Query 024229
Match_columns 270
No_of_seqs 139 out of 266
Neff 3.1
Searched_HMMs 29240
Date Mon Mar 25 04:36:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024229.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/024229hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1qyp_A RNA polymerase II; tran 77.8 1.5 5.3E-05 30.3 2.7 38 57-94 15-55 (57)
2 1tfi_A Transcriptional elongat 77.1 1.4 4.7E-05 30.6 2.3 37 57-93 9-48 (50)
3 3h0g_I DNA-directed RNA polyme 62.5 9.6 0.00033 29.8 4.5 37 58-94 73-112 (113)
4 1twf_I B12.6, DNA-directed RNA 55.5 7.3 0.00025 30.9 2.8 41 57-97 72-115 (122)
5 2fiy_A Protein FDHE homolog; F 52.6 5.3 0.00018 36.6 1.7 36 57-93 222-264 (309)
6 3po3_S Transcription elongatio 48.6 6.7 0.00023 33.2 1.6 37 57-93 137-176 (178)
7 1pqv_S STP-alpha, transcriptio 45.3 8.6 0.0003 34.9 1.9 37 57-93 268-307 (309)
8 1gnf_A Transcription factor GA 42.9 13 0.00043 25.7 2.0 41 57-101 4-44 (46)
9 3qt1_I DNA-directed RNA polyme 41.4 5.6 0.00019 32.5 0.0 38 57-94 92-132 (133)
10 3dfx_A Trans-acting T-cell-spe 39.5 22 0.00075 26.0 2.9 44 56-103 6-49 (63)
11 4hc9_A Trans-acting T-cell-spe 36.1 14 0.00047 29.5 1.5 49 52-104 54-102 (115)
12 3nw0_A Non-structural maintena 34.9 5.9 0.0002 34.7 -0.9 38 57-95 193-230 (238)
13 4gat_A Nitrogen regulatory pro 32.5 38 0.0013 24.8 3.3 45 55-103 7-51 (66)
14 3cw1_L U1 small nuclear ribonu 31.7 12 0.0004 28.5 0.4 17 81-97 2-18 (77)
15 1tie_A Erythrina trypsin inhib 30.9 12 0.00042 31.4 0.5 20 15-36 126-146 (172)
16 1z2q_A LM5-1; membrane protein 30.5 49 0.0017 24.3 3.6 30 55-93 19-48 (84)
17 2k2d_A Ring finger and CHY zin 30.3 18 0.0006 27.2 1.2 12 58-69 56-67 (79)
18 1k82_A Formamidopyrimidine-DNA 29.4 16 0.00056 32.3 1.0 29 57-90 240-268 (268)
19 1ee8_A MUTM (FPG) protein; bet 29.0 18 0.0006 32.1 1.1 29 57-90 235-263 (266)
20 3u6p_A Formamidopyrimidine-DNA 27.9 18 0.00062 32.2 1.0 29 57-90 245-273 (273)
21 2xzf_A Formamidopyrimidine-DNA 27.6 18 0.00063 32.0 1.0 29 57-90 242-270 (271)
22 2kae_A GATA-type transcription 24.5 21 0.00071 26.6 0.7 49 53-104 4-52 (71)
23 2gmg_A Hypothetical protein PF 23.4 29 0.00098 27.9 1.3 12 58-69 85-96 (105)
24 1pft_A TFIIB, PFTFIIBN; N-term 22.7 39 0.0013 22.4 1.7 33 56-94 4-36 (50)
25 1k3x_A Endonuclease VIII; hydr 22.5 23 0.00079 31.2 0.7 29 57-90 234-262 (262)
No 1
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=77.77 E-value=1.5 Score=30.32 Aligned_cols=38 Identities=18% Similarity=0.586 Sum_probs=26.1
Q ss_pred ccCCCCCCCCCcceeeecccCCCCC---chhhhhccccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQP---RHFCKTCRRYWTA 94 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~CrRyWT~ 94 (270)
.++||+|...+..|--.+-.+...| .|.|..|.--|+.
T Consensus 15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~ 55 (57)
T 1qyp_A 15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS 55 (57)
T ss_dssp ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence 4789999984444443344444445 3899999999976
No 2
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=77.13 E-value=1.4 Score=30.65 Aligned_cols=37 Identities=19% Similarity=0.667 Sum_probs=28.3
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 93 (270)
...||+|...+.-|=-.+..+...|- |.|..|..-|.
T Consensus 9 ~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~ 48 (50)
T 1tfi_A 9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 48 (50)
T ss_dssp CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred ccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence 36899999888777666666665553 88999998885
No 3
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=62.46 E-value=9.6 Score=29.84 Aligned_cols=37 Identities=19% Similarity=0.424 Sum_probs=25.0
Q ss_pred cCCCCCCCCCcceeeecccCCCCCc---hhhhhccccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWTA 94 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~ 94 (270)
.+||+|...+..|--.+-.+...|- |.|..|..-|++
T Consensus 73 ~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~ 112 (113)
T 3h0g_I 73 KECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE 112 (113)
T ss_dssp SCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred cCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence 7899999876554333333333332 889999999974
No 4
>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...
Probab=55.53 E-value=7.3 Score=30.92 Aligned_cols=41 Identities=20% Similarity=0.490 Sum_probs=29.6
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccccCCc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWTAGGS 97 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~GGt 97 (270)
...||+|...+.-|--.+-.+...|- |.|..|.--|+..-.
T Consensus 72 ~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~nn~ 115 (122)
T 1twf_I 72 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK 115 (122)
T ss_dssp CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCTT
T ss_pred CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccCCh
Confidence 37899999876665555555554443 899999999988643
No 5
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1
Probab=52.60 E-value=5.3 Score=36.61 Aligned_cols=36 Identities=17% Similarity=0.540 Sum_probs=26.1
Q ss_pred ccCCCCCCCCCcceeeecccC-----C-CC-Cchhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYS-----F-SQ-PRHFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~-----~-~Q-PR~fCk~CrRyWT 93 (270)
..+||.|.+. .+.-|+.--. . .. --+.|..|+.|+-
T Consensus 222 R~~C~~Cg~~-~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~YlK 264 (309)
T 2fiy_A 222 RIKCSHCEES-KHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLK 264 (309)
T ss_dssp TTSCSSSCCC-SCCEEECCCC-CCCSTTCSEEEEEETTTTEEEE
T ss_pred CcCCcCCCCC-CCeeEEEecCccccCCCcceEEEEcccccchHh
Confidence 4789999998 4677775443 1 22 2389999999983
No 6
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A
Probab=48.60 E-value=6.7 Score=33.20 Aligned_cols=37 Identities=19% Similarity=0.603 Sum_probs=23.2
Q ss_pred ccCCCCCCCCCcceeeecccCCCCC---chhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQP---RHFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~CrRyWT 93 (270)
...||+|...+..|--.+-.+..-| -|.|..|..-|.
T Consensus 137 ~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~ 176 (178)
T 3po3_S 137 RFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK 176 (178)
T ss_dssp SSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred CcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCCeec
Confidence 4689999976654322222222222 388999999985
No 7
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A
Probab=45.29 E-value=8.6 Score=34.89 Aligned_cols=37 Identities=19% Similarity=0.615 Sum_probs=23.5
Q ss_pred ccCCCCCCCCCcceeeecccCCCCC---chhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQP---RHFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~CrRyWT 93 (270)
...||+|...+..|-=.+..+...| -|.|..|..-|.
T Consensus 268 ~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~ 307 (309)
T 1pqv_S 268 RFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307 (309)
T ss_pred cccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCcee
Confidence 4689999965544422233333333 288999999885
No 8
>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A
Probab=42.91 E-value=13 Score=25.67 Aligned_cols=41 Identities=22% Similarity=0.536 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNV 101 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnv 101 (270)
...|-.|...+|-. .-.- .....+|-+|.-||-..|..|-+
T Consensus 4 ~~~C~~C~tt~Tp~--WR~g--p~G~~LCNaCGl~~k~~~~~RP~ 44 (46)
T 1gnf_A 4 ARECVNCGATATPL--WRRD--RTGHYLCNACGLYHKMNGQNRPL 44 (46)
T ss_dssp SCCCTTTCCCCCSS--CBCC--TTCCCBCSHHHHHHHHTCSCCCC
T ss_pred CCCCCCcCCCCCCc--CccC--CCCCccchHHHHHHHHcCCCCCC
Confidence 46699999887752 1111 12238999999999999998743
No 9
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=41.42 E-value=5.6 Score=32.52 Aligned_cols=38 Identities=26% Similarity=0.621 Sum_probs=0.0
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhccccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWTA 94 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~ 94 (270)
...||+|...+..|=..+-.+...|- |.|..|.--|.+
T Consensus 92 ~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~C~~~w~e 132 (133)
T 3qt1_I 92 DRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKE 132 (133)
T ss_dssp -----------------------------------------
T ss_pred cCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCCCCCEeCc
Confidence 37899999876654333333333332 889999999975
No 10
>3dfx_A Trans-acting T-cell-specific transcription factor GATA-3; activator, DNA-binding, metal-binding, nucleus; HET: DNA; 2.70A {Mus musculus} PDB: 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A*
Probab=39.52 E-value=22 Score=25.96 Aligned_cols=44 Identities=18% Similarity=0.488 Sum_probs=31.6
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccC
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPV 103 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPV 103 (270)
....|-.|...+|-. .-.- .....+|-+|.=||-..|..|-+.+
T Consensus 6 ~~~~C~~C~tt~Tp~--WR~g--p~G~~LCNACGl~~~~~~~~RP~~~ 49 (63)
T 3dfx_A 6 AGTSCANCQTTTTTL--WRRN--ANGDPVCNACGLYYKLHNINRPLTM 49 (63)
T ss_dssp TTCCCTTTCCSCCSS--CCCC--TTSCCCCHHHHHHHHHHSSCCCGGG
T ss_pred CCCcCCCcCCCCCCc--cCCC--CCCCchhhHHHHHHHHcCCCCCcCc
Confidence 346699999887752 1111 1223899999999999999887765
No 11
>4hc9_A Trans-acting T-cell-specific transcription factor; zinc finger, GATA transcription factor, DNA bridging, transc DNA complex; HET: DNA; 1.60A {Homo sapiens} PDB: 4hc7_A* 4hca_A* 3dfx_A* 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A* 1gnf_A 1y0j_A 2l6y_A 2l6z_A
Probab=36.14 E-value=14 Score=29.47 Aligned_cols=49 Identities=18% Similarity=0.451 Sum_probs=35.4
Q ss_pred CCcccccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccCC
Q 024229 52 PQRERVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPVG 104 (270)
Q Consensus 52 p~~~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPVG 104 (270)
+.......|-.|...+|-- .- .-+..+.+|-+|.-||...|..|-+-+-
T Consensus 54 ~~~~~~~~C~~C~t~~tp~--WR--r~~~g~~lCNaCgl~~~~~~~~rp~~~~ 102 (115)
T 4hc9_A 54 AARRAGTSCANCQTTTTTL--WR--RNANGDPVCNACGLYYKLHNINRPLTMK 102 (115)
T ss_dssp CCCCTTCCCTTTCCSCCSS--CE--ECTTSCEECHHHHHHHHHHSSCCCGGGC
T ss_pred ccccccccCCCcCCCCcce--eE--ECCCCCCcchHHHHHHHHhCCCCCcccc
Confidence 3445578999999988742 11 1123368999999999999998877653
No 12
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Probab=34.87 E-value=5.9 Score=34.70 Aligned_cols=38 Identities=21% Similarity=0.454 Sum_probs=30.7
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccC
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAG 95 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~G 95 (270)
+..|+.|...=+..|+.+= -.++...-|..|++.|+..
T Consensus 193 g~~C~~C~~~~H~~C~~~~-~~~~~~~~CP~C~~~W~~~ 230 (238)
T 3nw0_A 193 GQSCETCGIRMHLPCVAKY-FQSNAEPRCPHCNDYWPHE 230 (238)
T ss_dssp CEECSSSCCEECHHHHHHH-TTTCSSCBCTTTCCBCCSC
T ss_pred CcccCccChHHHHHHHHHH-HHhCCCCCCCCCCCCCCCC
Confidence 4779999999999998654 3456678899999999875
No 13
>4gat_A Nitrogen regulatory protein AREA; DNA binding protein, transcription factor, zinc binding domain, complex (transcription regulation/DNA); HET: DNA; NMR {Emericella nidulans} SCOP: g.39.1.1 PDB: 5gat_A* 6gat_A* 7gat_A*
Probab=32.49 E-value=38 Score=24.81 Aligned_cols=45 Identities=16% Similarity=0.452 Sum_probs=31.8
Q ss_pred ccccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccC
Q 024229 55 ERVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPV 103 (270)
Q Consensus 55 ~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPV 103 (270)
.....|-.|.+.+|-- .=. ...-+ .+|-+|.-||-.-|.+|-+-.
T Consensus 7 ~~~~~C~~C~t~~Tp~-WR~--gp~G~-~LCNaCGl~~~~~~~~RP~~~ 51 (66)
T 4gat_A 7 NGPTTCTNCFTQTTPL-WRR--NPEGQ-PLCNACGLFLKLHGVVRPLSL 51 (66)
T ss_dssp SSSCCCTTTCCCCCSS-CEE--ETTTE-EECHHHHHHHHHHCSCCCGGG
T ss_pred CCCCCCCCCCCCCCCc-CCc--CCCCC-CccHHHHHHHHHcCCCCchhh
Confidence 3457899999988751 111 11222 899999999999999876644
No 14
>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, finger, RNA recognition motif, 5' splice site; 5.49A {Homo sapiens} PDB: 1uw2_A 2vrd_A
Probab=31.72 E-value=12 Score=28.55 Aligned_cols=17 Identities=29% Similarity=0.903 Sum_probs=14.7
Q ss_pred CchhhhhcccccccCCc
Q 024229 81 PRHFCKTCRRYWTAGGS 97 (270)
Q Consensus 81 PR~fCk~CrRyWT~GGt 97 (270)
|||||+=|..|.|+.-.
T Consensus 2 PkYyCdYCd~~lt~Ds~ 18 (77)
T 3cw1_L 2 PKFYCDYCDTYLTHDSP 18 (77)
T ss_pred CCcccccCCceecCCCH
Confidence 89999999999987643
No 15
>1tie_A Erythrina trypsin inhibitor; proteinase inhibitor (trypsin); 2.50A {Erythrina caffra} SCOP: b.42.4.1
Probab=30.86 E-value=12 Score=31.40 Aligned_cols=20 Identities=40% Similarity=0.732 Sum_probs=16.5
Q ss_pred ccccccc-ccCCCCccccccccc
Q 024229 15 YYNLLYC-FCNPSPICKGIGFVT 36 (270)
Q Consensus 15 ~~~~~~~-~~~~~~~~~~i~~~~ 36 (270)
.|+|+|| +| ...|.-||+..
T Consensus 126 ~YKL~~Cp~c--~~~C~dvGi~~ 146 (172)
T 1tie_A 126 SYKLLYCEGK--HEKCASIGINR 146 (172)
T ss_dssp EEEEEEECST--TTCEEEEEEEE
T ss_pred cEEEEEeCCC--CCccccceEEE
Confidence 5999999 67 56799999874
No 16
>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}
Probab=30.53 E-value=49 Score=24.28 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=20.0
Q ss_pred ccccCCCCCCCCCcceeeecccCCCCCchhhhhcccccc
Q 024229 55 ERVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWT 93 (270)
Q Consensus 55 ~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT 93 (270)
.+...|..|... | ++..-||-|+.|.+-.=
T Consensus 19 ~~~~~C~~C~~~---F------s~~~RrHHCR~CG~v~C 48 (84)
T 1z2q_A 19 EDAPACNGCGCV---F------TTTVRRHHCRNCGYVLC 48 (84)
T ss_dssp TTCCBCTTTCCB---C------CTTSCCEECTTTCCEEC
T ss_pred CCCCCCcCcCCc---c------ccchhcccccCCCcEEC
Confidence 345678888765 3 34467888888876543
No 17
>2k2d_A Ring finger and CHY zinc finger domain- containing protein 1; zinc-binding protein, cytoplasm, metal-binding, nucleus, metal binding protein; NMR {Homo sapiens}
Probab=30.26 E-value=18 Score=27.17 Aligned_cols=12 Identities=33% Similarity=0.808 Sum_probs=11.1
Q ss_pred cCCCCCCCCCcc
Q 024229 58 LNCPRCNSTDTK 69 (270)
Q Consensus 58 ~~CPRC~S~~Tk 69 (270)
++||.|.|.||+
T Consensus 56 ~kC~~C~SyNTr 67 (79)
T 2k2d_A 56 MKCKICESYNTA 67 (79)
T ss_dssp CCCTTTSCCCEE
T ss_pred ccCcCCCCcCeE
Confidence 489999999998
No 18
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=29.43 E-value=16 Score=32.30 Aligned_cols=29 Identities=14% Similarity=0.462 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||-.|++
T Consensus 240 g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 268 (268)
T 1k82_A 240 GEPCRVCGTPIVATKH-A----QRATFYCRQCQK 268 (268)
T ss_dssp TSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 4679999987766544 2 355599999985
No 19
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken STR genomics/proteomics initiative, RSGI, structural genomics; 1.90A {Thermus thermophilus} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=29.03 E-value=18 Score=32.12 Aligned_cols=29 Identities=31% Similarity=0.709 Sum_probs=21.4
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ -.+.-|||..|++
T Consensus 235 g~pC~~CG~~I~~~~~-----~gR~t~~CP~CQ~ 263 (266)
T 1ee8_A 235 GLPCPACGRPVERRVV-----AGRGTHFCPTCQG 263 (266)
T ss_dssp TSBCTTTCCBCEEEES-----SSCEEEECTTTTT
T ss_pred CCCCCCCCCEeeEEEE-----CCCceEECCCCCC
Confidence 4679999987666433 2356699999997
No 20
>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair, sequence context; HET: DNA 08Q; 1.60A {Geobacillus stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A* 3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A* 2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A* 3sar_A* 3sav_A* ...
Probab=27.93 E-value=18 Score=32.18 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||-.|++
T Consensus 245 g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 273 (273)
T 3u6p_A 245 GNPCKRCGTPIEKTVV-A----GRGTHYCPRCQR 273 (273)
T ss_dssp TSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred cCCCCCCCCeEEEEEE-C----CCCeEECCCCCC
Confidence 4689999987666433 2 255599999985
No 21
>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET: VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A* 1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A 1pjj_A*
Probab=27.59 E-value=18 Score=31.96 Aligned_cols=29 Identities=28% Similarity=0.677 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||..|++
T Consensus 242 G~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 270 (271)
T 2xzf_A 242 GEKCSRCGAEIQKIKV-A----GRGTHFCPVCQQ 270 (271)
T ss_dssp TSBCTTTCCBCEEEEE-T----TEEEEECTTTSC
T ss_pred CCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 4679999987666543 2 355599999986
No 22
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=24.50 E-value=21 Score=26.65 Aligned_cols=49 Identities=20% Similarity=0.365 Sum_probs=32.7
Q ss_pred CcccccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccCC
Q 024229 53 QRERVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPVG 104 (270)
Q Consensus 53 ~~~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPVG 104 (270)
..+....|-.|...+|-. +-.-..... .+|-+|.=||-..|+.|-+..-
T Consensus 4 ~~~~~~~C~nC~tt~Tp~--WRrg~~~~g-~LCNACGl~~~~~~~~RP~~~~ 52 (71)
T 2kae_A 4 MNKKSFQCSNCSVTETIR--WRNIRSKEG-IQCNACFIYQRKYNKTRPVTAV 52 (71)
T ss_dssp ----CCCCSSSCCSCCSS--CCCCSSSSC-CCSSHHHHHHHHHHSCCCTHHH
T ss_pred CCCCCCcCCccCCCCCCc--cccCCCCCC-ccchHHHHHHHHhCCCCCcccc
Confidence 345568899999998852 222111222 8999999999999998876543
No 23
>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82
Probab=23.39 E-value=29 Score=27.87 Aligned_cols=12 Identities=33% Similarity=0.828 Sum_probs=9.9
Q ss_pred cCCCCCCCCCcc
Q 024229 58 LNCPRCNSTDTK 69 (270)
Q Consensus 58 ~~CPRC~S~~Tk 69 (270)
..||+|.|.+..
T Consensus 85 srCP~CkSe~Ie 96 (105)
T 2gmg_A 85 SRCPKCKSEWIE 96 (105)
T ss_dssp SSCSSSCCCCBC
T ss_pred CCCcCCCCCccC
Confidence 569999998876
No 24
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=22.74 E-value=39 Score=22.36 Aligned_cols=33 Identities=18% Similarity=0.476 Sum_probs=22.0
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCchhhhhccccccc
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTA 94 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~ 94 (270)
..+.||.|.+.+-.| ...+-...|..|+.-+..
T Consensus 4 ~~~~CP~C~~~~l~~------d~~~gelvC~~CG~v~~e 36 (50)
T 1pft_A 4 KQKVCPACESAELIY------DPERGEIVCAKCGYVIEE 36 (50)
T ss_dssp SCCSCTTTSCCCEEE------ETTTTEEEESSSCCBCCC
T ss_pred ccEeCcCCCCcceEE------cCCCCeEECcccCCcccc
Confidence 357899998854332 234556999999776544
No 25
>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*
Probab=22.47 E-value=23 Score=31.16 Aligned_cols=29 Identities=31% Similarity=0.605 Sum_probs=20.3
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||-.|++
T Consensus 234 g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 262 (262)
T 1k3x_A 234 GEPCERCGSIIEKTTL-S----SRPFYWCPGCQH 262 (262)
T ss_dssp TSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred cCCCCCCCCEeEEEEE-C----CCCeEECCCCCC
Confidence 4579999987655433 2 345599999985
Done!