~~~   43 (89)
T 2rpp_A           16 TLEVCRQFQRGTCSRSDEECKFAHPPKS   43 (89)
T ss_dssp             EECBCHHHHHTCCCCCTTTSSSBCCCSS
T ss_pred             hhhhchHHhcCCCCCCCCCCCCcCCCcc
Confidence            46799999999999998 9999999865

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.37  E-value=2.1e-05  Score=57.53  Aligned_cols=27  Identities=48%  Similarity=1.159  Sum_probs=23.9

Q ss_pred             ccccchhhhcccccCCC-Ccccccchhc
Q 030923            4 ERGVCRAFQRGECTRGD-GCKFSHNEQR   30 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~-~crfshd~~~   30 (169)
                      ...||..|++|.|++|+ .|+|+|+...
T Consensus        19 k~~VCr~FlrG~C~rgd~~C~FsH~~~~   46 (98)
T 2e5s_A           19 KLEVCREFQRGNCARGETDCRFAHPADS   46 (98)
T ss_dssp             EEEBCSHHHHTCCSSHHHHCSSBCCSSC
T ss_pred             hhhhhHHHhcCcCCCCCCCCCCcCCchh
Confidence            46799999999999999 6999999854

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=97.17  E-value=0.00011  Score=50.03  Aligned_cols=25  Identities=32%  Similarity=0.797  Sum_probs=22.8

Q ss_pred             ccccchhhhcccccCCCCcccccchh
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      ...||+.|++|.|++| .|+|.|.++
T Consensus        41 ~~~vC~~flkG~C~r~-~C~y~H~~~   65 (70)
T 3d2q_A           41 TVTVCMDYIKGRCSRE-KCKYFHPPA   65 (70)
T ss_dssp             EEEBCHHHHTTCCCCT-TCCSBCCCH
T ss_pred             cceeccccCcCCCCCC-CcCeeCCHH
Confidence            4689999999999999 999999865

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=97.16  E-value=0.00011  Score=52.45  Aligned_cols=25  Identities=28%  Similarity=0.623  Sum_probs=22.9

Q ss_pred             ccccchhhhcccccCCCCcccccchh
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      ...||+.|++|.|+++ .|+|.|.+.
T Consensus        42 ~~~vC~dflkG~C~r~-~C~y~H~~~   66 (83)
T 3d2n_A           42 RVIACFDSLKGRCSRE-NCKYLHPPP   66 (83)
T ss_dssp             EEECCHHHHTTCCCCS-SCSSCCCCH
T ss_pred             ceeehhHhhhccccCC-CcceeCChH
Confidence            3689999999999999 999999876

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=97.02  E-value=0.00015  Score=50.10  Aligned_cols=26  Identities=38%  Similarity=0.926  Sum_probs=23.4

Q ss_pred             ccccchhhhcccccCCCCcccccchh
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      ...||.-|++|.|..|+.|.|+|+..
T Consensus        15 k~~vCk~fl~G~C~~G~~C~fsH~~~   40 (72)
T 2rhk_C           15 KTVVCKHWLRGLCKKGDQCEFLHEYD   40 (72)
T ss_dssp             CCSBCHHHHTTCCCCGGGSSSBCSCC
T ss_pred             cCeeCHHHhcCCCCCCCCCCCccccc
Confidence            35699999999999999999999964

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.94  E-value=0.00027  Score=48.85  Aligned_cols=27  Identities=37%  Similarity=0.871  Sum_probs=24.0

Q ss_pred             ccccchhhhcccccCCCCcccccchhc
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQR   30 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~~   30 (169)
                      ...||.-|++|.|.+|+.|.|+|+...
T Consensus         9 k~~~C~~fl~G~C~~G~~C~fsH~~~~   35 (77)
T 2d9n_A            9 KTVVCKHWLRGLCKKGDQCEFLHEYDM   35 (77)
T ss_dssp             TTSBCHHHHTTCCSCTTSSSSBCSCCT
T ss_pred             cceeCHhHccCcCCCCCCCCCcccccc
Confidence            346999999999999999999999764

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=96.80  E-value=0.00035  Score=50.67  Aligned_cols=25  Identities=28%  Similarity=0.626  Sum_probs=23.0

Q ss_pred             ccccchhhhcccccCCCCcccccchh
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      ...||+.|++|.|+++ .|+|.|.+.
T Consensus        50 ~~~vC~dflkG~C~r~-~Cky~H~~~   74 (89)
T 2rpp_A           50 RVIACFDSLKGRCSRE-NCKYLHPPT   74 (89)
T ss_dssp             BEEBCHHHHHTCCCCT-TCCSBCCCH
T ss_pred             ceeeehhhhhCcCCCC-CcceecCHH
Confidence            4689999999999999 999999876

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.78  E-value=0.00035  Score=51.01  Aligned_cols=26  Identities=31%  Similarity=0.751  Sum_probs=23.4

Q ss_pred             cccccchhhhcccccCCCCcccccchh
Q 030923            3 EERGVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         3 e~~~vc~afq~gec~rg~~crfshd~~   29 (169)
                      +...||+.|++|.|+++ .|+|.|...
T Consensus        54 ~~~~vC~~flkG~C~r~-~C~y~H~~~   79 (98)
T 2e5s_A           54 NTVTVCMDYIKGRCMRE-KCKYFHPPA   79 (98)
T ss_dssp             CEEEBCHHHHHTCCCCT-TCCSBCCCH
T ss_pred             CccccchhhccCCCCCC-CcCccCChH
Confidence            45689999999999999 999999874

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=96.46  E-value=0.0012  Score=47.90  Aligned_cols=24  Identities=29%  Similarity=0.915  Sum_probs=21.3

Q ss_pred             ccccchhhhcccccCCCCcccccc
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHN   27 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd   27 (169)
                      ...||..|++|.|.+|+.|+|+|+
T Consensus        12 k~~lC~~f~~G~C~~G~~C~f~H~   35 (98)
T 2cqe_A           12 KRELCKFYITGFCARAENCPYMHG   35 (98)
T ss_dssp             CCSBCTTTTTTCCSCSTTCSSBSS
T ss_pred             CCccCcccccCcCCCCCCCCCCCC
Confidence            456899999999999999999998

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=96.42  E-value=0.0011  Score=44.38  Aligned_cols=28  Identities=29%  Similarity=0.794  Sum_probs=23.6

Q ss_pred             cccchhhh-cccccCCCCcccccchhccc
Q 030923            5 RGVCRAFQ-RGECTRGDGCKFSHNEQRAA   32 (169)
Q Consensus         5 ~~vc~afq-~gec~rg~~crfshd~~~~a   32 (169)
                      ..+|..|+ +|.|..|+.|+|+|+.....
T Consensus        12 t~~C~~f~~~G~C~~G~~C~f~H~~~e~~   40 (77)
T 1m9o_A           12 TELCRTYSESGRCRYGAKCQFAHGLGELR   40 (77)
T ss_dssp             SCCCSGGGGTSCCTTTTTCSSCSSSCCGG
T ss_pred             chhCHHhhhCCCcCCCCCccCCCCChhhc
Confidence            46899885 99999999999999986443

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=95.59  E-value=0.0041  Score=45.07  Aligned_cols=24  Identities=38%  Similarity=0.922  Sum_probs=21.6

Q ss_pred             ccchhh-hcccccCCCCcccccchh
Q 030923            6 GVCRAF-QRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~af-q~gec~rg~~crfshd~~   29 (169)
                      .||..| ++|.|..|+.|+|+|...
T Consensus        37 ~~C~~f~~~G~C~~G~~C~f~H~~~   61 (98)
T 2cqe_A           37 FPCKLYHTTGNCINGDDCMFSHDPL   61 (98)
T ss_dssp             SBCSHHHHTSCCSSCTTCSSBCCCC
T ss_pred             CcCcCcccCCcCCCCCCCcccCCCC
Confidence            589999 699999999999999864

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=94.85  E-value=0.0048  Score=41.31  Aligned_cols=24  Identities=38%  Similarity=1.002  Sum_probs=0.0

Q ss_pred             ccchhhh-cccccCCCCcccccchh
Q 030923            6 GVCRAFQ-RGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq-~gec~rg~~crfshd~~   29 (169)
                      .+|..|+ .|.|.+|+.|+|.|+..
T Consensus        51 ~~C~~f~~~G~C~~G~~C~f~H~~~   75 (77)
T 1m9o_A           51 ELCHKFKLQGRCPYGSRCHFIHNPT   75 (77)
T ss_dssp             -------------------------
T ss_pred             CcccchhhCcCCCCcCcCCCCCCCC
Confidence            5897664 89999999999999864

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.57  E-value=0.013  Score=41.55  Aligned_cols=24  Identities=33%  Similarity=1.056  Sum_probs=22.1

Q ss_pred             ccchhhhcccccCCCCcccccchh
Q 030923            6 GVCRAFQRGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq~gec~rg~~crfshd~~   29 (169)
                      -+|-.|++|.|..|+.|.|-|.+.
T Consensus        21 ~LC~~~~~G~C~~G~~C~FAHG~~   44 (69)
T 2d9m_A           21 SICDRYMNGTCPEGNSCKFAHGNA   44 (69)
T ss_dssp             SBCHHHHHSCCSSCSSCSSBSSHH
T ss_pred             ccCcccCcCCCCCCCccCCcCCHH
Confidence            479999999999999999999875

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.51  E-value=0.014  Score=40.06  Aligned_cols=25  Identities=28%  Similarity=0.739  Sum_probs=22.2

Q ss_pred             cccchhhhc-ccccCCCCcccccchhc
Q 030923            5 RGVCRAFQR-GECTRGDGCKFSHNEQR   30 (169)
Q Consensus         5 ~~vc~afq~-gec~rg~~crfshd~~~   30 (169)
                      ..||.-|++ |.|. |+.|+|.|....
T Consensus        38 ~~~C~~f~~~G~C~-~~~C~f~H~~~~   63 (77)
T 2d9n_A           38 MPECYFYSKFGECS-NKECPFLHIDPE   63 (77)
T ss_dssp             SCBCHHHHHTCCCC-CSSCSSBCCCTT
T ss_pred             CCCCcccCCCCccC-CCCeeccCCCcc
Confidence            468999999 9999 999999998753

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=93.33  E-value=0.027  Score=38.66  Aligned_cols=25  Identities=28%  Similarity=0.764  Sum_probs=22.1

Q ss_pred             cccchhhhc-ccccCCCCcccccchhc
Q 030923            5 RGVCRAFQR-GECTRGDGCKFSHNEQR   30 (169)
Q Consensus         5 ~~vc~afq~-gec~rg~~crfshd~~~   30 (169)
                      ..||.-|++ |.|.. +.|+|.|....
T Consensus        44 ~~~C~~f~~~G~C~~-~~C~y~H~~p~   69 (72)
T 2rhk_C           44 MSECYFYSKFGECSN-KECPFLHIDPE   69 (72)
T ss_dssp             CCBCHHHHHHSCCSB-TTCCSBCCCCC
T ss_pred             CCcccccCCCCCCCC-CCeeccCCCcc
Confidence            468999999 99999 99999998643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=92.01  E-value=0.041  Score=45.25  Aligned_cols=23  Identities=30%  Similarity=0.722  Sum_probs=21.1

Q ss_pred             ccchhhhcccccCCCCcccccch
Q 030923            6 GVCRAFQRGECTRGDGCKFSHNE   28 (169)
Q Consensus         6 ~vc~afq~gec~rg~~crfshd~   28 (169)
                      -+|.-|.+|.|.+|+.|.|-|..
T Consensus        71 ~~C~ffakG~C~~G~~C~y~H~l   93 (240)
T 3u1l_A           71 FFCLFFAKGMCCLGPKCEYLHHI   93 (240)
T ss_dssp             SBCHHHHTTCCSCGGGCSSBBSC
T ss_pred             eEcCccccCCCCCCCCCCccCCC
Confidence            38999999999999999999963

---

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	169
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	95.71
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	95.32
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	94.91
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	93.14
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	85.63

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.71  E-value=0.002  Score=39.40  Aligned_cols=24  Identities=33%  Similarity=0.948  Sum_probs=20.4

Q ss_pred             ccchhhh-cccccCCCCcccccchh
Q 030923            6 GVCRAFQ-RGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq-~gec~rg~~crfshd~~   29 (169)
                      -.|..|+ .|-|..|+.|.|.|++.
T Consensus        10 ~lC~~~~~~g~C~~G~~C~FAHg~~   34 (40)
T d1m9oa_          10 ELCRTYSESGRCRYGAKCQFAHGLG   34 (40)
T ss_dssp             CCCSGGGGTSCCTTTTTCSSCSSSC
T ss_pred             ccChhhhcCCcCCCCCCCCCCCCHH
Confidence            4798886 59999999999999654

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0019  Score=38.49  Aligned_cols=24  Identities=42%  Similarity=0.988  Sum_probs=20.7

Q ss_pred             ccchhhhc-ccccCCCCcccccchh
Q 030923            6 GVCRAFQR-GECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq~-gec~rg~~crfshd~~   29 (169)
                      -+|..|+. |.|..|+.|.|.|+++
T Consensus         9 ~lC~~f~~~g~C~yG~~C~FaHg~~   33 (34)
T d1rgoa2           9 ELCRTFHTIGFCPYGPRCHFIHNAD   33 (34)
T ss_dssp             SBCHHHHHHSCCTTGGGCSSBCCSC
T ss_pred             hhccccCCCCcCCCCCcccCcCCCC
Confidence            46888865 9999999999999874

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.91  E-value=0.0035  Score=37.59  Aligned_cols=24  Identities=38%  Similarity=1.045  Sum_probs=20.8

Q ss_pred             ccchhhh-cccccCCCCcccccchh
Q 030923            6 GVCRAFQ-RGECTRGDGCKFSHNEQ   29 (169)
Q Consensus         6 ~vc~afq-~gec~rg~~crfshd~~   29 (169)
                      -+|..|+ .|-|..|+.|.|-|.+.
T Consensus         7 ~lC~~~~~~g~C~~G~~C~FAHg~~   31 (36)
T d1rgoa1           7 ELCRPFEESGTCKYGEKCQFAHGFH   31 (36)
T ss_dssp             SBCHHHHHHSCCTTGGGCSSBSSGG
T ss_pred             hhCcchhcCCcCCCCCcCCCcCCHH
Confidence            3798875 69999999999999875

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.14  E-value=0.014  Score=38.59  Aligned_cols=17  Identities=47%  Similarity=1.083  Sum_probs=14.5

Q ss_pred             cccccCCCCcccccchh
Q 030923           13 RGECTRGDGCKFSHNEQ   29 (169)
Q Consensus        13 ~gec~rg~~crfshd~~   29 (169)
                      .+.|-.|+.|+|||++-
T Consensus         9 g~kCy~gd~C~FSH~pL   25 (56)
T d2cqea1           9 TGNCINGDDCMFSHDPL   25 (56)
T ss_dssp             TSCCSSCTTCSSBCCCC
T ss_pred             CCcccCCCcccccCCcc
Confidence            45899999999999754

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.63  E-value=0.19  Score=29.26  Aligned_cols=25  Identities=28%  Similarity=0.914  Sum_probs=21.9

Q ss_pred             ccccchhhhcccccCCCCcccccch
Q 030923            4 ERGVCRAFQRGECTRGDGCKFSHNE   28 (169)
Q Consensus         4 ~~~vc~afq~gec~rg~~crfshd~   28 (169)
                      ...+|--...|-|++|..|.|-|++
T Consensus         5 kkelCKfYvqGyCtrgenC~ymH~e   29 (29)
T d2cqea2           5 KRELCKFYITGFCARAENCPYMHGD   29 (29)
T ss_dssp             CCSBCTTTTTTCCSCSTTCSSBSSS
T ss_pred             hhhhhhhheeeeecCCcCcccccCC
Confidence            3568888899999999999999975