Psyllid ID: psy4296

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100---
Protein Sequence
MGKCCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTGM
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccEEcccccccccccccccccccccccEEEEHHHHHHHccccccccHHHHccHcccccEHEEEccccccccccccccccHHHHHHHHHHHHHEHcccc
Coil and Loop (DISEMBL)
mgkccagiiqdpsfqapgvlvpfplrhitgdrsVVCKHWLRglckkgdqceflheydmtkmpecyfysrfnachnkecpflhidpdsmieaSVGMVHRVDTGM
Flexible Loop (DISEMBL)
mgkccagiiqdpsfqapgVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTGM
Low Complexity Region (SEG)
MGKCCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTGM
Disordered region (IsUnstruct)
***CCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVG*********
Disordered Region (DISOPRED)
***CCAG*************************SVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTG*
Disordered Region (DISEMBL)
MGKCCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTGM
Disordered Region (DISPRO)
*GKCCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTG*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGKCCAGIIQDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHRVDTGM
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	103	2.2.26 [Sep-21-2011]
O95639	269	Cleavage and polyadenylat	yes	N/A	0.650	0.249	0.820	7e-30
Q66KE3	269	Cleavage and polyadenylat	yes	N/A	0.650	0.249	0.820	1e-29
Q6DJP7	269	Cleavage and polyadenylat	N/A	N/A	0.650	0.249	0.820	1e-29
Q5FVR7	243	Cleavage and polyadenylat	yes	N/A	0.650	0.275	0.820	2e-29
O19137	243	Cleavage and polyadenylat	yes	N/A	0.650	0.275	0.820	2e-29
A6NMK7	179	Putative cleavage and pol	no	N/A	0.601	0.346	0.709	8e-23
Q8BQZ5	211	Cleavage and polyadenylat	yes	N/A	0.466	0.227	0.854	1e-20
Q59T36	215	mRNA 3'-end-processing pr	N/A	N/A	0.640	0.306	0.579	4e-17
Q4IPA4	255	mRNA 3'-end-processing pr	no	N/A	0.640	0.258	0.552	2e-16
Q6BTT1	223	mRNA 3'-end-processing pr	yes	N/A	0.640	0.295	0.565	2e-16

>sp|O95639|CPSF4_HUMAN Cleavage and polyadenylation specificity factor subunit 4 OS=Homo sapiens GN=CPSF4 PE=1 SV=1

 Score =  129 bits (323), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).
Homo sapiens (taxid: 9606)

>sp|Q66KE3|CPSF4_XENTR Cleavage and polyadenylation specificity factor subunit 4 OS=Xenopus tropicalis GN=cpsf4 PE=2 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Cpsf4 binds RNA polymers with a preference for poly(U).

Xenopus tropicalis (taxid: 8364)

>sp|Q6DJP7|CPSF4_XENLA Cleavage and polyadenylation specificity factor subunit 4 OS=Xenopus laevis GN=cpsf4 PE=2 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Cpsf4 binds RNA polymers with a preference for poly(U).

Xenopus laevis (taxid: 8355)

>sp|Q5FVR7|CPSF4_RAT Cleavage and polyadenylation specificity factor subunit 4 OS=Rattus norvegicus GN=Cpsf4 PE=2 SV=1

 Score =  127 bits (320), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

Rattus norvegicus (taxid: 10116)

>sp|O19137|CPSF4_BOVIN Cleavage and polyadenylation specificity factor subunit 4 OS=Bos taurus GN=CPSF4 PE=2 SV=1

 Score =  127 bits (320), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

Bos taurus (taxid: 9913)

>sp|A6NMK7|CPS4L_HUMAN Putative cleavage and polyadenylation specificity factor subunit 4-like protein OS=Homo sapiens GN=CPSF4L PE=2 SV=3

 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 52/62 (83%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RH  G++ VVCKHWLRGLCKKGD C+FLH+YD+T+MPECYFYS+F  C NKEC FLH+
Sbjct: 56  PFRHDRGEKMVVCKHWLRGLCKKGDHCKFLHQYDLTRMPECYFYSKFGDCSNKECSFLHV 115

Query: 84  DP 85
            P
Sbjct: 116 KP 117

Homo sapiens (taxid: 9606)

>sp|Q8BQZ5|CPSF4_MOUSE Cleavage and polyadenylation specificity factor subunit 4 OS=Mus musculus GN=Cpsf4 PE=2 SV=1

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 41/48 (85%), Positives = 46/48 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFN 71
           P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F 
Sbjct: 56  PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFG 103

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

Mus musculus (taxid: 10090)

>sp|Q59T36|YTH1_CANAL mRNA 3'-end-processing protein YTH1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=YTH1 PE=3 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/69 (57%), Positives = 49/69 (71%), Gaps = 3/69 (4%)

Query: 24  PLRHITG--DRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNAC-HNKECPF 80
           P +H++      +VCKHWLRGLCKKGD CEFLHEY++ KMPEC FYS+   C    EC +
Sbjct: 57  PNKHVSAMYSNKIVCKHWLRGLCKKGDHCEFLHEYNLRKMPECLFYSKNGYCTQTSECLY 116

Query: 81  LHIDPDSMI 89
           LH+DP S I
Sbjct: 117 LHVDPQSKI 125

Component of the cleavage factor I (CF I) involved in pre-mRNA 3'-end processing.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

>sp|Q4IPA4|YTH1_GIBZE mRNA 3'-end-processing protein YTH1 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=YTH1 PE=3 SV=2

 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 51/76 (67%), Gaps = 10/76 (13%)

Query: 24  PLRHIT---------GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACH 74
           P RH++         G  S+VCKHWLRGLCKKG+ CEFLHEY++ KMPEC F+ R   C 
Sbjct: 58  PERHVSDSKTSQPTGGLNSLVCKHWLRGLCKKGEHCEFLHEYNLRKMPECNFFMRNGYCS 117

Query: 75  N-KECPFLHIDPDSMI 89
           N  EC +LHIDP S +
Sbjct: 118 NGDECLYLHIDPQSRL 133

Component of the cleavage factor I (CF I) involved in pre-mRNA 3'-end processing.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

>sp|Q6BTT1|YTH1_DEBHA mRNA 3'-end-processing protein YTH1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=YTH1 PE=3 SV=2

 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/69 (56%), Positives = 48/69 (69%), Gaps = 3/69 (4%)

Query: 24  PLRHITG--DRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNAC-HNKECPF 80
           P +H++      +VCKHWLRGLCKK D CEFLHEY++ KMPEC FYS+   C    EC +
Sbjct: 57  PHKHVSSMYSNKIVCKHWLRGLCKKNDHCEFLHEYNLRKMPECLFYSKNGFCTQTPECLY 116

Query: 81  LHIDPDSMI 89
           LH+DP S I
Sbjct: 117 LHVDPQSKI 125

Component of the cleavage factor I (CF I) involved in pre-mRNA 3'-end processing.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

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	103
239792848	148	ACYPI007246 [Acyrthosiphon pisum]	0.776	0.540	0.724	4e-31
242021708	233	Cleavage and polyadenylation specificity	0.650	0.287	0.895	9e-31
332373586	294	unknown [Dendroctonus ponderosae]	0.650	0.227	0.895	1e-30
347968471	296	AGAP013044-PA [Anopheles gambiae str. PE	0.650	0.226	0.895	2e-30
312377105	251	hypothetical protein AND_11711 [Anophele	0.650	0.266	0.895	2e-30
237681208	280	cleavage and polyadenylation specific fa	0.650	0.239	0.880	2e-30
117935458	320	IP02511p [Drosophila melanogaster]	0.650	0.209	0.880	3e-30
847869	296	zinc finger protein [Drosophila melanoga	0.650	0.226	0.880	3e-30
390176610	282	GA17582 [Drosophila pseudoobscura pseudo	0.650	0.237	0.880	3e-30
17137188	296	clipper [Drosophila melanogaster] gi|729	0.650	0.226	0.880	3e-30

>gi|239792848|dbj|BAH72717.1| ACYPI007246 [Acyrthosiphon pisum]

 Score =  138 bits (347), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 63/87 (72%), Positives = 71/87 (81%), Gaps = 7/87 (8%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P+RH+ GDR+VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFY+RFNACHNKECPFLHI
Sbjct: 56  PMRHVRGDRTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYARFNACHNKECPFLHI 115

Query: 84  DPDSMIE-------ASVGMVHRVDTGM 103
           DP+S ++         V M H V+  M
Sbjct: 116 DPESKLKDCPWYDRGFVAMAHIVNINM 142

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242021708|ref|XP_002431285.1| Cleavage and polyadenylation specificity factor 30 kDa subunit, putative [Pediculus humanus corporis] gi|212516553|gb|EEB18547.1| Cleavage and polyadenylation specificity factor 30 kDa subunit, putative [Pediculus humanus corporis]

 Score =  137 bits (345), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 64/67 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 56  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 115

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 116 DPESKIK 122

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332373586|gb|AEE61934.1| unknown [Dendroctonus ponderosae]

 Score =  136 bits (343), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 64/67 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 57  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 116

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 117 DPESKIK 123

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347968471|ref|XP_003436228.1| AGAP013044-PA [Anopheles gambiae str. PEST] gi|333467988|gb|EGK96785.1| AGAP013044-PA [Anopheles gambiae str. PEST]

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 64/67 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 59  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 118

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 119 DPESKIK 125

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312377105|gb|EFR24020.1| hypothetical protein AND_11711 [Anopheles darlingi]

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 64/67 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 83  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 142

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 143 DPESKIK 149

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|237681208|ref|NP_001153741.1| cleavage and polyadenylation specific factor 4, 30kDa [Tribolium castaneum] gi|270004678|gb|EFA01126.1| hypothetical protein TcasGA2_TC010339 [Tribolium castaneum]

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 64/67 (95%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RH+ GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 57  PFRHVRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 116

Query: 84  DPDSMIE 90
           DP+S I+
Sbjct: 117 DPESKIK 123

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|117935458|gb|ABK57069.1| IP02511p [Drosophila melanogaster]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 82  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 141

Query: 84  DPDSMIE 90
           DP S ++
Sbjct: 142 DPQSKVK 148

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|847869|gb|AAA67954.1| zinc finger protein [Drosophila melanogaster]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 58  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 117

Query: 84  DPDSMIE 90
           DP S ++
Sbjct: 118 DPQSKVK 124

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390176610|ref|XP_001356742.2| GA17582 [Drosophila pseudoobscura pseudoobscura] gi|388858696|gb|EAL33807.2| GA17582 [Drosophila pseudoobscura pseudoobscura]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 58  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 117

Query: 84  DPDSMIE 90
           DP S ++
Sbjct: 118 DPQSKVK 124

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17137188|ref|NP_477156.1| clipper [Drosophila melanogaster] gi|7296160|gb|AAF51453.1| clipper [Drosophila melanogaster] gi|90855755|gb|ABE01239.1| IP02509p [Drosophila melanogaster] gi|220952324|gb|ACL88705.1| Clp-PA [synthetic construct] gi|220958742|gb|ACL91914.1| Clp-PA [synthetic construct]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 24  PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
           P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct: 58  PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 117

Query: 84  DPDSMIE 90
           DP S ++
Sbjct: 118 DPQSKVK 124

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	103
FB|FBgn0015621	296	Clp "Clipper" [Drosophila mela	0.650	0.226	0.880	2.5e-33
UNIPROTKB|E1BV31	243	CPSF4 "Uncharacterized protein	0.650	0.275	0.820	8.8e-31
UNIPROTKB|O19137	243	CPSF4 "Cleavage and polyadenyl	0.650	0.275	0.820	8.8e-31
UNIPROTKB|E2RBM0	164	CPSF4 "Uncharacterized protein	0.650	0.408	0.820	8.8e-31
UNIPROTKB|J9P398	269	CPSF4 "Uncharacterized protein	0.650	0.249	0.820	8.8e-31
UNIPROTKB|B7Z7B0	191	CPSF4 "Cleavage and polyadenyl	0.650	0.350	0.820	8.8e-31
UNIPROTKB|C9K0K2	112	CPSF4 "Cleavage and polyadenyl	0.650	0.598	0.820	8.8e-31
UNIPROTKB|H7C016	229	CPSF4 "Cleavage and polyadenyl	0.650	0.292	0.820	8.8e-31
UNIPROTKB|O95639	269	CPSF4 "Cleavage and polyadenyl	0.650	0.249	0.820	8.8e-31
UNIPROTKB|F1REX3	269	LOC100518830 "Uncharacterized	0.650	0.249	0.820	8.8e-31

FB|FBgn0015621 Clp "Clipper" [Drosophila melanogaster (taxid:7227)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI GDR++VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI
Sbjct:    58 PFRHIRGDRTIVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 117

Query:    84 DPDSMIE 90
             DP S ++
Sbjct:   118 DPQSKVK 124

GO:0004521 "endoribonuclease activity" evidence=IDA

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

GO:0006379 "mRNA cleavage" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|E1BV31 CPSF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    56 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   116 DPESKIK 122

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

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

UNIPROTKB|O19137 CPSF4 "Cleavage and polyadenylation specificity factor subunit 4" [Bos taurus (taxid:9913)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    56 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   116 DPESKIK 122

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

GO:0005739 "mitochondrion" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2RBM0 CPSF4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    54 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 113

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   114 DPESKIK 120

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J9P398 CPSF4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    56 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   116 DPESKIK 122

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|B7Z7B0 CPSF4 "Cleavage and polyadenylation-specificity factor subunit 4" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:     3 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 62

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:    63 DPESKIK 69

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|C9K0K2 CPSF4 "Cleavage and polyadenylation-specificity factor subunit 4" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:     3 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 62

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:    63 DPESKIK 69

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|H7C016 CPSF4 "Cleavage and polyadenylation-specificity factor subunit 4" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    23 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 82

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:    83 DPESKIK 89

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|O95639 CPSF4 "Cleavage and polyadenylation specificity factor subunit 4" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    56 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   116 DPESKIK 122

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0019048 "virus-host interaction" evidence=TAS

GO:0019054 "modulation by virus of host cellular process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0046778 "modification by virus of host mRNA processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|F1REX3 LOC100518830 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 55/67 (82%), Positives = 62/67 (92%)

Query:    24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI 83
             P RHI+G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHI
Sbjct:    56 PFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHI 115

Query:    84 DPDSMIE 90
             DP+S I+
Sbjct:   116 DPESKIK 122

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q06102	YTH1_YEAST	No assigned EC number	0.5362	0.6407	0.3173	yes	N/A
Q6FTL0	YTH1_CANGA	No assigned EC number	0.5507	0.6407	0.3157	yes	N/A
Q6C922	YTH1_YARLI	No assigned EC number	0.5652	0.6407	0.3419	yes	N/A
O95639	CPSF4_HUMAN	No assigned EC number	0.8208	0.6504	0.2490	yes	N/A
Q8BQZ5	CPSF4_MOUSE	No assigned EC number	0.8541	0.4660	0.2274	yes	N/A
Q758T3	YTH1_ASHGO	No assigned EC number	0.5285	0.6504	0.3205	yes	N/A
Q5FVR7	CPSF4_RAT	No assigned EC number	0.8208	0.6504	0.2757	yes	N/A
Q6CKU1	YTH1_KLULA	No assigned EC number	0.5142	0.6504	0.3190	yes	N/A
O19137	CPSF4_BOVIN	No assigned EC number	0.8208	0.6504	0.2757	yes	N/A
Q6BTT1	YTH1_DEBHA	No assigned EC number	0.5652	0.6407	0.2959	yes	N/A
Q66KE3	CPSF4_XENTR	No assigned EC number	0.8208	0.6504	0.2490	yes	N/A
Q9UTD1	YTH1_SCHPO	No assigned EC number	0.6206	0.5533	0.3352	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	103
COG5084	285	COG5084, YTH1, Cleavage and polyadenylation specif	1e-18
smart00356	27	smart00356, ZnF_C3H1, zinc finger	1e-04

>gnl|CDD|227416 COG5084, YTH1, Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

 Score = 78.0 bits (192), Expect = 1e-18
 Identities = 32/70 (45%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 21  VPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSRFNACHN-KE 77
            P    +     SVVCK +LRGLCK G  CEFLHEYD+     P C  +S   +C +   
Sbjct: 92  TPNNHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPS 151

Query: 78  CPFLHIDPDS 87
           C + HIDPDS
Sbjct: 152 CGYSHIDPDS 161

Length = 285

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

 Score = 36.1 bits (84), Expect = 1e-04
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEY 56
          ++ +CK + RG C +GD+C+F H  
Sbjct: 3  KTELCKFFKRGYCPRGDRCKFAHPL 27

Length = 27

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	103
KOG1492|consensus	377		99.59
KOG1040|consensus	325		99.58
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	98.94
KOG1492|consensus	377		98.81
KOG1040|consensus	325		98.66
KOG2494|consensus	331		98.41
smart00356	27	ZnF_C3H1 zinc finger.	98.24
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.22
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	98.16
KOG4791|consensus	667		98.14
KOG1677|consensus	332		98.04
KOG1763|consensus	343		97.92
KOG1595|consensus	528		97.39
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	97.23
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	97.23
KOG4791|consensus	667		97.2
smart00356	27	ZnF_C3H1 zinc finger.	97.0
KOG2185|consensus	486		96.7
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	96.55
PF10650	23	zf-C3H1: Putative zinc-finger domain; InterPro: IP	96.41
KOG2494|consensus	331		96.34
KOG2333|consensus	614		95.45
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	95.2
PF10650	23	zf-C3H1: Putative zinc-finger domain; InterPro: IP	95.01
KOG1039|consensus	344		94.77
KOG1677|consensus	332		94.11
KOG1595|consensus	528		94.08
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	93.15
KOG1039|consensus	344		92.73
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	91.49
COG5152	259	Uncharacterized conserved protein, contains RING a	90.66
KOG0153|consensus	377		90.49
KOG2185|consensus	486		90.31
KOG3702|consensus	681		90.31
KOG0153|consensus	377		80.97

>KOG1492|consensus

Probab=99.59  E-value=3.3e-16  Score=119.13  Aligned_cols=80  Identities=24%  Similarity=0.593  Sum_probs=75.1

Q ss_pred             CCCCCCCCCCCCCCCCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCCCCCCCCcCcHHH
Q psy4296          16 APGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGM   95 (103)
Q Consensus        16 ~~g~g~~C~f~H~~~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~~~~~~~~~C~~f   95 (103)
                      ..|+|.+|+|.|++ .+..+|..||+|.|.+.+.|.++|++++++.|.|+||+- |.|.+++|+|.|+.-++.+++|.+|
T Consensus       217 icgkgaacrfvhep-trkticpkflngrcnkaedcnlsheldprripacryfll-gkcnnpncryvhihysenapicfef  294 (377)
T KOG1492|consen  217 ICGKGAACRFVHEP-TRKTICPKFLNGRCNKAEDCNLSHELDPRRIPACRYFLL-GKCNNPNCRYVHIHYSENAPICFEF  294 (377)
T ss_pred             cccCCceeeeeccc-cccccChHHhcCccCchhcCCcccccCccccchhhhhhh-ccCCCCCceEEEEeecCCCceeeee
Confidence            35678999999996 789999999999999999999999999999999999998 9999999999999999999999988


Q ss_pred             Hh
Q psy4296          96 VH   97 (103)
Q Consensus        96 ~~   97 (103)
                      +.
T Consensus       295 ak  296 (377)
T KOG1492|consen  295 AK  296 (377)
T ss_pred             hh
Confidence            75

>KOG1040|consensus

Probab=99.58  E-value=1e-15  Score=120.13  Aligned_cols=83  Identities=53%  Similarity=0.959  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCCC---CCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCC-CCCCCCCCCCCCCCcCcH
Q psy4296          18 GVLVPFPLRHIT---GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHN-KECPFLHIDPDSMIEASV   93 (103)
Q Consensus        18 g~g~~C~f~H~~---~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~-~~C~y~H~~~~~~~~~C~   93 (103)
                      +++..|+.+|..   +++..||+|||+|.|++||.|.|+|++++.++++|.||...|.|++ .+|+|.|+.|++..++|.
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~vcK~~l~glC~kgD~C~Flhe~~~~k~rec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~  138 (325)
T KOG1040|consen   59 ERGPICPKSHNDVSDSRGKVVCKHWLRGLCKKGDQCEFLHEYDLTKMRECKFFSLFGECTNGKDCPYLHGDPQTAIKKCK  138 (325)
T ss_pred             cCCCCCccccCCccccCCceeehhhhhhhhhccCcCcchhhhhhcccccccccccccccccccCCcccCCChhhhhhccc
Confidence            345889999997   6789999999999999999999999999999999999999999999 699999999999999998


Q ss_pred             HHHhhhc
Q psy4296          94 GMVHRVD  100 (103)
Q Consensus        94 ~f~~~~~  100 (103)
                      .+..+..
T Consensus       139 ~~~~g~c  145 (325)
T KOG1040|consen  139 WYKEGFC  145 (325)
T ss_pred             hhhhccC
Confidence            7766654

>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

Probab=98.94  E-value=1.1e-09  Score=84.99  Aligned_cols=76  Identities=43%  Similarity=0.821  Sum_probs=68.5

Q ss_pred             CCCCCCCCC--CCCcccccccccCCCCCCCCCCCCccCCCCc--ccccccccccccCCC-CCCCCCCCCCCCCCcCcHHH
Q psy4296          21 VPFPLRHIT--GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSRFNACHN-KECPFLHIDPDSMIEASVGM   95 (103)
Q Consensus        21 ~~C~f~H~~--~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~--~p~C~~f~~~G~C~~-~~C~y~H~~~~~~~~~C~~f   95 (103)
                      .++++.|..  ..+..+|++|+.|.|..+..|.|+|+++..+  ++.|++|...|.|+. ..|.|.|+.|+.....|..+
T Consensus        90 ~s~~~~~~~~~~~s~V~c~~~~~g~c~s~~~c~~lh~~d~~~s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~~~~~~~~~  169 (285)
T COG5084          90 LSTPNNHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQY  169 (285)
T ss_pred             ccCCccccCccccCCcccchhccccCcCCCccccccCCCcccccCCCcccccccceeccCCCCCccccCccccccccccc
Confidence            478999986  3688899999999999999999999999888  999999955599999 49999999999999999877


Q ss_pred             H
Q psy4296          96 V   96 (103)
Q Consensus        96 ~   96 (103)
                      .
T Consensus       170 ~  170 (285)
T COG5084         170 S  170 (285)
T ss_pred             C
Confidence            6

>KOG1492|consensus

Probab=98.81  E-value=2e-09  Score=82.21  Aligned_cols=68  Identities=24%  Similarity=0.498  Sum_probs=60.8

Q ss_pred             CCCCC---CCCCCCCCC-CCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCC-CCCCCCCC
Q psy4296          16 APGVL---VPFPLRHIT-GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNK-ECPFLHID   84 (103)
Q Consensus        16 ~~g~g---~~C~f~H~~-~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~-~C~y~H~~   84 (103)
                      ..|++   +.|.++|+- +++.+.|||||.|.|.+. +|+|.|.--.++.|+|.-|.++|+|..+ .|.-.|+.
T Consensus       240 lngrcnkaedcnlsheldprripacryfllgkcnnp-ncryvhihysenapicfefakygfcelgtscknqhil  312 (377)
T KOG1492|consen  240 LNGRCNKAEDCNLSHELDPRRIPACRYFLLGKCNNP-NCRYVHIHYSENAPICFEFAKYGFCELGTSCKNQHIL  312 (377)
T ss_pred             hcCccCchhcCCcccccCccccchhhhhhhccCCCC-CceEEEEeecCCCceeeeehhcceeccccccccceee
Confidence            45555   899999995 689999999999999986 7999999888999999999999999996 99999974

>KOG1040|consensus

Probab=98.66  E-value=1.4e-08  Score=80.05  Aligned_cols=82  Identities=20%  Similarity=0.347  Sum_probs=67.0

Q ss_pred             CcCCCCC---CCCCCCCCCC-CCcccccccc-cCCCCCCCCCCCCccCCCCcccccccccccccCCC-CCCCCCCCCCCC
Q psy4296          14 FQAPGVL---VPFPLRHITG-DRSVVCKHWL-RGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHN-KECPFLHIDPDS   87 (103)
Q Consensus        14 f~~~g~g---~~C~f~H~~~-~~~~vC~~fl-~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~-~~C~y~H~~~~~   87 (103)
                      |+..|.+   +.|.|+|+.. .+.+.|.||. .|.|.++.+|+|.|....+....|.+|.+ |.|.. +.|++.|+..  
T Consensus        82 ~~l~glC~kgD~C~Flhe~~~~k~rec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~~~~~-g~c~~g~~c~~~h~~~--  158 (325)
T KOG1040|consen   82 HWLRGLCKKGDQCEFLHEYDLTKMRECKFFSLFGECTNGKDCPYLHGDPQTAIKKCKWYKE-GFCRGGPSCKKRHERK--  158 (325)
T ss_pred             hhhhhhhhccCcCcchhhhhhcccccccccccccccccccCCcccCCChhhhhhccchhhh-ccCCCcchhhhhhhcc--
Confidence            6666664   9999999863 4677886666 59999999999999876677888999999 99999 4999999976  


Q ss_pred             CCcCcHHHHhhhc
Q psy4296          88 MIEASVGMVHRVD  100 (103)
Q Consensus        88 ~~~~C~~f~~~~~  100 (103)
                        ..|...+.++.
T Consensus       159 --~~c~~y~~gfC  169 (325)
T KOG1040|consen  159 --VLCPPYNAGFC  169 (325)
T ss_pred             --cCCCchhhhhc
Confidence              57777766654

>KOG2494|consensus

Probab=98.41  E-value=8.8e-08  Score=75.33  Aligned_cols=55  Identities=27%  Similarity=0.716  Sum_probs=46.0

Q ss_pred             CCcccccccccCCCCCCCC-CCCCccCCCC-----cccccccccccccCCCCCCCCCCCCCC
Q psy4296          31 DRSVVCKHWLRGLCKKGDQ-CEFLHEYDMT-----KMPECYFYSRFNACHNKECPFLHIDPD   86 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~-C~f~H~~~~~-----~~p~C~~f~~~G~C~~~~C~y~H~~~~   86 (103)
                      ....|||-||+|.|.+||. |.|.|....-     +...|..+++ |.|++++|+|.|-...
T Consensus        35 l~~eVCReF~rn~C~R~d~~CkfaHP~~~~~V~~g~v~aC~Ds~k-grCsR~nCkylHpp~h   95 (331)
T KOG2494|consen   35 LTLEVCREFLRNTCSRGDRECKFAHPPKNCQVSNGRVIACFDSQK-GRCSRENCKYLHPPQH   95 (331)
T ss_pred             hHHHHHHHHHhccccCCCccccccCCCCCCCccCCeEEEEecccc-CccCcccceecCCChh
Confidence            3677999999999999997 9999975432     2455999999 9999999999997543

>smart00356 ZnF_C3H1 zinc finger

Probab=98.24  E-value=7.8e-07  Score=45.24  Aligned_cols=24  Identities=42%  Similarity=1.070  Sum_probs=21.6

Q ss_pred             CcccccccccCCCCCCCCCCCCcc
Q psy4296          32 RSVVCKHWLRGLCKKGDQCEFLHE   55 (103)
Q Consensus        32 ~~~vC~~fl~G~C~~Gd~C~f~H~   55 (103)
                      +..+|++|++|.|.+|++|+|+|+
T Consensus         3 k~~~C~~~~~g~C~~g~~C~~~H~   26 (27)
T smart00356        3 KTELCKFFKRGYCPYGDRCKFAHP   26 (27)
T ss_pred             CCCcCcCccCCCCCCCCCcCCCCc
Confidence            567899999999999999999996

>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=98.22  E-value=2.1e-07  Score=48.34  Aligned_cols=24  Identities=38%  Similarity=1.083  Sum_probs=18.8

Q ss_pred             Cccccccccc-CCCCCCCCCCCCcc
Q psy4296          32 RSVVCKHWLR-GLCKKGDQCEFLHE   55 (103)
Q Consensus        32 ~~~vC~~fl~-G~C~~Gd~C~f~H~   55 (103)
                      ++++|++|++ |.|..|++|.|+|+
T Consensus         2 k~~~C~~f~~~g~C~~G~~C~f~H~   26 (27)
T PF00642_consen    2 KTKLCRFFMRTGTCPFGDKCRFAHG   26 (27)
T ss_dssp             TSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred             ccccChhhccCCccCCCCCcCccCC
Confidence            5789999998 99999999999996

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 ....

>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

Probab=98.16  E-value=2.6e-06  Score=66.20  Aligned_cols=73  Identities=23%  Similarity=0.464  Sum_probs=62.6

Q ss_pred             CCcCCCCC---CCCCCCCCCC-CC--ccccccc-ccCCCCCCCCCCCCccCCCCcccccccccc--cccCCCC-CCCCCC
Q psy4296          13 SFQAPGVL---VPFPLRHITG-DR--SVVCKHW-LRGLCKKGDQCEFLHEYDMTKMPECYFYSR--FNACHNK-ECPFLH   82 (103)
Q Consensus        13 ~f~~~g~g---~~C~f~H~~~-~~--~~vC~~f-l~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~--~G~C~~~-~C~y~H   82 (103)
                      +|+..|++   ..|.|.|+.. .+  ...|++| +.|.|..|..|.++|....+..++|.+|.+  .+.|.++ .|++.|
T Consensus       108 ~~~~~g~c~s~~~c~~lh~~d~~~s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~~~~~~~~~~~~~~~f~p~g~~c~~~H  187 (285)
T COG5084         108 KFFLRGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQYSGATYGFCPLGASCKFSH  187 (285)
T ss_pred             chhccccCcCCCccccccCCCcccccCCCcccccccceeccCCCCCccccCcccccccccccCcccccccCCCCcccccc
Confidence            36666765   8999999973 34  7889999 889999999999999988888999999994  5999996 999999


Q ss_pred             CCC
Q psy4296          83 IDP   85 (103)
Q Consensus        83 ~~~   85 (103)
                      +.-
T Consensus       188 ~~~  190 (285)
T COG5084         188 TLK  190 (285)
T ss_pred             ccc
Confidence            964

>KOG4791|consensus

Probab=98.14  E-value=8.4e-07  Score=73.31  Aligned_cols=68  Identities=26%  Similarity=0.554  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCCC--CCcccccccccCCCCCCCCCCCCccCCCCc--ccccccccccccCCCCCCCCCCCCC
Q psy4296          17 PGVLVPFPLRHITG--DRSVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSRFNACHNKECPFLHIDP   85 (103)
Q Consensus        17 ~g~g~~C~f~H~~~--~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~--~p~C~~f~~~G~C~~~~C~y~H~~~   85 (103)
                      .-+++.|+|+|...  ....+|++|+.+.|-+. .|+|+|.--..+  -..|.|+.++..|.+.+|-|+|..|
T Consensus        14 cKk~d~c~~rh~E~al~n~t~C~~w~~~~~C~k-~C~YRHSe~~~kr~e~~CYwe~~p~gC~k~~CgfRH~~p   85 (667)
T KOG4791|consen   14 CKKGDSCPFRHCEAALGNETVCTLWQEGRCCRK-VCRYRHSEIDKKRSEIPCYWENQPTGCQKLNCGFRHNRP   85 (667)
T ss_pred             hhccCcCcchhhHHHhcCcchhhhhhhcCcccc-cccchhhHHhhhcCcccceeecCCCccCCCccccccCCC
Confidence            34469999999963  57789999999875543 699999754433  3349999984459999999999764

>KOG1677|consensus

Probab=98.04  E-value=3.5e-06  Score=65.25  Aligned_cols=55  Identities=27%  Similarity=0.777  Sum_probs=46.8

Q ss_pred             Cccccccccc-CCCCC-CCCCCCCccCCCCc---------------ccccccccccccCCCC-CCCCCCCCCC
Q psy4296          32 RSVVCKHWLR-GLCKK-GDQCEFLHEYDMTK---------------MPECYFYSRFNACHNK-ECPFLHIDPD   86 (103)
Q Consensus        32 ~~~vC~~fl~-G~C~~-Gd~C~f~H~~~~~~---------------~p~C~~f~~~G~C~~~-~C~y~H~~~~   86 (103)
                      ++++|++|.+ |.|.+ |++|.|.|.....+               ..+|.+|+++|.|..| +|.|.|..++
T Consensus       131 kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~  203 (332)
T KOG1677|consen  131 KTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPSSENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPE  203 (332)
T ss_pred             cCCcceeeecCccccccCchhhhcCCcccccccccchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcc
Confidence            6778999997 99999 99999998755332               4569999999999996 9999998763

>KOG1763|consensus

Probab=97.92  E-value=2e-06  Score=67.34  Aligned_cols=57  Identities=33%  Similarity=0.841  Sum_probs=45.7

Q ss_pred             CCcccccccccCCCCCCCCCCCCccCCCCc------------------------------------ccccccccc-----
Q psy4296          31 DRSVVCKHWLRGLCKKGDQCEFLHEYDMTK------------------------------------MPECYFYSR-----   69 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~------------------------------------~p~C~~f~~-----   69 (103)
                      .+..+|-||.+|.|.+|+.|.|||++...+                                    ..||+||+.     
T Consensus        90 PKSvvCafFk~g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeAvE~~  169 (343)
T KOG1763|consen   90 PKSVVCAFFKQGTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEAVENG  169 (343)
T ss_pred             chHHHHHHHhccCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHHHhcC
Confidence            478899999999999999999999866321                                    127999964     


Q ss_pred             -cc---cCCCC--CCCCCCCCCCC
Q psy4296          70 -FN---ACHNK--ECPFLHIDPDS   87 (103)
Q Consensus        70 -~G---~C~~~--~C~y~H~~~~~   87 (103)
                       +|   .|.+|  .|.|+|..|.-
T Consensus       170 kYGWfW~CPnGg~~C~YrHaLP~G  193 (343)
T KOG1763|consen  170 KYGWFWECPNGGDKCIYRHALPEG  193 (343)
T ss_pred             CccceeECCCCCCeeeeeecCCcc
Confidence             34   49996  69999998863

>KOG1595|consensus

Probab=97.39  E-value=0.00013  Score=60.65  Aligned_cols=64  Identities=25%  Similarity=0.516  Sum_probs=48.3

Q ss_pred             CCCCCCCCCC-C----------CCcccccccccCCCCCCCCCCCCccCCCC-------cccccccccccccCCCCCCCCC
Q psy4296          20 LVPFPLRHIT-G----------DRSVVCKHWLRGLCKKGDQCEFLHEYDMT-------KMPECYFYSRFNACHNKECPFL   81 (103)
Q Consensus        20 g~~C~f~H~~-~----------~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~-------~~p~C~~f~~~G~C~~~~C~y~   81 (103)
                      +..|||.|.. +          .+-..|.-|-+|.|.+||+|.|.|..-..       ++..|+--   |.|.+.-|-|.
T Consensus       212 wteCPf~HpgEkARRRDPRkyhYs~tpCPefrkG~C~rGD~CEyaHgvfEcwLHPa~YRT~~CkDg---~~C~RrvCfFA  288 (528)
T KOG1595|consen  212 WTECPFAHPGEKARRRDPRKYHYSSTPCPEFRKGSCERGDSCEYAHGVFECWLHPARYRTRKCKDG---GYCPRRVCFFA  288 (528)
T ss_pred             cccCCccCCCcccccCCcccccccCccCcccccCCCCCCCccccccceehhhcCHHHhccccccCC---CCCccceEeee
Confidence            4899999942 1          25668999999999999999999974321       23446655   67888899999


Q ss_pred             CCCCC
Q psy4296          82 HIDPD   86 (103)
Q Consensus        82 H~~~~   86 (103)
                      |+..+
T Consensus       289 H~~eq  293 (528)
T KOG1595|consen  289 HSPEQ  293 (528)
T ss_pred             cChHH
Confidence            98543

>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=97.23  E-value=6.2e-05  Score=38.91  Aligned_cols=24  Identities=33%  Similarity=0.672  Sum_probs=18.2

Q ss_pred             cccccccccccccCCCC-CCCCCCC
Q psy4296          60 KMPECYFYSRFNACHNK-ECPFLHI   83 (103)
Q Consensus        60 ~~p~C~~f~~~G~C~~~-~C~y~H~   83 (103)
                      ++++|++|++.|.|..+ +|+|.|.
T Consensus         2 k~~~C~~f~~~g~C~~G~~C~f~H~   26 (27)
T PF00642_consen    2 KTKLCRFFMRTGTCPFGDKCRFAHG   26 (27)
T ss_dssp             TSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred             ccccChhhccCCccCCCCCcCccCC
Confidence            35689999999999995 9999996

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 ....

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

Probab=97.23  E-value=0.0002  Score=34.31  Aligned_cols=18  Identities=44%  Similarity=0.982  Sum_probs=11.7

Q ss_pred             cccccccCCCCCCCCCCCCc
Q psy4296          35 VCKHWLRGLCKKGDQCEFLH   54 (103)
Q Consensus        35 vC~~fl~G~C~~Gd~C~f~H   54 (103)
                      +|+||..  |+++++|+|+|
T Consensus         1 ~Ck~~~~--C~~~~~C~f~H   18 (19)
T PF14608_consen    1 PCKFGPN--CTNGDNCPFSH   18 (19)
T ss_pred             CCcCcCC--CCCCCcCccCC
Confidence            3666654  77776677776

>KOG4791|consensus

Probab=97.20  E-value=8.2e-05  Score=61.80  Aligned_cols=51  Identities=27%  Similarity=0.630  Sum_probs=42.9

Q ss_pred             cccccccccCCCCCCCCCCCCccCCCC-cccccccccccccCCCCCCCCCCCC
Q psy4296          33 SVVCKHWLRGLCKKGDQCEFLHEYDMT-KMPECYFYSRFNACHNKECPFLHID   84 (103)
Q Consensus        33 ~~vC~~fl~G~C~~Gd~C~f~H~~~~~-~~p~C~~f~~~G~C~~~~C~y~H~~   84 (103)
                      ...|.||+...|+++|.|+|+|.-+.. +..+|++|+. +.|-+..|+|+|..
T Consensus         3 ~~dcyff~ys~cKk~d~c~~rh~E~al~n~t~C~~w~~-~~~C~k~C~YRHSe   54 (667)
T KOG4791|consen    3 GEDCYFFFYSTCKKGDSCPFRHCEAALGNETVCTLWQE-GRCCRKVCRYRHSE   54 (667)
T ss_pred             cccchhhhhhhhhccCcCcchhhHHHhcCcchhhhhhh-cCcccccccchhhH
Confidence            457999999999999999999986643 4677999999 66666699999974

>smart00356 ZnF_C3H1 zinc finger

Probab=97.00  E-value=0.00065  Score=34.14  Aligned_cols=23  Identities=35%  Similarity=0.756  Sum_probs=19.3

Q ss_pred             cccccccccccccCCCC-CCCCCCC
Q psy4296          60 KMPECYFYSRFNACHNK-ECPFLHI   83 (103)
Q Consensus        60 ~~p~C~~f~~~G~C~~~-~C~y~H~   83 (103)
                      +.++|++|.. |.|..+ +|+|+|.
T Consensus         3 k~~~C~~~~~-g~C~~g~~C~~~H~   26 (27)
T smart00356        3 KTELCKFFKR-GYCPYGDRCKFAHP   26 (27)
T ss_pred             CCCcCcCccC-CCCCCCCCcCCCCc
Confidence            4567999965 999995 9999996

>KOG2185|consensus

Probab=96.70  E-value=0.00067  Score=55.37  Aligned_cols=26  Identities=38%  Similarity=0.890  Sum_probs=20.4

Q ss_pred             CcccccccccCCCCCCCCCCCCccCC
Q psy4296          32 RSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        32 ~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      .+.+|.|||.|.|+-+.+|+|||.+.
T Consensus       139 sMkpC~ffLeg~CRF~enCRfSHG~~  164 (486)
T KOG2185|consen  139 SMKPCKFFLEGRCRFGENCRFSHGLD  164 (486)
T ss_pred             hhccchHhhccccccCcccccccCcc
Confidence            45678888888888888888888755

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

Probab=96.55  E-value=0.0004  Score=53.33  Aligned_cols=56  Identities=34%  Similarity=0.844  Sum_probs=44.1

Q ss_pred             CCcccccccccCCCCCCCCCCCCccCCCCc----------------------------ccccccccc------cc---cC
Q psy4296          31 DRSVVCKHWLRGLCKKGDQCEFLHEYDMTK----------------------------MPECYFYSR------FN---AC   73 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~----------------------------~p~C~~f~~------~G---~C   73 (103)
                      .++.+|-.|+++.|.+|+.|.|+|.....+                            -.||+||+.      +|   .|
T Consensus        83 pK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~C  162 (299)
T COG5252          83 PKTVVCALFLNKTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWTC  162 (299)
T ss_pred             chhHHHHHhccCccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceeeC
Confidence            477899999999999999999999843210                            236999954      23   49


Q ss_pred             CCC--CCCCCCCCCC
Q psy4296          74 HNK--ECPFLHIDPD   86 (103)
Q Consensus        74 ~~~--~C~y~H~~~~   86 (103)
                      .++  .|.|.|..|.
T Consensus       163 Png~~~C~y~H~Lp~  177 (299)
T COG5252         163 PNGNMRCSYIHKLPD  177 (299)
T ss_pred             CCCCceeeeeeccCc
Confidence            996  9999999876

>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger

Probab=96.41  E-value=0.0021  Score=32.38  Aligned_cols=21  Identities=24%  Similarity=0.657  Sum_probs=13.2

Q ss_pred             ccccccccccCCCCCCCCCCC
Q psy4296          63 ECYFYSRFNACHNKECPFLHI   83 (103)
Q Consensus        63 ~C~~f~~~G~C~~~~C~y~H~   83 (103)
                      .|.|.++.|.|.+++|.|.|.
T Consensus         2 lC~yEl~Gg~Cnd~~C~~QHf   22 (23)
T PF10650_consen    2 LCPYELTGGVCNDPDCEFQHF   22 (23)
T ss_pred             CCccccCCCeeCCCCCCcccc
Confidence            466666633666666666664

>KOG2494|consensus

Probab=96.34  E-value=0.0039  Score=49.48  Aligned_cols=43  Identities=19%  Similarity=0.405  Sum_probs=32.9

Q ss_pred             cCCCCC---CC-CCCCCCCC------CCcccccccccCCCCCCCCCCCCccCCC
Q psy4296          15 QAPGVL---VP-FPLRHITG------DRSVVCKHWLRGLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        15 ~~~g~g---~~-C~f~H~~~------~~~~vC~~fl~G~C~~Gd~C~f~H~~~~   58 (103)
                      |++|.|   +. |+|.|-+.      .+...|-.|++|.|.+ ++|+|.|....
T Consensus        43 F~rn~C~R~d~~CkfaHP~~~~~V~~g~v~aC~Ds~kgrCsR-~nCkylHpp~h   95 (331)
T KOG2494|consen   43 FLRNTCSRGDRECKFAHPPKNCQVSNGRVIACFDSQKGRCSR-ENCKYLHPPQH   95 (331)
T ss_pred             HHhccccCCCccccccCCCCCCCccCCeEEEEeccccCccCc-ccceecCCChh
Confidence            345554   45 99999963      3566799999999999 47999998553

>KOG2333|consensus

Probab=95.45  E-value=0.0074  Score=50.58  Aligned_cols=51  Identities=31%  Similarity=0.802  Sum_probs=42.2

Q ss_pred             cccccccccC---CCCCCCCCCCCccCCC---Cc----ccccccccccccCCCC-CCCCCCC
Q psy4296          33 SVVCKHWLRG---LCKKGDQCEFLHEYDM---TK----MPECYFYSRFNACHNK-ECPFLHI   83 (103)
Q Consensus        33 ~~vC~~fl~G---~C~~Gd~C~f~H~~~~---~~----~p~C~~f~~~G~C~~~-~C~y~H~   83 (103)
                      ..+|.-.++|   .|..||+|+|.|+.+.   .+    -|.|.+|.+.|.|..+ .|+|+=.
T Consensus        76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Dig~~Cp~f~s~G~Cp~G~~CRFl~a  137 (614)
T KOG2333|consen   76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDIGPSCPVFESLGFCPYGFKCRFLGA  137 (614)
T ss_pred             hccChHhhcCCCccCcccccccccccHHHHHhccCcccCCccceeeccccCCccceeehhhc
Confidence            5689888887   6999999999999763   11    4679999999999998 9999744

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

Probab=95.20  E-value=0.014  Score=27.79  Aligned_cols=17  Identities=47%  Similarity=1.112  Sum_probs=14.4

Q ss_pred             ccccccccccCCCC-CCCCCC
Q psy4296          63 ECYFYSRFNACHNK-ECPFLH   82 (103)
Q Consensus        63 ~C~~f~~~G~C~~~-~C~y~H   82 (103)
                      +|+||.   .|+++ +|+|.|
T Consensus         1 ~Ck~~~---~C~~~~~C~f~H   18 (19)
T PF14608_consen    1 PCKFGP---NCTNGDNCPFSH   18 (19)
T ss_pred             CCcCcC---CCCCCCcCccCC
Confidence            488885   49997 999999

>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger

Probab=95.01  E-value=0.013  Score=29.42  Aligned_cols=21  Identities=38%  Similarity=0.814  Sum_probs=17.7

Q ss_pred             ccccccccC-CCCCCCCCCCCcc
Q psy4296          34 VVCKHWLRG-LCKKGDQCEFLHE   55 (103)
Q Consensus        34 ~vC~~fl~G-~C~~Gd~C~f~H~   55 (103)
                      ++|.|-+.| .|... +|.|.|-
T Consensus         1 ~lC~yEl~Gg~Cnd~-~C~~QHf   22 (23)
T PF10650_consen    1 PLCPYELTGGVCNDP-DCEFQHF   22 (23)
T ss_pred             CCCccccCCCeeCCC-CCCcccc
Confidence            479999998 99875 6999994

>KOG1039|consensus

Probab=94.77  E-value=0.012  Score=47.03  Aligned_cols=25  Identities=36%  Similarity=0.797  Sum_probs=23.3

Q ss_pred             ccccccccCCCCCCCCCCCCccCCC
Q psy4296          34 VVCKHWLRGLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        34 ~vC~~fl~G~C~~Gd~C~f~H~~~~   58 (103)
                      .||+||++|.|..|+.|+|+|....
T Consensus         9 tic~~~~~g~c~~g~~cr~~h~~~~   33 (344)
T KOG1039|consen    9 TICKYYQKGNCKFGDLCRLSHSLPD   33 (344)
T ss_pred             hhhhhcccccccccceeeeeccCch
Confidence            8999999999999999999998773

>KOG1677|consensus

Probab=94.11  E-value=0.03  Score=43.33  Aligned_cols=39  Identities=26%  Similarity=0.544  Sum_probs=31.1

Q ss_pred             CCCCCCCCCCCC----------------CCccccccccc-CCCCCCCCCCCCccCC
Q psy4296          19 VLVPFPLRHITG----------------DRSVVCKHWLR-GLCKKGDQCEFLHEYD   57 (103)
Q Consensus        19 ~g~~C~f~H~~~----------------~~~~vC~~fl~-G~C~~Gd~C~f~H~~~   57 (103)
                      .|+.|.|-|...                .++++|.+|++ |.|.+|..|.|.|...
T Consensus       147 ~ge~crfah~~~e~r~~~~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~  202 (332)
T KOG1677|consen  147 RGEQCRFAHGLEELRLPSSENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEP  202 (332)
T ss_pred             cCchhhhcCCcccccccccchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCc
Confidence            356787766531                36789999997 9999999999999865

>KOG1595|consensus

Probab=94.08  E-value=0.055  Score=45.44  Aligned_cols=49  Identities=18%  Similarity=0.461  Sum_probs=37.7

Q ss_pred             CcccccccccCCCCCCCCCCCCccCC-CCc---------ccccccccccccCCCC-CCCCCCCC
Q psy4296          32 RSVVCKHWLRGLCKKGDQCEFLHEYD-MTK---------MPECYFYSRFNACHNK-ECPFLHID   84 (103)
Q Consensus        32 ~~~vC~~fl~G~C~~Gd~C~f~H~~~-~~~---------~p~C~~f~~~G~C~~~-~C~y~H~~   84 (103)
                      |+.-|.   ++.|..+-.|||.|.-. +++         -.+|.-|.+ |.|.+| .|-|.|..
T Consensus       200 Kir~C~---R~~shDwteCPf~HpgEkARRRDPRkyhYs~tpCPefrk-G~C~rGD~CEyaHgv  259 (528)
T KOG1595|consen  200 KIRRCS---RPRSHDWTECPFAHPGEKARRRDPRKYHYSSTPCPEFRK-GSCERGDSCEYAHGV  259 (528)
T ss_pred             eecccC---CccCCCcccCCccCCCcccccCCcccccccCccCccccc-CCCCCCCccccccce
Confidence            666675   45888898999999332 222         345999999 999995 99999974

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=93.15  E-value=0.076  Score=42.20  Aligned_cols=51  Identities=27%  Similarity=0.649  Sum_probs=37.5

Q ss_pred             ccccccc-cCCCCC---CCCCCCC---ccCCCCc---------ccccccccccccCCCC-CCCCCCCC
Q psy4296          34 VVCKHWL-RGLCKK---GDQCEFL---HEYDMTK---------MPECYFYSRFNACHNK-ECPFLHID   84 (103)
Q Consensus        34 ~vC~~fl-~G~C~~---Gd~C~f~---H~~~~~~---------~p~C~~f~~~G~C~~~-~C~y~H~~   84 (103)
                      .+|.-|- .|.|..   |+.|.|+   |.++..+         +.+|..|.+.|.|..+ +|.|.|..
T Consensus       231 ~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd  298 (351)
T COG5063         231 ELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGD  298 (351)
T ss_pred             HHhhccCcCCCCccccccccccccccccccccccccccccccccCCccchhhcccCccccccccccCC
Confidence            5785554 588888   8888888   8755322         4568888888888886 88888864

>KOG1039|consensus

Probab=92.73  E-value=0.046  Score=43.76  Aligned_cols=32  Identities=25%  Similarity=0.665  Sum_probs=27.3

Q ss_pred             ccCCCCcccccccccccccCCCC-CCCCCCCCCC
Q psy4296          54 HEYDMTKMPECYFYSRFNACHNK-ECPFLHIDPD   86 (103)
Q Consensus        54 H~~~~~~~p~C~~f~~~G~C~~~-~C~y~H~~~~   86 (103)
                      |++..+...+|+||++ |.|..+ .|+|.|+.|.
T Consensus         1 ~d~~~~~~tic~~~~~-g~c~~g~~cr~~h~~~~   33 (344)
T KOG1039|consen    1 HDLSLSQETICKYYQK-GNCKFGDLCRLSHSLPD   33 (344)
T ss_pred             Cccccccchhhhhccc-ccccccceeeeeccCch
Confidence            5666666688999999 999995 9999999985

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=91.49  E-value=0.31  Score=38.79  Aligned_cols=56  Identities=21%  Similarity=0.292  Sum_probs=43.8

Q ss_pred             CCccccccccc-CCCCCCCCCCCCccCCCCc-----------ccccccccccccCCC-CCCCCCCCCCC
Q psy4296          31 DRSVVCKHWLR-GLCKKGDQCEFLHEYDMTK-----------MPECYFYSRFNACHN-KECPFLHIDPD   86 (103)
Q Consensus        31 ~~~~vC~~fl~-G~C~~Gd~C~f~H~~~~~~-----------~p~C~~f~~~G~C~~-~~C~y~H~~~~   86 (103)
                      -+++.|.-|.. |.|..|..|.|.|......           -.+|+-++.+|.|.. ++|.++|..-.
T Consensus       272 frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~~~~~~~~y~~~~crt~~~~g~~p~g~~~c~~~dkkn  340 (351)
T COG5063         272 FRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPSGGAVCKSFDKKN  340 (351)
T ss_pred             cccCCccchhhcccCccccccccccCChhhccccccccccccccccccccccCccCCCCchhhccccch
Confidence            37789999986 9999999999999744211           235998988888988 48999987543

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

Probab=90.66  E-value=0.092  Score=39.71  Aligned_cols=27  Identities=41%  Similarity=0.910  Sum_probs=22.6

Q ss_pred             Ccccccccc-cCCCCCCCCCCCCccCCC
Q psy4296          32 RSVVCKHWL-RGLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        32 ~~~vC~~fl-~G~C~~Gd~C~f~H~~~~   58 (103)
                      ...||+-|. .|.|-+||+|.|+|+.++
T Consensus       140 qpdVCKdyk~TGYCGYGDsCKflH~R~D  167 (259)
T COG5152         140 QPDVCKDYKETGYCGYGDSCKFLHDRSD  167 (259)
T ss_pred             CcccccchhhcccccCCchhhhhhhhhh
Confidence            556897776 599999999999999773

>KOG0153|consensus

Probab=90.49  E-value=0.13  Score=41.38  Aligned_cols=27  Identities=33%  Similarity=0.961  Sum_probs=24.1

Q ss_pred             CCcccccccccCCCCCCCCCCCCccCC
Q psy4296          31 DRSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      .+..||-||..|.|++|++|+|.|+..
T Consensus       159 n~p~Icsf~v~geckRG~ec~yrhEkp  185 (377)
T KOG0153|consen  159 NRPHICSFFVKGECKRGAECPYRHEKP  185 (377)
T ss_pred             CCCccccceeeccccccccccccccCC
Confidence            356689999999999999999999966

>KOG2185|consensus

Probab=90.31  E-value=0.12  Score=42.48  Aligned_cols=61  Identities=21%  Similarity=0.316  Sum_probs=36.1

Q ss_pred             CCCCCCCCCCCCCccccccccc--CC-CCCCCCCCCCccCCCCcccccccccccccCCC-CCCCCCCCC
Q psy4296          20 LVPFPLRHITGDRSVVCKHWLR--GL-CKKGDQCEFLHEYDMTKMPECYFYSRFNACHN-KECPFLHID   84 (103)
Q Consensus        20 g~~C~f~H~~~~~~~vC~~fl~--G~-C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~-~~C~y~H~~   84 (103)
                      |..|.+.|+....  +|-|-..  |. =..+..=.|+|.. -+.|.+|.||+. |.|.. .+|+|+|-.
T Consensus        99 GsKcsaph~ss~g--l~yHna~I~g~E~sarvRVlfl~PT-h~sMkpC~ffLe-g~CRF~enCRfSHG~  163 (486)
T KOG2185|consen   99 GSKCSAPHTSSRG--LYYHNARIIGFEGSARVRVLFLTPT-HESMKPCKFFLE-GRCRFGENCRFSHGL  163 (486)
T ss_pred             CCcccccccCCcc--ceecceeEEeeccccceEEEeecCc-chhhccchHhhc-cccccCcccccccCc
Confidence            5678888875322  2211110  10 0122234566642 334777999999 99999 499999974

>KOG3702|consensus

Probab=90.31  E-value=0.55  Score=40.58  Aligned_cols=74  Identities=20%  Similarity=0.425  Sum_probs=39.6

Q ss_pred             cccCCCCcCCCCCCCCCCCCCCCC----C------cccccccccC-----CCCCCCCCCCCccCCCC-----c-------
Q psy4296           8 IIQDPSFQAPGVLVPFPLRHITGD----R------SVVCKHWLRG-----LCKKGDQCEFLHEYDMT-----K-------   60 (103)
Q Consensus         8 ~~~~p~f~~~g~g~~C~f~H~~~~----~------~~vC~~fl~G-----~C~~Gd~C~f~H~~~~~-----~-------   60 (103)
                      ++.+|++..+-..+.|.|-|....    .      ...|.+-+-|     .|.+-| |.|+|....-     .       
T Consensus       543 ~l~~Cky~~~Ct~a~Ce~~HPtaa~~~~s~p~k~fa~~~~ks~p~Ck~~~kCtasD-C~~sH~~~~~pvq~t~ip~~~~~  621 (681)
T KOG3702|consen  543 ILTRCKYGPACTSAECEFAHPTAAENAKSLPNKKFASKCLKSHPGCKFGKKCTASD-CNYSHAGRRIPVQPTRIPPPFPG  621 (681)
T ss_pred             eeccccCCCcCCchhhhhcCCcchhhhhccccccccccceeccccccccccccccc-CcccccCCCCCCccccCCCCCCC
Confidence            455666665555677777776521    1      1122222221     366554 7777754331     0       


Q ss_pred             ---ccccccccccccCCCCCCCCCCCCC
Q psy4296          61 ---MPECYFYSRFNACHNKECPFLHIDP   85 (103)
Q Consensus        61 ---~p~C~~f~~~G~C~~~~C~y~H~~~   85 (103)
                         +..|+|+   +.|.+..|+|.|-..
T Consensus       622 ~ti~~~CrY~---pnCrnm~C~F~HPk~  646 (681)
T KOG3702|consen  622 GTIRGLCRYR---PNCRNMQCKFYHPKT  646 (681)
T ss_pred             CCccccceec---cCcCCccccccCCcc
Confidence               1237776   567777777777543

>KOG0153|consensus

Probab=80.97  E-value=1  Score=36.47  Aligned_cols=25  Identities=32%  Similarity=0.869  Sum_probs=21.7

Q ss_pred             ccccccccccccCCCC-CCCCCCCCCC
Q psy4296          61 MPECYFYSRFNACHNK-ECPFLHIDPD   86 (103)
Q Consensus        61 ~p~C~~f~~~G~C~~~-~C~y~H~~~~   86 (103)
                      ..+|.||.+ |.|+++ +|+|.|..|.
T Consensus       161 p~Icsf~v~-geckRG~ec~yrhEkp~  186 (377)
T KOG0153|consen  161 PHICSFFVK-GECKRGAECPYRHEKPP  186 (377)
T ss_pred             Cccccceee-ccccccccccccccCCC
Confidence            347999999 999985 9999999983

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	103
2d9n_A	77	Solution Structure Of Ccch Type Zinc-Finger Domain		9e-28
2rhk_C	72	Crystal Structure Of Influenza A Ns1a Protein In Co		7e-26

>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In Cleavage And Polyadenylation Specificity Factor Length = 77

Iteration: 1
 Score =  118 bits (295), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 51/62 (82%), Positives = 58/62 (93%)
Query: 29 TGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSM 88
          +G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHIDP+S 
Sbjct: 6  SGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESK 65
Query: 89 IE 90
          I+
Sbjct: 66 IK 67

>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex With F2f3 Fragment Of Human Cellular Factor Cpsf30, Northeast Structural Genomics Targets Or8c And Hr6309a Length = 72

Iteration: 1
 Score =  112 bits (279), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 54/59 (91%)
Query: 31 DRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMI 89
          +++VVCKHWLRGLCKKGDQCEFLHEYDMTKM ECYFYS+F  C NKECPFLHIDP+S I
Sbjct: 14 EKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSNKECPFLHIDPESKI 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	103
2rhk_C	72	Cleavage and polyadenylation specificity factor su	3e-25
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	1e-23
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	2e-05
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	2e-11
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	5e-06
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	9e-06
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	2e-05
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	2e-05
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	8e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-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 = 89.1 bits (221), Expect = 3e-25
 Identities = 50/62 (80%), Positives = 57/62 (91%)

Query: 26 RHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDP 85
           H++G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKM ECYFYS+F  C NKECPFLHIDP
Sbjct: 9  SHMSGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSNKECPFLHIDP 68

Query: 86 DS 87
          +S
Sbjct: 69 ES 70

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

 Score = 84.9 bits (210), Expect = 1e-23
 Identities = 50/58 (86%), Positives = 55/58 (94%)

Query: 30 GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDS 87
          G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F  C NKECPFLHIDP+S
Sbjct: 7  GEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPES 64

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

 Score = 38.3 bits (89), Expect = 2e-05
 Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 1/46 (2%)

Query: 24 PLRH-ITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS 68
             H     +   C  + +       +C FLH    +K+ +C +  
Sbjct: 28 EFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESKIKDCPWSG 73

>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 Length = 98

 Score = 54.3 bits (130), Expect = 2e-11
 Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDP 85
          +  +CK ++ G C + + C ++H       P   +++  N  +  +C F H   
Sbjct: 12 KRELCKFYITGFCARAENCPYMHGD----FPCKLYHTTGNCINGDDCMFSHDPL 61

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens} Length = 89

 Score = 40.6 bits (94), Expect = 5e-06
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 22 PFPLRHITGDRSVVCKHWLRGLCKKGDQ-CEFLH-----EYDMTKMPECYFYSRFNACHN 75
            P+R        VC+ + RG C + D+ C+F H     + +  ++  C+   +   C  
Sbjct: 6  SGPVRDTKWLTLEVCRQFQRGTCSRSDEECKFAHPPKSCQVENGRVIACFDSLK-GRCSR 64

Query: 76 KECPFLHIDP 85
          + C +LH   
Sbjct: 65 ENCKYLHPPT 74

>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 Length = 70

 Score = 39.3 bits (91), Expect = 9e-06
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 9/60 (15%)

Query: 31 DRSVVCKHWLRGLCKKGD-QCEFLHEYDMT-------KMPECYFYSRFNACHNKECPFLH 82
          DR  VC+ + RG C +G+  C F H  D T        +  C  Y +   C  ++C + H
Sbjct: 4  DRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIK-GRCSREKCKYFH 62

>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} Length = 83

 Score = 38.9 bits (90), Expect = 2e-05
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 35 VCKHWLRGLCKKGD-QCEFLHEYDMT-----KMPECYFYSRFNACHNKECPFLHIDP 85
          VC+ + RG C + D +C+F H          ++  C+   +   C  + C +LH  P
Sbjct: 11 VCREFQRGTCSRPDTECKFAHPSKSCQVENGRVIACFDSLK-GRCSRENCKYLHPPP 66

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 98

 Score = 39.1 bits (90), Expect = 2e-05
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 9/69 (13%)

Query: 22 PFPLRHITGDRSVVCKHWLRGLCKKGD-QCEFLHEYDMT-------KMPECYFYSRFNAC 73
              + +  D+  VC+ + RG C +G+  C F H  D T        +  C  Y +   C
Sbjct: 9  TATQKLLRTDKLEVCREFQRGNCARGETDCRFAHPADSTMIDTSDNTVTVCMDYIK-GRC 67

Query: 74 HNKECPFLH 82
            ++C + H
Sbjct: 68 MREKCKYFH 76

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

 Score = 36.9 bits (85), Expect = 8e-05
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 11/58 (18%)

Query: 36 CKHWLR-GLCKKGDQCEFLH---------EYDMTKMPECYFYSRFNACHN-KECPFLH 82
          C+ +   G C+ G +C+F H          +   K   C+ +     C     C F+H
Sbjct: 15 CRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIH 72

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 5/52 (9%)

Query: 26  RHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKE 77
           R     +   C  + +G+C  G +CE+LH      +P+     +        
Sbjct: 63  RGDNDGQLFFCLFFAKGMCCLGPKCEYLHH-----IPDEEDIGKLALRTEVL 109

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	103
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	99.83
2rhk_C	72	Cleavage and polyadenylation specificity factor su	99.79
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	99.64
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	99.59
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	99.55
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	99.55
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	99.48
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	99.37
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.29
2rhk_C	72	Cleavage and polyadenylation specificity factor su	98.86
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.8
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	98.78
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.65
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	98.53
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	98.29
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	98.25
2lhn_A	80	Nuclear polyadenylated RNA-binding protein NAB2; n	97.33
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	97.53
2lhn_A	80	Nuclear polyadenylated RNA-binding protein NAB2; n	96.64
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	97.09
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	97.07
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	96.97
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.47
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	95.34
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	95.17
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	91.98

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

Probab=99.83  E-value=1.5e-21  Score=123.55  Aligned_cols=68  Identities=74%  Similarity=1.424  Sum_probs=64.5

Q ss_pred             CCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCCCCCCCCcCcHHHHhh
Q psy4296          31 DRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHR   98 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~~~~~~~~~C~~f~~~   98 (103)
                      .++.+|+||++|.|++|++|+|+|+++..++++|+||++.|.|.+++|+|+|+.|+.++++|++|..+
T Consensus         8 ~k~~~C~~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~~~~C~f~H~~~~~~~~~C~~f~~g   75 (77)
T 2d9n_A            8 EKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESKIKDCPWSGPS   75 (77)
T ss_dssp             CTTSBCHHHHTTCCSCTTSSSSBCSCCTTTSCBCHHHHHTCCCCCSSCSSBCCCTTSSCSSSSCCTTT
T ss_pred             CcceeCHhHccCcCCCCCCCCCccccccCcCCCCcccCCCCccCCCCeeccCCCccccCCCCcccccC
Confidence            68899999999999999999999999999999999999989999889999999999999999999865

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

Probab=99.79  E-value=3e-20  Score=116.58  Aligned_cols=62  Identities=81%  Similarity=1.648  Sum_probs=55.4

Q ss_pred             CCCCCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCCCCCCC
Q psy4296          27 HITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDSM   88 (103)
Q Consensus        27 H~~~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~~~~~~   88 (103)
                      |....+.++|+||++|.|++|++|+|+|+++..++++|+||+++|.|++++|+|+|+.|+++
T Consensus        10 ~~~~~k~~vCk~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~~~~C~y~H~~p~~k   71 (72)
T 2rhk_C           10 HMSGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSNKECPFLHIDPESK   71 (72)
T ss_dssp             SSSCCCCSBCHHHHTTCCCCGGGSSSBCSCCTTSCCBCHHHHHHSCCSBTTCCSBCCCCC--
T ss_pred             cCCCCcCeeCHHHhcCCCCCCCCCCCccccccccCCcccccCCCCCCCCCCeeccCCCcccc
Confidence            33347889999999999999999999999999999999999998999999999999998765

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

Probab=99.64  E-value=2.4e-17  Score=108.81  Aligned_cols=66  Identities=24%  Similarity=0.615  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCCCcccccccccCCCCCCC-CCCCCccCC-------CCcccccccccccccCCCCCCCCCCCCCC
Q psy4296          20 LVPFPLRHITGDRSVVCKHWLRGLCKKGD-QCEFLHEYD-------MTKMPECYFYSRFNACHNKECPFLHIDPD   86 (103)
Q Consensus        20 g~~C~f~H~~~~~~~vC~~fl~G~C~~Gd-~C~f~H~~~-------~~~~p~C~~f~~~G~C~~~~C~y~H~~~~   86 (103)
                      +..++..+..+++..||++|++|.|.+|| .|+|+|+.+       ..++++|++|++ |.|++++|+|.|+.+.
T Consensus         7 ~~~~~~K~~~~~k~~VCr~FlrG~C~rgd~~C~FsH~~~~~~~~~~~~~~~vC~~flk-G~C~r~~C~y~H~~~~   80 (98)
T 2e5s_A            7 GSTATQKLLRTDKLEVCREFQRGNCARGETDCRFAHPADSTMIDTSDNTVTVCMDYIK-GRCMREKCKYFHPPAH   80 (98)
T ss_dssp             CSSCCCCCCCSSEEEBCSHHHHTCCSSHHHHCSSBCCSSCCSCCTTTCEEEBCHHHHH-TCCCCTTCCSBCCCHH
T ss_pred             CccccccccChhhhhhhHHHhcCcCCCCCCCCCCcCCchhccccccCCccccchhhcc-CCCCCCCcCccCChHH
Confidence            34677777777899999999999999998 799999975       357899999999 9999999999998753

>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=99.59  E-value=2.2e-16  Score=98.13  Aligned_cols=54  Identities=31%  Similarity=0.819  Sum_probs=48.1

Q ss_pred             CCcccccccccCCCCCCC-CCCCCccCC-------CCcccccccccccccCCCCCCCCCCCCC
Q psy4296          31 DRSVVCKHWLRGLCKKGD-QCEFLHEYD-------MTKMPECYFYSRFNACHNKECPFLHIDP   85 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd-~C~f~H~~~-------~~~~p~C~~f~~~G~C~~~~C~y~H~~~   85 (103)
                      .+..||++|++|.|.+|+ .|+|+|+..       ..++++|++|++ |.|++++|+|+|+.+
T Consensus         4 ~k~~vC~~f~~G~C~rg~~~C~f~H~~~~~~~~~~~~~~~vC~~flk-G~C~r~~C~y~H~~~   65 (70)
T 3d2q_A            4 DRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIK-GRCSREKCKYFHPPA   65 (70)
T ss_dssp             CEEEBCHHHHTTCCSSCTTTCSSBCCCTTSCCBTTTTEEEBCHHHHT-TCCCCTTCCSBCCCH
T ss_pred             ccchhCHHHhcCCCCCCCCCCCCccCcccccccccCCcceeccccCc-CCCCCCCcCeeCCHH
Confidence            577899999999999999 599999753       456899999999 999999999999864

>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=99.55  E-value=1.2e-15  Score=99.16  Aligned_cols=66  Identities=24%  Similarity=0.564  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCCcccccccccCCCCCCC-CCCCCccCCC-----CcccccccccccccCCCCCCCCCCCCCC
Q psy4296          20 LVPFPLRHITGDRSVVCKHWLRGLCKKGD-QCEFLHEYDM-----TKMPECYFYSRFNACHNKECPFLHIDPD   86 (103)
Q Consensus        20 g~~C~f~H~~~~~~~vC~~fl~G~C~~Gd-~C~f~H~~~~-----~~~p~C~~f~~~G~C~~~~C~y~H~~~~   86 (103)
                      +..++++++...+.+||+.|++|.|.+|| .|+|+|....     .++++|.+|++ |.|++++|+|.|..+.
T Consensus         4 ~~~~~~~~~~~~~~~VCrdFlrG~C~r~d~~CrfsH~~~~~~v~~~~~~vC~dflk-G~C~r~~Cky~H~~~h   75 (89)
T 2rpp_A            4 GSSGPVRDTKWLTLEVCRQFQRGTCSRSDEECKFAHPPKSCQVENGRVIACFDSLK-GRCSRENCKYLHPPTH   75 (89)
T ss_dssp             CCCSCCCSCSSSEECBCHHHHHTCCCCCTTTSSSBCCCSSSCCBTTBEEBCHHHHH-TCCCCTTCCSBCCCHH
T ss_pred             cccccccCCCcchhhhchHHhcCCCCCCCCCCCCcCCCccccccCCceeeehhhhh-CcCCCCCcceecCHHH
Confidence            45788888876789999999999999998 9999998764     47899999999 9999999999998653

>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=99.55  E-value=1.3e-15  Score=100.37  Aligned_cols=65  Identities=20%  Similarity=0.531  Sum_probs=54.6

Q ss_pred             CCCCC--CCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCC-CCCCCCCCCCCCCCcCcHH
Q psy4296          25 LRHIT--GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHN-KECPFLHIDPDSMIEASVG   94 (103)
Q Consensus        25 f~H~~--~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~-~~C~y~H~~~~~~~~~C~~   94 (103)
                      |+|+.  +.++.+|+||++|.|++|++|+|+|+     .++|++|+..|.|.+ ++|+|.|......++.|..
T Consensus         3 ~sH~~~~~~k~~lC~~f~~G~C~~G~~C~f~H~-----~~~C~~f~~~G~C~~G~~C~f~H~~~~~~~~~~l~   70 (98)
T 2cqe_A            3 SGSSGELPKKRELCKFYITGFCARAENCPYMHG-----DFPCKLYHTTGNCINGDDCMFSHDPLTEETRELLD   70 (98)
T ss_dssp             CCCCCCCSCCCSBCTTTTTTCCSCSTTCSSBSS-----SSBCSHHHHTSCCSSCTTCSSBCCCCCHHHHHHHH
T ss_pred             ccccCCCCCCCccCcccccCcCCCCCCCCCCCC-----CCcCcCcccCCcCCCCCCCcccCCCCcccchhHHh
Confidence            78886  36899999999999999999999998     567999975599999 4999999976655555543

>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=99.48  E-value=1.6e-14  Score=92.81  Aligned_cols=55  Identities=27%  Similarity=0.709  Sum_probs=48.9

Q ss_pred             CCcccccccccCCCCCCC-CCCCCccCC-----CCcccccccccccccCCCCCCCCCCCCCC
Q psy4296          31 DRSVVCKHWLRGLCKKGD-QCEFLHEYD-----MTKMPECYFYSRFNACHNKECPFLHIDPD   86 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd-~C~f~H~~~-----~~~~p~C~~f~~~G~C~~~~C~y~H~~~~   86 (103)
                      .+.+||++|++|.|.+|| .|+|+|...     ..++++|.+|++ |.|.++.|+|.|..+.
T Consensus         7 ~~~~VCr~FlrG~C~r~d~~C~f~H~~~~~~~~~~~~~vC~dflk-G~C~r~~C~y~H~~~~   67 (83)
T 3d2n_A            7 LTLEVCREFQRGTCSRPDTECKFAHPSKSCQVENGRVIACFDSLK-GRCSRENCKYLHPPPH   67 (83)
T ss_dssp             GEEEBCTTGGGTCCCSCTTTCSSBCCCTTCCEETTEEECCHHHHT-TCCCCSSCSSCCCCHH
T ss_pred             ccchhcHHHhcCCCCCCCCCCCCcCCCccccccCCceeehhHhhh-ccccCCCcceeCChHH
Confidence            477899999999999997 999999975     345899999999 9999999999998653

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

Probab=99.37  E-value=1.7e-13  Score=86.37  Aligned_cols=58  Identities=19%  Similarity=0.375  Sum_probs=50.0

Q ss_pred             CCCcCCCCC---CCCCCCCCCC-CCccccccccc-CCCCCCCCCCCCccCCCCcccccccccccc
Q psy4296          12 PSFQAPGVL---VPFPLRHITG-DRSVVCKHWLR-GLCKKGDQCEFLHEYDMTKMPECYFYSRFN   71 (103)
Q Consensus        12 p~f~~~g~g---~~C~f~H~~~-~~~~vC~~fl~-G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G   71 (103)
                      .+|++.|.+   +.|+|+|+.. .++++|+||++ |.|. |+.|+|+|.....++++|.+|++ |
T Consensus        13 C~~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~-~~~C~f~H~~~~~~~~~C~~f~~-g   75 (77)
T 2d9n_A           13 CKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECS-NKECPFLHIDPESKIKDCPWSGP-S   75 (77)
T ss_dssp             CHHHHTTCCSCTTSSSSBCSCCTTTSCBCHHHHHTCCCC-CSSCSSBCCCTTSSCSSSSCCTT-T
T ss_pred             CHhHccCcCCCCCCCCCccccccCcCCCCcccCCCCccC-CCCeeccCCCccccCCCCccccc-C
Confidence            346667775   7899999963 57789999999 9999 78999999998888999999998 5

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

Probab=99.29  E-value=1.1e-12  Score=81.61  Aligned_cols=55  Identities=22%  Similarity=0.597  Sum_probs=25.8

Q ss_pred             CCcccccccc-cCCCCCCCCCCCCccCCCCc---------ccccccccccccCCCC-CCCCCCCCC
Q psy4296          31 DRSVVCKHWL-RGLCKKGDQCEFLHEYDMTK---------MPECYFYSRFNACHNK-ECPFLHIDP   85 (103)
Q Consensus        31 ~~~~vC~~fl-~G~C~~Gd~C~f~H~~~~~~---------~p~C~~f~~~G~C~~~-~C~y~H~~~   85 (103)
                      .++.+|++|+ .|.|.+|++|.|+|+.....         ..+|++|...|.|.++ +|+|.|...
T Consensus        10 ~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~~~~~~~~k~~~C~~f~~~G~C~~G~~C~f~H~~~   75 (77)
T 1m9o_A           10 YKTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPT   75 (77)
T ss_dssp             CCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGTC--------------------------------
T ss_pred             ccchhCHHhhhCCCcCCCCCccCCCCChhhccccccccccCCcccchhhCcCCCCcCcCCCCCCCC
Confidence            6889999997 79999999999999875432         4679977766999995 999999864

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

Probab=98.86  E-value=3.6e-10  Score=70.37  Aligned_cols=47  Identities=19%  Similarity=0.316  Sum_probs=38.8

Q ss_pred             CCCcCCCCC---CCCCCCCCC-CCCccccccccc-CCCCCCCCCCCCccCCCC
Q psy4296          12 PSFQAPGVL---VPFPLRHIT-GDRSVVCKHWLR-GLCKKGDQCEFLHEYDMT   59 (103)
Q Consensus        12 p~f~~~g~g---~~C~f~H~~-~~~~~vC~~fl~-G~C~~Gd~C~f~H~~~~~   59 (103)
                      .+|++.|.+   +.|+|+|+. ..++++|+||++ |.|.+ ++|+|+|.....
T Consensus        19 Ck~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~~-~~C~y~H~~p~~   70 (72)
T 2rhk_C           19 CKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSN-KECPFLHIDPES   70 (72)
T ss_dssp             CHHHHTTCCCCGGGSSSBCSCCTTSCCBCHHHHHHSCCSB-TTCCSBCCCCC-
T ss_pred             CHHHhcCCCCCCCCCCCccccccccCCcccccCCCCCCCC-CCeeccCCCccc
Confidence            357777875   789999996 367889999999 99999 899999986544

>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=98.80  E-value=1.6e-09  Score=71.04  Aligned_cols=49  Identities=29%  Similarity=0.459  Sum_probs=39.7

Q ss_pred             CCCcCCCCC---CCCCCCCCCCCCcccccccc-cCCCCCCCCCCCCccCCCCccccc
Q psy4296          12 PSFQAPGVL---VPFPLRHITGDRSVVCKHWL-RGLCKKGDQCEFLHEYDMTKMPEC   64 (103)
Q Consensus        12 p~f~~~g~g---~~C~f~H~~~~~~~vC~~fl-~G~C~~Gd~C~f~H~~~~~~~p~C   64 (103)
                      .+|+..|.+   +.|+|+|+    ..+|++|+ +|.|.+|+.|+|+|......++.|
T Consensus        16 C~~f~~G~C~~G~~C~f~H~----~~~C~~f~~~G~C~~G~~C~f~H~~~~~~~~~~   68 (98)
T 2cqe_A           16 CKFYITGFCARAENCPYMHG----DFPCKLYHTTGNCINGDDCMFSHDPLTEETREL   68 (98)
T ss_dssp             CTTTTTTCCSCSTTCSSBSS----SSBCSHHHHTSCCSSCTTCSSBCCCCCHHHHHH
T ss_pred             CcccccCcCCCCCCCCCCCC----CCcCcCcccCCcCCCCCCCcccCCCCcccchhH
Confidence            357777875   78999999    67899996 899999999999999765544433

>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=98.78  E-value=1.2e-09  Score=67.50  Aligned_cols=43  Identities=19%  Similarity=0.491  Sum_probs=35.7

Q ss_pred             CCcCCCCC---C-CCCCCCCC--------CCCcccccccccCCCCCCCCCCCCccC
Q psy4296          13 SFQAPGVL---V-PFPLRHIT--------GDRSVVCKHWLRGLCKKGDQCEFLHEY   56 (103)
Q Consensus        13 ~f~~~g~g---~-~C~f~H~~--------~~~~~vC~~fl~G~C~~Gd~C~f~H~~   56 (103)
                      ++++.|++   + .|+|+|+.        +.++++|++|++|.|.+| +|+|+|..
T Consensus        10 ~~f~~G~C~rg~~~C~f~H~~~~~~~~~~~~~~~vC~~flkG~C~r~-~C~y~H~~   64 (70)
T 3d2q_A           10 REYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSRE-KCKYFHPP   64 (70)
T ss_dssp             HHHHTTCCSSCTTTCSSBCCCTTSCCBTTTTEEEBCHHHHTTCCCCT-TCCSBCCC
T ss_pred             HHHhcCCCCCCCCCCCCccCcccccccccCCcceeccccCcCCCCCC-CcCeeCCH
Confidence            45677776   5 59999974        246889999999999999 89999974

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

Probab=98.65  E-value=2.8e-09  Score=70.02  Aligned_cols=44  Identities=18%  Similarity=0.460  Sum_probs=37.5

Q ss_pred             CCcCCCCC---C-CCCCCCCCC--------CCcccccccccCCCCCCCCCCCCccCC
Q psy4296          13 SFQAPGVL---V-PFPLRHITG--------DRSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        13 ~f~~~g~g---~-~C~f~H~~~--------~~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      ++|..|++   + .|+|+|+..        .+.++|++|++|.|.++ +|+|+|...
T Consensus        24 r~FlrG~C~rgd~~C~FsH~~~~~~~~~~~~~~~vC~~flkG~C~r~-~C~y~H~~~   79 (98)
T 2e5s_A           24 REFQRGNCARGETDCRFAHPADSTMIDTSDNTVTVCMDYIKGRCMRE-KCKYFHPPA   79 (98)
T ss_dssp             SHHHHTCCSSHHHHCSSBCCSSCCSCCTTTCEEEBCHHHHHTCCCCT-TCCSBCCCH
T ss_pred             HHHhcCcCCCCCCCCCCcCCchhccccccCCccccchhhccCCCCCC-CcCccCChH
Confidence            57777887   3 699999963        57889999999999999 899999754

>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=98.53  E-value=4.1e-08  Score=62.67  Aligned_cols=44  Identities=23%  Similarity=0.446  Sum_probs=36.5

Q ss_pred             CCcCCCCC---C-CCCCCCCCC------CCcccccccccCCCCCCCCCCCCccCC
Q psy4296          13 SFQAPGVL---V-PFPLRHITG------DRSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        13 ~f~~~g~g---~-~C~f~H~~~------~~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      ++|++|++   + .|+|+|+..      .+.++|.+|++|.|.++ +|+|+|...
T Consensus        13 r~FlrG~C~r~d~~C~f~H~~~~~~~~~~~~~vC~dflkG~C~r~-~C~y~H~~~   66 (83)
T 3d2n_A           13 REFQRGTCSRPDTECKFAHPSKSCQVENGRVIACFDSLKGRCSRE-NCKYLHPPP   66 (83)
T ss_dssp             TTGGGTCCCSCTTTCSSBCCCTTCCEETTEEECCHHHHTTCCCCS-SCSSCCCCH
T ss_pred             HHHhcCCCCCCCCCCCCcCCCccccccCCceeehhHhhhccccCC-CcceeCChH
Confidence            45666886   3 999999963      35899999999999998 799999754

>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=98.29  E-value=1.2e-07  Score=61.25  Aligned_cols=43  Identities=23%  Similarity=0.463  Sum_probs=35.2

Q ss_pred             CcCCCCC---C-CCCCCCCCC------CCcccccccccCCCCCCCCCCCCccCC
Q psy4296          14 FQAPGVL---V-PFPLRHITG------DRSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        14 f~~~g~g---~-~C~f~H~~~------~~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      .|++|++   + .|+|+|+..      .+.++|.+|++|.|.++ +|+|+|...
T Consensus        22 dFlrG~C~r~d~~CrfsH~~~~~~v~~~~~~vC~dflkG~C~r~-~Cky~H~~~   74 (89)
T 2rpp_A           22 QFQRGTCSRSDEECKFAHPPKSCQVENGRVIACFDSLKGRCSRE-NCKYLHPPT   74 (89)
T ss_dssp             HHHHTCCCCCTTTSSSBCCCSSSCCBTTBEEBCHHHHHTCCCCT-TCCSBCCCH
T ss_pred             HHhcCCCCCCCCCCCCcCCCccccccCCceeeehhhhhCcCCCC-CcceecCHH
Confidence            4455775   4 899999964      37899999999999998 799999754

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

Probab=98.25  E-value=3.7e-07  Score=56.27  Aligned_cols=44  Identities=23%  Similarity=0.605  Sum_probs=12.6

Q ss_pred             CcCCCCC---CCCCCCCCCC----------CCcccccccc-cCCCCCCCCCCCCccCC
Q psy4296          14 FQAPGVL---VPFPLRHITG----------DRSVVCKHWL-RGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        14 f~~~g~g---~~C~f~H~~~----------~~~~vC~~fl-~G~C~~Gd~C~f~H~~~   57 (103)
                      |...|.+   +.|+|.|+..          .++.+|++|+ .|.|.+|+.|.|+|...
T Consensus        18 f~~~G~C~~G~~C~f~H~~~e~~~~~~~~~~k~~~C~~f~~~G~C~~G~~C~f~H~~~   75 (77)
T 1m9o_A           18 YSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPT   75 (77)
T ss_dssp             GGGTSCCTTTTTCSSCSSSCCGGGTC--------------------------------
T ss_pred             hhhCCCcCCCCCccCCCCChhhccccccccccCCcccchhhCcCCCCcCcCCCCCCCC
Confidence            4356764   8999999963          1357998555 79999999999999753

>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein; NMR {Saccharomyces cerevisiae S288C}

Probab=97.33  E-value=5.3e-07  Score=57.31  Aligned_cols=62  Identities=24%  Similarity=0.448  Sum_probs=47.4

Q ss_pred             cCCCCcCCCCCCCCCCCCCCCCCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCC
Q psy4296          10 QDPSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI   83 (103)
Q Consensus        10 ~~p~f~~~g~g~~C~f~H~~~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~   83 (103)
                      +..+|...-....|+|.|..  ...+|++++  .|++- .|.|.|..    ...|+|+.   .|++.+|+|.|.
T Consensus        10 e~CKf~~~Ctn~~C~f~Hp~--~~~~Cr~g~--~C~~~-~C~f~HP~----~~~Crf~~---~C~n~~C~F~Hp   71 (80)
T 2lhn_A           10 EQCKFGTHCTNKRCKYRHAR--SHIMCREGA--NCTRI-DCLFGHPI----NEDCRFGV---NCKNIYCLFRHP   71 (80)
Confidence            34456665555899999984  456899886  89985 59999952    23599885   599999999994

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

Probab=97.53  E-value=6.1e-05  Score=55.94  Aligned_cols=42  Identities=31%  Similarity=0.717  Sum_probs=28.0

Q ss_pred             cccccccccC-----CCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCCC
Q psy4296          33 SVVCKHWLRG-----LCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHID   84 (103)
Q Consensus        33 ~~vC~~fl~G-----~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~~   84 (103)
                      ..||.+| +|     .|+.++.|..+|        +|++|++ |.|....|...|..
T Consensus       151 PeiC~~Y-kG~g~~g~C~~~~~C~kLH--------IC~~Fl~-G~C~f~~CkRsH~~  197 (229)
T 3u9g_A          151 PEICKSY-KGEGRKQTCGQPQPCERLH--------ICEHFTR-GNCSYLNCLRSHNL  197 (229)
T ss_dssp             CCBCTTC-CCSSSCCSCSSSSCCCSBC--------SCHHHHT-TCCCCSSCSSCCCT
T ss_pred             chHHHHh-CCCCCCCcCCCCCCCccee--------ccchhhc-CCcCCCCccCccCc
Confidence            3467777 63     676666677766        4777777 77776677777765

>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein; NMR {Saccharomyces cerevisiae S288C}

Probab=96.64  E-value=1.4e-05  Score=50.63  Aligned_cols=44  Identities=23%  Similarity=0.462  Sum_probs=36.9

Q ss_pred             CCcccccccccCCCCCCCCCCCCccCCCCcccccccccccccCCCCCCCCCCC
Q psy4296          31 DRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHI   83 (103)
Q Consensus        31 ~~~~vC~~fl~G~C~~Gd~C~f~H~~~~~~~p~C~~f~~~G~C~~~~C~y~H~   83 (103)
                      +..+.|+||.  .|++ +.|+|.|...   .++|+|+.   .|++.+|.|.|-
T Consensus         7 ~~~e~CKf~~--~Ctn-~~C~f~Hp~~---~~~Cr~g~---~C~~~~C~f~HP   50 (80)
T 2lhn_A            7 KSLEQCKFGT--HCTN-KRCKYRHARS---HIMCREGA---NCTRIDCLFGHP   50 (80)
Confidence            5678899998  8999 7899999642   35799995   599999999994

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

Probab=97.09  E-value=0.00027  Score=52.46  Aligned_cols=40  Identities=23%  Similarity=0.316  Sum_probs=29.4

Q ss_pred             CCCC--CCCCCCCCCCCCcccccccccCCCCCCCCCCCCccCCC
Q psy4296          17 PGVL--VPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        17 ~g~g--~~C~f~H~~~~~~~vC~~fl~G~C~~Gd~C~f~H~~~~   58 (103)
                      +|.|  ..|.|...= .+.-||++|++|.|+. .+|.-+|+...
T Consensus       158 kG~g~~g~C~~~~~C-~kLHIC~~Fl~G~C~f-~~CkRsH~~~~  199 (229)
T 3u9g_A          158 KGEGRKQTCGQPQPC-ERLHICEHFTRGNCSY-LNCLRSHNLMD  199 (229)
T ss_dssp             CCSSSCCSCSSSSCC-CSBCSCHHHHTTCCCC-SSCSSCCCTTS
T ss_pred             CCCCCCCcCCCCCCC-cceeccchhhcCCcCC-CCccCccCccC
Confidence            5554  677777664 5777888888888888 57888887644

>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=97.07  E-value=0.00028  Score=40.94  Aligned_cols=28  Identities=25%  Similarity=0.617  Sum_probs=21.5

Q ss_pred             CCccccccccc-CCCCCCCCCCCCccCCC
Q psy4296          31 DRSVVCKHWLR-GLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        31 ~~~~vC~~fl~-G~C~~Gd~C~f~H~~~~   58 (103)
                      ..+.||+-|.. |.|.+|.+|+++|+.++
T Consensus        18 ~~~~iC~~FSayGwCp~G~~Cp~SHDiDl   46 (50)
T 2fc6_A           18 HPTSICDNFSAYGWCPLGPQCPQSHDISG   46 (50)
T ss_dssp             CCSCBCSHHHHTCCCTTGGGCSSBCCCCC
T ss_pred             cccchhhhccccccCCCCCCCCccccCCC
Confidence            46778866664 88888888888888765

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

Probab=96.97  E-value=0.00051  Score=42.36  Aligned_cols=33  Identities=27%  Similarity=0.689  Sum_probs=26.2

Q ss_pred             CCCCCCCCCcccccccccCCCCCCCCCCCCccCC
Q psy4296          24 PLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYD   57 (103)
Q Consensus        24 ~f~H~~~~~~~vC~~fl~G~C~~Gd~C~f~H~~~   57 (103)
                      .++... .+..+|+.|+.|.|..|+.|.|.|...
T Consensus        12 ~~R~P~-~k~~LC~~~~~G~C~~G~~C~FAHG~~   44 (69)
T 2d9m_A           12 QHRFPT-GYFSICDRYMNGTCPEGNSCKFAHGNA   44 (69)
T ss_dssp             CCCCCC-SCCSBCHHHHHSCCSSCSSCSSBSSHH
T ss_pred             cccCCC-CCcccCcccCcCCCCCCCccCCcCCHH
Confidence            344432 567999999999999999999999743

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

Probab=96.47  E-value=0.00062  Score=50.51  Aligned_cols=27  Identities=30%  Similarity=0.785  Sum_probs=23.5

Q ss_pred             CcccccccccCCCCCCCCCCCCccCCC
Q psy4296          32 RSVVCKHWLRGLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        32 ~~~vC~~fl~G~C~~Gd~C~f~H~~~~   58 (103)
                      +..+|-||.+|.|.+|++|+|+|....
T Consensus        69 ~~~~C~ffakG~C~~G~~C~y~H~lPt   95 (240)
T 3u1l_A           69 QLFFCLFFAKGMCCLGPKCEYLHHIPD   95 (240)
T ss_dssp             CCSBCHHHHTTCCSCGGGCSSBBSCCC
T ss_pred             CCeEcCccccCCCCCCCCCCccCCCCC
Confidence            455999999999999999999998543

>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=95.34  E-value=0.014  Score=33.70  Aligned_cols=36  Identities=19%  Similarity=0.324  Sum_probs=27.1

Q ss_pred             CCCCccCC-CCcccccccccccccCCCC-CCCCCCCCC
Q psy4296          50 CEFLHEYD-MTKMPECYFYSRFNACHNK-ECPFLHIDP   85 (103)
Q Consensus        50 C~f~H~~~-~~~~p~C~~f~~~G~C~~~-~C~y~H~~~   85 (103)
                      |-+.+... .....+|.-|..+|+|.++ +|+++|...
T Consensus         8 cclp~~~~~~~~~~iC~~FSayGwCp~G~~Cp~SHDiD   45 (50)
T 2fc6_A            8 CCLPPATHRPHPTSICDNFSAYGWCPLGPQCPQSHDIS   45 (50)
T ss_dssp             CCCCTTSCCCCCSCBCSHHHHTCCCTTGGGCSSBCCCC
T ss_pred             ccCCCcccCccccchhhhccccccCCCCCCCCccccCC
Confidence            44444322 2467889999999999996 999999853

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

Probab=95.17  E-value=0.0041  Score=46.05  Aligned_cols=26  Identities=31%  Similarity=0.796  Sum_probs=22.6

Q ss_pred             ccccccccccccCCCC-CCCCCCCCCCC
Q psy4296          61 MPECYFYSRFNACHNK-ECPFLHIDPDS   87 (103)
Q Consensus        61 ~p~C~~f~~~G~C~~~-~C~y~H~~~~~   87 (103)
                      ..+|.||.+ |.|.+| +|+|+|..|..
T Consensus        70 ~~~C~ffak-G~C~~G~~C~y~H~lPt~   96 (240)
T 3u1l_A           70 LFFCLFFAK-GMCCLGPKCEYLHHIPDE   96 (240)
T ss_dssp             CSBCHHHHT-TCCSCGGGCSSBBSCCCH
T ss_pred             CeEcCcccc-CCCCCCCCCCccCCCCCc
Confidence            347999999 999996 89999998863

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

Probab=91.98  E-value=0.071  Score=32.65  Aligned_cols=32  Identities=22%  Similarity=0.545  Sum_probs=24.7

Q ss_pred             CCccCCCCcccccccccccccCCCC-CCCCCCCC
Q psy4296          52 FLHEYDMTKMPECYFYSRFNACHNK-ECPFLHID   84 (103)
Q Consensus        52 f~H~~~~~~~p~C~~f~~~G~C~~~-~C~y~H~~   84 (103)
                      ..|.....+...|..|.. |.|..+ .|.|.|-.
T Consensus        11 W~~R~P~~k~~LC~~~~~-G~C~~G~~C~FAHG~   43 (69)
T 2d9m_A           11 WQHRFPTGYFSICDRYMN-GTCPEGNSCKFAHGN   43 (69)
T ss_dssp             CCCCCCCSCCSBCHHHHH-SCCSSCSSCSSBSSH
T ss_pred             ccccCCCCCcccCcccCc-CCCCCCCccCCcCCH
Confidence            344445566788999966 999995 99999963

---

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	103
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	98.67
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	97.96
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	97.75
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	97.71
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	97.52
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	97.02
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	96.49
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	95.94
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	95.54
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	95.5
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	95.11
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	95.1

>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=98.67  E-value=5.8e-09  Score=52.72  Aligned_cols=26  Identities=23%  Similarity=0.935  Sum_probs=24.0

Q ss_pred             CCCcccccccccCCCCCCCCCCCCcc
Q psy4296          30 GDRSVVCKHWLRGLCKKGDQCEFLHE   55 (103)
Q Consensus        30 ~~~~~vC~~fl~G~C~~Gd~C~f~H~   55 (103)
                      +++..+|+||++|.|.+|++|+|.|.
T Consensus         3 ~kkkelCKfYvqGyCtrgenC~ymH~   28 (29)
T d2cqea2           3 PKKRELCKFYITGFCARAENCPYMHG   28 (29)
T ss_dssp             SCCCSBCTTTTTTCCSCSTTCSSBSS
T ss_pred             chhhhhhhhheeeeecCCcCcccccC
Confidence            47889999999999999999999995

>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=97.96  E-value=2.7e-06  Score=46.10  Aligned_cols=28  Identities=25%  Similarity=0.764  Sum_probs=24.4

Q ss_pred             CCccccccccc-CCCCCCCCCCCCccCCC
Q psy4296          31 DRSVVCKHWLR-GLCKKGDQCEFLHEYDM   58 (103)
Q Consensus        31 ~~~~vC~~fl~-G~C~~Gd~C~f~H~~~~   58 (103)
                      .++.+|++|++ |.|.+|+.|.|+|....
T Consensus         7 yKT~lC~~~~~~g~C~~G~~C~FAHg~~E   35 (40)
T d1m9oa_           7 YKTELCRTYSESGRCRYGAKCQFAHGLGE   35 (40)
T ss_dssp             CCSCCCSGGGGTSCCTTTTTCSSCSSSCC
T ss_pred             cccccChhhhcCCcCCCCCCCCCCCCHHH
Confidence            68999999986 99999999999997543

>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=97.75  E-value=3.3e-06  Score=44.28  Aligned_cols=30  Identities=30%  Similarity=0.832  Sum_probs=25.5

Q ss_pred             CCCCCCCccccccccc-CCCCCCCCCCCCccC
Q psy4296          26 RHITGDRSVVCKHWLR-GLCKKGDQCEFLHEY   56 (103)
Q Consensus        26 ~H~~~~~~~vC~~fl~-G~C~~Gd~C~f~H~~   56 (103)
                      +|. ..++.+|++|.. |.|..|+.|.|+|..
T Consensus         2 rhp-kyKT~lC~~f~~~g~C~yG~~C~FaHg~   32 (34)
T d1rgoa2           2 RHP-KYKTELCRTFHTIGFCPYGPRCHFIHNA   32 (34)
T ss_dssp             CCT-TTTCSBCHHHHHHSCCTTGGGCSSBCCS
T ss_pred             CCC-CccchhccccCCCCcCCCCCcccCcCCC
Confidence            354 379999999986 999999999999974

>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=97.71  E-value=2.4e-06  Score=45.30  Aligned_cols=27  Identities=30%  Similarity=0.913  Sum_probs=23.8

Q ss_pred             CCccccccccc-CCCCCCCCCCCCccCC
Q psy4296          31 DRSVVCKHWLR-GLCKKGDQCEFLHEYD   57 (103)
Q Consensus        31 ~~~~vC~~fl~-G~C~~Gd~C~f~H~~~   57 (103)
                      -++.+|++|.. |.|.+|++|.|.|...
T Consensus         4 yKT~lC~~~~~~g~C~~G~~C~FAHg~~   31 (36)
T d1rgoa1           4 YKTELCRPFEESGTCKYGEKCQFAHGFH   31 (36)
T ss_dssp             TTSSBCHHHHHHSCCTTGGGCSSBSSGG
T ss_pred             cchhhCcchhcCCcCCCCCcCCCcCCHH
Confidence            58999999985 9999999999999754

>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=97.52  E-value=2.4e-05  Score=39.08  Aligned_cols=24  Identities=33%  Similarity=0.814  Sum_probs=20.6

Q ss_pred             CcccccccccccccCCCC-CCCCCCC
Q psy4296          59 TKMPECYFYSRFNACHNK-ECPFLHI   83 (103)
Q Consensus        59 ~~~p~C~~f~~~G~C~~~-~C~y~H~   83 (103)
                      .+...|+||.. |+|+++ +|+|+|.
T Consensus         4 kkkelCKfYvq-GyCtrgenC~ymH~   28 (29)
T d2cqea2           4 KKRELCKFYIT-GFCARAENCPYMHG   28 (29)
T ss_dssp             CCCSBCTTTTT-TCCSCSTTCSSBSS
T ss_pred             hhhhhhhhhee-eeecCCcCcccccC
Confidence            34567999999 999995 9999995

>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=97.02  E-value=8.8e-05  Score=42.52  Aligned_cols=23  Identities=35%  Similarity=0.686  Sum_probs=18.3

Q ss_pred             cccccccC-CCCCCCCCCCCccCC
Q psy4296          35 VCKHWLRG-LCKKGDQCEFLHEYD   57 (103)
Q Consensus        35 vC~~fl~G-~C~~Gd~C~f~H~~~   57 (103)
                      .|+||..| .|..||+|.|||.+.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~pL   25 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHDPL   25 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCCCC
T ss_pred             CcceeecCCcccCCCcccccCCcc
Confidence            58888865 699999999999643

>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=96.49  E-value=0.00099  Score=35.50  Aligned_cols=27  Identities=30%  Similarity=0.503  Sum_probs=22.5

Q ss_pred             cccccccccccccCCCC-CCCCCCCCCC
Q psy4296          60 KMPECYFYSRFNACHNK-ECPFLHIDPD   86 (103)
Q Consensus        60 ~~p~C~~f~~~G~C~~~-~C~y~H~~~~   86 (103)
                      +...|++|.+.|.|..+ +|.|.|...+
T Consensus         8 KT~lC~~~~~~g~C~~G~~C~FAHg~~E   35 (40)
T d1m9oa_           8 KTELCRTYSESGRCRYGAKCQFAHGLGE   35 (40)
T ss_dssp             CSCCCSGGGGTSCCTTTTTCSSCSSSCC
T ss_pred             ccccChhhhcCCcCCCCCCCCCCCCHHH
Confidence            46679999888999995 9999997643

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Target of EGR1 protein 1, TOE1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.94  E-value=0.0013  Score=34.35  Aligned_cols=25  Identities=28%  Similarity=0.724  Sum_probs=12.1

Q ss_pred             CCcccccccc-cCCCCCCCCCCCCcc
Q psy4296          31 DRSVVCKHWL-RGLCKKGDQCEFLHE   55 (103)
Q Consensus        31 ~~~~vC~~fl-~G~C~~Gd~C~f~H~   55 (103)
                      ..+.||..|. -|.|.+|.+|+.||+
T Consensus        11 ~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          11 HPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CccchhhhhhhccccCCCCCCcccCc
Confidence            3445553333 255555555555553

>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=95.54  E-value=0.001  Score=34.70  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=21.7

Q ss_pred             cccccccccccccCCCC-CCCCCCCCC
Q psy4296          60 KMPECYFYSRFNACHNK-ECPFLHIDP   85 (103)
Q Consensus        60 ~~p~C~~f~~~G~C~~~-~C~y~H~~~   85 (103)
                      ++..|++|.+.|.|..+ +|.|.|...
T Consensus         5 KT~lC~~~~~~g~C~~G~~C~FAHg~~   31 (36)
T d1rgoa1           5 KTELCRPFEESGTCKYGEKCQFAHGFH   31 (36)
T ss_dssp             TSSBCHHHHHHSCCTTGGGCSSBSSGG
T ss_pred             chhhCcchhcCCcCCCCCcCCCcCCHH
Confidence            45679999877999995 999999753

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Target of EGR1 protein 1, TOE1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.50  E-value=0.0021  Score=33.48  Aligned_cols=26  Identities=23%  Similarity=0.419  Sum_probs=22.9

Q ss_pred             CCcccccccccccccCCCC-CCCCCCC
Q psy4296          58 MTKMPECYFYSRFNACHNK-ECPFLHI   83 (103)
Q Consensus        58 ~~~~p~C~~f~~~G~C~~~-~C~y~H~   83 (103)
                      .....+|.-|..+|+|.++ +||.+|.
T Consensus        10 ~~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          10 PHPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CCccchhhhhhhccccCCCCCCcccCc
Confidence            4557889999999999996 9999995

>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=95.11  E-value=0.0036  Score=35.56  Aligned_cols=25  Identities=28%  Similarity=0.612  Sum_probs=20.6

Q ss_pred             ccccccccccCCC-CCCCCCCCCCCC
Q psy4296          63 ECYFYSRFNACHN-KECPFLHIDPDS   87 (103)
Q Consensus        63 ~C~~f~~~G~C~~-~~C~y~H~~~~~   87 (103)
                      +|+||...+.|.+ ++|.|+|...+.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~pLt~   27 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHDPLTE   27 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCCCCCH
T ss_pred             CcceeecCCcccCCCcccccCCccCH
Confidence            4999998679999 599999976543

>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=95.10  E-value=0.0024  Score=32.86  Aligned_cols=26  Identities=23%  Similarity=0.515  Sum_probs=22.5

Q ss_pred             CcccccccccccccCCCC-CCCCCCCC
Q psy4296          59 TKMPECYFYSRFNACHNK-ECPFLHID   84 (103)
Q Consensus        59 ~~~p~C~~f~~~G~C~~~-~C~y~H~~   84 (103)
                      -++..|+.|...|.|..+ +|.|.|..
T Consensus         6 yKT~lC~~f~~~g~C~yG~~C~FaHg~   32 (34)
T d1rgoa2           6 YKTELCRTFHTIGFCPYGPRCHFIHNA   32 (34)
T ss_dssp             TTCSBCHHHHHHSCCTTGGGCSSBCCS
T ss_pred             ccchhccccCCCCcCCCCCcccCcCCC
Confidence            456789999988999995 99999974