Query 040161
Match_columns 366
No_of_seqs 137 out of 202
Neff 2.2
Searched_HMMs 29240
Date Mon Mar 25 08:44:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040161.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/040161hhsearch_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 84.1 0.85 2.9E-05 32.5 3.3 38 87-124 15-55 (57)
2 1tfi_A Transcriptional elongat 81.3 1.1 3.9E-05 32.1 3.0 38 86-123 8-48 (50)
3 3h0g_I DNA-directed RNA polyme 75.6 4 0.00014 32.9 5.0 38 87-124 72-112 (113)
4 3po3_S Transcription elongatio 71.2 2.9 0.0001 36.3 3.4 38 86-123 136-176 (178)
5 2fiy_A Protein FDHE homolog; F 70.8 1.8 6.2E-05 40.6 2.2 36 86-122 221-263 (309)
6 1twf_I B12.6, DNA-directed RNA 64.2 6.6 0.00023 32.0 4.0 40 87-126 72-114 (122)
7 1pqv_S STP-alpha, transcriptio 60.1 4.5 0.00015 37.6 2.6 37 87-123 268-307 (309)
8 1k82_A Formamidopyrimidine-DNA 57.4 4 0.00014 37.0 1.7 31 85-120 238-268 (268)
9 1ee8_A MUTM (FPG) protein; bet 57.0 4.4 0.00015 36.8 1.9 31 85-120 233-263 (266)
10 3u6p_A Formamidopyrimidine-DNA 55.9 4.4 0.00015 36.9 1.7 31 85-120 243-273 (273)
11 2xzf_A Formamidopyrimidine-DNA 55.2 4.6 0.00016 36.6 1.7 31 85-120 240-270 (271)
12 3nw0_A Non-structural maintena 51.4 2.5 8.4E-05 37.9 -0.7 39 86-125 192-230 (238)
13 1k3x_A Endonuclease VIII; hydr 49.0 6 0.0002 35.7 1.4 30 86-120 233-262 (262)
14 3qt1_I DNA-directed RNA polyme 46.2 4.2 0.00015 34.1 0.0 38 87-124 92-132 (133)
15 3cw1_L U1 small nuclear ribonu 45.8 5.6 0.00019 31.3 0.6 17 111-127 2-18 (77)
16 1gnf_A Transcription factor GA 40.4 17 0.00058 25.9 2.4 42 86-131 3-44 (46)
17 2js4_A UPF0434 protein BB2007; 39.2 25 0.00087 26.7 3.3 34 83-123 4-37 (70)
18 1pft_A TFIIB, PFTFIIBN; N-term 37.3 24 0.00081 24.2 2.7 33 86-124 4-36 (50)
19 2jny_A Uncharacterized BCR; st 32.3 16 0.00056 27.7 1.3 34 82-122 5-38 (67)
20 2jr6_A UPF0434 protein NMA0874 32.0 23 0.00079 26.8 2.1 33 83-122 4-36 (68)
21 3dfx_A Trans-acting T-cell-spe 31.5 36 0.0012 25.7 3.0 48 83-134 3-50 (63)
22 2pk7_A Uncharacterized protein 29.9 23 0.00077 26.9 1.7 31 85-122 6-36 (69)
23 2gmg_A Hypothetical protein PF 29.9 25 0.00085 29.2 2.1 14 86-99 83-96 (105)
24 2kpi_A Uncharacterized protein 29.5 44 0.0015 24.3 3.1 33 81-122 4-38 (56)
25 2k2d_A Ring finger and CHY zin 28.8 21 0.00071 27.6 1.4 13 87-99 55-67 (79)
26 1wd2_A Ariadne-1 protein homol 28.8 41 0.0014 24.5 2.9 42 86-127 5-49 (60)
27 4gat_A Nitrogen regulatory pro 27.0 41 0.0014 25.5 2.7 45 85-133 7-51 (66)
28 2hf1_A Tetraacyldisaccharide-1 24.9 23 0.00078 26.8 0.9 32 84-122 5-36 (68)
29 1y02_A CARP2, FYVE-ring finger 21.8 32 0.0011 28.5 1.3 37 82-127 14-50 (120)
30 1p91_A Ribosomal RNA large sub 21.5 57 0.002 27.0 2.8 39 88-135 3-42 (269)
31 1k81_A EIF-2-beta, probable tr 21.3 30 0.001 23.2 0.9 31 88-122 1-31 (36)
32 2kae_A GATA-type transcription 20.2 30 0.001 26.7 0.8 49 83-134 4-52 (71)
No 1
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=84.12 E-value=0.85 Score=32.52 Aligned_cols=38 Identities=18% Similarity=0.590 Sum_probs=25.8
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCC---ccccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWTK 124 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT~ 124 (366)
..+||+|...+..|--.+-.....| .|.|..|.--|..
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 5789999984444433333333444 3999999999976
No 2
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=81.29 E-value=1.1 Score=32.09 Aligned_cols=38 Identities=18% Similarity=0.614 Sum_probs=28.4
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT 123 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT 123 (366)
....||+|...+..|--.+..+...|- |.|..|..-|.
T Consensus 8 ~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~ 48 (50)
T 1tfi_A 8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 48 (50)
T ss_dssp CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred CccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence 347899999887776665555555553 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=75.61 E-value=4 Score=32.88 Aligned_cols=38 Identities=18% Similarity=0.424 Sum_probs=24.9
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCc---cccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTK 124 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~ 124 (366)
..+||+|...+..|-..+-.....|- |.|..|...|.+
T Consensus 72 ~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~ 112 (113)
T 3h0g_I 72 DKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE 112 (113)
T ss_dssp CSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred ccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence 38999999876544333333222222 889999999974
No 4
>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=71.18 E-value=2.9 Score=36.31 Aligned_cols=38 Identities=16% Similarity=0.603 Sum_probs=23.1
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCC---cccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWT 123 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT 123 (366)
....||+|...+..|--.+-....-| -|.|..|..-|.
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 34799999975544322222222222 388999999995
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=70.80 E-value=1.8 Score=40.64 Aligned_cols=36 Identities=19% Similarity=0.613 Sum_probs=26.5
Q ss_pred CCcCCCCCCCCCceeeeecCcC-------CCCCccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYN-------LTQPRHFCKTCRRYW 122 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn-------~~QPRhfCksCrRYW 122 (366)
...+||.|... .++-|+.--. ...--+.|+.|+.|+
T Consensus 221 ~R~~C~~Cg~~-~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~Yl 263 (309)
T 2fiy_A 221 VRIKCSHCEES-KHLAYLSLEHDGQPAEKAVLRAETCPSCQGYL 263 (309)
T ss_dssp CTTSCSSSCCC-SCCEEECCCC-CCCSTTCSEEEEEETTTTEEE
T ss_pred cCcCCcCCCCC-CCeeEEEecCccccCCCcceEEEEcccccchH
Confidence 46789999998 4777875444 122238999999998
No 6
>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=64.21 E-value=6.6 Score=31.98 Aligned_cols=40 Identities=20% Similarity=0.520 Sum_probs=28.4
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccccCc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTKGG 126 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~GG 126 (366)
...||+|...+.-|-..+-.....|- |.|..|...|...-
T Consensus 72 ~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~nn 114 (122)
T 1twf_I 72 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQ 114 (122)
T ss_dssp CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCT
T ss_pred CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccCC
Confidence 47899999876555444444444443 89999999998753
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=60.11 E-value=4.5 Score=37.57 Aligned_cols=37 Identities=16% Similarity=0.623 Sum_probs=22.7
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCC---cccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWT 123 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT 123 (366)
...||+|...+..|-=.+......| -|.|..|..-|.
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 4689999955544322222222223 289999999985
No 8
>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=57.35 E-value=4 Score=37.01 Aligned_cols=31 Identities=13% Similarity=0.500 Sum_probs=22.7
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+..+||||...-.|.-+ . .+.-|||..|++
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 346789999987766544 2 355599999985
No 9
>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=57.04 E-value=4.4 Score=36.83 Aligned_cols=31 Identities=29% Similarity=0.738 Sum_probs=22.9
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+..+||||...-.|.-+ . .+.-|||..|++
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 356789999987666544 2 355699999997
No 10
>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=55.91 E-value=4.4 Score=36.93 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=22.4
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+..+||||...-.|.-+ . .+.-|||..|++
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 355799999987666543 2 255599999985
No 11
>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=55.20 E-value=4.6 Score=36.62 Aligned_cols=31 Identities=26% Similarity=0.697 Sum_probs=22.8
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+..+||||...-.|.-+ . .+.-|||..|++
T Consensus 240 R~G~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 270 (271)
T 2xzf_A 240 KTGEKCSRCGAEIQKIKV-A----GRGTHFCPVCQQ 270 (271)
T ss_dssp CTTSBCTTTCCBCEEEEE-T----TEEEEECTTTSC
T ss_pred CCCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 356789999987766544 2 255599999996
No 12
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Probab=51.36 E-value=2.5 Score=37.94 Aligned_cols=39 Identities=21% Similarity=0.573 Sum_probs=30.9
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccC
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKG 125 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~G 125 (366)
....|+.|...=+..|+++=. ..+....|..|++.|...
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 357899998888888986543 456678999999999875
No 13
>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=49.01 E-value=6 Score=35.71 Aligned_cols=30 Identities=27% Similarity=0.623 Sum_probs=21.5
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+.+||||...-.|.-+ . .+.-|||..|++
T Consensus 233 ~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 262 (262)
T 1k3x_A 233 DGEPCERCGSIIEKTTL-S----SRPFYWCPGCQH 262 (262)
T ss_dssp TTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CcCCCCCCCCEeEEEEE-C----CCCeEECCCCCC
Confidence 45689999987665433 2 345599999985
No 14
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=46.17 E-value=4.2 Score=34.14 Aligned_cols=38 Identities=24% Similarity=0.630 Sum_probs=0.0
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCC---ccccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWTK 124 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT~ 124 (366)
...||+|...+..|-..+-.....| -|.|..|..-|..
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 4799999987654433333322222 2889999999975
No 15
>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=45.79 E-value=5.6 Score=31.31 Aligned_cols=17 Identities=29% Similarity=0.929 Sum_probs=15.0
Q ss_pred CcccccccccccccCcc
Q 040161 111 PRHFCKTCRRYWTKGGA 127 (366)
Q Consensus 111 PRhfCksCrRYWT~GGt 127 (366)
|||||+-|..|.|+.-.
T Consensus 2 PkYyCdYCd~~lt~Ds~ 18 (77)
T 3cw1_L 2 PKFYCDYCDTYLTHDSP 18 (77)
T ss_pred CCcccccCCceecCCCH
Confidence 89999999999988754
No 16
>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=40.37 E-value=17 Score=25.93 Aligned_cols=42 Identities=19% Similarity=0.510 Sum_probs=30.1
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNV 131 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNV 131 (366)
+...|-.|...+|-. +..- .....+|-+|.-||-+.|..|-+
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 457899999887752 2211 12238999999999999987743
No 17
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=39.18 E-value=25 Score=26.71 Aligned_cols=34 Identities=21% Similarity=0.379 Sum_probs=23.4
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccc
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWT 123 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT 123 (366)
.--+.+.||.|... .-|- .......|+.|++-+-
T Consensus 4 ~LL~iL~CP~ck~~---L~~~----~~~~~LiC~~cg~~YP 37 (70)
T 2js4_A 4 RLLDILVCPVCKGR---LEFQ----RAQAELVCNADRLAFP 37 (70)
T ss_dssp CCCCCCBCTTTCCB---EEEE----TTTTEEEETTTTEEEE
T ss_pred HHhhheECCCCCCc---CEEe----CCCCEEEcCCCCceec
Confidence 44578999999983 3332 2356789999987653
No 18
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=37.29 E-value=24 Score=24.16 Aligned_cols=33 Identities=18% Similarity=0.534 Sum_probs=22.5
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTK 124 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~ 124 (366)
..+.||.|.+.+-.| ...+-...|+.|+.-+..
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 457899998854333 223556999999876653
No 19
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1
Probab=32.28 E-value=16 Score=27.65 Aligned_cols=34 Identities=12% Similarity=0.175 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCCceeeeecCcCCCCCccccccccccc
Q 040161 82 SGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW 122 (366)
Q Consensus 82 p~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW 122 (366)
+.--+.+.||.|... .-|- ...-...|+.|++-+
T Consensus 5 ~~LLeiL~CP~ck~~---L~~~----~~~g~LvC~~c~~~Y 38 (67)
T 2jny_A 5 PQLLEVLACPKDKGP---LRYL----ESEQLLVNERLNLAY 38 (67)
T ss_dssp GGGTCCCBCTTTCCB---CEEE----TTTTEEEETTTTEEE
T ss_pred HHHHHHhCCCCCCCc---CeEe----CCCCEEEcCCCCccc
Confidence 344578999999983 3332 235678999998755
No 20
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=32.03 E-value=23 Score=26.81 Aligned_cols=33 Identities=12% Similarity=0.256 Sum_probs=22.5
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCccccccccccc
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW 122 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW 122 (366)
.--+.+.||.|.. +.-|- ...-...|+.|++-+
T Consensus 4 ~LL~iL~CP~ck~---~L~~~----~~~~~LiC~~cg~~Y 36 (68)
T 2jr6_A 4 KFLDILVCPVTKG---RLEYH----QDKQELWSRQAKLAY 36 (68)
T ss_dssp SSSCCCBCSSSCC---BCEEE----TTTTEEEETTTTEEE
T ss_pred HHhhheECCCCCC---cCeEe----CCCCEEEcCCCCcEe
Confidence 3457899999996 33332 234678999998755
No 21
>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=31.49 E-value=36 Score=25.74 Aligned_cols=48 Identities=15% Similarity=0.470 Sum_probs=34.4
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccCC
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIG 134 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVG 134 (366)
.+.....|-.|...+|-. +-.- .....+|-+|.=||-+.|..|-+.+-
T Consensus 3 ~~~~~~~C~~C~tt~Tp~--WR~g--p~G~~LCNACGl~~~~~~~~RP~~~~ 50 (63)
T 3dfx_A 3 ARRAGTSCANCQTTTTTL--WRRN--ANGDPVCNACGLYYKLHNINRPLTMK 50 (63)
T ss_dssp CCCTTCCCTTTCCSCCSS--CCCC--TTSCCCCHHHHHHHHHHSSCCCGGGC
T ss_pred CCCCCCcCCCcCCCCCCc--cCCC--CCCCchhhHHHHHHHHcCCCCCcCcC
Confidence 445667899999987742 2111 12238999999999999998877653
No 22
>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=29.88 E-value=23 Score=26.93 Aligned_cols=31 Identities=16% Similarity=0.318 Sum_probs=21.5
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW 122 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW 122 (366)
-+.+.||.|... .-| ....-...|+.|++-+
T Consensus 6 LeiL~CP~ck~~---L~~----~~~~~~LiC~~cg~~Y 36 (69)
T 2pk7_A 6 LDILACPICKGP---LKL----SADKTELISKGAGLAY 36 (69)
T ss_dssp GGTCCCTTTCCC---CEE----CTTSSEEEETTTTEEE
T ss_pred HhheeCCCCCCc---CeE----eCCCCEEEcCCCCcEe
Confidence 467899999964 222 2335678999998755
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=29.87 E-value=25 Score=29.19 Aligned_cols=14 Identities=36% Similarity=0.786 Sum_probs=9.5
Q ss_pred CCcCCCCCCCCCce
Q 040161 86 QNLRCPRCDSSNTK 99 (366)
Q Consensus 86 e~~~CPRC~S~nTK 99 (366)
.+-.||+|.|.+-.
T Consensus 83 kPsrCP~CkSe~Ie 96 (105)
T 2gmg_A 83 IPSRCPKCKSEWIE 96 (105)
T ss_dssp CCSSCSSSCCCCBC
T ss_pred CCCCCcCCCCCccC
Confidence 45677777777655
No 24
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=29.48 E-value=44 Score=24.30 Aligned_cols=33 Identities=21% Similarity=0.578 Sum_probs=23.0
Q ss_pred CCCCCCCcCCCCCCCCCceeeeecCcCCCCCccccc--cccccc
Q 040161 81 NSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCK--TCRRYW 122 (366)
Q Consensus 81 ~p~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCk--sCrRYW 122 (366)
.+.--+.+.||.|... .- |.. ....|+ .|++-|
T Consensus 4 d~~lL~iL~CP~c~~~---L~-~~~-----~~L~C~~~~c~~~Y 38 (56)
T 2kpi_A 4 EAGLLEILACPACHAP---LE-ERD-----AELICTGQDCGLAY 38 (56)
T ss_dssp CCSCTTSCCCSSSCSC---EE-EET-----TEEEECSSSCCCEE
T ss_pred CHHHHhheeCCCCCCc---ce-ecC-----CEEEcCCcCCCcEE
Confidence 3445678999999984 22 332 678899 898654
No 25
>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=28.81 E-value=21 Score=27.63 Aligned_cols=13 Identities=38% Similarity=0.892 Sum_probs=11.4
Q ss_pred CcCCCCCCCCCce
Q 040161 87 NLRCPRCDSSNTK 99 (366)
Q Consensus 87 ~~~CPRC~S~nTK 99 (366)
..+||.|.|.||+
T Consensus 55 g~kC~~C~SyNTr 67 (79)
T 2k2d_A 55 GMKCKICESYNTA 67 (79)
T ss_dssp CCCCTTTSCCCEE
T ss_pred cccCcCCCCcCeE
Confidence 3489999999998
No 26
>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1
Probab=28.78 E-value=41 Score=24.53 Aligned_cols=42 Identities=24% Similarity=0.507 Sum_probs=30.1
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCC---CcccccccccccccCcc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQ---PRHFCKTCRRYWTKGGA 127 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~Q---PRhfCksCrRYWT~GGt 127 (366)
...+||.|...-.|----|.-.-.. --+||-.|.+-|..-|.
T Consensus 5 ~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~~~~~ 49 (60)
T 1wd2_A 5 NTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGS 49 (60)
T ss_dssp CCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGGGT
T ss_pred cceECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcccCCC
Confidence 4579999999888866544333333 35899999999987654
No 27
>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=27.03 E-value=41 Score=25.48 Aligned_cols=45 Identities=20% Similarity=0.546 Sum_probs=32.3
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccC
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPI 133 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPV 133 (366)
.....|-.|...+|-. .-. .. .-..+|-+|.-||-.-|.+|-+-.
T Consensus 7 ~~~~~C~~C~t~~Tp~--WR~-gp-~G~~LCNaCGl~~~~~~~~RP~~~ 51 (66)
T 4gat_A 7 NGPTTCTNCFTQTTPL--WRR-NP-EGQPLCNACGLFLKLHGVVRPLSL 51 (66)
T ss_dssp SSSCCCTTTCCCCCSS--CEE-ET-TTEEECHHHHHHHHHHCSCCCGGG
T ss_pred CCCCCCCCCCCCCCCc--CCc-CC-CCCCccHHHHHHHHHcCCCCchhh
Confidence 4678999999988752 111 11 222899999999999999877644
No 28
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1
Probab=24.86 E-value=23 Score=26.84 Aligned_cols=32 Identities=22% Similarity=0.436 Sum_probs=21.8
Q ss_pred CCCCcCCCCCCCCCceeeeecCcCCCCCccccccccccc
Q 040161 84 NNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW 122 (366)
Q Consensus 84 ~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW 122 (366)
--+.+.||.|.. ..-|- ...-...|+.|++-+
T Consensus 5 LL~iL~CP~ck~---~L~~~----~~~~~LiC~~cg~~Y 36 (68)
T 2hf1_A 5 FLEILVCPLCKG---PLVFD----KSKDELICKGDRLAF 36 (68)
T ss_dssp CEEECBCTTTCC---BCEEE----TTTTEEEETTTTEEE
T ss_pred HhhheECCCCCC---cCeEe----CCCCEEEcCCCCcEe
Confidence 346789999996 33332 235668999998755
No 29
>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1
Probab=21.83 E-value=32 Score=28.46 Aligned_cols=37 Identities=19% Similarity=0.477 Sum_probs=21.4
Q ss_pred CCCCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcc
Q 040161 82 SGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGA 127 (366)
Q Consensus 82 p~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGt 127 (366)
++......|..|... | +...-||-|+.|.+.+=..=.
T Consensus 14 ~Pd~~~~~C~~C~~~---F------s~~~RkHHCR~CG~ifC~~Cs 50 (120)
T 1y02_A 14 SPTGLEPSCKSCGAH---F------ANTARKQTCLDCKKNFCMTCS 50 (120)
T ss_dssp ------CCCTTTCCC---C------SSGGGCEECTTTCCEECGGGE
T ss_pred cCccccCcccCcCCc---c------ccccccccCCCCCCeeCHHHh
Confidence 345556789999875 3 233678999998877654433
No 30
>1p91_A Ribosomal RNA large subunit methyltransferase A; RLMA, RRMA, 23S rRNA, NESG, structural genomics, PSI, protein structure initiative; HET: SAM; 2.80A {Escherichia coli} SCOP: c.66.1.33
Probab=21.45 E-value=57 Score=27.03 Aligned_cols=39 Identities=18% Similarity=0.503 Sum_probs=24.9
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCccccccccccc-ccCcccccccCCC
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW-TKGGALRNVPIGG 135 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW-T~GGtLRNVPVGG 135 (366)
+.||.|...... ...-+.|..|..|- .++|-+.-+++-.
T Consensus 3 ~~Cp~C~~~~~~---------~~~~~~C~~~~~~~~~~~Gy~~~~~~~~ 42 (269)
T 1p91_A 3 FSCPLCHQPLSR---------EKNSYICPQRHQFDMAKEGYVNLLPVQH 42 (269)
T ss_dssp BBCTTTCCBCEE---------ETTEEECTTCCEEEBCTTSCEECSCSSS
T ss_pred ccCCCCCcccee---------CCCEEECCCCCcCCcCCCEEEEeecccc
Confidence 689999875433 12347898888774 4567655555533
No 31
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1
Probab=21.29 E-value=30 Score=23.25 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=20.6
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCccccccccccc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYW 122 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYW 122 (366)
..||-|.+.+|++--= ...--..|++|...+
T Consensus 1 VlC~~C~~peT~l~~~----~~~~~l~C~aCG~~~ 31 (36)
T 1k81_A 1 VICRECGKPDTKIIKE----GRVHLLKCMACGAIR 31 (36)
T ss_dssp CCCSSSCSCEEEEEEE----TTEEEEEEETTTEEE
T ss_pred CCCcCCCCCCcEEEEe----CCcEEEEhhcCCCcc
Confidence 3699999999997541 112225688886544
No 32
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=20.17 E-value=30 Score=26.68 Aligned_cols=49 Identities=22% Similarity=0.390 Sum_probs=33.0
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccCC
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIG 134 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVG 134 (366)
+.++...|-.|...+|- .+-.-..... .+|-+|.=||-+.|..|-+..-
T Consensus 4 ~~~~~~~C~nC~tt~Tp--~WRrg~~~~g-~LCNACGl~~~~~~~~RP~~~~ 52 (71)
T 2kae_A 4 MNKKSFQCSNCSVTETI--RWRNIRSKEG-IQCNACFIYQRKYNKTRPVTAV 52 (71)
T ss_dssp ----CCCCSSSCCSCCS--SCCCCSSSSC-CCSSHHHHHHHHHHSCCCTHHH
T ss_pred CCCCCCcCCccCCCCCC--ccccCCCCCC-ccchHHHHHHHHhCCCCCcccc
Confidence 45577999999999875 2332111222 8999999999999998877543
Done!