Citrus Sinensis ID: 031295

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160--
Protein Sequence
MLKLISESYIPSKWIFLMHPFDSNVNEENRYYTQLSLPPNSDLDPPPLDMQNLDIEDPEDQVDSDTEEEVENVDKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTGKAF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEcccccccEEEcccccccccccccccEEccccccccccccccccHHHccccccccccccccccccccccccccccccccccHHHccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccEccccccc
Coil and Loop (DISEMBL)
MLKLISEsyipskwiflmhpfdsnvneenryytqlslppnsdldpppldmqnldiedpedqvdsdteeevenvdknnkqvdevtgnqmtrrkfcypqrpgvhdcsyylrtgrcrfgmsckfnhpvprqiqSLNQSINSNTVsiemnpnnsansnrmstgkaf
Flexible Loop (DISEMBL)
MLKLISESYIPSKWIFLMHPFDSNVNEENRYYTQLSLPPNSDLDPPPLDMQNLDIEDPEDQVDSDTEeevenvdknnkqvdevtgnqmtrrkfcypqrpgvHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIemnpnnsansnrmstgkaf
Low Complexity Region (SEG)
MLKLISESYIPSKWIFLMHPFDSNVNEENRYYTQlslppnsdldpppldMQNLDIEDPEDQVDSDTeeevenvdknnkqvdEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTGKAF
Disordered region (IsUnstruct)
*****SESYIPSKWIFLMHPFDSNVNEENRYY*********************************************************RRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPV*************************************
Disordered Region (DISOPRED)
**KLISESYIPSKW************************************************************************************PGVHDCSYYLRTGRCRFGMSCKFNH*******************IEMNPNNSANSNRMSTGKAF
Disordered Region (DISEMBL)
MLKLISESYIPSKWIFLMHPFDSNVNEENRYYTQLSLPPNSDLDPPPLDMQNLDIED****************DKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSA***********
Disordered Region (DISPRO)
*LKLISESYIPSKWIFLMHPFDSNVNEENRYYTQLSLPPNSDLDPPPLDMQNLDIEDP***********************************CYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPV*************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLKLISESYIPSKWIFLMHPFDSNVNEENRYYTQLSLPPNSDLDPPPLDMQNLDIEDPEDQVDSDTEEEVENVDKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTGKAF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	162	2.2.26 [Sep-21-2011]
Q9STM4	448	Zinc finger CCCH domain-c	yes	no	0.209	0.075	0.666	2e-10
Q9SQU4	462	Zinc finger CCCH domain-c	no	no	0.216	0.075	0.657	1e-09
Q5RJC5	435	Zinc finger CCCH domain-c	no	no	0.580	0.216	0.316	2e-09
Q2R4J4	444	Zinc finger CCCH domain-c	yes	no	0.518	0.189	0.348	2e-09
Q2QT65	454	Zinc finger CCCH domain-c	no	no	0.259	0.092	0.568	8e-09
Q8GXX7	397	Zinc finger CCCH domain-c	no	no	0.203	0.083	0.657	9e-09
Q5JLB5	439	Zinc finger CCCH domain-c	no	no	0.203	0.075	0.685	1e-08
Q0DBW8	279	Zinc finger CCCH domain-c	no	no	0.216	0.125	0.638	3e-08
Q9SWF9	417	Zinc finger CCCH domain-c	N/A	no	0.203	0.079	0.628	4e-08
Q6NPN3	465	Zinc finger CCCH domain-c	no	no	0.228	0.079	0.513	5e-08

>sp|Q9STM4|C3H43_ARATH Zinc finger CCCH domain-containing protein 43 OS=Arabidopsis thaliana GN=At3g48440 PE=1 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/36 (66%), Positives = 29/36 (80%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           YP RPG  DCS+Y+RTG C+FG SCKFNHP+ R+ Q
Sbjct: 107 YPVRPGAEDCSFYMRTGSCKFGSSCKFNHPLARKFQ 142

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SQU4|C3H34_ARATH Zinc finger CCCH domain-containing protein 34 OS=Arabidopsis thaliana GN=At3g06410 PE=2 SV=2

 Score = 62.8 bits (151), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 30/35 (85%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
           YP RPG  +CSYYLRTG+C+FG++C+FNHPVP  +
Sbjct: 145 YPLRPGEKECSYYLRTGQCKFGLTCRFNHPVPLAV 179

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RJC5|C3H67_ARATH Zinc finger CCCH domain-containing protein 67 OS=Arabidopsis thaliana GN=At5g63260 PE=2 SV=2

 Score = 62.0 bits (149), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 55/101 (54%), Gaps = 7/101 (6%)

Query: 50  MQNLDIEDPEDQVDSDTEEEVENVDKNNK------QVDEVTGNQMTRRKFCYPQRPGVHD 103
           ++N+ ++D   ++         NV+ +++      Q +E  G++  R    YP RP   D
Sbjct: 48  LRNVGLDDSAKELSVPISVPQGNVETDSRALFGSDQKEEEEGSE-KRMMMVYPVRPDSED 106

Query: 104 CSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIE 144
           CS+Y+RTG C++G SCKFNHPV R++Q   + +      +E
Sbjct: 107 CSFYMRTGSCKYGSSCKFNHPVRRKLQIGRERVRERDEDVE 147

Arabidopsis thaliana (taxid: 3702)

>sp|Q2R4J4|C3H63_ORYSJ Zinc finger CCCH domain-containing protein 63 OS=Oryza sativa subsp. japonica GN=Os11g0472000 PE=2 SV=2

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 75  KNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQ 134
           K N   D        R K  YPQR G  +C YYL+TG C+FG +CKF+H  PR+  ++  
Sbjct: 78  KFNHPADRKMAVAAARMKGEYPQRIGQPECQYYLKTGTCKFGATCKFHH--PREKAAIAT 135

Query: 135 SINSNTVSIEMNPNNSANSNRMSTGK 160
            +  N +   + PN    +  + TG+
Sbjct: 136 RVQLNALGYPLRPNEKECAYYLRTGQ 161

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QT65|C3H66_ORYSJ Zinc finger CCCH domain-containing protein 66 OS=Oryza sativa subsp. japonica GN=Os12g0405100 PE=2 SV=1

 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 31/44 (70%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINS 138
           YP+R G  DCSYY+RTG CRFGM+CKFNHP  R++      +N 
Sbjct: 63  YPERIGEPDCSYYMRTGLCRFGMTCKFNHPPNRKLAVAAARMNG 106

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8GXX7|C3H33_ARATH Zinc finger CCCH domain-containing protein 33 OS=Arabidopsis thaliana GN=ZFN1 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 29/35 (82%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
           YP+RPG  DCSYY+RTG CRFG +C+FNHP  R++
Sbjct: 37  YPERPGEPDCSYYIRTGLCRFGSTCRFNHPRDREL 71

Arabidopsis thaliana (taxid: 3702)

>sp|Q5JLB5|C3H12_ORYSJ Zinc finger CCCH domain-containing protein 12 OS=Oryza sativa subsp. japonica GN=Os01g0917400 PE=2 SV=2

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 28/35 (80%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
           YP+R G  DC+YYLRTG CRFGMSC+FNHP  R +
Sbjct: 77  YPERSGEPDCTYYLRTGLCRFGMSCRFNHPQDRNL 111

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0DBW8|C3H42_ORYSJ Zinc finger CCCH domain-containing protein 42 OS=Oryza sativa subsp. japonica GN=Os06g0519400 PE=2 SV=1

 Score = 57.8 bits (138), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/36 (63%), Positives = 29/36 (80%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           +PQRPG HDC +YLR GRC++GM+C+FNHP  R  Q
Sbjct: 117 HPQRPGEHDCLHYLRFGRCKYGMNCRFNHPPDRLPQ 152

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SWF9|ZFNL_PEA Zinc finger CCCH domain-containing protein ZFN-like OS=Pisum sativum PE=2 SV=1

 Score = 57.4 bits (137), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/35 (62%), Positives = 28/35 (80%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
           YP+ PG  DCSYY+RTG CRFG +C+FNHP  R++
Sbjct: 27  YPEHPGEPDCSYYIRTGLCRFGATCRFNHPPNRKL 61

Pisum sativum (taxid: 3888)

>sp|Q6NPN3|C3H58_ARATH Zinc finger CCCH domain-containing protein 58 OS=Arabidopsis thaliana GN=At5g18550 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 31/37 (83%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQS 131
           +P RPG  +CSY++RTG+C+FG +C+++HPVP  +Q+
Sbjct: 142 FPLRPGEKECSYFMRTGQCKFGSTCRYHHPVPPGVQA 178

Arabidopsis thaliana (taxid: 3702)

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	162
297816042	447	zinc finger (CCCH-type) family protein [	0.438	0.158	0.387	6e-10
356557823	481	PREDICTED: zinc finger CCCH domain-conta	0.314	0.106	0.452	6e-09
359491687	481	PREDICTED: zinc finger CCCH domain-conta	0.407	0.137	0.444	8e-09
225456787	484	PREDICTED: zinc finger CCCH domain-conta	0.407	0.136	0.444	8e-09
255540399	495	nucleic acid binding protein, putative [	0.345	0.113	0.482	1e-08
15228379	448	zinc finger CCCH domain-containing prote	0.209	0.075	0.666	1e-08
356507323	570	PREDICTED: zinc finger CCCH domain-conta	0.314	0.089	0.465	1e-08
357447361	482	Zinc finger CCCH domain-containing prote	0.308	0.103	0.433	4e-08
334188594	451	zinc finger CCCH domain-containing prote	0.506	0.181	0.359	4e-08
79395677	462	zinc finger CCCH domain-containing prote	0.216	0.075	0.657	5e-08

>gi|297816042|ref|XP_002875904.1| zinc finger (CCCH-type) family protein [Arabidopsis lyrata subsp. lyrata] gi|297321742|gb|EFH52163.1| zinc finger (CCCH-type) family protein [Arabidopsis lyrata subsp. lyrata]

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 36/93 (38%), Positives = 49/93 (52%), Gaps = 22/93 (23%)

Query: 60  DQVDSDTEEEVENVDKNNKQVDE---VTGNQMTR-------------------RKFCYPQ 97
           D+V  +  E + +V ++N  +D    VT NQ                      R+  YP 
Sbjct: 50  DEVTKEKSETIVSVSESNGGLDSNVVVTSNQEEEEEEDGDDYGDGWSENESEMRETVYPV 109

Query: 98  RPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           RPG  DCS+Y+RTG C+FG SCKFNHP+ R+IQ
Sbjct: 110 RPGAEDCSFYMRTGSCKFGSSCKFNHPLARKIQ 142

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557823|ref|XP_003547210.1| PREDICTED: zinc finger CCCH domain-containing protein 58-like [Glycine max]

 Score = 65.9 bits (159), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 35/53 (66%)

Query: 78  KQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           +Q        M+   + YP RPG  +CSYY++TG+C+FG +CKF+HPVP  +Q
Sbjct: 120 RQAGGTAATPMSLSYYGYPLRPGEKECSYYVKTGQCKFGATCKFHHPVPAGVQ 172

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491687|ref|XP_003634306.1| PREDICTED: zinc finger CCCH domain-containing protein 43 isoform 2 [Vitis vinifera]

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/72 (44%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 59  EDQVDSDTEEEVENVDKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMS 118
           E +   D EE+ EN++      DE         +F YP RP   DCS+YLRTG C+FG +
Sbjct: 96  EVKASDDEEEQCENLE------DESAAKDDKSARFQYPVRPDAVDCSFYLRTGTCKFGSN 149

Query: 119 CKFNHPVPRQIQ 130
           CKFNHP+ R+ Q
Sbjct: 150 CKFNHPIRRKNQ 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225456787|ref|XP_002277300.1| PREDICTED: zinc finger CCCH domain-containing protein 43 isoform 1 [Vitis vinifera] gi|297733636|emb|CBI14883.3| unnamed protein product [Vitis vinifera]

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/72 (44%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 59  EDQVDSDTEEEVENVDKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMS 118
           E +   D EE+ EN++      DE         +F YP RP   DCS+YLRTG C+FG +
Sbjct: 96  EVKASDDEEEQCENLE------DESAAKDDKSARFQYPVRPDAVDCSFYLRTGTCKFGSN 149

Query: 119 CKFNHPVPRQIQ 130
           CKFNHP+ R+ Q
Sbjct: 150 CKFNHPIRRKNQ 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540399|ref|XP_002511264.1| nucleic acid binding protein, putative [Ricinus communis] gi|223550379|gb|EEF51866.1| nucleic acid binding protein, putative [Ricinus communis]

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 40/58 (68%), Gaps = 2/58 (3%)

Query: 81  DEVTGNQMTRR--KFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSI 136
           DE + N + RR  ++ YP RP   DCSYY++TG C+FG +CKFNHPV R++Q   + +
Sbjct: 125 DERSNNGVNRRHNQYQYPVRPEAEDCSYYMKTGTCKFGSNCKFNHPVKRKMQVSKEKV 182

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15228379|ref|NP_190414.1| zinc finger CCCH domain-containing protein 43 [Arabidopsis thaliana] gi|62901491|sp|Q9STM4.1|C3H43_ARATH RecName: Full=Zinc finger CCCH domain-containing protein 43; Short=AtC3H43; AltName: Full=Zinc finger CCCH domain-containing protein ZFN-like 6 gi|4678344|emb|CAB41154.1| putative protein [Arabidopsis thaliana] gi|194272236|gb|ACF37203.1| At3g48440 [Arabidopsis thaliana] gi|332644896|gb|AEE78417.1| zinc finger CCCH domain-containing protein 43 [Arabidopsis thaliana]

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/36 (66%), Positives = 29/36 (80%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           YP RPG  DCS+Y+RTG C+FG SCKFNHP+ R+ Q
Sbjct: 107 YPVRPGAEDCSFYMRTGSCKFGSSCKFNHPLARKFQ 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507323|ref|XP_003522417.1| PREDICTED: zinc finger CCCH domain-containing protein 43-like [Glycine max]

 Score = 64.3 bits (155), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 38/58 (65%)

Query: 74  DKNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQS 131
           DK    V+ V G + + R   YP RP   DC++YL+TG C+FG +CKFNHP+ R+ Q+
Sbjct: 209 DKVGGDVEGVKGERSSGRAQQYPLRPEAEDCAFYLKTGTCKFGFNCKFNHPLRRKNQA 266

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357447361|ref|XP_003593956.1| Zinc finger CCCH domain-containing protein [Medicago truncatula] gi|355483004|gb|AES64207.1| Zinc finger CCCH domain-containing protein [Medicago truncatula]

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 36/53 (67%)

Query: 78  KQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
           KQ      + ++   + YP RPG  +CSY+++TG+C+FG +CKF+HPVP  +Q
Sbjct: 120 KQTGATDASPVSLNYYGYPLRPGEKECSYFVKTGQCKFGATCKFDHPVPASVQ 172

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334188594|ref|NP_001190604.1| zinc finger CCCH domain-containing protein 67 [Arabidopsis thaliana] gi|332010342|gb|AED97725.1| zinc finger CCCH domain-containing protein 67 [Arabidopsis thaliana]

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 52/89 (58%), Gaps = 7/89 (7%)

Query: 50  MQNLDIEDPEDQVDSDTEEEVENVDKNNK------QVDEVTGNQMTRRKFCYPQRPGVHD 103
           ++N+ ++D   ++         NV+ +++      Q +E  G++  R    YP RP   D
Sbjct: 48  LRNVGLDDSAKELSVPISVPQGNVETDSRALFGSDQKEEEEGSE-KRMMMVYPVRPDSED 106

Query: 104 CSYYLRTGRCRFGMSCKFNHPVPRQIQSL 132
           CS+Y+RTG C++G SCKFNHPV R++Q L
Sbjct: 107 CSFYMRTGSCKYGSSCKFNHPVRRKLQDL 135

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79395677|ref|NP_187292.2| zinc finger CCCH domain-containing protein 34 [Arabidopsis thaliana] gi|150387824|sp|Q9SQU4.2|C3H34_ARATH RecName: Full=Zinc finger CCCH domain-containing protein 34; Short=AtC3H34; AltName: Full=Zinc finger CCCH domain-containing protein ZFN-like 2 gi|110741372|dbj|BAF02236.1| hypothetical protein [Arabidopsis thaliana] gi|332640868|gb|AEE74389.1| zinc finger CCCH domain-containing protein 34 [Arabidopsis thaliana]

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 30/35 (85%)

Query: 95  YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
           YP RPG  +CSYYLRTG+C+FG++C+FNHPVP  +
Sbjct: 145 YPLRPGEKECSYYLRTGQCKFGLTCRFNHPVPLAV 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	162
TAIR|locus:2081066	462	AT3G06410 [Arabidopsis thalian	0.222	0.077	0.666	1.3e-10
TAIR|locus:2101170	448	AT3G48440 [Arabidopsis thalian	0.222	0.080	0.666	2.5e-10
TAIR|locus:2075477	397	ZFN1 "zinc finger protein 1" [	0.216	0.088	0.657	9e-10
TAIR|locus:2171407	375	ZFN3 "zinc finger nuclease 3"	0.395	0.170	0.378	6e-09
TAIR|locus:2182988	465	AT5G18550 [Arabidopsis thalian	0.246	0.086	0.5	1.1e-08
TAIR|locus:2087775	524	HUA1 "ENHANCER OF AG-4 1" [Ara	0.345	0.106	0.421	1.4e-08
TAIR|locus:2043368	468	AT2G47850 [Arabidopsis thalian	0.197	0.068	0.625	5.1e-08
TAIR|locus:2013763	321	AT1G29570 [Arabidopsis thalian	0.283	0.143	0.434	1.1e-07
TAIR|locus:2010562	404	AT1G04990 [Arabidopsis thalian	0.216	0.086	0.540	1.4e-07
TAIR|locus:1006230718	82	AT1G48195 [Arabidopsis thalian	0.364	0.719	0.365	2.3e-07

TAIR|locus:2081066 AT3G06410 [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 1.3e-10, P = 1.3e-10
 Identities = 24/36 (66%), Positives = 31/36 (86%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
             YP RPG  +CSYYLRTG+C+FG++C+FNHPVP  +Q
Sbjct:   145 YPLRPGEKECSYYLRTGQCKFGLTCRFNHPVPLAVQ 180

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:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2101170 AT3G48440 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 24/36 (66%), Positives = 29/36 (80%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ 130
             YP RPG  DCS+Y+RTG C+FG SCKFNHP+ R+ Q
Sbjct:   107 YPVRPGAEDCSFYMRTGSCKFGSSCKFNHPLARKFQ 142

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:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2075477 ZFN1 "zinc finger protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 9.0e-10, P = 9.0e-10
 Identities = 23/35 (65%), Positives = 29/35 (82%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129
             YP+RPG  DCSYY+RTG CRFG +C+FNHP  R++
Sbjct:    37 YPERPGEPDCSYYIRTGLCRFGSTCRFNHPRDREL 71

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=TAS

GO:0004518 "nuclease activity" evidence=TAS

GO:0005829 "cytosol" evidence=IDA

GO:0010313 "phytochrome binding" evidence=IPI

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0048027 "mRNA 5'-UTR binding" evidence=IPI

TAIR|locus:2171407 ZFN3 "zinc finger nuclease 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 6.0e-09, P = 6.0e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSN 154
             YP+R G  +C +YL+TG C+FG++CKF+HP  R    ++ S++ N +S  + PN    S 
Sbjct:    84 YPERIGQPECEFYLKTGTCKFGVTCKFHHP--RNKAGIDGSVSVNVLSYPLRPNEDDCSY 141

Query:   155 RMSTGK 160
              +  G+
Sbjct:   142 FLRIGQ 147

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=TAS

GO:0004518 "nuclease activity" evidence=TAS

TAIR|locus:2182988 AT5G18550 [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 20/40 (50%), Positives = 33/40 (82%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQ 134
             +P RPG  +CSY++RTG+C+FG +C+++HPVP  +Q+ +Q
Sbjct:   142 FPLRPGEKECSYFMRTGQCKFGSTCRYHHPVPPGVQAPSQ 181

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:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2087775 HUA1 "ENHANCER OF AG-4 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 1.4e-08, P = 1.4e-08
 Identities = 24/57 (42%), Positives = 39/57 (68%)

Query:    96 PQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSAN 152
             P+RP    C++Y++TG+C+FG+SCKF+HP   Q+ S +Q I S+ V +   P+ + N
Sbjct:   266 PERPSEPMCTFYMKTGKCKFGLSCKFHHPKDIQLPSSSQDIGSS-VGLTSEPDATNN 321

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA;TAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001709 "cell fate determination" evidence=TAS

GO:0003723 "RNA binding" evidence=ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2043368 AT2G47850 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 5.1e-08, P = 5.1e-08
 Identities = 20/32 (62%), Positives = 28/32 (87%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126
             YP R G ++CSYYL+TG+C+FG++CKF+HP P
Sbjct:   133 YPVREGDNECSYYLKTGQCKFGITCKFHHPQP 164

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

TAIR|locus:2013763 AT1G29570 [Arabidopsis thaliana (taxid:3702)]

 Score = 127 (49.8 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 20/46 (43%), Positives = 28/46 (60%)

Query:    82 EVTGNQMTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPR 127
             ++   +  R+   YP RPG  DC +YL+ G CR+  SC+FNHP  R
Sbjct:    39 QIQSKERMRQSSPYPVRPGKKDCQFYLKNGLCRYRSSCRFNHPTQR 84

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0048445 "carpel morphogenesis" evidence=RCA

TAIR|locus:2010562 AT1G04990 [Arabidopsis thaliana (taxid:3702)]

 Score = 128 (50.1 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 20/37 (54%), Positives = 27/37 (72%)

Query:    95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHP--VPRQI 129
             YP RPG  DC +YLRTG C +G SC++NHP  +P+ +
Sbjct:    44 YPDRPGERDCQFYLRTGLCGYGSSCRYNHPTHLPQDV 80

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:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:1006230718 AT1G48195 [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 2.3e-07, P = 2.3e-07
 Identities = 23/63 (36%), Positives = 33/63 (52%)

Query:    88 MTRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNP 147
             M+  KF  P+RPG  +CSYYLRTG C    +CK++HP  + I         N   + + P
Sbjct:     1 MSEEKF--PERPGEPECSYYLRTGNCYLKQNCKYHHP--KNITPSEPQCTLNDKGLPLRP 56

Query:   148 NNS 150
               +
Sbjct:    57 GQA 59


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.131   0.399    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      162       132   0.00091  102 3  11 22  0.41    31
                                                     30  0.43    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  596 (63 KB)
  Total size of DFA:  147 KB (2089 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  13.67u 0.09s 13.76t   Elapsed:  00:00:01
  Total cpu time:  13.67u 0.09s 13.76t   Elapsed:  00:00:01
  Start:  Fri May 10 20:35:23 2013   End:  Fri May 10 20:35:24 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	162
pfam00642	27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	6e-07
smart00356	27	smart00356, ZnF_C3H1, zinc finger	3e-04

>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)

 Score = 43.3 bits (103), Expect = 6e-07
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 104 CSYYLRTGRCRFGMSCKFNHPV 125
           C ++ RTG C++G  CKF H  
Sbjct: 6   CRFFSRTGTCKYGDRCKFAHGQ 27

Length = 27

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

 Score = 36.1 bits (84), Expect = 3e-04
 Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 1/27 (3%)

Query: 98  RPGVHDCSYYLRTGRCRFGMSCKFNHP 124
           +     C ++ + G C  G  CKF HP
Sbjct: 1   KYKTELCKFF-KRGYCPRGDRCKFAHP 26

Length = 27

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	162
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.74
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	98.29
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	98.26
smart00356	27	ZnF_C3H1 zinc finger.	98.08
KOG2185	486	consensus Predicted RNA-processing protein, contai	97.06
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.57
COG5152	259	Uncharacterized conserved protein, contains RING a	95.99
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.36
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	94.69
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	94.03
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	92.64
KOG2333	614	consensus Uncharacterized conserved protein [Gener	90.43
KOG1763	343	consensus Uncharacterized conserved protein, conta	87.23
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	85.38
KOG1040	325	consensus Polyadenylation factor I complex, subuni	81.39

>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=98.74  E-value=2.5e-09  Score=62.99  Aligned_cols=26  Identities=38%  Similarity=1.000  Sum_probs=21.1

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCC
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPV  125 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~  125 (162)
                      ..++|.+|+++|.|+||++|+|.|+.
T Consensus         2 k~~~C~~f~~~g~C~~G~~C~f~H~~   27 (27)
T PF00642_consen    2 KTKLCRFFMRTGTCPFGDKCRFAHGE   27 (27)
T ss_dssp             TSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred             ccccChhhccCCccCCCCCcCccCCC
Confidence            57899999999999999999999973

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 ....

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

Probab=98.29  E-value=4.2e-07  Score=76.66  Aligned_cols=36  Identities=28%  Similarity=0.706  Sum_probs=32.8

Q ss_pred             cCCCCCCCCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295           93 FCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus        93 ~~~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      ..++.+.+.++|.+|++||.|+||.+|+|+|+.+..
T Consensus       169 ~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~  204 (332)
T KOG1677|consen  169 VGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPED  204 (332)
T ss_pred             hcCCCCCCCcCCCccccCCCCCCCCcCeecCCCccc
Confidence            467889999999999999999999999999998843

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

Probab=98.26  E-value=5.8e-07  Score=75.82  Aligned_cols=63  Identities=21%  Similarity=0.364  Sum_probs=53.5

Q ss_pred             cCCCCCCCCCCCccchhccCCCC-CCCCccCCCCCcccccccccccCcceeeccCCCCCccchhcccC
Q 031295           93 FCYPQRPGVHDCSYYLRTGRCRF-GMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTG  159 (162)
Q Consensus        93 ~~~P~RPg~~~C~fYmKTG~CRF-G~~CKFnHP~~~~s~~~~~~vn~~~V~lp~rP~n~~~~~~~~~g  159 (162)
                      ...|++-+.+.|.+|+++|.|+| |.+|||+|+........    ....++.+.++....|.+|.++|
T Consensus       124 ~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~----~~~~~~~~~~~kt~lC~~f~~tG  187 (332)
T KOG1677|consen  124 ERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS----SENQVGNPPKYKTKLCPKFQKTG  187 (332)
T ss_pred             ccCcccccCCcceeeecCccccccCchhhhcCCcccccccc----cchhhcCCCCCCCcCCCccccCC
Confidence            56788899999999999999999 99999999998643111    22468899999999999999987

>smart00356 ZnF_C3H1 zinc finger

Probab=98.08  E-value=2.6e-06  Score=48.18  Aligned_cols=23  Identities=39%  Similarity=1.152  Sum_probs=21.2

Q ss_pred             CCCCccchhccCCCCCCCCccCCC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHP  124 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP  124 (162)
                      ..+|++| ++|.|++|++|+|.|.
T Consensus         4 ~~~C~~~-~~g~C~~g~~C~~~H~   26 (27)
T smart00356        4 TELCKFF-KRGYCPYGDRCKFAHP   26 (27)
T ss_pred             CCcCcCc-cCCCCCCCCCcCCCCc
Confidence            4589999 8899999999999996

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

Probab=97.06  E-value=0.00023  Score=66.01  Aligned_cols=40  Identities=35%  Similarity=0.901  Sum_probs=32.6

Q ss_pred             cccCcCCCCCCCCCCCccchhccCCCCCCCCccCCCCCccc
Q 031295           89 TRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI  129 (162)
Q Consensus        89 ~~~~~~~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s  129 (162)
                      ++-..-+|.-..-.+|.|||. |.||||.+|||.|-.....
T Consensus       128 vRVlfl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V~l  167 (486)
T KOG2185|consen  128 VRVLFLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLDVPL  167 (486)
T ss_pred             eEEEeecCcchhhccchHhhc-cccccCcccccccCcccch
Confidence            344456787777899999987 9999999999999877543

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=96.57  E-value=0.0013  Score=36.35  Aligned_cols=19  Identities=37%  Similarity=0.966  Sum_probs=16.5

Q ss_pred             CCccchhccCCCCCCCCccCCC
Q 031295          103 DCSYYLRTGRCRFGMSCKFNHP  124 (162)
Q Consensus       103 ~C~fYmKTG~CRFG~~CKFnHP  124 (162)
                      .|+|+..   |++|++|.|.||
T Consensus         1 ~Ck~~~~---C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGPN---CTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcCC---CCCCCcCccCCc
Confidence            4898843   999999999998

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

Probab=95.99  E-value=0.0022  Score=55.34  Aligned_cols=26  Identities=42%  Similarity=0.791  Sum_probs=24.3

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      ..+|.=|-.||.|.||++|||-|.++
T Consensus       141 pdVCKdyk~TGYCGYGDsCKflH~R~  166 (259)
T COG5152         141 PDVCKDYKETGYCGYGDSCKFLHDRS  166 (259)
T ss_pred             cccccchhhcccccCCchhhhhhhhh
Confidence            36899999999999999999999987

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.36  E-value=0.0046  Score=54.04  Aligned_cols=39  Identities=28%  Similarity=0.627  Sum_probs=33.1

Q ss_pred             CCCCCCCCCCccchhccCCCCCCCCccCCCCCccccccc
Q 031295           95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLN  133 (162)
Q Consensus        95 ~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s~~~~  133 (162)
                      |-...++..|.||.|+|.||+|+.|+-.|-++..++..+
T Consensus         9 fgtekdKv~c~fy~k~gacR~gdrcsR~h~kpt~s~t~l   47 (260)
T KOG2202|consen    9 FGTEKDKVNCSFYFKIGACRHGDRCSRLHEKPTFSQTVL   47 (260)
T ss_pred             hcccccccccchHHhhcccccccHHHHhhcccccchHHH
Confidence            444577899999999999999999999999998775533

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

Probab=94.69  E-value=0.012  Score=52.78  Aligned_cols=25  Identities=40%  Similarity=1.150  Sum_probs=23.1

Q ss_pred             CCCccchhccCCCCCCCCccCCCCCc
Q 031295          102 HDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus       102 ~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      .+|.||.+ |.|+||+.|+|.|-.+.
T Consensus         9 tic~~~~~-g~c~~g~~cr~~h~~~~   33 (344)
T KOG1039|consen    9 TICKYYQK-GNCKFGDLCRLSHSLPD   33 (344)
T ss_pred             hhhhhccc-ccccccceeeeeccCch
Confidence            89999966 99999999999999884

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

Probab=94.03  E-value=0.017  Score=51.75  Aligned_cols=26  Identities=42%  Similarity=0.779  Sum_probs=24.0

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      .-+|.=|--||.|.||++|||.|.+.
T Consensus       186 pDicKdykeTgycg~gdSckFlh~r~  211 (313)
T KOG1813|consen  186 PDICKDYKETGYCGYGDSCKFLHDRS  211 (313)
T ss_pred             chhhhhhHhhCcccccchhhhhhhhh
Confidence            35899999999999999999999986

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

Probab=92.64  E-value=0.043  Score=49.49  Aligned_cols=26  Identities=38%  Similarity=0.850  Sum_probs=23.4

Q ss_pred             CCCCccchhccCCCCCCC-CccCCCCCc
Q 031295          101 VHDCSYYLRTGRCRFGMS-CKFNHPVPR  127 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~-CKFnHP~~~  127 (162)
                      -.+|+-|+| |.|.=|++ |||.||...
T Consensus        37 ~eVCReF~r-n~C~R~d~~CkfaHP~~~   63 (331)
T KOG2494|consen   37 LEVCREFLR-NTCSRGDRECKFAHPPKN   63 (331)
T ss_pred             HHHHHHHHh-ccccCCCccccccCCCCC
Confidence            379999977 99999999 999999874

>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]

Probab=90.43  E-value=0.11  Score=49.87  Aligned_cols=36  Identities=22%  Similarity=0.594  Sum_probs=27.4

Q ss_pred             CCCCccchhc--cCCCCCCCCccCCCCCcccccccccc
Q 031295          101 VHDCSYYLRT--GRCRFGMSCKFNHPVPRQIQSLNQSI  136 (162)
Q Consensus       101 ~~~C~fYmKT--G~CRFG~~CKFnHP~~~~s~~~~~~v  136 (162)
                      -..|.--.+.  -.|.||++|||.|..+.-...-...|
T Consensus        76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Di  113 (614)
T KOG2333|consen   76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDI  113 (614)
T ss_pred             hccChHhhcCCCccCcccccccccccHHHHHhccCccc
Confidence            4679999887  68999999999999986443333334

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

Probab=87.23  E-value=0.2  Score=45.40  Aligned_cols=32  Identities=28%  Similarity=0.726  Sum_probs=27.0

Q ss_pred             CCCCCCCCccchhccCCCCCCCCccCCCCCccc
Q 031295           97 QRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI  129 (162)
Q Consensus        97 ~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s  129 (162)
                      +-|-.-+|.|| +.|.|.=|+.|||.|.-....
T Consensus        88 vDPKSvvCafF-k~g~C~KG~kCKFsHdl~~~~  119 (343)
T KOG1763|consen   88 VDPKSVVCAFF-KQGTCTKGDKCKFSHDLAVER  119 (343)
T ss_pred             CCchHHHHHHH-hccCCCCCCcccccchHHHhh
Confidence            34667899999 889999999999999876543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=85.38  E-value=0.32  Score=42.73  Aligned_cols=28  Identities=29%  Similarity=0.471  Sum_probs=25.7

Q ss_pred             CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295           98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus        98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      ++.+..|.+|.++ .|..|..|-|.|...
T Consensus       149 ~~rea~C~~~e~~-~C~rG~~CnFmH~k~  176 (260)
T KOG2202|consen  149 DFREAICGQFERT-ECSRGGACNFMHVKR  176 (260)
T ss_pred             chhhhhhcccccc-cCCCCCcCcchhhhh
Confidence            7788999999886 999999999999984

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]

Probab=81.39  E-value=0.6  Score=41.81  Aligned_cols=28  Identities=36%  Similarity=0.721  Sum_probs=24.8

Q ss_pred             CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295           98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus        98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      --++.+|.||++ |.|+-|+.|-|.|-.+
T Consensus        74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~~  101 (325)
T KOG1040|consen   74 SRGKVVCKHWLR-GLCKKGDQCEFLHEYD  101 (325)
T ss_pred             cCCceeehhhhh-hhhhccCcCcchhhhh
Confidence            457899999977 9999999999999774

---

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	162
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	5e-05
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 8/21 (38%), Positives = 10/21 (47%)

Query: 104 CSYYLRTGRCRFGMSCKFNHP 124
           C  +   GRC +G  C F H 
Sbjct: 53  CHKFKLQGRCPYGSRCHFIHN 73

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 104 CSYYLRTGRCRFGMSCKFNHPV 125
           C  Y  +GRCR+G  C+F H +
Sbjct: 15  CRTYSESGRCRYGAKCQFAHGL 36

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 38.7 bits (89), Expect = 4e-04
 Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 26/99 (26%)

Query: 2   LKLISESYI--PSKWIFLMHPFDSNVN-------------EENRYYTQLS-LPPNSDLDP 45
           L +I+ES     + W    H     +              E  + + +LS  PP++ +  
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389

Query: 46  PPLDM--QNLDIEDPEDQVDSDTEEEVEN---VDKNNKQ 79
             L +   ++   D    V+     ++     V+K  K+
Sbjct: 390 ILLSLIWFDVIKSDVMVVVN-----KLHKYSLVEKQPKE 423

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	162
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	98.45
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.34
2rhk_C	72	Cleavage and polyadenylation specificity factor su	98.31
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.24
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	98.14
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	97.61
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	97.23
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	96.97
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	96.69
2rhk_C	72	Cleavage and polyadenylation specificity factor su	96.65
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	96.44
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	96.4
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.09
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	95.94
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	95.86
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	95.85
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	94.29
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	93.83
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	91.1
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	91.0
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	90.58

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

Probab=98.45  E-value=1.3e-07  Score=64.09  Aligned_cols=52  Identities=25%  Similarity=0.426  Sum_probs=28.0

Q ss_pred             CCCCCCCccchhccCCCCCCCCccCCCCCcccccccccccCcceeeccCCCCCccchhcccC
Q 031295           98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTG  159 (162)
Q Consensus        98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s~~~~~~vn~~~V~lp~rP~n~~~~~~~~~g  159 (162)
                      +....+|++|+++|.|+||++|+|.|.........          ...+....+|.+|..+|
T Consensus         9 ~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~~~----------~~~~~k~~~C~~f~~~G   60 (77)
T 1m9o_A            9 RYKTELCRTYSESGRCRYGAKCQFAHGLGELRQAN----------RHPKYKTELCHKFKLQG   60 (77)
T ss_dssp             CCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGTC---------------------------
T ss_pred             CccchhCHHhhhCCCcCCCCCccCCCCChhhcccc----------ccccccCCcccchhhCc
Confidence            45678999999999999999999999987532211          11133456787777666

>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=98.34  E-value=3.1e-07  Score=66.84  Aligned_cols=31  Identities=23%  Similarity=0.447  Sum_probs=25.3

Q ss_pred             cCCCCCCCCCCCccchhccCCCCCCCCccCCC
Q 031295           93 FCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHP  124 (162)
Q Consensus        93 ~~~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP  124 (162)
                      +.+..+....+|+||+ +|.|++|++|+|.|+
T Consensus         5 H~~~~~~k~~lC~~f~-~G~C~~G~~C~f~H~   35 (98)
T 2cqe_A            5 SSGELPKKRELCKFYI-TGFCARAENCPYMHG   35 (98)
T ss_dssp             CCCCCSCCCSBCTTTT-TTCCSCSTTCSSBSS
T ss_pred             ccCCCCCCCccCcccc-cCcCCCCCCCCCCCC
Confidence            4556666788999995 799999999999998

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

Probab=98.31  E-value=2e-07  Score=64.50  Aligned_cols=43  Identities=26%  Similarity=0.381  Sum_probs=34.4

Q ss_pred             CCCCCCCccchhccCCCCCCCCccCCCCCcccccccccccCcceeeccCCCCCccchhcccCc
Q 031295           98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTGK  160 (162)
Q Consensus        98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s~~~~~~vn~~~V~lp~rP~n~~~~~~~~~g~  160 (162)
                      .....+|+||++ |.|+.|++|+|.|+.+..                   ...+|.||+++|.
T Consensus        13 ~~k~~vCk~fl~-G~C~~G~~C~fsH~~~~~-------------------~~~~C~~f~~~G~   55 (72)
T 2rhk_C           13 GEKTVVCKHWLR-GLCKKGDQCEFLHEYDMT-------------------KMSECYFYSKFGE   55 (72)
T ss_dssp             CCCCSBCHHHHT-TCCCCGGGSSSBCSCCTT-------------------SCCBCHHHHHHSC
T ss_pred             CCcCeeCHHHhc-CCCCCCCCCCCccccccc-------------------cCCcccccCCCCC
Confidence            355789999988 999999999999996531                   2457999988663

>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=98.24  E-value=2.1e-07  Score=67.76  Aligned_cols=59  Identities=19%  Similarity=0.332  Sum_probs=45.2

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCCcccc-c-ccccccCcceeeccCCCCCccchhcccCcC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVPRQIQ-S-LNQSINSNTVSIEMNPNNSANSNRMSTGKA  161 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~~s~-~-~~~~vn~~~V~lp~rP~n~~~~~~~~~g~~  161 (162)
                      ..+|.||+++|.|++|++|+|.|+...... . ..+.+  ..-..+.+.++.-|..+.|+|-+
T Consensus        36 ~~~C~~f~~~G~C~~G~~C~f~H~~~~~~~~~~l~~~l--~~~~~~~~~~e~e~~~~~k~~~~   96 (98)
T 2cqe_A           36 DFPCKLYHTTGNCINGDDCMFSHDPLTEETRELLDKML--ADDAEAGAEDEKEVEELKKSGPS   96 (98)
T ss_dssp             SSBCSHHHHTSCCSSCTTCSSBCCCCCHHHHHHHHHHH--HHHHHSCCCCCCCCCCSCCCCCC
T ss_pred             CCcCcCcccCCcCCCCCCCcccCCCCcccchhHHhhhc--chhhhhccCCcHHHHHHHHcCCC
Confidence            578999999999999999999999764221 1 11222  33457899999999999999854

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

Probab=98.14  E-value=9.6e-07  Score=61.21  Aligned_cols=27  Identities=33%  Similarity=0.667  Sum_probs=23.9

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCCCc
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      ...+|+||++ |.|+.|++|+|.|+...
T Consensus         9 k~~~C~~fl~-G~C~~G~~C~fsH~~~~   35 (77)
T 2d9n_A            9 KTVVCKHWLR-GLCKKGDQCEFLHEYDM   35 (77)
T ss_dssp             TTSBCHHHHT-TCCSCTTSSSSBCSCCT
T ss_pred             cceeCHhHcc-CcCCCCCCCCCcccccc
Confidence            3579999988 99999999999999763

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

Probab=97.61  E-value=8.4e-06  Score=55.07  Aligned_cols=27  Identities=30%  Similarity=0.704  Sum_probs=0.0

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCCC
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      ...+|.+|+++|.|+||.+|+|.|+..
T Consensus        49 k~~~C~~f~~~G~C~~G~~C~f~H~~~   75 (77)
T 1m9o_A           49 KTELCHKFKLQGRCPYGSRCHFIHNPT   75 (77)
T ss_dssp             ---------------------------
T ss_pred             cCCcccchhhCcCCCCcCcCCCCCCCC
Confidence            357899998999999999999999864

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

Probab=97.23  E-value=8.5e-05  Score=52.38  Aligned_cols=24  Identities=42%  Similarity=0.783  Sum_probs=22.1

Q ss_pred             CCCccchhccCCCCCCCCccCCCCC
Q 031295          102 HDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       102 ~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      ..|..| .+|.|+||++|.|.|-..
T Consensus        21 ~LC~~~-~~G~C~~G~~C~FAHG~~   44 (69)
T 2d9m_A           21 SICDRY-MNGTCPEGNSCKFAHGNA   44 (69)
T ss_dssp             SBCHHH-HHSCCSSCSSCSSBSSHH
T ss_pred             ccCccc-CcCCCCCCCccCCcCCHH
Confidence            899999 679999999999999765

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

Probab=96.97  E-value=0.00035  Score=48.22  Aligned_cols=26  Identities=31%  Similarity=0.833  Sum_probs=23.5

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCCc
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      .++|.||+++|.|. |++|+|.|..+.
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            46899999999999 999999998764

>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=96.69  E-value=0.0006  Score=46.34  Aligned_cols=25  Identities=36%  Similarity=0.885  Sum_probs=21.9

Q ss_pred             CCCccchhccCCCCCC-CCccCCCCCc
Q 031295          102 HDCSYYLRTGRCRFGM-SCKFNHPVPR  127 (162)
Q Consensus       102 ~~C~fYmKTG~CRFG~-~CKFnHP~~~  127 (162)
                      ++|++|+ .|.|+-|+ .|+|.|+.+.
T Consensus         7 ~vC~~f~-~G~C~rg~~~C~f~H~~~~   32 (70)
T 3d2q_A            7 EVCREYQ-RGNCNRGENDCRFAHPADS   32 (70)
T ss_dssp             EBCHHHH-TTCCSSCTTTCSSBCCCTT
T ss_pred             hhCHHHh-cCCCCCCCCCCCCccCccc
Confidence            6899995 59999999 4999999874

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

Probab=96.65  E-value=0.00065  Score=46.75  Aligned_cols=26  Identities=31%  Similarity=0.800  Sum_probs=23.7

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCCc
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      .++|.||++.|.|.+ ++|+|.|..+.
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            568999999999999 99999998764

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

Probab=96.44  E-value=0.00041  Score=50.53  Aligned_cols=27  Identities=33%  Similarity=0.858  Sum_probs=24.0

Q ss_pred             CCCCccchhccCCCCCC-CCccCCCCCcc
Q 031295          101 VHDCSYYLRTGRCRFGM-SCKFNHPVPRQ  128 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~-~CKFnHP~~~~  128 (162)
                      .++|++|++ |.|+-|+ .|+|.|+.+..
T Consensus        20 ~~VCr~Flr-G~C~rgd~~C~FsH~~~~~   47 (98)
T 2e5s_A           20 LEVCREFQR-GNCARGETDCRFAHPADST   47 (98)
T ss_dssp             EEBCSHHHH-TCCSSHHHHCSSBCCSSCC
T ss_pred             hhhhHHHhc-CcCCCCCCCCCCcCCchhc
Confidence            469999988 9999999 79999998753

>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=96.40  E-value=0.0015  Score=46.45  Aligned_cols=26  Identities=35%  Similarity=0.761  Sum_probs=23.3

Q ss_pred             CCCCccchhccCCCCCC-CCccCCCCCc
Q 031295          101 VHDCSYYLRTGRCRFGM-SCKFNHPVPR  127 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~-~CKFnHP~~~  127 (162)
                      .++|++|++ |.|.=|+ .|+|.||...
T Consensus         9 ~~VCr~Flr-G~C~r~d~~C~f~H~~~~   35 (83)
T 3d2n_A            9 LEVCREFQR-GTCSRPDTECKFAHPSKS   35 (83)
T ss_dssp             EEBCTTGGG-TCCCSCTTTCSSBCCCTT
T ss_pred             chhcHHHhc-CCCCCCCCCCCCcCCCcc
Confidence            368999988 9999996 9999999874

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

Probab=96.09  E-value=0.0017  Score=53.51  Aligned_cols=30  Identities=23%  Similarity=0.752  Sum_probs=25.9

Q ss_pred             CCCCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295           98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus        98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      +....+|.||.| |.|+.|+.|.|.|..+..
T Consensus        67 ~~~~~~C~ffak-G~C~~G~~C~y~H~lPt~   96 (240)
T 3u1l_A           67 DGQLFFCLFFAK-GMCCLGPKCEYLHHIPDE   96 (240)
T ss_dssp             TTCCSBCHHHHT-TCCSCGGGCSSBBSCCCH
T ss_pred             CCCCeEcCcccc-CCCCCCCCCCccCCCCCc
Confidence            445679999988 999999999999988764

>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=95.94  E-value=0.003  Score=45.57  Aligned_cols=26  Identities=35%  Similarity=0.789  Sum_probs=23.8

Q ss_pred             CCCCccchhccCCCCCC-CCccCCCCCc
Q 031295          101 VHDCSYYLRTGRCRFGM-SCKFNHPVPR  127 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~-~CKFnHP~~~  127 (162)
                      .++|+.|++ |.|.=|+ .|+|.||...
T Consensus        17 ~~VCrdFlr-G~C~r~d~~CrfsH~~~~   43 (89)
T 2rpp_A           17 LEVCRQFQR-GTCSRSDEECKFAHPPKS   43 (89)
T ss_dssp             ECBCHHHHH-TCCCCCTTTSSSBCCCSS
T ss_pred             hhhchHHhc-CCCCCCCCCCCCcCCCcc
Confidence            479999988 9999998 9999999886

>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=95.86  E-value=0.0029  Score=42.94  Aligned_cols=24  Identities=42%  Similarity=0.948  Sum_probs=22.1

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      .++|.+|++ |.|..| +|+|.|+..
T Consensus        42 ~~vC~~flk-G~C~r~-~C~y~H~~~   65 (70)
T 3d2q_A           42 VTVCMDYIK-GRCSRE-KCKYFHPPA   65 (70)
T ss_dssp             EEBCHHHHT-TCCCCT-TCCSBCCCH
T ss_pred             ceeccccCc-CCCCCC-CcCeeCCHH
Confidence            589999988 999999 999999976

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

Probab=95.85  E-value=0.0028  Score=46.14  Aligned_cols=27  Identities=37%  Similarity=0.807  Sum_probs=23.7

Q ss_pred             CCCCCCccchhccCCCCCCCCccCCCCCc
Q 031295           99 PGVHDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus        99 Pg~~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      ...++|.+|+| |.|..| +|+|.|+...
T Consensus        54 ~~~~vC~~flk-G~C~r~-~C~y~H~~~~   80 (98)
T 2e5s_A           54 NTVTVCMDYIK-GRCMRE-KCKYFHPPAH   80 (98)
T ss_dssp             CEEEBCHHHHH-TCCCCT-TCCSBCCCHH
T ss_pred             Cccccchhhcc-CCCCCC-CcCccCChHH
Confidence            34589999988 999999 9999999874

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=94.29  E-value=0.02  Score=38.32  Aligned_cols=30  Identities=20%  Similarity=0.481  Sum_probs=27.5

Q ss_pred             CCCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295           99 PGVHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus        99 Pg~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      ....+|.-|...|.|+.|..|.+.|..+..
T Consensus        18 ~~~~iC~~FSayGwCp~G~~Cp~SHDiDl~   47 (50)
T 2fc6_A           18 HPTSICDNFSAYGWCPLGPQCPQSHDISGP   47 (50)
T ss_dssp             CCSCBCSHHHHTCCCTTGGGCSSBCCCCCC
T ss_pred             cccchhhhccccccCCCCCCCCccccCCCC
Confidence            467999999999999999999999999864

>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=93.83  E-value=0.022  Score=40.35  Aligned_cols=26  Identities=42%  Similarity=0.850  Sum_probs=23.1

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCCcc
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      .++|.+|+| |.|.-| +|+|-|+....
T Consensus        43 ~~vC~dflk-G~C~r~-~C~y~H~~~~l   68 (83)
T 3d2n_A           43 VIACFDSLK-GRCSRE-NCKYLHPPPHL   68 (83)
T ss_dssp             EECCHHHHT-TCCCCS-SCSSCCCCHHH
T ss_pred             eeehhHhhh-ccccCC-CcceeCChHHH
Confidence            489999988 999999 99999998754

>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=91.10  E-value=0.078  Score=38.12  Aligned_cols=26  Identities=38%  Similarity=0.754  Sum_probs=23.0

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCCcc
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      ..+|..|+| |.|.-+ +|||-|+....
T Consensus        51 ~~vC~dflk-G~C~r~-~Cky~H~~~hl   76 (89)
T 2rpp_A           51 VIACFDSLK-GRCSRE-NCKYLHPPTHL   76 (89)
T ss_dssp             EEBCHHHHH-TCCCCT-TCCSBCCCHHH
T ss_pred             eeeehhhhh-CcCCCC-CcceecCHHHH
Confidence            589999987 999998 99999998754

>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein; 1.80A {Rattus norvegicus}

Probab=91.00  E-value=0.074  Score=44.62  Aligned_cols=24  Identities=29%  Similarity=0.812  Sum_probs=19.3

Q ss_pred             CCCccchhccCCCCCCCCccCCCCCc
Q 031295          102 HDCSYYLRTGRCRFGMSCKFNHPVPR  127 (162)
Q Consensus       102 ~~C~fYmKTG~CRFG~~CKFnHP~~~  127 (162)
                      -+|.+|++ |.||| .+||..|....
T Consensus       176 HIC~~Fl~-G~C~f-~~CkRsH~~~~  199 (229)
T 3u9g_A          176 HICEHFTR-GNCSY-LNCLRSHNLMD  199 (229)
T ss_dssp             CSCHHHHT-TCCCC-SSCSSCCCTTS
T ss_pred             eccchhhc-CCcCC-CCccCccCccC
Confidence            46788866 99999 79999998753

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=90.58  E-value=0.048  Score=45.27  Aligned_cols=26  Identities=31%  Similarity=0.884  Sum_probs=0.0

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPVPRQ  128 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~~~~  128 (162)
                      .+..|.|=   ..|-||.+|||.||-...
T Consensus       191 ~~~~~~~~---~~~~~~~~~~~~~~~~~~  216 (223)
T 3v33_A          191 RKQPCPYG---RKCTYGIKCRFFHPERPS  216 (223)
T ss_dssp             -----------------------------
T ss_pred             CCCCCCCC---cccccCCcceecCCccCC
Confidence            47789986   479999999999998643

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	162
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	7e-04
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	0.003

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

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]

 Score = 33.5 bits (77), Expect = 7e-04
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 104 CSYYLRTGRCRFGMSCKFNH 123
           C  +  +G C++G  C+F H
Sbjct: 9   CRPFEESGTCKYGEKCQFAH 28

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

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]

 Score = 32.0 bits (73), Expect = 0.003
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 104 CSYYLRTGRCRFGMSCKFNH 123
           C  Y  +GRCR+G  C+F H
Sbjct: 12  CRTYSESGRCRYGAKCQFAH 31

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	162
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	97.94
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	97.86
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	97.79
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	96.09
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	95.01

>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=97.94  E-value=2.1e-06  Score=52.96  Aligned_cols=27  Identities=37%  Similarity=0.928  Sum_probs=24.3

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCCC
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      ..+.|++|+++|.|+||++|.|.|-..
T Consensus         8 KT~lC~~~~~~g~C~~G~~C~FAHg~~   34 (40)
T d1m9oa_           8 KTELCRTYSESGRCRYGAKCQFAHGLG   34 (40)
T ss_dssp             CSCCCSGGGGTSCCTTTTTCSSCSSSC
T ss_pred             ccccChhhhcCCcCCCCCCCCCCCCHH
Confidence            357899999999999999999999765

>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=97.86  E-value=1.2e-06  Score=53.12  Aligned_cols=26  Identities=27%  Similarity=0.798  Sum_probs=23.8

Q ss_pred             CCCCccchhccCCCCCCCCccCCCCC
Q 031295          101 VHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       101 ~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      .+.|++|.++|.|.||++|.|.|-.+
T Consensus         6 T~lC~~~~~~g~C~~G~~C~FAHg~~   31 (36)
T d1rgoa1           6 TELCRPFEESGTCKYGEKCQFAHGFH   31 (36)
T ss_dssp             SSBCHHHHHHSCCTTGGGCSSBSSGG
T ss_pred             hhhCcchhcCCcCCCCCcCCCcCCHH
Confidence            47899999999999999999999765

>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=97.79  E-value=2.2e-06  Score=51.51  Aligned_cols=27  Identities=26%  Similarity=0.630  Sum_probs=24.1

Q ss_pred             CCCCCccchhccCCCCCCCCccCCCCC
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHPVP  126 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP~~  126 (162)
                      --..|.+|.++|.|.||++|.|.|-.+
T Consensus         7 KT~lC~~f~~~g~C~yG~~C~FaHg~~   33 (34)
T d1rgoa2           7 KTELCRTFHTIGFCPYGPRCHFIHNAD   33 (34)
T ss_dssp             TCSBCHHHHHHSCCTTGGGCSSBCCSC
T ss_pred             cchhccccCCCCcCCCCCcccCcCCCC
Confidence            357899999999999999999999753

>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=96.09  E-value=0.0014  Score=38.27  Aligned_cols=24  Identities=25%  Similarity=0.682  Sum_probs=21.2

Q ss_pred             CCCCCccchhccCCCCCCCCccCCC
Q 031295          100 GVHDCSYYLRTGRCRFGMSCKFNHP  124 (162)
Q Consensus       100 g~~~C~fYmKTG~CRFG~~CKFnHP  124 (162)
                      -+..|.||++ |.|-=|.+|.|-|-
T Consensus         5 kkelCKfYvq-GyCtrgenC~ymH~   28 (29)
T d2cqea2           5 KRELCKFYIT-GFCARAENCPYMHG   28 (29)
T ss_dssp             CCSBCTTTTT-TCCSCSTTCSSBSS
T ss_pred             hhhhhhhhee-eeecCCcCcccccC
Confidence            4689999965 99999999999994

>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=95.01  E-value=0.0042  Score=40.86  Aligned_cols=23  Identities=39%  Similarity=0.834  Sum_probs=20.6

Q ss_pred             CCccchhccCCCCCCCCccCCCC
Q 031295          103 DCSYYLRTGRCRFGMSCKFNHPV  125 (162)
Q Consensus       103 ~C~fYmKTG~CRFG~~CKFnHP~  125 (162)
                      .|.||-..+.|--|++|||.|..
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~p   24 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHDP   24 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCCC
T ss_pred             CcceeecCCcccCCCcccccCCc
Confidence            59999878899999999999954