Query 011016
Match_columns 495
No_of_seqs 152 out of 266
Neff 3.3
Searched_HMMs 29240
Date Mon Mar 25 19:03:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011016.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/011016hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_I DNA-directed RNA polyme 73.5 3.8 0.00013 35.0 4.7 45 128-174 65-112 (113)
2 1tfi_A Transcriptional elongat 68.3 3.8 0.00013 30.9 3.0 37 137-173 9-48 (50)
3 1qyp_A RNA polymerase II; tran 67.6 3.2 0.00011 31.3 2.6 38 137-174 15-55 (57)
4 1twf_I B12.6, DNA-directed RNA 56.4 14 0.00048 31.9 4.9 47 128-176 65-114 (122)
5 4f02_C Eukaryotic translation 51.2 4.3 0.00015 27.5 0.6 13 423-435 1-13 (27)
6 3dfx_A Trans-acting T-cell-spe 47.5 9.9 0.00034 30.2 2.3 43 137-183 7-49 (63)
7 2fiy_A Protein FDHE homolog; F 46.1 9.4 0.00032 38.1 2.5 35 137-172 222-263 (309)
8 3po3_S Transcription elongatio 44.5 13 0.00046 34.2 3.0 35 136-173 136-176 (178)
9 1gnf_A Transcription factor GA 41.8 13 0.00046 27.7 2.1 41 137-181 4-44 (46)
10 1k82_A Formamidopyrimidine-DNA 41.1 9.5 0.00032 36.9 1.6 29 137-170 240-268 (268)
11 2xzf_A Formamidopyrimidine-DNA 39.5 10 0.00035 36.6 1.6 28 138-170 243-270 (271)
12 1ee8_A MUTM (FPG) protein; bet 39.4 11 0.00036 36.6 1.6 29 137-170 235-263 (266)
13 1pqv_S STP-alpha, transcriptio 38.8 14 0.00048 36.5 2.4 34 137-173 268-307 (309)
14 3u6p_A Formamidopyrimidine-DNA 38.1 10 0.00034 36.9 1.2 28 138-170 246-273 (273)
15 1k3x_A Endonuclease VIII; hydr 34.8 12 0.00042 35.9 1.3 28 138-170 235-262 (262)
16 3cw1_L U1 small nuclear ribonu 30.2 14 0.00048 30.5 0.6 17 161-177 2-18 (77)
17 3nw0_A Non-structural maintena 28.4 9.7 0.00033 36.3 -0.7 38 137-175 193-230 (238)
18 3qt1_I DNA-directed RNA polyme 26.5 14 0.00047 32.8 0.0 44 129-174 86-132 (133)
19 2jny_A Uncharacterized BCR; st 26.2 23 0.0008 28.2 1.3 31 135-172 8-38 (67)
20 2pk7_A Uncharacterized protein 25.2 30 0.001 27.6 1.8 30 136-172 7-36 (69)
21 2js4_A UPF0434 protein BB2007; 25.0 41 0.0014 26.9 2.5 32 135-173 6-37 (70)
22 1wii_A Hypothetical UPF0222 pr 24.6 53 0.0018 27.3 3.2 42 131-173 17-58 (85)
23 4hc9_A Trans-acting T-cell-spe 23.3 42 0.0015 29.0 2.5 44 136-183 58-101 (115)
24 1pft_A TFIIB, PFTFIIBN; N-term 22.7 48 0.0016 24.0 2.3 33 136-174 4-36 (50)
25 2jr6_A UPF0434 protein NMA0874 22.5 31 0.001 27.5 1.3 30 136-172 7-36 (68)
26 2vut_I AREA, nitrogen regulato 22.4 27 0.00093 25.7 0.9 40 138-181 2-41 (43)
27 2kpi_A Uncharacterized protein 21.0 52 0.0018 25.2 2.3 29 135-172 8-38 (56)
28 2gmg_A Hypothetical protein PF 20.5 53 0.0018 28.5 2.5 17 133-149 80-96 (105)
29 4gat_A Nitrogen regulatory pro 20.4 67 0.0023 25.5 2.9 46 134-183 6-51 (66)
No 1
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=73.54 E-value=3.8 Score=35.02 Aligned_cols=45 Identities=20% Similarity=0.419 Sum_probs=27.5
Q ss_pred ccccCCCCCccCCCCCCCCCCceeeecccCCCCC---ccccccccccccc
Q 011016 128 EKTLKKPDKILPCPRCNSMDTKFCYYNNYNVNQP---RHFCKNCQRYWTA 174 (495)
Q Consensus 128 ~~~l~~p~~~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~C~RyWT~ 174 (495)
+..|++ ....||+|...+..|-..+-.....| -|.|.+|.-.|..
T Consensus 65 ~~tlp~--~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~ 112 (113)
T 3h0g_I 65 DPTLPR--SDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE 112 (113)
T ss_dssp CSSSCB--CCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred cccCCC--cccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence 456644 33799999987654422222222222 2889999999974
No 2
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=68.26 E-value=3.8 Score=30.89 Aligned_cols=37 Identities=16% Similarity=0.693 Sum_probs=26.8
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCc---ccccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPR---HFCKNCQRYWT 173 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~C~RyWT 173 (495)
...||+|...+.-|--.+..+...|- |.|.+|..-|.
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 46899999877766555555444443 89999998885
No 3
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=67.55 E-value=3.2 Score=31.27 Aligned_cols=38 Identities=18% Similarity=0.578 Sum_probs=24.6
Q ss_pred ccCCCCCCCCCCceeeecccCCCCC---ccccccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQP---RHFCKNCQRYWTA 174 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~C~RyWT~ 174 (495)
.++||+|...+..|--.+-.....| .|.|..|.--|..
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 4689999984433332232233334 3899999999976
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=56.39 E-value=14 Score=31.90 Aligned_cols=47 Identities=21% Similarity=0.504 Sum_probs=31.0
Q ss_pred ccccCCCCCccCCCCCCCCCCceeeecccCCCCCc---ccccccccccccCC
Q 011016 128 EKTLKKPDKILPCPRCNSMDTKFCYYNNYNVNQPR---HFCKNCQRYWTAGG 176 (495)
Q Consensus 128 ~~~l~~p~~~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~C~RyWT~GG 176 (495)
+..+++- ...||+|...+.-|-..+-.....|- |.|.+|.-.|....
T Consensus 65 ~~t~p~t--~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~nn 114 (122)
T 1twf_I 65 DPTLPRS--DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQ 114 (122)
T ss_dssp CTTSCCC--CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCT
T ss_pred ccccccc--CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccCC
Confidence 3455443 46899999876555444433333332 89999999998864
No 5
>4f02_C Eukaryotic translation initiation factor 4 gamma; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens}
Probab=51.16 E-value=4.3 Score=27.52 Aligned_cols=13 Identities=54% Similarity=0.889 Sum_probs=10.8
Q ss_pred ceeecCCCccccc
Q 011016 423 KTLRIDDPGDAAK 435 (495)
Q Consensus 423 KTLRIDDp~EAAK 435 (495)
|||||-||+.-.|
T Consensus 1 k~irirdpnqggk 13 (27)
T 4f02_C 1 KTIRIRDPNQGGK 13 (27)
T ss_pred CcceecCccccch
Confidence 7999999987554
No 6
>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=47.49 E-value=9.9 Score=30.19 Aligned_cols=43 Identities=16% Similarity=0.464 Sum_probs=31.8
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCcccccccccccccCCccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNVPV 183 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~GG~lRnVPv 183 (495)
...|-.|....|-. +-.- .....+|-+|.-||-..|.+|-+.+
T Consensus 7 ~~~C~~C~tt~Tp~--WR~g--p~G~~LCNACGl~~~~~~~~RP~~~ 49 (63)
T 3dfx_A 7 GTSCANCQTTTTTL--WRRN--ANGDPVCNACGLYYKLHNINRPLTM 49 (63)
T ss_dssp TCCCTTTCCSCCSS--CCCC--TTSCCCCHHHHHHHHHHSSCCCGGG
T ss_pred CCcCCCcCCCCCCc--cCCC--CCCCchhhHHHHHHHHcCCCCCcCc
Confidence 45899999988753 2221 1223899999999999999887765
No 7
>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=46.12 E-value=9.4 Score=38.07 Aligned_cols=35 Identities=20% Similarity=0.534 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCceeeecccC-------CCCCccccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYN-------VNQPRHFCKNCQRYW 172 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~-------~~QPR~fCk~C~RyW 172 (495)
...||.|... .++-||.--. ...--+.|..|+.|+
T Consensus 222 R~~C~~Cg~~-~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~Yl 263 (309)
T 2fiy_A 222 RIKCSHCEES-KHLAYLSLEHDGQPAEKAVLRAETCPSCQGYL 263 (309)
T ss_dssp TTSCSSSCCC-SCCEEECCCC-CCCSTTCSEEEEEETTTTEEE
T ss_pred CcCCcCCCCC-CCeeEEEecCccccCCCcceEEEEcccccchH
Confidence 4678888887 4666665433 112237888888887
No 8
>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=44.52 E-value=13 Score=34.17 Aligned_cols=35 Identities=20% Similarity=0.634 Sum_probs=22.8
Q ss_pred CccCCCCCCCCCCceeeecccC---CCCC---cccccccccccc
Q 011016 136 KILPCPRCNSMDTKFCYYNNYN---VNQP---RHFCKNCQRYWT 173 (495)
Q Consensus 136 ~~~~CPRC~S~~TkfcyyNNy~---~~QP---R~fCk~C~RyWT 173 (495)
....||+|...+. ||...+ ..-| -|.|..|..-|.
T Consensus 136 ~~~~Cp~C~~~~a---~~~q~Q~rsaDE~mt~f~~C~~C~~~w~ 176 (178)
T 3po3_S 136 DRFTCGKCKEKKV---SYYQLQTRSAAAPLTTFCTCEACGNRWK 176 (178)
T ss_dssp SSSCCSSSCCSCE---ECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred CCcCCCCCCCCce---EEEEeecccCCCCCcEEEEcCCCCCeec
Confidence 3579999996554 443332 1112 388999999995
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=41.84 E-value=13 Score=27.71 Aligned_cols=41 Identities=20% Similarity=0.493 Sum_probs=29.9
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCcccccccccccccCCccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNV 181 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~GG~lRnV 181 (495)
...|-.|....|-. +-.-. ....+|-+|.-||-..|.+|-+
T Consensus 4 ~~~C~~C~tt~Tp~--WR~gp--~G~~LCNaCGl~~k~~~~~RP~ 44 (46)
T 1gnf_A 4 ARECVNCGATATPL--WRRDR--TGHYLCNACGLYHKMNGQNRPL 44 (46)
T ss_dssp SCCCTTTCCCCCSS--CBCCT--TCCCBCSHHHHHHHHTCSCCCC
T ss_pred CCCCCCcCCCCCCc--CccCC--CCCccchHHHHHHHHcCCCCCC
Confidence 46799999988753 22221 2238999999999999998743
No 10
>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=41.09 E-value=9.5 Score=36.89 Aligned_cols=29 Identities=21% Similarity=0.544 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 170 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~R 170 (495)
..+||||...=.|.-+ . .+.-|||..||+
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 3589999987666543 2 355599999995
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=39.51 E-value=10 Score=36.62 Aligned_cols=28 Identities=32% Similarity=0.689 Sum_probs=20.8
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccccc
Q 011016 138 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 170 (495)
Q Consensus 138 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~R 170 (495)
.+||||...=.|.-+ . .+.-|||..||+
T Consensus 243 ~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 270 (271)
T 2xzf_A 243 EKCSRCGAEIQKIKV-A----GRGTHFCPVCQQ 270 (271)
T ss_dssp SBCTTTCCBCEEEEE-T----TEEEEECTTTSC
T ss_pred CCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 589999887666533 2 355599999997
No 12
>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=39.39 E-value=11 Score=36.60 Aligned_cols=29 Identities=34% Similarity=0.778 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 170 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~R 170 (495)
..+||||...=.|.-+ . .+.-|||..||+
T Consensus 235 g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 263 (266)
T 1ee8_A 235 GLPCPACGRPVERRVV-A----GRGTHFCPTCQG 263 (266)
T ss_dssp TSBCTTTCCBCEEEES-S----SCEEEECTTTTT
T ss_pred CCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 3589999887665433 2 355699999997
No 13
>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=38.85 E-value=14 Score=36.52 Aligned_cols=34 Identities=21% Similarity=0.692 Sum_probs=22.1
Q ss_pred ccCCCCCCCCCCceeeeccc---CCCCC---cccccccccccc
Q 011016 137 ILPCPRCNSMDTKFCYYNNY---NVNQP---RHFCKNCQRYWT 173 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy---~~~QP---R~fCk~C~RyWT 173 (495)
...||+|...+ |||... .-..| -|.|..|..-|.
T Consensus 268 ~~~C~~C~~~~---~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~ 307 (309)
T 1pqv_S 268 RFTCGKCKEKK---VSYYQLQTRSADEPLTTFCTCEACGNRWK 307 (309)
T ss_pred cccCCCCCCCe---eEEEEeecccCCCCCcEEEEeCCCCCcee
Confidence 46899999554 444332 22222 289999999885
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=38.08 E-value=10 Score=36.88 Aligned_cols=28 Identities=36% Similarity=0.812 Sum_probs=20.3
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccccc
Q 011016 138 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 170 (495)
Q Consensus 138 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~R 170 (495)
.+||||...=.|.-+ . .+.-|||..||+
T Consensus 246 ~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 273 (273)
T 3u6p_A 246 NPCKRCGTPIEKTVV-A----GRGTHYCPRCQR 273 (273)
T ss_dssp SBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CCCCCCCCeEEEEEE-C----CCCeEECCCCCC
Confidence 499999877655433 2 255599999995
No 15
>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=34.80 E-value=12 Score=35.90 Aligned_cols=28 Identities=36% Similarity=0.820 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccccc
Q 011016 138 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 170 (495)
Q Consensus 138 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~R 170 (495)
.+||||...=.|.= +. .+.-|||..||+
T Consensus 235 ~pC~~CG~~I~~~~-~~----gR~t~~CP~CQ~ 262 (262)
T 1k3x_A 235 EPCERCGSIIEKTT-LS----SRPFYWCPGCQH 262 (262)
T ss_dssp SBCTTTCCBCEEEE-ET----TEEEEECTTTCC
T ss_pred CCCCCCCCEeEEEE-EC----CCCeEECCCCCC
Confidence 48999987765543 22 345599999995
No 16
>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=30.19 E-value=14 Score=30.49 Aligned_cols=17 Identities=29% Similarity=0.931 Sum_probs=15.1
Q ss_pred CcccccccccccccCCc
Q 011016 161 PRHFCKNCQRYWTAGGT 177 (495)
Q Consensus 161 PR~fCk~C~RyWT~GG~ 177 (495)
|||||.-|..|.|+.-.
T Consensus 2 PkYyCdYCd~~lt~Ds~ 18 (77)
T 3cw1_L 2 PKFYCDYCDTYLTHDSP 18 (77)
T ss_pred CCcccccCCceecCCCH
Confidence 89999999999988754
No 17
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Probab=28.45 E-value=9.7 Score=36.34 Aligned_cols=38 Identities=18% Similarity=0.510 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCcccccccccccccC
Q 011016 137 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAG 175 (495)
Q Consensus 137 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~G 175 (495)
+..|+.|...=+..|+++=+ ..+...-|..|+..|...
T Consensus 193 g~~C~~C~~~~H~~C~~~~~-~~~~~~~CP~C~~~W~~~ 230 (238)
T 3nw0_A 193 GQSCETCGIRMHLPCVAKYF-QSNAEPRCPHCNDYWPHE 230 (238)
T ss_dssp CEECSSSCCEECHHHHHHHT-TTCSSCBCTTTCCBCCSC
T ss_pred CcccCccChHHHHHHHHHHH-HhCCCCCCCCCCCCCCCC
Confidence 45788888777888875543 456678899999999876
No 18
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=26.51 E-value=14 Score=32.84 Aligned_cols=44 Identities=27% Similarity=0.604 Sum_probs=0.0
Q ss_pred cccCCCCCccCCCCCCCCCCceeeecccCCCCC---ccccccccccccc
Q 011016 129 KTLKKPDKILPCPRCNSMDTKFCYYNNYNVNQP---RHFCKNCQRYWTA 174 (495)
Q Consensus 129 ~~l~~p~~~~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~C~RyWT~ 174 (495)
.+|++ ....||+|...+.-|-..+-.....| -|.|..|.--|..
T Consensus 86 ptlp~--t~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~C~~~w~e 132 (133)
T 3qt1_I 86 PTLPR--SDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKE 132 (133)
T ss_dssp -------------------------------------------------
T ss_pred ccCCc--ccCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCCCCCEeCc
Confidence 45543 34799999987655422222222222 2789999999975
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=26.21 E-value=23 Score=28.20 Aligned_cols=31 Identities=13% Similarity=0.235 Sum_probs=21.2
Q ss_pred CCccCCCCCCCCCCceeeecccCCCCCccccccccccc
Q 011016 135 DKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYW 172 (495)
Q Consensus 135 ~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyW 172 (495)
-.++.||.|... .-| ....-...|+.|++-+
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 2335668899997655
No 20
>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=25.17 E-value=30 Score=27.60 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=20.6
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCccccccccccc
Q 011016 136 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYW 172 (495)
Q Consensus 136 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyW 172 (495)
.++.||.|... .- | ........|++|++-+
T Consensus 7 eiL~CP~ck~~---L~-~---~~~~~~LiC~~cg~~Y 36 (69)
T 2pk7_A 7 DILACPICKGP---LK-L---SADKTELISKGAGLAY 36 (69)
T ss_dssp GTCCCTTTCCC---CE-E---CTTSSEEEETTTTEEE
T ss_pred hheeCCCCCCc---Ce-E---eCCCCEEEcCCCCcEe
Confidence 57899999964 22 2 3345668899997654
No 21
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=25.05 E-value=41 Score=26.92 Aligned_cols=32 Identities=22% Similarity=0.464 Sum_probs=21.7
Q ss_pred CCccCCCCCCCCCCceeeecccCCCCCcccccccccccc
Q 011016 135 DKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWT 173 (495)
Q Consensus 135 ~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT 173 (495)
-.++.||.|... .-| ........|++|++-+-
T Consensus 6 L~iL~CP~ck~~---L~~----~~~~~~LiC~~cg~~YP 37 (70)
T 2js4_A 6 LDILVCPVCKGR---LEF----QRAQAELVCNADRLAFP 37 (70)
T ss_dssp CCCCBCTTTCCB---EEE----ETTTTEEEETTTTEEEE
T ss_pred hhheECCCCCCc---CEE----eCCCCEEEcCCCCceec
Confidence 357899999983 332 23356688999976553
No 22
>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4
Probab=24.61 E-value=53 Score=27.35 Aligned_cols=42 Identities=17% Similarity=0.286 Sum_probs=31.7
Q ss_pred cCCCCCccCCCCCCCCCCceeeecccCCCCCcccccccccccc
Q 011016 131 LKKPDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWT 173 (495)
Q Consensus 131 l~~p~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT 173 (495)
+.+-+....||.|+..++=-|-+.- ...-.+.-|+.|+-.+.
T Consensus 17 ~~~L~t~F~CPfCnh~~sV~vkidk-~~~~g~l~C~~Cg~~~~ 58 (85)
T 1wii_A 17 TGTLETQFTCPFCNHEKSCDVKMDR-ARNTGVISCTVCLEEFQ 58 (85)
T ss_dssp CCCCSSCCCCTTTCCSSCEEEEEET-TTTEEEEEESSSCCEEE
T ss_pred CCCCCCeEcCCCCCCCCeEEEEEEc-cCCEEEEEcccCCCeEE
Confidence 3566788999999999877777653 34467788999987654
No 23
>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=23.35 E-value=42 Score=29.00 Aligned_cols=44 Identities=16% Similarity=0.445 Sum_probs=33.0
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCcccccccccccccCCccccccc
Q 011016 136 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNVPV 183 (495)
Q Consensus 136 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~GG~lRnVPv 183 (495)
..+.|-.|....|-. .-. -...+.+|-+|.-||-..|..|-+-+
T Consensus 58 ~~~~C~~C~t~~tp~--WRr--~~~g~~lCNaCgl~~~~~~~~rp~~~ 101 (115)
T 4hc9_A 58 AGTSCANCQTTTTTL--WRR--NANGDPVCNACGLYYKLHNINRPLTM 101 (115)
T ss_dssp TTCCCTTTCCSCCSS--CEE--CTTSCEECHHHHHHHHHHSSCCCGGG
T ss_pred ccccCCCcCCCCcce--eEE--CCCCCCcchHHHHHHHHhCCCCCccc
Confidence 357999999988752 211 12236899999999999999887766
No 24
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=22.69 E-value=48 Score=23.99 Aligned_cols=33 Identities=21% Similarity=0.519 Sum_probs=22.1
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCccccccccccccc
Q 011016 136 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTA 174 (495)
Q Consensus 136 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~ 174 (495)
..+.||.|.+.+-.| ...+-...|..|+.-+..
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 457899998754332 223556999999776543
No 25
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=22.52 E-value=31 Score=27.50 Aligned_cols=30 Identities=17% Similarity=0.495 Sum_probs=20.4
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCccccccccccc
Q 011016 136 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYW 172 (495)
Q Consensus 136 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyW 172 (495)
.++.||.|.. ..-| ........|++|++-+
T Consensus 7 ~iL~CP~ck~---~L~~----~~~~~~LiC~~cg~~Y 36 (68)
T 2jr6_A 7 DILVCPVTKG---RLEY----HQDKQELWSRQAKLAY 36 (68)
T ss_dssp CCCBCSSSCC---BCEE----ETTTTEEEETTTTEEE
T ss_pred hheECCCCCC---cCeE----eCCCCEEEcCCCCcEe
Confidence 5789999996 3322 2334668899997654
No 26
>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=22.43 E-value=27 Score=25.68 Aligned_cols=40 Identities=18% Similarity=0.530 Sum_probs=28.7
Q ss_pred cCCCCCCCCCCceeeecccCCCCCcccccccccccccCCccccc
Q 011016 138 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNV 181 (495)
Q Consensus 138 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~GG~lRnV 181 (495)
..|-.|....|-. +-.- . ....+|-+|.-||-..|.+|-+
T Consensus 2 ~~C~~C~tt~Tp~--WR~g-p-~G~~LCNaCGl~~k~~~~~RP~ 41 (43)
T 2vut_I 2 TTCTNCFTQTTPL--WRRN-P-EGQPLCNACGLFLKLHGVVRPL 41 (43)
T ss_dssp CCCSSSCCCCCSC--CEEC-T-TSCEECHHHHHHHHHHSSCCCC
T ss_pred CcCCccCCCCCCc--cccC-C-CCCcccHHHHHHHHHhCCCCCC
Confidence 4688898887753 2221 1 2238999999999999998754
No 27
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=20.96 E-value=52 Score=25.15 Aligned_cols=29 Identities=24% Similarity=0.670 Sum_probs=20.3
Q ss_pred CCccCCCCCCCCCCceeeecccCCCCCccccc--cccccc
Q 011016 135 DKILPCPRCNSMDTKFCYYNNYNVNQPRHFCK--NCQRYW 172 (495)
Q Consensus 135 ~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk--~C~RyW 172 (495)
-.++.||.|... . -|+. ....|. .|++-+
T Consensus 8 L~iL~CP~c~~~---L-~~~~-----~~L~C~~~~c~~~Y 38 (56)
T 2kpi_A 8 LEILACPACHAP---L-EERD-----AELICTGQDCGLAY 38 (56)
T ss_dssp TTSCCCSSSCSC---E-EEET-----TEEEECSSSCCCEE
T ss_pred HhheeCCCCCCc---c-eecC-----CEEEcCCcCCCcEE
Confidence 467899999984 2 2333 667899 897654
No 28
>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=20.46 E-value=53 Score=28.53 Aligned_cols=17 Identities=24% Similarity=0.448 Sum_probs=11.0
Q ss_pred CCCCccCCCCCCCCCCc
Q 011016 133 KPDKILPCPRCNSMDTK 149 (495)
Q Consensus 133 ~p~~~~~CPRC~S~~Tk 149 (495)
..++.-.||+|.|.+..
T Consensus 80 ~~~kPsrCP~CkSe~Ie 96 (105)
T 2gmg_A 80 EINIPSRCPKCKSEWIE 96 (105)
T ss_dssp CSSCCSSCSSSCCCCBC
T ss_pred cCCCCCCCcCCCCCccC
Confidence 33444578888887655
No 29
>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=20.40 E-value=67 Score=25.55 Aligned_cols=46 Identities=17% Similarity=0.501 Sum_probs=32.9
Q ss_pred CCCccCCCCCCCCCCceeeecccCCCCCcccccccccccccCCccccccc
Q 011016 134 PDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNVPV 183 (495)
Q Consensus 134 p~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~C~RyWT~GG~lRnVPv 183 (495)
+.....|-.|...+|-. .-. ...- ..+|-+|.-||-..|.+|-+-.
T Consensus 6 ~~~~~~C~~C~t~~Tp~--WR~-gp~G-~~LCNaCGl~~~~~~~~RP~~~ 51 (66)
T 4gat_A 6 QNGPTTCTNCFTQTTPL--WRR-NPEG-QPLCNACGLFLKLHGVVRPLSL 51 (66)
T ss_dssp SSSSCCCTTTCCCCCSS--CEE-ETTT-EEECHHHHHHHHHHCSCCCGGG
T ss_pred CCCCCCCCCCCCCCCCc--CCc-CCCC-CCccHHHHHHHHHcCCCCchhh
Confidence 34567999999988762 111 1122 2899999999999999876655
Done!