Query 002804
Match_columns 879
No_of_seqs 233 out of 1374
Neff 3.6
Searched_HMMs 29240
Date Tue Mar 26 18:25:47 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/002804.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1516-1519//hhsearch_pdb/002804hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2d9n_A Cleavage and polyadenyl 1.0 1 1 100.9 5.0 67 467-538 5-75 (77)
2 2cqe_A KIAA1064 protein; CCCH 1.0 1 1 89.7 5.1 59 492-553 3-61 (98)
3 2e5s_A Otthump00000018578; ZF- 1.0 1 1 89.3 0.6 58 468-526 15-78 (98)
4 2rhk_C Cleavage and polyadenyl 1.0 1 1 87.5 2.6 56 467-526 11-67 (72)
5 2cqe_A KIAA1064 protein; CCCH 1.0 1 1 83.7 6.4 50 469-526 10-60 (98)
6 3d2q_A Muscleblind-like protei 1.0 1 1 82.2 2.7 55 470-525 3-63 (70)
7 2d9n_A Cleavage and polyadenyl 1.0 1 1 80.4 5.1 63 503-571 10-75 (77)
8 3u9g_A Zinc finger CCCH-type a 1.0 1 1 79.8 3.6 73 474-554 90-199 (229)
9 2rhk_C Cleavage and polyadenyl 1.0 1 1 78.6 2.3 52 503-555 16-70 (72)
10 1m9o_A Tristetraproline; Cys3H 1.0 1 1 78.2 3.6 70 465-554 5-76 (77)
No 1
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=100.95 Aligned_cols=67 Identities=30% Similarity=0.639 Sum_probs=55.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCC---CCCCCCCCCCCC
Q ss_conf 557775222222314678899999977788878777723444423-789899999999999---988872643669
Q 002804 467 NLKPKTVKYCHHYLKGRCQEGDKCKFSHDTVPLTKSTKACCHFAR-NSCMKGDNCPFDHDL---SKYPCENFVAKG 538 (879)
Q Consensus 467 ~~DPKs~vVCrfFlkG~CkKGdkCkFSHD~sp~RKktkvCk~FLk-GsCKkGDnCpFSH~l---ssipCk~Fls~G 538 (879)
....|+ ++|+||++|.|.+|+.|+|+|+..+. +. ++|++|++ |.|. +++|+|.|.. ...+|.+|. +|
T Consensus 5 ~~~~k~-~~C~~fl~G~C~~G~~C~fsH~~~~~-~~-~~C~~f~~~G~C~-~~~C~f~H~~~~~~~~~C~~f~-~g 75 (77)
T 2d9n_A 5 SSGEKT-VVCKHWLRGLCKKGDQCEFLHEYDMT-KM-PECYFYSKFGECS-NKECPFLHIDPESKIKDCPWSG-PS 75 (77)
T ss_dssp CSCCTT-SBCHHHHTTCCSCTTSSSSBCSCCTT-TS-CBCHHHHHTCCCC-CSSCSSBCCCTTSSCSSSSCCT-TT
T ss_pred CCCCCC-EECHHHCCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCCCCCC-CCCEECCCCCCCCCCCCCCCCC-CC
T ss_conf 888866-06974705867897898885566547-69-8885368878668-9896453888535687785433-67
No 2
>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=1.00 E-value=1 Score=89.75 Aligned_cols=59 Identities=29% Similarity=0.732 Sum_probs=30.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 77788878777723444423789899999999999988872643669899999998999999
Q 002804 492 FSHDTVPLTKSTKACCHFARNSCMKGDNCPFDHDLSKYPCENFVAKGFCNRGDNCLFSHKLP 553 (879)
Q Consensus 492 FSHD~sp~RKktkvCk~FLkGsCKkGDnCpFSH~lssipCk~Fls~G~CprGdkC~FaH~~p 553 (879)
|+|+....++. .+|++|+.|.|++|+.|+|+|+ ..+|++|+.+|.|++|+.|+|.|...
T Consensus 3 ~sH~~~~~~k~-~lC~~f~~G~C~~G~~C~f~H~--~~~C~~f~~~G~C~~G~~C~f~H~~~ 61 (98)
T 2cqe_A 3 SGSSGELPKKR-ELCKFYITGFCARAENCPYMHG--DFPCKLYHTTGNCINGDDCMFSHDPL 61 (98)
T ss_dssp CCCCCCCSCCC-SBCTTTTTTCCSCSTTCSSBSS--SSBCSHHHHTSCCSSCTTCSSBCCCC
T ss_pred CCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 66657777877-4581203675789997887888--99591815588689989883538887
No 3
>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=89.35 Aligned_cols=58 Identities=22% Similarity=0.769 Sum_probs=43.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 577752222223146788999-999777888787-----77723444423789899999999999
Q 002804 468 LKPKTVKYCHHYLKGRCQEGD-KCKFSHDTVPLT-----KSTKACCHFARNSCMKGDNCPFDHDL 526 (879)
Q Consensus 468 ~DPKs~vVCrfFlkG~CkKGd-kCkFSHD~sp~R-----KktkvCk~FLkGsCKkGDnCpFSH~l 526 (879)
.++.+..+|++|++|.|.+|+ .|+|+|+..... ...++|.+|++|.|.++ +|+|.|..
T Consensus 15 ~~~~k~~VCr~FlrG~C~rgd~~C~FsH~~~~~~~~~~~~~~~vC~~flkG~C~r~-~C~y~H~~ 78 (98)
T 2e5s_A 15 LRTDKLEVCREFQRGNCARGETDCRFAHPADSTMIDTSDNTVTVCMDYIKGRCMRE-KCKYFHPP 78 (98)
T ss_dssp CCSSEEEBCSHHHHTCCSSHHHHCSSBCCSSCCSCCTTTCEEEBCHHHHHTCCCCT-TCCSBCCC
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCHHHCCCCCCCC-CCCCCCCH
T ss_conf 57135265288703967799998878678310024456896645550166999899-72743882
No 4
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}
Probab=1.00 E-value=1 Score=87.53 Aligned_cols=56 Identities=34% Similarity=0.774 Sum_probs=41.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCC
Q ss_conf 557775222222314678899999977788878777723444423-789899999999999
Q 002804 467 NLKPKTVKYCHHYLKGRCQEGDKCKFSHDTVPLTKSTKACCHFAR-NSCMKGDNCPFDHDL 526 (879)
Q Consensus 467 ~~DPKs~vVCrfFlkG~CkKGdkCkFSHD~sp~RKktkvCk~FLk-GsCKkGDnCpFSH~l 526 (879)
+..++. ++|+||++|.|.+|+.|+|+|+..+. +. ++|++|++ |.|.+ ++|+|.|..
T Consensus 11 ~~~~k~-~vCk~fl~G~C~~G~~C~fsH~~~~~-~~-~~C~~f~~~G~C~~-~~C~y~H~~ 67 (72)
T 2rhk_C 11 MSGEKT-VVCKHWLRGLCKKGDQCEFLHEYDMT-KM-SECYFYSKFGECSN-KECPFLHID 67 (72)
T ss_dssp SSCCCC-SBCHHHHTTCCCCGGGSSSBCSCCTT-SC-CBCHHHHHHSCCSB-TTCCSBCCC
T ss_pred CCCCCC-EECHHHHCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCCCCCCC-CCEECCCCC
T ss_conf 778868-04977866988898898776366436-59-73664587787789-984231878
No 5
>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=1.00 E-value=1 Score=83.69 Aligned_cols=50 Identities=30% Similarity=0.853 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCC
Q ss_conf 777522222231467889999997778887877772344442-3789899999999999
Q 002804 469 KPKTVKYCHHYLKGRCQEGDKCKFSHDTVPLTKSTKACCHFA-RNSCMKGDNCPFDHDL 526 (879)
Q Consensus 469 DPKs~vVCrfFlkG~CkKGdkCkFSHD~sp~RKktkvCk~FL-kGsCKkGDnCpFSH~l 526 (879)
..|+ .+|+||++|.|.+|+.|+|+|+. .+|++|+ .|.|.+|+.|+|.|..
T Consensus 10 ~~k~-~lC~~f~~G~C~~G~~C~f~H~~-------~~C~~f~~~G~C~~G~~C~f~H~~ 60 (98)
T 2cqe_A 10 PKKR-ELCKFYITGFCARAENCPYMHGD-------FPCKLYHTTGNCINGDDCMFSHDP 60 (98)
T ss_dssp SCCC-SBCTTTTTTCCSCSTTCSSBSSS-------SBCSHHHHTSCCSSCTTCSSBCCC
T ss_pred CCCC-CCCCCCCCCCCCCCCCCCCCCCC-------CCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 7877-45812036757899978878889-------959181558868998988353888
No 6
>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=1.00 E-value=1 Score=82.19 Aligned_cols=55 Identities=22% Similarity=0.774 Sum_probs=39.0
Q ss_pred CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 7752222223146788999-99977788878-----77772344442378989999999999
Q 002804 470 PKTVKYCHHYLKGRCQEGD-KCKFSHDTVPL-----TKSTKACCHFARNSCMKGDNCPFDHD 525 (879)
Q Consensus 470 PKs~vVCrfFlkG~CkKGd-kCkFSHD~sp~-----RKktkvCk~FLkGsCKkGDnCpFSH~ 525 (879)
+.+..+|++|++|.|.+|+ .|+|+|+.... ...+++|.+|++|.|.++ +|+|.|.
T Consensus 3 ~~k~~vC~~f~~G~C~rg~~~C~f~H~~~~~~~~~~~~~~~vC~~flkG~C~r~-~C~y~H~ 63 (70)
T 3d2q_A 3 TDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSRE-KCKYFHP 63 (70)
T ss_dssp -CEEEBCHHHHTTCCSSCTTTCSSBCCCTTSCCBTTTTEEEBCHHHHTTCCCCT-TCCSBCC
T ss_pred CCCCHHCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCC-CCCEECC
T ss_conf 640112887734977898998878567422334356896606631174898999-7483589
No 7
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=80.38 Aligned_cols=63 Identities=30% Similarity=0.584 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 7234444237898999999999999---88872643669899999998999999999999999988988889
Q 002804 503 TKACCHFARNSCMKGDNCPFDHDLS---KYPCENFVAKGFCNRGDNCLFSHKLPPKEQDPPTPSTCTPELKP 571 (879)
Q Consensus 503 tkvCk~FLkGsCKkGDnCpFSH~ls---sipCk~Fls~G~CprGdkC~FaH~~p~~k~~Psas~vCtp~Lkg 571 (879)
..+|++|++|.|++|+.|+|+|++. ..+|++|+.+|.|. |+.|+|.|..+.... ..|..++.+
T Consensus 10 ~~~C~~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~-~~~C~f~H~~~~~~~-----~~C~~f~~g 75 (77)
T 2d9n_A 10 TVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECS-NKECPFLHIDPESKI-----KDCPWSGPS 75 (77)
T ss_dssp TSBCHHHHTTCCSCTTSSSSBCSCCTTTSCBCHHHHHTCCCC-CSSCSSBCCCTTSSC-----SSSSCCTTT
T ss_pred CEECHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEECCCCCCCCCC-----CCCCCCCCC
T ss_conf 606974705867897898885566547698885368878668-989645388853568-----778543367
No 8
>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein; 1.80A {Rattus norvegicus}
Probab=1.00 E-value=1 Score=79.83 Aligned_cols=73 Identities=34% Similarity=0.725 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCC----CCCCCCCCCCCCCCC----------------------------CCCCCCCCCCCC-----CCCC
Q ss_conf 222223146788----999999777888787----------------------------777234444237-----8989
Q 002804 474 KYCHHYLKGRCQ----EGDKCKFSHDTVPLT----------------------------KSTKACCHFARN-----SCMK 516 (879)
Q Consensus 474 vVCrfFlkG~Ck----KGdkCkFSHD~sp~R----------------------------KktkvCk~FLkG-----sCKk 516 (879)
-+|+||+.|.|. .+..|+|+|+..... -.+.+|.+| +| .|..
T Consensus 90 HLCK~~l~G~C~~~~~~~~~Ck~SHdi~s~~N~~vLk~h~l~~L~~~eL~~LLLQnDp~lLPeiC~~Y-kG~g~~g~C~~ 168 (229)
T 3u9g_A 90 HLCKLNLLGRCHYAQSQRNLCKYSHDVLSEQNFQILKNHELSGLNQEELACLLVQSDPFFLPEICKSY-KGEGRKQTCGQ 168 (229)
T ss_dssp CCCHHHHTTCCGGGTCCSSCCSSCSCTTCHHHHHHHHHTTCTTCCHHHHHHHHHTTCGGGSCCBCTTC-CCSSSCCSCSS
T ss_pred EECHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHEECCCCCCCCCHHHHHH-CCCCCCCCCCC
T ss_conf 10065540857766677787664533476567999987573437875763100168886676578871-78898786899
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99999999999888726436698999999989999999
Q 002804 517 GDNCPFDHDLSKYPCENFVAKGFCNRGDNCLFSHKLPP 554 (879)
Q Consensus 517 GDnCpFSH~lssipCk~Fls~G~CprGdkC~FaH~~p~ 554 (879)
++.|...| +|.+|+ +|.|.+ ..|+..|....
T Consensus 169 ~~~C~kLH-----IC~~Fl-~G~C~f-~~CkRsH~~~~ 199 (229)
T 3u9g_A 169 PQPCERLH-----ICEHFT-RGNCSY-LNCLRSHNLMD 199 (229)
T ss_dssp SSCCCSBC-----SCHHHH-TTCCCC-SSCSSCCCTTS
T ss_pred CCCCCCEE-----CCCHHH-CCCCCC-CCCCCCCCCCC
T ss_conf 99986410-----102233-498378-87668667667
No 9
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}
Probab=1.00 E-value=1 Score=78.60 Aligned_cols=52 Identities=35% Similarity=0.704 Sum_probs=45.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 7234444237898999999999999---8887264366989999999899999999
Q 002804 503 TKACCHFARNSCMKGDNCPFDHDLS---KYPCENFVAKGFCNRGDNCLFSHKLPPK 555 (879)
Q Consensus 503 tkvCk~FLkGsCKkGDnCpFSH~ls---sipCk~Fls~G~CprGdkC~FaH~~p~~ 555 (879)
..+|++|++|.|++|+.|+|+|++. .++|++|+..|.|.+ +.|+|.|..+..
T Consensus 16 ~~vCk~fl~G~C~~G~~C~fsH~~~~~~~~~C~~f~~~G~C~~-~~C~y~H~~p~~ 70 (72)
T 2rhk_C 16 TVVCKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSN-KECPFLHIDPES 70 (72)
T ss_dssp CSBCHHHHTTCCCCGGGSSSBCSCCTTSCCBCHHHHHHSCCSB-TTCCSBCCCCC-
T ss_pred CEECHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCEECCCCCCCC
T ss_conf 8049778669888988987763664365973664587787789-984231878455
No 10
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Probab=1.00 E-value=1 Score=78.19 Aligned_cols=70 Identities=31% Similarity=0.669 Sum_probs=50.9
Q ss_pred CCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCC
Q ss_conf 8855777522222231-467889999997778887877772344442378989999999999-99888726436698999
Q 002804 465 PQNLKPKTVKYCHHYL-KGRCQEGDKCKFSHDTVPLTKSTKACCHFARNSCMKGDNCPFDHD-LSKYPCENFVAKGFCNR 542 (879)
Q Consensus 465 ~~~~DPKs~vVCrfFl-kG~CkKGdkCkFSHD~sp~RKktkvCk~FLkGsCKkGDnCpFSH~-lssipCk~Fls~G~Cpr 542 (879)
.+....|+ .+|++|+ .|.|.+|+.|+|+|+....+.. . .|. ....+|++|...|+|++
T Consensus 5 ~~~~~~kt-~~C~~f~~~G~C~~G~~C~f~H~~~e~~~~-~------------------~~~~~k~~~C~~f~~~G~C~~ 64 (77)
T 1m9o_A 5 TTSSRYKT-ELCRTYSESGRCRYGAKCQFAHGLGELRQA-N------------------RHPKYKTELCHKFKLQGRCPY 64 (77)
T ss_dssp CCSSCCCS-CCCSGGGGTSCCTTTTTCSSCSSSCCGGGT-C---------------------------------------
T ss_pred CCCCCCCC-HHCHHHHHCCCCCCCCCCCCCCCCHHHCCC-C------------------CCCCCCCCCCCCHHHCCCCCC
T ss_conf 78887624-028776618974899984688788100562-3------------------344566783652630969789
Q ss_pred CCCCCCCCCCCC
Q ss_conf 999989999999
Q 002804 543 GDNCLFSHKLPP 554 (879)
Q Consensus 543 GdkC~FaH~~p~ 554 (879)
|+.|+|.|....
T Consensus 65 G~~C~f~H~~~e 76 (77)
T 1m9o_A 65 GSRCHFIHNPTE 76 (77)
T ss_dssp ------------
T ss_pred CCCCCCCCCCCC
T ss_conf 686888897988
Done!