Query 042156
Match_columns 336
No_of_seqs 143 out of 202
Neff 2.3
Searched_HMMs 29240
Date Mon Mar 25 05:19:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042156.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042156hhsearch_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 79.9 1.2 4.1E-05 31.5 2.7 38 38-75 15-55 (57)
2 1tfi_A Transcriptional elongat 79.3 1.6 5.4E-05 31.1 3.2 39 36-74 7-48 (50)
3 3h0g_I DNA-directed RNA polyme 73.9 4.7 0.00016 32.2 5.0 41 35-75 69-112 (113)
4 2fiy_A Protein FDHE homolog; F 67.9 2.2 7.5E-05 39.8 2.0 37 36-73 220-263 (309)
5 1twf_I B12.6, DNA-directed RNA 64.5 6.5 0.00022 31.8 4.0 43 35-77 69-114 (122)
6 3po3_S Transcription elongatio 56.8 5.2 0.00018 34.5 2.3 38 37-74 136-176 (178)
7 1pqv_S STP-alpha, transcriptio 55.4 6 0.00021 36.5 2.6 38 37-74 267-307 (309)
8 3dfx_A Trans-acting T-cell-spe 51.1 11 0.00036 28.4 2.8 46 36-85 5-50 (63)
9 1gnf_A Transcription factor GA 44.5 13 0.00043 26.4 2.2 42 37-82 3-44 (46)
10 3cw1_L U1 small nuclear ribonu 43.0 6.8 0.00023 30.6 0.7 17 62-78 2-18 (77)
11 3qt1_I DNA-directed RNA polyme 42.3 5.3 0.00018 33.3 0.0 40 36-75 90-132 (133)
12 1k82_A Formamidopyrimidine-DNA 40.6 11 0.00036 34.0 1.7 31 36-71 238-268 (268)
13 1ee8_A MUTM (FPG) protein; bet 40.4 11 0.00039 33.9 1.9 31 36-71 233-263 (266)
14 3u6p_A Formamidopyrimidine-DNA 39.1 12 0.00039 34.0 1.7 31 36-71 243-273 (273)
15 3nw0_A Non-structural maintena 39.0 4.8 0.00016 35.8 -0.8 39 37-76 192-230 (238)
16 2xzf_A Formamidopyrimidine-DNA 38.5 12 0.00041 33.7 1.7 32 35-71 239-270 (271)
17 4gat_A Nitrogen regulatory pro 34.1 27 0.00091 26.3 2.7 45 36-84 7-51 (66)
18 1k3x_A Endonuclease VIII; hydr 33.2 15 0.0005 32.9 1.4 31 36-71 232-262 (262)
19 2kae_A GATA-type transcription 33.2 3.4 0.00012 31.7 -2.4 48 35-85 5-52 (71)
20 4hc9_A Trans-acting T-cell-spe 32.7 29 0.001 28.2 3.0 46 36-85 57-102 (115)
21 2gmg_A Hypothetical protein PF 29.5 28 0.00096 28.6 2.3 15 36-50 82-96 (105)
22 1pft_A TFIIB, PFTFIIBN; N-term 29.1 35 0.0012 23.1 2.4 33 37-75 4-36 (50)
23 2vut_I AREA, nitrogen regulato 27.2 18 0.00062 25.2 0.7 41 39-83 2-42 (43)
24 2akl_A PHNA-like protein PA012 25.9 45 0.0015 28.8 3.0 33 37-77 26-58 (138)
25 2zjr_Z 50S ribosomal protein L 25.7 28 0.00096 25.6 1.5 30 35-78 27-56 (60)
26 2k2d_A Ring finger and CHY zin 25.2 26 0.00087 26.9 1.3 12 39-50 56-67 (79)
27 2jny_A Uncharacterized BCR; st 24.4 27 0.00094 26.2 1.3 31 36-73 8-38 (67)
28 2pk7_A Uncharacterized protein 22.8 34 0.0012 25.7 1.6 30 37-73 7-36 (69)
29 2con_A RUH-035 protein, NIN on 22.6 24 0.00083 27.5 0.7 36 37-87 14-49 (79)
30 1ffk_W Ribosomal protein L37AE 21.1 38 0.0013 26.1 1.5 44 35-85 24-67 (73)
31 2jr6_A UPF0434 protein NMA0874 20.9 35 0.0012 25.6 1.3 31 36-73 6-36 (68)
32 1nui_A DNA primase/helicase; z 20.8 42 0.0014 28.8 1.9 30 37-72 13-42 (255)
No 1
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=79.90 E-value=1.2 Score=31.51 Aligned_cols=38 Identities=21% Similarity=0.597 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWTQ 75 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT~ 75 (336)
..+||+|...+..|--.+-.....| .|.|..|.--|+.
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 5789999985444433333333444 3899999999976
No 2
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=79.33 E-value=1.6 Score=31.08 Aligned_cols=39 Identities=21% Similarity=0.579 Sum_probs=29.1
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWT 74 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 74 (336)
.....||+|...+..|--.+..+...|- |.|..|..-|.
T Consensus 7 t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~ 48 (50)
T 1tfi_A 7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 48 (50)
T ss_dssp CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred eCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence 3467899999888777665555555553 89999998885
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=73.91 E-value=4.7 Score=32.21 Aligned_cols=41 Identities=20% Similarity=0.469 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWTQ 75 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~ 75 (336)
+....+||+|...+..|-..+-.+...|- |.|..|.--|+.
T Consensus 69 p~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~ 112 (113)
T 3h0g_I 69 PRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE 112 (113)
T ss_dssp CBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred CCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence 34458999999877554333333322222 889999999974
No 4
>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=67.89 E-value=2.2 Score=39.81 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCCCceeeeecccC-------CCCCccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYS-------LSQPRYFCKTCRRYW 73 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~-------~~QPRhfCksCrRYW 73 (336)
-...+||.|... .++-|+.--. ..---+.|..|+.|+
T Consensus 220 ~~R~~C~~Cg~~-~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~Yl 263 (309)
T 2fiy_A 220 YVRIKCSHCEES-KHLAYLSLEHDGQPAEKAVLRAETCPSCQGYL 263 (309)
T ss_dssp CCTTSCSSSCCC-SCCEEECCCC-CCCSTTCSEEEEEETTTTEEE
T ss_pred ecCcCCcCCCCC-CCeeEEEecCccccCCCcceEEEEcccccchH
Confidence 357899999998 4677775443 112238999999997
No 5
>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=64.47 E-value=6.5 Score=31.81 Aligned_cols=43 Identities=19% Similarity=0.515 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccCc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWTQGG 77 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~GG 77 (336)
+.....||+|...+.-|-..+-.+-..|- |.|..|.--|+..-
T Consensus 69 p~t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~nn 114 (122)
T 1twf_I 69 PRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQ 114 (122)
T ss_dssp CCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCT
T ss_pred cccCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccCC
Confidence 33467899999876665444444444443 89999999998753
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=56.82 E-value=5.2 Score=34.50 Aligned_cols=38 Identities=18% Similarity=0.565 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCC---cccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWT 74 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT 74 (336)
....||+|...+..|--.+-.+-.-| -|.|..|..-|.
T Consensus 136 ~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~ 176 (178)
T 3po3_S 136 DRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK 176 (178)
T ss_dssp SSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred CCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCCeec
Confidence 35789999976654322222222222 388999999995
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=55.40 E-value=6 Score=36.47 Aligned_cols=38 Identities=18% Similarity=0.576 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCC---cccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWT 74 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT 74 (336)
....||+|...+..|-=.+..+-..| -|.|..|..-|.
T Consensus 267 ~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~ 307 (309)
T 1pqv_S 267 DRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307 (309)
T ss_pred ccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCcee
Confidence 35789999966544422222222223 289999999885
No 8
>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=51.09 E-value=11 Score=28.38 Aligned_cols=46 Identities=15% Similarity=0.446 Sum_probs=33.6
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
.....|-.|...+|-. +-.- .....+|-+|.-||-..|+.|-+.+-
T Consensus 5 ~~~~~C~~C~tt~Tp~--WR~g--p~G~~LCNACGl~~~~~~~~RP~~~~ 50 (63)
T 3dfx_A 5 RAGTSCANCQTTTTTL--WRRN--ANGDPVCNACGLYYKLHNINRPLTMK 50 (63)
T ss_dssp CTTCCCTTTCCSCCSS--CCCC--TTSCCCCHHHHHHHHHHSSCCCGGGC
T ss_pred CCCCcCCCcCCCCCCc--cCCC--CCCCchhhHHHHHHHHcCCCCCcCcC
Confidence 4577899999987752 2111 12238999999999999998877763
No 9
>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=44.47 E-value=13 Score=26.37 Aligned_cols=42 Identities=21% Similarity=0.605 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNV 82 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNV 82 (336)
....|..|...+|-. +-.- .....+|-+|.-||-..|.+|-+
T Consensus 3 ~~~~C~~C~tt~Tp~--WR~g--p~G~~LCNaCGl~~k~~~~~RP~ 44 (46)
T 1gnf_A 3 EARECVNCGATATPL--WRRD--RTGHYLCNACGLYHKMNGQNRPL 44 (46)
T ss_dssp CSCCCTTTCCCCCSS--CBCC--TTCCCBCSHHHHHHHHTCSCCCC
T ss_pred CCCCCCCcCCCCCCc--CccC--CCCCccchHHHHHHHHcCCCCCC
Confidence 456799999887753 2111 12238999999999999998743
No 10
>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=43.01 E-value=6.8 Score=30.59 Aligned_cols=17 Identities=29% Similarity=1.038 Sum_probs=14.7
Q ss_pred CcccccccccccccCcc
Q 042156 62 PRYFCKTCRRYWTQGGT 78 (336)
Q Consensus 62 PRhfCksCrRYWT~GGt 78 (336)
|||||+-|..|.|+.-.
T Consensus 2 PkYyCdYCd~~lt~Ds~ 18 (77)
T 3cw1_L 2 PKFYCDYCDTYLTHDSP 18 (77)
T ss_pred CCcccccCCceecCCCH
Confidence 89999999999987644
No 11
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=42.32 E-value=5.3 Score=33.30 Aligned_cols=40 Identities=28% Similarity=0.692 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWTQ 75 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT~ 75 (336)
.....||+|...+..|-..+-.+..-| -|.|..|.--|..
T Consensus 90 ~t~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~C~~~w~e 132 (133)
T 3qt1_I 90 RSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKE 132 (133)
T ss_dssp -------------------------------------------
T ss_pred cccCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCCCCCEeCc
Confidence 345789999987765433333322222 2889999999975
No 12
>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=40.62 E-value=11 Score=34.05 Aligned_cols=31 Identities=13% Similarity=0.536 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|.-+ . .+.-|||..|++
T Consensus 238 R~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 268 (268)
T 1k82_A 238 RKGEPCRVCGTPIVATKH-A----QRATFYCRQCQK 268 (268)
T ss_dssp CTTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred cCCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 445789999987666544 2 355599999985
No 13
>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=40.41 E-value=11 Score=33.86 Aligned_cols=31 Identities=23% Similarity=0.536 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|.-+ . .+.-|||..|++
T Consensus 233 R~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 263 (266)
T 1ee8_A 233 REGLPCPACGRPVERRVV-A----GRGTHFCPTCQG 263 (266)
T ss_dssp CTTSBCTTTCCBCEEEES-S----SCEEEECTTTTT
T ss_pred cCCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 455789999987666533 1 355699999997
No 14
>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=39.10 E-value=12 Score=33.96 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|.-+ . .+.-|||..|++
T Consensus 243 R~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 273 (273)
T 3u6p_A 243 RQGNPCKRCGTPIEKTVV-A----GRGTHYCPRCQR 273 (273)
T ss_dssp CTTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CCcCCCCCCCCeEEEEEE-C----CCCeEECCCCCC
Confidence 345689999987666433 2 355599999985
No 15
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Probab=39.02 E-value=4.8 Score=35.84 Aligned_cols=39 Identities=26% Similarity=0.565 Sum_probs=30.5
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccccccC
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQG 76 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~G 76 (336)
....|+.|...=+..|++.=. ..+....|..|+..|+..
T Consensus 192 ~g~~C~~C~~~~H~~C~~~~~-~~~~~~~CP~C~~~W~~~ 230 (238)
T 3nw0_A 192 QGQSCETCGIRMHLPCVAKYF-QSNAEPRCPHCNDYWPHE 230 (238)
T ss_dssp SCEECSSSCCEECHHHHHHHT-TTCSSCBCTTTCCBCCSC
T ss_pred CCcccCccChHHHHHHHHHHH-HhCCCCCCCCCCCCCCCC
Confidence 357788888888888886543 456678999999999865
No 16
>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=38.52 E-value=12 Score=33.69 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
.....+||||...=.|.-+ . .+.-|||..|++
T Consensus 239 gR~G~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 270 (271)
T 2xzf_A 239 GKTGEKCSRCGAEIQKIKV-A----GRGTHFCPVCQQ 270 (271)
T ss_dssp TCTTSBCTTTCCBCEEEEE-T----TEEEEECTTTSC
T ss_pred cCCCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 3455789999987666543 2 345599999986
No 17
>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=34.07 E-value=27 Score=26.29 Aligned_cols=45 Identities=18% Similarity=0.517 Sum_probs=32.6
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccC
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPV 84 (336)
..+..|-.|...+|-. .-. ...-+ .+|-+|.-||-.-|++|-+..
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 4578999999988752 111 11222 899999999999999877665
No 18
>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=33.22 E-value=15 Score=32.94 Aligned_cols=31 Identities=32% Similarity=0.777 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||+|...=.|.-+ . .+.-|||..|++
T Consensus 232 R~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 262 (262)
T 1k3x_A 232 RDGEPCERCGSIIEKTTL-S----SRPFYWCPGCQH 262 (262)
T ss_dssp CTTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CCcCCCCCCCCEeEEEEE-C----CCCeEECCCCCC
Confidence 445689999987655433 2 344599999985
No 19
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=33.20 E-value=3.4 Score=31.71 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=33.2
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
......|-.|...+|-. +-.-.... ..+|-+|.-||-+.|+.|-+..-
T Consensus 5 ~~~~~~C~nC~tt~Tp~--WRrg~~~~-g~LCNACGl~~~~~~~~RP~~~~ 52 (71)
T 2kae_A 5 NKKSFQCSNCSVTETIR--WRNIRSKE-GIQCNACFIYQRKYNKTRPVTAV 52 (71)
T ss_dssp ---CCCCSSSCCSCCSS--CCCCSSSS-CCCSSHHHHHHHHHHSCCCTHHH
T ss_pred CCCCCcCCccCCCCCCc--cccCCCCC-CccchHHHHHHHHhCCCCCcccc
Confidence 45678999999998752 33211122 28999999999999998877664
No 20
>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=32.71 E-value=29 Score=28.15 Aligned_cols=46 Identities=15% Similarity=0.434 Sum_probs=34.3
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
.....|-.|...+|-. .-. -..-+.+|-+|.-||..-|..|-+.+-
T Consensus 57 ~~~~~C~~C~t~~tp~--WRr--~~~g~~lCNaCgl~~~~~~~~rp~~~~ 102 (115)
T 4hc9_A 57 RAGTSCANCQTTTTTL--WRR--NANGDPVCNACGLYYKLHNINRPLTMK 102 (115)
T ss_dssp CTTCCCTTTCCSCCSS--CEE--CTTSCEECHHHHHHHHHHSSCCCGGGC
T ss_pred cccccCCCcCCCCcce--eEE--CCCCCCcchHHHHHHHHhCCCCCcccc
Confidence 4578999999988742 111 122368999999999999999887774
No 21
>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=29.53 E-value=28 Score=28.62 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCCce
Q 042156 36 PQPQKCPRCESLNTK 50 (336)
Q Consensus 36 ~~~~~CPRC~S~nTK 50 (336)
..+-.||+|.|.+..
T Consensus 82 ~kPsrCP~CkSe~Ie 96 (105)
T 2gmg_A 82 NIPSRCPKCKSEWIE 96 (105)
T ss_dssp SCCSSCSSSCCCCBC
T ss_pred CCCCCCcCCCCCccC
Confidence 456778888887654
No 22
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=29.11 E-value=35 Score=23.11 Aligned_cols=33 Identities=21% Similarity=0.556 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 75 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~ 75 (336)
..+.||.|.+.+-.| ....-...|+.|+.-+..
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 467899998854333 223456899999876543
No 23
>2vut_I AREA, nitrogen regulatory protein AREA; transcription regulation, protein-protein interactions, metal-binding, nitrate assimilation; HET: NAD; 2.3A {Emericella nidulans} SCOP: g.39.1.1 PDB: 2vus_I* 2vuu_I*
Probab=27.22 E-value=18 Score=25.16 Aligned_cols=41 Identities=17% Similarity=0.531 Sum_probs=28.4
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccccccccCccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVP 83 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVP 83 (336)
..|-.|...+|-. +-.- .....+|-+|.-||-..|++|-+.
T Consensus 2 ~~C~~C~tt~Tp~--WR~g--p~G~~LCNaCGl~~k~~~~~RP~~ 42 (43)
T 2vut_I 2 TTCTNCFTQTTPL--WRRN--PEGQPLCNACGLFLKLHGVVRPLS 42 (43)
T ss_dssp CCCSSSCCCCCSC--CEEC--TTSCEECHHHHHHHHHHSSCCCCC
T ss_pred CcCCccCCCCCCc--cccC--CCCCcccHHHHHHHHHhCCCCCCC
Confidence 5688888877642 1111 122389999999999999987653
No 24
>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5
Probab=25.85 E-value=45 Score=28.82 Aligned_cols=33 Identities=24% Similarity=0.574 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGG 77 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 77 (336)
....||.|.|..|-. ...-+.|..|.-=|+...
T Consensus 26 ~lP~CP~C~seytYe--------Dg~l~vCPeC~hEW~~~~ 58 (138)
T 2akl_A 26 TLPPCPQCNSEYTYE--------DGALLVCPECAHEWSPNE 58 (138)
T ss_dssp CSCCCTTTCCCCCEE--------CSSSEEETTTTEEECTTT
T ss_pred cCCCCCCCCCcceEe--------cCCeEECCccccccCCcc
Confidence 467899999987743 456699999999997554
No 25
>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...
Probab=25.73 E-value=28 Score=25.64 Aligned_cols=30 Identities=30% Similarity=0.817 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGT 78 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGt 78 (336)
.+....||.|... + .|.+.|.+|.-| +|-.
T Consensus 27 ~p~l~~c~~cG~~--~----------~pH~vc~~CG~Y--~gr~ 56 (60)
T 2zjr_Z 27 APNLTECPQCHGK--K----------LSHHICPNCGYY--DGRQ 56 (60)
T ss_dssp CCCCEECTTTCCE--E----------CTTBCCTTTCBS--SSBC
T ss_pred CCCceECCCCCCE--e----------CCceEcCCCCcC--CCEE
Confidence 4578889999875 3 899999999977 5543
No 26
>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=25.20 E-value=26 Score=26.91 Aligned_cols=12 Identities=58% Similarity=0.941 Sum_probs=11.0
Q ss_pred CCCCCCCCCCce
Q 042156 39 QKCPRCESLNTK 50 (336)
Q Consensus 39 ~~CPRC~S~nTK 50 (336)
.+||.|.|.||+
T Consensus 56 ~kC~~C~SyNTr 67 (79)
T 2k2d_A 56 MKCKICESYNTA 67 (79)
T ss_dssp CCCTTTSCCCEE
T ss_pred ccCcCCCCcCeE
Confidence 389999999998
No 27
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1
Probab=24.37 E-value=27 Score=26.20 Aligned_cols=31 Identities=13% Similarity=0.169 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYW 73 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYW 73 (336)
-..+.||.|... .-| ....-...|+.|++-+
T Consensus 8 LeiL~CP~ck~~---L~~----~~~~g~LvC~~c~~~Y 38 (67)
T 2jny_A 8 LEVLACPKDKGP---LRY----LESEQLLVNERLNLAY 38 (67)
T ss_dssp TCCCBCTTTCCB---CEE----ETTTTEEEETTTTEEE
T ss_pred HHHhCCCCCCCc---CeE----eCCCCEEEcCCCCccc
Confidence 357899999983 222 2235568899998754
No 28
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1
Probab=22.80 E-value=34 Score=25.67 Aligned_cols=30 Identities=17% Similarity=0.299 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYW 73 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYW 73 (336)
..+.||.|...-. | ....-...|+.|++-+
T Consensus 7 eiL~CP~ck~~L~---~----~~~~~~LiC~~cg~~Y 36 (69)
T 2pk7_A 7 DILACPICKGPLK---L----SADKTELISKGAGLAY 36 (69)
T ss_dssp GTCCCTTTCCCCE---E----CTTSSEEEETTTTEEE
T ss_pred hheeCCCCCCcCe---E----eCCCCEEEcCCCCcEe
Confidence 4789999996422 2 2335668899998754
No 29
>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1
Probab=22.63 E-value=24 Score=27.48 Aligned_cols=36 Identities=28% Similarity=0.483 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCC
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGG 87 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVGGG 87 (336)
-.+.|-.|-... ..-.|+||..|. +.||+-|+|.-.
T Consensus 14 ~iLrC~aCf~~t----------~~~~k~FCp~CG-----n~TL~Rvsvsvd 49 (79)
T 2con_A 14 YILRCHGCFKTT----------SDMNRVFCGHCG-----NKTLKKVSVTIN 49 (79)
T ss_dssp EEEECSSSCCEE----------SCSSCCSCSSSC-----CSCCEEEECBCC
T ss_pred eeeEecccceEC----------CCcccccccccC-----cccceEEEEEEC
Confidence 367788886542 457899999995 469999988543
No 30
>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*
Probab=21.09 E-value=38 Score=26.12 Aligned_cols=44 Identities=23% Similarity=0.393 Sum_probs=30.3
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
+...+.||.|....-|= ..----.|+.|.+-|+.|.-..+.|.+
T Consensus 24 q~~ky~C~fCgk~~vkR-------~a~GIW~C~~C~~~~AGGAy~~~T~~~ 67 (73)
T 1ffk_W 24 HKKKYKCPVCGFPKLKR-------ASTSIWVCGHCGYKIAGGAYTPETVAG 67 (73)
T ss_pred cccCccCCCCCCceeEE-------EEeEEEECCCCCcEEECCCccccccce
Confidence 35788999998755441 001126799999999888776666654
No 31
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=20.93 E-value=35 Score=25.58 Aligned_cols=31 Identities=10% Similarity=0.273 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYW 73 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYW 73 (336)
-..+.||.|... .-| ....-...|+.|++-+
T Consensus 6 L~iL~CP~ck~~---L~~----~~~~~~LiC~~cg~~Y 36 (68)
T 2jr6_A 6 LDILVCPVTKGR---LEY----HQDKQELWSRQAKLAY 36 (68)
T ss_dssp SCCCBCSSSCCB---CEE----ETTTTEEEETTTTEEE
T ss_pred hhheECCCCCCc---CeE----eCCCCEEEcCCCCcEe
Confidence 357899999963 222 2234668899998754
No 32
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2
Probab=20.80 E-value=42 Score=28.85 Aligned_cols=30 Identities=20% Similarity=0.613 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRY 72 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRY 72 (336)
.+.+||-|...+. |-.|.. --++|..|..+
T Consensus 13 ~~~~CP~Cg~~d~-~~~~~d-----g~~~C~~Cg~~ 42 (255)
T 1nui_A 13 YHIPCDNCGSSDG-NSLFSD-----GHTFCYVCEKW 42 (255)
T ss_dssp EEECCSSSCCSSC-EEEETT-----SCEEETTTCCE
T ss_pred cCCcCCCCCCCCC-ceEeCC-----CCeecccCCCc
Confidence 4789999998653 665642 24999999853
Done!