Query 020288
Match_columns 328
No_of_seqs 141 out of 254
Neff 3.3
Searched_HMMs 29240
Date Mon Mar 25 14:38:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020288.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/020288hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1tfi_A Transcriptional elongat 79.1 1.1 3.8E-05 32.0 2.3 38 76-113 8-48 (50)
2 1qyp_A RNA polymerase II; tran 78.5 0.97 3.3E-05 32.3 1.9 38 77-114 15-55 (57)
3 2fiy_A Protein FDHE homolog; F 71.8 1.7 5.9E-05 41.0 2.3 35 77-112 222-263 (309)
4 3h0g_I DNA-directed RNA polyme 69.7 2.4 8.4E-05 34.3 2.5 39 76-114 71-112 (113)
5 1twf_I B12.6, DNA-directed RNA 61.4 6.7 0.00023 32.1 3.6 40 76-115 71-113 (122)
6 1gnf_A Transcription factor GA 57.2 6 0.00021 28.0 2.3 42 76-121 3-44 (46)
7 2kae_A GATA-type transcription 55.8 1.3 4.5E-05 34.1 -1.5 50 72-124 3-52 (71)
8 3po3_S Transcription elongatio 55.0 4.7 0.00016 35.2 1.7 37 77-113 137-176 (178)
9 3dfx_A Trans-acting T-cell-spe 52.6 12 0.0004 28.2 3.3 46 74-123 4-49 (63)
10 1pqv_S STP-alpha, transcriptio 52.4 7.6 0.00026 36.3 2.8 37 77-113 268-307 (309)
11 1k82_A Formamidopyrimidine-DNA 52.0 4.9 0.00017 36.8 1.4 30 76-110 239-268 (268)
12 3u6p_A Formamidopyrimidine-DNA 51.0 5.2 0.00018 36.8 1.4 30 76-110 244-273 (273)
13 1ee8_A MUTM (FPG) protein; bet 51.0 5.4 0.00018 36.6 1.5 30 76-110 234-263 (266)
14 2xzf_A Formamidopyrimidine-DNA 50.1 5.5 0.00019 36.4 1.4 30 76-110 241-270 (271)
15 3nw0_A Non-structural maintena 48.7 2.4 8.3E-05 38.3 -1.2 39 76-115 192-230 (238)
16 3qt1_I DNA-directed RNA polyme 45.4 4.4 0.00015 34.1 0.0 38 77-114 92-132 (133)
17 4gat_A Nitrogen regulatory pro 44.5 22 0.00075 26.8 3.7 46 74-123 6-51 (66)
18 1k3x_A Endonuclease VIII; hydr 43.8 7.1 0.00024 35.5 1.1 30 76-110 233-262 (262)
19 1z2q_A LM5-1; membrane protein 42.8 13 0.00044 28.3 2.3 31 74-113 18-48 (84)
20 3cw1_L U1 small nuclear ribonu 39.8 7.1 0.00024 30.6 0.4 17 101-117 2-18 (77)
21 2k2d_A Ring finger and CHY zin 38.1 12 0.0004 29.0 1.3 14 77-90 55-68 (79)
22 4hc9_A Trans-acting T-cell-spe 36.1 28 0.00095 28.5 3.4 46 74-123 56-101 (115)
23 1pft_A TFIIB, PFTFIIBN; N-term 30.9 24 0.00081 24.2 1.9 33 76-114 4-36 (50)
24 2gmg_A Hypothetical protein PF 29.6 28 0.00095 28.7 2.4 14 76-89 83-96 (105)
25 2zjr_Z 50S ribosomal protein L 29.2 24 0.00082 26.1 1.7 24 76-111 29-52 (60)
26 2vut_I AREA, nitrogen regulato 28.9 19 0.00063 25.1 1.0 41 78-122 2-42 (43)
27 2jny_A Uncharacterized BCR; st 26.7 20 0.0007 27.0 1.0 30 76-112 9-38 (67)
28 2pk7_A Uncharacterized protein 25.8 25 0.00085 26.6 1.3 30 76-112 7-36 (69)
29 2jr6_A UPF0434 protein NMA0874 23.2 26 0.00089 26.4 1.0 30 76-112 7-36 (68)
30 2js4_A UPF0434 protein BB2007; 22.7 45 0.0015 25.2 2.2 35 76-117 7-42 (70)
31 2kdx_A HYPA, hydrogenase/ureas 20.1 54 0.0018 26.1 2.3 14 77-90 89-103 (119)
No 1
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=79.07 E-value=1.1 Score=32.03 Aligned_cols=38 Identities=21% Similarity=0.617 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhcccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWT 113 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT 113 (328)
...+||+|...+..|--.+..+...|- |.|..|..-|.
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 347899999888777665665555553 89999998885
No 2
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=78.50 E-value=0.97 Score=32.29 Aligned_cols=38 Identities=18% Similarity=0.601 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcC---chhhhhhhccccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWTR 114 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT~ 114 (328)
..+||+|...+..|--.+-.+...| .|.|..|.--|+.
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 5789999985444433333344444 4899999999976
No 3
>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=71.84 E-value=1.7 Score=41.05 Aligned_cols=35 Identities=20% Similarity=0.624 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCcceeeecCCC-------CCcCchhhhhhhccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYS-------LSQPRHFCKACRRYW 112 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~-------~~QPR~fCk~CrRyw 112 (328)
..+||.|.++ .++-|+.--. ...--+.|..|+.|+
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 5799999998 4677875443 222348999999998
No 4
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=69.67 E-value=2.4 Score=34.28 Aligned_cols=39 Identities=18% Similarity=0.372 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT~ 114 (328)
...+||+|...+..|-..+-.+...|- |.|..|.--|++
T Consensus 71 ~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~ 112 (113)
T 3h0g_I 71 SDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE 112 (113)
T ss_dssp CCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred cccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence 348999999877554333333332222 889999999974
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=61.36 E-value=6.7 Score=32.07 Aligned_cols=40 Identities=20% Similarity=0.489 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhcccccC
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWTRG 115 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT~G 115 (328)
....||+|...+.-|-..+-.+...|- |.|..|.--|+..
T Consensus 71 t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~n 113 (122)
T 1twf_I 71 SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD 113 (122)
T ss_dssp CCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred cCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccC
Confidence 347899999876665444444444443 8999999999875
No 6
>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=57.21 E-value=6 Score=28.03 Aligned_cols=42 Identities=24% Similarity=0.509 Sum_probs=30.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCcccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNV 121 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnv 121 (328)
+...|-.|..++|-. +-.-. ....+|-+|.-||-..|..|-+
T Consensus 3 ~~~~C~~C~tt~Tp~--WR~gp--~G~~LCNaCGl~~k~~~~~RP~ 44 (46)
T 1gnf_A 3 EARECVNCGATATPL--WRRDR--TGHYLCNACGLYHKMNGQNRPL 44 (46)
T ss_dssp CSCCCTTTCCCCCSS--CBCCT--TCCCBCSHHHHHHHHTCSCCCC
T ss_pred CCCCCCCcCCCCCCc--CccCC--CCCccchHHHHHHHHcCCCCCC
Confidence 457899999988753 22221 2238999999999999998754
No 7
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=55.79 E-value=1.3 Score=34.13 Aligned_cols=50 Identities=22% Similarity=0.351 Sum_probs=33.9
Q ss_pred CCCCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccccccccC
Q 020288 72 PHTEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPVG 124 (328)
Q Consensus 72 p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPvG 124 (328)
+.++....|-.|..++|-. .-.-..... .+|-+|.-||-..++.|-+..=
T Consensus 3 ~~~~~~~~C~nC~tt~Tp~--WRrg~~~~g-~LCNACGl~~~~~~~~RP~~~~ 52 (71)
T 2kae_A 3 HMNKKSFQCSNCSVTETIR--WRNIRSKEG-IQCNACFIYQRKYNKTRPVTAV 52 (71)
T ss_dssp -----CCCCSSSCCSCCSS--CCCCSSSSC-CCSSHHHHHHHHHHSCCCTHHH
T ss_pred CCCCCCCcCCccCCCCCCc--cccCCCCCC-ccchHHHHHHHHhCCCCCcccc
Confidence 3456779999999998863 333111222 8999999999999998877653
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=55.04 E-value=4.7 Score=35.22 Aligned_cols=37 Identities=22% Similarity=0.653 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcC---chhhhhhhcccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWT 113 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT 113 (328)
..+||+|...+..|--.+-.+..-| -|.|..|..-|.
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 3689999976654322222222222 388999999995
No 9
>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=52.60 E-value=12 Score=28.18 Aligned_cols=46 Identities=20% Similarity=0.494 Sum_probs=33.6
Q ss_pred CCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCcccccccc
Q 020288 74 TEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPV 123 (328)
Q Consensus 74 pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPv 123 (328)
++....|-.|..++|-. .-.-. ....+|-+|.-||-..|+.|-+.+
T Consensus 4 ~~~~~~C~~C~tt~Tp~--WR~gp--~G~~LCNACGl~~~~~~~~RP~~~ 49 (63)
T 3dfx_A 4 RRAGTSCANCQTTTTTL--WRRNA--NGDPVCNACGLYYKLHNINRPLTM 49 (63)
T ss_dssp CCTTCCCTTTCCSCCSS--CCCCT--TSCCCCHHHHHHHHHHSSCCCGGG
T ss_pred CCCCCcCCCcCCCCCCc--cCCCC--CCCchhhHHHHHHHHcCCCCCcCc
Confidence 34567899999988753 22221 122899999999999999887765
No 10
>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=52.41 E-value=7.6 Score=36.34 Aligned_cols=37 Identities=22% Similarity=0.665 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcC---chhhhhhhcccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWT 113 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT 113 (328)
...||+|...+..|-=.+..+...| -|.|..|..-|.
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 3689999966544422222333333 288999999885
No 11
>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=52.02 E-value=4.9 Score=36.79 Aligned_cols=30 Identities=13% Similarity=0.455 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||||...-.|.-+ . .+.-|||..|++
T Consensus 239 ~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 268 (268)
T 1k82_A 239 KGEPCRVCGTPIVATKH-A----QRATFYCRQCQK 268 (268)
T ss_dssp TTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 35789999987766543 2 355699999985
No 12
>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=50.99 E-value=5.2 Score=36.77 Aligned_cols=30 Identities=27% Similarity=0.645 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||||...=.|.-+ . .+.-|||..|++
T Consensus 244 ~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 273 (273)
T 3u6p_A 244 QGNPCKRCGTPIEKTVV-A----GRGTHYCPRCQR 273 (273)
T ss_dssp TTSBCTTTCCBCEEEEE-T----TEEEEECTTTCC
T ss_pred CcCCCCCCCCeEEEEEE-C----CCCeEECCCCCC
Confidence 35689999987666533 2 355699999985
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=50.99 E-value=5.4 Score=36.56 Aligned_cols=30 Identities=27% Similarity=0.692 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||||...-.|.-+ . .+.-|||..|++
T Consensus 234 ~g~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 263 (266)
T 1ee8_A 234 EGLPCPACGRPVERRVV-A----GRGTHFCPTCQG 263 (266)
T ss_dssp TTSBCTTTCCBCEEEES-S----SCEEEECTTTTT
T ss_pred CCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 35789999987666533 2 356699999997
No 14
>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=50.05 E-value=5.5 Score=36.43 Aligned_cols=30 Identities=30% Similarity=0.709 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||||...-.|.-+ . .+.-|||..|++
T Consensus 241 ~G~pC~~CG~~I~~~~~-~----gR~t~~CP~CQ~ 270 (271)
T 2xzf_A 241 TGEKCSRCGAEIQKIKV-A----GRGTHFCPVCQQ 270 (271)
T ss_dssp TTSBCTTTCCBCEEEEE-T----TEEEEECTTTSC
T ss_pred CCCCCCCCCCEeeEEEE-C----CCceEECCCCCC
Confidence 35789999987766543 2 355699999996
No 15
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Probab=48.69 E-value=2.4 Score=38.29 Aligned_cols=39 Identities=21% Similarity=0.457 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccC
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRG 115 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~G 115 (328)
++.+|+.|...=+..|+.+= -.++....|..|+..|+..
T Consensus 192 ~g~~C~~C~~~~H~~C~~~~-~~~~~~~~CP~C~~~W~~~ 230 (238)
T 3nw0_A 192 QGQSCETCGIRMHLPCVAKY-FQSNAEPRCPHCNDYWPHE 230 (238)
T ss_dssp SCEECSSSCCEECHHHHHHH-TTTCSSCBCTTTCCBCCSC
T ss_pred CCcccCccChHHHHHHHHHH-HHhCCCCCCCCCCCCCCCC
Confidence 35778888888888887543 3456678899999999865
No 16
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=45.38 E-value=4.4 Score=34.08 Aligned_cols=38 Identities=26% Similarity=0.631 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcC---chhhhhhhccccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWTR 114 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT~ 114 (328)
..+||+|...+..|-..+-.+...| -|.|..|.--|++
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 4789999987765433333333222 3889999999975
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=44.48 E-value=22 Score=26.82 Aligned_cols=46 Identities=22% Similarity=0.514 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCcccccccc
Q 020288 74 TEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPV 123 (328)
Q Consensus 74 pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPv 123 (328)
+.....|-.|.+++|-- +=..- .-+ .+|-+|.-||-.-|++|-+..
T Consensus 6 ~~~~~~C~~C~t~~Tp~-WR~gp--~G~-~LCNaCGl~~~~~~~~RP~~~ 51 (66)
T 4gat_A 6 QNGPTTCTNCFTQTTPL-WRRNP--EGQ-PLCNACGLFLKLHGVVRPLSL 51 (66)
T ss_dssp SSSSCCCTTTCCCCCSS-CEEET--TTE-EECHHHHHHHHHHCSCCCGGG
T ss_pred CCCCCCCCCCCCCCCCc-CCcCC--CCC-CccHHHHHHHHHcCCCCchhh
Confidence 34568999999988762 11111 122 899999999999999877655
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=43.75 E-value=7.1 Score=35.54 Aligned_cols=30 Identities=30% Similarity=0.600 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||+|...-.|.-+ . .+.-|||..|++
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 34689999987666432 2 355599999985
No 19
>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}
Probab=42.81 E-value=13 Score=28.32 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccc
Q 020288 74 TEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWT 113 (328)
Q Consensus 74 pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT 113 (328)
.++...|..|... | ++..-||-|+.|.+-.=
T Consensus 18 d~~~~~C~~C~~~---F------s~~~RrHHCR~CG~v~C 48 (84)
T 1z2q_A 18 DEDAPACNGCGCV---F------TTTVRRHHCRNCGYVLC 48 (84)
T ss_dssp TTTCCBCTTTCCB---C------CTTSCCEECTTTCCEEC
T ss_pred CCCCCCCcCcCCc---c------ccchhcccccCCCcEEC
Confidence 3456788888765 3 34467898988876543
No 20
>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=39.83 E-value=7.1 Score=30.55 Aligned_cols=17 Identities=29% Similarity=0.923 Sum_probs=14.9
Q ss_pred CchhhhhhhcccccCcc
Q 020288 101 PRHFCKACRRYWTRGGA 117 (328)
Q Consensus 101 PR~fCk~CrRywT~GG~ 117 (328)
|||||+-|..|.|+.-.
T Consensus 2 PkYyCdYCd~~lt~Ds~ 18 (77)
T 3cw1_L 2 PKFYCDYCDTYLTHDSP 18 (77)
T ss_pred CCcccccCCceecCCCH
Confidence 89999999999987744
No 21
>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=38.07 E-value=12 Score=29.00 Aligned_cols=14 Identities=43% Similarity=0.731 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCcce
Q 020288 77 PLKCPRCDSTNTKF 90 (328)
Q Consensus 77 ~~~CPRC~S~~Tkf 90 (328)
+++||.|.|.||+.
T Consensus 55 g~kC~~C~SyNTr~ 68 (79)
T 2k2d_A 55 GMKCKICESYNTAQ 68 (79)
T ss_dssp CCCCTTTSCCCEEE
T ss_pred cccCcCCCCcCeEe
Confidence 45999999999983
No 22
>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=28 Score=28.52 Aligned_cols=46 Identities=20% Similarity=0.511 Sum_probs=34.3
Q ss_pred CCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCcccccccc
Q 020288 74 TEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPV 123 (328)
Q Consensus 74 pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPv 123 (328)
......|-.|...+|-- .-. . ..-+.+|-+|.-||..-|..|-+.+
T Consensus 56 ~~~~~~C~~C~t~~tp~--WRr-~-~~g~~lCNaCgl~~~~~~~~rp~~~ 101 (115)
T 4hc9_A 56 RRAGTSCANCQTTTTTL--WRR-N-ANGDPVCNACGLYYKLHNINRPLTM 101 (115)
T ss_dssp CCTTCCCTTTCCSCCSS--CEE-C-TTSCEECHHHHHHHHHHSSCCCGGG
T ss_pred ccccccCCCcCCCCcce--eEE-C-CCCCCcchHHHHHHHHhCCCCCccc
Confidence 34568999999988752 111 1 2236899999999999999887776
No 23
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=30.93 E-value=24 Score=24.15 Aligned_cols=33 Identities=18% Similarity=0.464 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~ 114 (328)
..++||.|.+.+-.| ....-...|+.|+.-+..
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 223456899999876654
No 24
>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=29.63 E-value=28 Score=28.69 Aligned_cols=14 Identities=36% Similarity=1.051 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCCcc
Q 020288 76 VPLKCPRCDSTNTK 89 (328)
Q Consensus 76 ~~~~CPRC~S~~Tk 89 (328)
.+-+||+|.|.+..
T Consensus 83 kPsrCP~CkSe~Ie 96 (105)
T 2gmg_A 83 IPSRCPKCKSEWIE 96 (105)
T ss_dssp CCSSCSSSCCCCBC
T ss_pred CCCCCcCCCCCccC
Confidence 34566666666544
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=29.19 E-value=24 Score=26.07 Aligned_cols=24 Identities=33% Similarity=0.904 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRY 111 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 111 (328)
....||.|... | .|.+.|.+|.-|
T Consensus 29 ~l~~c~~cG~~--~----------~pH~vc~~CG~Y 52 (60)
T 2zjr_Z 29 NLTECPQCHGK--K----------LSHHICPNCGYY 52 (60)
T ss_dssp CCEECTTTCCE--E----------CTTBCCTTTCBS
T ss_pred CceECCCCCCE--e----------CCceEcCCCCcC
Confidence 44789999875 3 799999999966
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=28.86 E-value=19 Score=25.12 Aligned_cols=41 Identities=20% Similarity=0.551 Sum_probs=29.0
Q ss_pred CCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccccccc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVP 122 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvP 122 (328)
..|-.|..++|-. +-.-. ....+|-+|.-||-..|++|-+.
T Consensus 2 ~~C~~C~tt~Tp~--WR~gp--~G~~LCNaCGl~~k~~~~~RP~~ 42 (43)
T 2vut_I 2 TTCTNCFTQTTPL--WRRNP--EGQPLCNACGLFLKLHGVVRPLS 42 (43)
T ss_dssp CCCSSSCCCCCSC--CEECT--TSCEECHHHHHHHHHHSSCCCCC
T ss_pred CcCCccCCCCCCc--cccCC--CCCcccHHHHHHHHHhCCCCCCC
Confidence 4688898887753 22211 12389999999999999988653
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=26.73 E-value=20 Score=26.99 Aligned_cols=30 Identities=17% Similarity=0.260 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYW 112 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyw 112 (328)
+.+.||.|... .-|- ...-...|+.|++-+
T Consensus 9 eiL~CP~ck~~---L~~~----~~~g~LvC~~c~~~Y 38 (67)
T 2jny_A 9 EVLACPKDKGP---LRYL----ESEQLLVNERLNLAY 38 (67)
T ss_dssp CCCBCTTTCCB---CEEE----TTTTEEEETTTTEEE
T ss_pred HHhCCCCCCCc---CeEe----CCCCEEEcCCCCccc
Confidence 56899999983 2222 234567899998755
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=25.80 E-value=25 Score=26.55 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYW 112 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyw 112 (328)
+.+.||.|...-+ | ....-...|+.|++-+
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 4589999996422 2 2334667899998754
No 29
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=23.23 E-value=26 Score=26.37 Aligned_cols=30 Identities=13% Similarity=0.319 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYW 112 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyw 112 (328)
+.+.||.|... .-|- ...-...|+.|++-+
T Consensus 7 ~iL~CP~ck~~---L~~~----~~~~~LiC~~cg~~Y 36 (68)
T 2jr6_A 7 DILVCPVTKGR---LEYH----QDKQELWSRQAKLAY 36 (68)
T ss_dssp CCCBCSSSCCB---CEEE----TTTTEEEETTTTEEE
T ss_pred hheECCCCCCc---CeEe----CCCCEEEcCCCCcEe
Confidence 56899999963 2222 234667899998654
No 30
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=22.72 E-value=45 Score=25.21 Aligned_cols=35 Identities=29% Similarity=0.525 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccc-cCcc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWT-RGGA 117 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT-~GG~ 117 (328)
+.+.||.|... .-|- ...-...|+.|++-+- +.|.
T Consensus 7 ~iL~CP~ck~~---L~~~----~~~~~LiC~~cg~~YPI~dGI 42 (70)
T 2js4_A 7 DILVCPVCKGR---LEFQ----RAQAELVCNADRLAFPVRDGV 42 (70)
T ss_dssp CCCBCTTTCCB---EEEE----TTTTEEEETTTTEEEEEETTE
T ss_pred hheECCCCCCc---CEEe----CCCCEEEcCCCCceecCCCCe
Confidence 56899999983 3222 2345678999987553 3443
No 31
>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}
Probab=20.15 E-value=54 Score=26.11 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=8.4
Q ss_pred CC-CCCCCCCCCcce
Q 020288 77 PL-KCPRCDSTNTKF 90 (328)
Q Consensus 77 ~~-~CPRC~S~~Tkf 90 (328)
.. .||.|.+.+.+|
T Consensus 89 ~~~~CP~Cgs~~~~i 103 (119)
T 2kdx_A 89 DYGVCEKCHSKNVII 103 (119)
T ss_dssp TTCCCSSSSSCCCEE
T ss_pred CCCcCccccCCCcEE
Confidence 44 566666666554
Done!