Query 029068
Match_columns 199
No_of_seqs 209 out of 1270
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 11:07:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029068.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/029068hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1gcc_A Ethylene responsive ele 99.9 3.8E-25 1.3E-29 154.6 6.6 60 16-75 2-62 (63)
2 3igm_B PF14_0633 protein; AP2 91.8 0.11 3.7E-06 37.0 2.8 27 12-40 3-30 (77)
3 1z1b_A Integrase; protein-DNA 85.5 0.98 3.4E-05 37.7 4.9 42 18-63 14-55 (356)
4 3jtz_A Integrase; four strande 82.8 3.3 0.00011 29.4 6.1 45 20-64 28-76 (88)
5 1u3e_M HNH homing endonuclease 81.9 0.21 7.2E-06 39.6 -0.7 38 17-57 109-146 (174)
6 3ju0_A Phage integrase; four s 72.2 8.6 0.00029 28.4 5.8 45 20-64 28-76 (108)
7 1b69_A Protein (integrase); in 48.3 25 0.00086 24.2 4.2 29 12-41 7-35 (69)
8 1x60_A Sporulation-specific N- 47.3 18 0.00061 24.1 3.4 24 38-61 45-68 (79)
9 2ftc_I Mitochondrial ribosomal 46.2 30 0.001 25.9 4.8 36 28-65 80-115 (118)
10 1uta_A FTSN, MSGA, cell divisi 42.5 31 0.0011 23.2 4.1 33 29-61 36-68 (81)
11 3eik_A Tata-box-binding protei 30.6 75 0.0026 26.3 5.2 50 13-65 73-123 (218)
12 3r8s_M 50S ribosomal protein L 29.7 58 0.002 25.0 4.1 35 28-65 92-126 (136)
13 1vq8_H 50S ribosomal protein L 28.0 44 0.0015 26.9 3.2 37 28-66 123-160 (171)
14 2pa2_A 60S ribosomal protein L 25.0 45 0.0015 26.2 2.8 38 27-66 93-131 (151)
15 2bn8_A CEDA, cell division act 24.9 29 0.001 24.5 1.5 38 14-54 37-74 (87)
No 1
>1gcc_A Ethylene responsive element binding factor 1; transcription factor, protein-DNA complex, ethylene inducible; HET: DNA; NMR {Arabidopsis thaliana} SCOP: d.10.1.2 PDB: 2gcc_A 3gcc_A
Probab=99.91 E-value=3.8e-25 Score=154.57 Aligned_cols=60 Identities=53% Similarity=1.007 Sum_probs=56.9
Q ss_pred ceeeEEeCCCCcEEEEEeeCC-CCeEEeeccCccHHHHHHHHHHHHHHhcCCCcccCCCCC
Q 029068 16 RYKGVRKRKWGKYVSEIRLPN-SRARIWLGSYDTAEKAARAFDAALFCLRGRSAKFNFPDN 75 (199)
Q Consensus 16 ~yrGV~~r~~gkW~A~I~~~~-~~kri~LGtf~t~eeAA~AYd~aa~~l~G~~a~~NFp~s 75 (199)
+||||++|++|||+|+|++|. +|+++|||+|+|+||||+|||.|+++++|.++.+|||++
T Consensus 2 ~yrGV~~r~~gkw~A~I~~~~~~g~r~~LGtf~T~eeAA~AyD~Aa~~~~G~~a~~NFp~~ 62 (63)
T 1gcc_A 2 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 62 (63)
T ss_dssp CCTTEEEETTTEEEEEEEETTTTSEEEEEEEESSHHHHHHHHHHHHHHHHSSCCCCSSCTT
T ss_pred CcccEeeCCCCcEEEEEccccCCCeEEEeeeCCCHHHHHHHHHHHHHHhcCcccccCCCCc
Confidence 699999999999999999886 479999999999999999999999999999999999975
No 2
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=91.79 E-value=0.11 Score=37.03 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=21.1
Q ss_pred CCCCceeeEEeCC-CCcEEEEEeeCCCCeE
Q 029068 12 RSDSRYKGVRKRK-WGKYVSEIRLPNSRAR 40 (199)
Q Consensus 12 ~n~S~yrGV~~r~-~gkW~A~I~~~~~~kr 40 (199)
..+|+|+||++.+ .+.|+|.-.+ +|++
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~e--~g~r 30 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFYD--GASR 30 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEEE--TTEE
T ss_pred CCCCCCCcEEeecCCceEEEEEec--CCeE
Confidence 5789999998874 6999999994 4543
No 3
>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP: d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3*
Probab=85.52 E-value=0.98 Score=37.70 Aligned_cols=42 Identities=19% Similarity=0.067 Sum_probs=31.5
Q ss_pred eeEEeCCCCcEEEEEeeCCCCeEEeeccCccHHHHHHHHHHHHHHh
Q 029068 18 KGVRKRKWGKYVSEIRLPNSRARIWLGSYDTAEKAARAFDAALFCL 63 (199)
Q Consensus 18 rGV~~r~~gkW~A~I~~~~~~kri~LGtf~t~eeAA~AYd~aa~~l 63 (199)
.||++++.|.|+.+++ .+|+++.+|. |..||..+...+...+
T Consensus 14 ~~v~~~~~g~~~~r~~--~~gk~~~~g~--t~~eA~~~a~~~~~~~ 55 (356)
T 1z1b_A 14 PNLYIRNNGYYCYRDP--RTGKEFGLGR--DRRIAITEAIQANIEL 55 (356)
T ss_dssp TTEEEETTTEEEEECT--TTCCEEEEES--CHHHHHHHHHHHHHHH
T ss_pred ccceecCCCeEEEEee--cCCeEEECCC--CHHHHHHHHHHHHHHH
Confidence 3577777789988765 6888999996 8888877766655443
No 4
>3jtz_A Integrase; four stranded beta-sheet, DNA binding protein; 1.30A {Yersinia pestis} PDB: 3rmp_A
Probab=82.79 E-value=3.3 Score=29.45 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=32.5
Q ss_pred EEeCCCC--cEEEEEeeCCCCeEEeeccCc--cHHHHHHHHHHHHHHhc
Q 029068 20 VRKRKWG--KYVSEIRLPNSRARIWLGSYD--TAEKAARAFDAALFCLR 64 (199)
Q Consensus 20 V~~r~~g--kW~A~I~~~~~~kri~LGtf~--t~eeAA~AYd~aa~~l~ 64 (199)
++.++.| .|+-+.+.....+++-||.|. |+++|....+++...+.
T Consensus 28 L~V~psG~K~w~~ryr~~Gk~~~~~LG~yp~~sL~~AR~~a~~~r~~l~ 76 (88)
T 3jtz_A 28 LLVKPGGSRHWYLKYRISGKESRIALGAYPAISLSDARQQREGIRKMLA 76 (88)
T ss_dssp EEECTTSCEEEEEEEEETTEEEEEEEEETTTSCHHHHHHHHHHHHHHHT
T ss_pred EEEecCCCEEEEEEEEeCCeEEEEEeECCCCCCHHHHHHHHHHHHHHHH
Confidence 3445544 599998843344679999997 68999888888777663
No 5
>1u3e_M HNH homing endonuclease; HNH catalytic motif, helix-turn-helix DNA binding domain, PR complex, DNA binding protein-DNA complex; 2.92A {Bacillus phage SPO1} SCOP: d.4.1.3 d.285.1.1
Probab=81.91 E-value=0.21 Score=39.57 Aligned_cols=38 Identities=16% Similarity=-0.007 Sum_probs=28.1
Q ss_pred eeeEEeCCCCcEEEEEeeCCCCeEEeeccCccHHHHHHHHH
Q 029068 17 YKGVRKRKWGKYVSEIRLPNSRARIWLGSYDTAEKAARAFD 57 (199)
Q Consensus 17 yrGV~~r~~gkW~A~I~~~~~~kri~LGtf~t~eeAA~AYd 57 (199)
.+||...+.++|.+.|. .. +.++||.|+|.+|||++|.
T Consensus 109 ~~g~~~~~~~k~~~vi~--~~-~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 109 SKAQQIAKIKNQKPIIV--IS-PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp HHHHHHHHHHTCCCEEE--EC-TTSCEEEESCHHHHHHHHT
T ss_pred eeeeeeccCCCCceEEE--Ec-CCceEEeeCCHHHHHHHHC
Confidence 45664422356888888 44 5678999999999999964
No 6
>3ju0_A Phage integrase; four stranded beta-sheet, DNA binding protein; 1.60A {Pectobacterium atrosepticum}
Probab=72.16 E-value=8.6 Score=28.36 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=31.9
Q ss_pred EEeCCCC--cEEEEEeeCCCCeEEeeccCc--cHHHHHHHHHHHHHHhc
Q 029068 20 VRKRKWG--KYVSEIRLPNSRARIWLGSYD--TAEKAARAFDAALFCLR 64 (199)
Q Consensus 20 V~~r~~g--kW~A~I~~~~~~kri~LGtf~--t~eeAA~AYd~aa~~l~ 64 (199)
++..+.| .|+-+.+.....+++-||.|. |+.+|....+.+...+.
T Consensus 28 L~V~psG~K~w~~rYr~~GK~~~~~LG~yp~~SLa~AR~~a~~~r~~l~ 76 (108)
T 3ju0_A 28 LLVHPNGSKYWRLSYRFEKKQRLLALGVYPAVSLADARQRRDEAKKLLA 76 (108)
T ss_dssp EEECTTSCEEEEEEEEETTEEEEEEEEEETTSCHHHHHHHHHHHHHHHH
T ss_pred EEEEcCCCEEEEEEEEEcCceEEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence 3445544 599998843334678999997 58888888877776663
No 7
>1b69_A Protein (integrase); integrase, DNA binding, transposition, complex, beta-sheet recognition; HET: DNA; NMR {Enterococcus faecalis} SCOP: d.10.1.1 PDB: 1tn9_A* 1bb8_A 2bb8_A
Probab=48.32 E-value=25 Score=24.23 Aligned_cols=29 Identities=21% Similarity=0.145 Sum_probs=21.7
Q ss_pred CCCCceeeEEeCCCCcEEEEEeeCCCCeEE
Q 029068 12 RSDSRYKGVRKRKWGKYVSEIRLPNSRARI 41 (199)
Q Consensus 12 ~n~S~yrGV~~r~~gkW~A~I~~~~~~kri 41 (199)
.+.--+.|+++|+.|+|+.++.+. .|++.
T Consensus 7 kgr~L~~GesqR~dG~Y~yry~d~-~Gkr~ 35 (69)
T 1b69_A 7 RGRILKTGESQRKDGRYLYKYIDS-FGEPQ 35 (69)
T ss_dssp SSSCCCTTEEECSSSCEEEEEECT-TSSEE
T ss_pred CCCccCCCeEEccCCcEEEEEEcC-CCCEE
Confidence 345667889999999999999964 35443
No 8
>1x60_A Sporulation-specific N-acetylmuramoyl-L-alanine amidase; CWLC, CWLCR, peptidoglycan, cell WALL lytic amidase, tandem repeats, hydrolase; NMR {Bacillus subtilis}
Probab=47.32 E-value=18 Score=24.15 Aligned_cols=24 Identities=13% Similarity=0.198 Sum_probs=18.7
Q ss_pred CeEEeeccCccHHHHHHHHHHHHH
Q 029068 38 RARIWLGSYDTAEKAARAFDAALF 61 (199)
Q Consensus 38 ~kri~LGtf~t~eeAA~AYd~aa~ 61 (199)
--|+++|.|.+.++|..+..+...
T Consensus 45 ~yRV~vGpf~~~~~A~~~~~~L~~ 68 (79)
T 1x60_A 45 LYKVQIGAFSSKDNADTLAARAKN 68 (79)
T ss_dssp EEEEEEEEESSHHHHHHHHHHHHH
T ss_pred EEEEEECCcCCHHHHHHHHHHHHH
Confidence 358889999999988888766554
No 9
>2ftc_I Mitochondrial ribosomal protein L16, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_I
Probab=46.16 E-value=30 Score=25.91 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=30.2
Q ss_pred EEEEEeeCCCCeEEeeccCccHHHHHHHHHHHHHHhcC
Q 029068 28 YVSEIRLPNSRARIWLGSYDTAEKAARAFDAALFCLRG 65 (199)
Q Consensus 28 W~A~I~~~~~~kri~LGtf~t~eeAA~AYd~aa~~l~G 65 (199)
|+|+|. .+..-+-++...+++.|.+|...|+.+|-+
T Consensus 80 wva~Vk--~G~ilfEi~g~~~~~~a~eAlr~a~~KlP~ 115 (118)
T 2ftc_I 80 YVTPVK--AGRLVVEMGGRCEFEEVQGFLDQVAHKLPF 115 (118)
T ss_pred EEEEEC--CCCEEEEEeccCCHHHHHHHHHHHHhhCCC
Confidence 999999 666667777778899999999999988744
No 10
>1uta_A FTSN, MSGA, cell division protein FTSN; bacterial cell division protein, RNP domain, transmembrane, inner membrane, repeat; NMR {Escherichia coli} SCOP: d.58.52.1
Probab=42.49 E-value=31 Score=23.24 Aligned_cols=33 Identities=21% Similarity=0.265 Sum_probs=23.1
Q ss_pred EEEEeeCCCCeEEeeccCccHHHHHHHHHHHHH
Q 029068 29 VSEIRLPNSRARIWLGSYDTAEKAARAFDAALF 61 (199)
Q Consensus 29 ~A~I~~~~~~kri~LGtf~t~eeAA~AYd~aa~ 61 (199)
.+.|.....--|+.+|-|.+.++|..+.++...
T Consensus 36 ~a~i~~~~~~yRV~vGpf~s~~~A~~~~~~L~~ 68 (81)
T 1uta_A 36 DSKITTNNGWNRVVIGPVKGKENADSTLNRLKM 68 (81)
T ss_dssp CEEEEECSSSEEEEESSCBTTTHHHHHHHHHHH
T ss_pred CeEEEeCCcEEEEEECCcCCHHHHHHHHHHHHH
Confidence 345543233468999999999999888766554
No 11
>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C
Probab=30.63 E-value=75 Score=26.34 Aligned_cols=50 Identities=16% Similarity=0.104 Sum_probs=39.4
Q ss_pred CCCceeeEEeC-CCCcEEEEEeeCCCCeEEeeccCccHHHHHHHHHHHHHHhcC
Q 029068 13 SDSRYKGVRKR-KWGKYVSEIRLPNSRARIWLGSYDTAEKAARAFDAALFCLRG 65 (199)
Q Consensus 13 n~S~yrGV~~r-~~gkW~A~I~~~~~~kri~LGtf~t~eeAA~AYd~aa~~l~G 65 (199)
+..+|-||.+| +.-|-.+-|. .+||-+..|. .+.|+|..|.++.+..++.
T Consensus 73 ePe~Fpglv~Rl~~Pk~t~LIF--~SGKiV~TGA-kS~e~a~~A~~ki~~~L~~ 123 (218)
T 3eik_A 73 NPKRFAAVIMRIREPKTTALIF--ASGKMVITGA-KSEKSSRMAAQRYAKIIHK 123 (218)
T ss_dssp CTTTCSSEEEEETTTTEEEEEC--TTSEEEEEEE-SSHHHHHHHHHHHHHHHHH
T ss_pred cCccCceEEEEecCCcEEEEEE--CCCeEEEEec-CCHHHHHHHHHHHHHHHHH
Confidence 34578898655 4467788888 8999988887 6799999999998887753
No 12
>3r8s_M 50S ribosomal protein L16; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_K 1p86_K 1vs8_M 1vs6_M 2aw4_M 2awb_M 1vt2_M 2i2v_M 2j28_M 2i2t_M* 2qao_M* 2qba_M* 2qbc_M* 2qbe_M 2qbg_M 2qbi_M* 2qbk_M* 2qov_M 2qox_M 2qoz_M* ...
Probab=29.71 E-value=58 Score=25.01 Aligned_cols=35 Identities=23% Similarity=0.135 Sum_probs=29.0
Q ss_pred EEEEEeeCCCCeEEeeccCccHHHHHHHHHHHHHHhcC
Q 029068 28 YVSEIRLPNSRARIWLGSYDTAEKAARAFDAALFCLRG 65 (199)
Q Consensus 28 W~A~I~~~~~~kri~LGtf~t~eeAA~AYd~aa~~l~G 65 (199)
|+|+|. .+..-+-++. .+++.|..|...|+.+|-+
T Consensus 92 wva~Vk--~G~ilfEi~g-~~~~~A~eAlr~a~~KLP~ 126 (136)
T 3r8s_M 92 WVALIQ--PGKVLYEMDG-VPEELAREAFKLAAAKLPI 126 (136)
T ss_dssp EEEEEC--TTCEEEEEES-SCHHHHHHHHHHHHTTCSS
T ss_pred EEEEEC--CCCEEEEEeC-CCHHHHHHHHHHHHhcCCC
Confidence 999999 6666677777 5999999999999988754
No 13
>1vq8_H 50S ribosomal protein L10E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: d.41.4.1 PDB: 1vq4_H* 1vq5_H* 1vq6_H* 1vq7_H* 1s72_H* 1vq9_H* 1vqk_H* 1vql_H* 1vqm_H* 1vqn_H* 1vqo_H* 1vqp_H* 2otj_H* 2otl_H* 2qa4_H* 2qex_H* 1yhq_H* 1yi2_H* 1yij_H* 1yit_H* ...
Probab=28.00 E-value=44 Score=26.87 Aligned_cols=37 Identities=14% Similarity=0.082 Sum_probs=27.0
Q ss_pred EEEEEeeCCCCeEEeecc-CccHHHHHHHHHHHHHHhcCC
Q 029068 28 YVSEIRLPNSRARIWLGS-YDTAEKAARAFDAALFCLRGR 66 (199)
Q Consensus 28 W~A~I~~~~~~kri~LGt-f~t~eeAA~AYd~aa~~l~G~ 66 (199)
|+|+|. .+..-+-+.. -.+++.|.+|...|+.+|-+.
T Consensus 123 wvArVk--~G~ilfei~~~~v~~~~A~eAlr~A~~KLP~k 160 (171)
T 1vq8_H 123 TAARVQ--AGEQLFTAYCNVEDAEHVKEAFRRAYNKITPS 160 (171)
T ss_dssp EEEEEC--TTCEEEEEEECTTTHHHHHHHHHHHGGGSSSC
T ss_pred EEEEEC--CCCEEEEEECcCCCHHHHHHHHHHHHhhCCCc
Confidence 999998 4444444443 368999999999999887543
No 14
>2pa2_A 60S ribosomal protein L10; QM protein, , structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.50A {Homo sapiens} SCOP: d.41.4.1
Probab=25.03 E-value=45 Score=26.24 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=27.5
Q ss_pred cEEEEEeeCCCCeEEeecc-CccHHHHHHHHHHHHHHhcCC
Q 029068 27 KYVSEIRLPNSRARIWLGS-YDTAEKAARAFDAALFCLRGR 66 (199)
Q Consensus 27 kW~A~I~~~~~~kri~LGt-f~t~eeAA~AYd~aa~~l~G~ 66 (199)
-|+|+|. .+..-+-+.. -.+++.|.+|...|+.+|-+.
T Consensus 93 ~wvArVk--~G~ilfei~~~~v~~~~A~eAlr~A~~KlP~k 131 (151)
T 2pa2_A 93 GTVARVH--IGQVIMSIRTKLQNKEHVIEALRRAKFKFPGR 131 (151)
T ss_dssp CCEEEEC--TTBEEEEEEECGGGHHHHHHHHHHHGGGSSSC
T ss_pred EEEEEEC--CCCEEEEEECCCCCHHHHHHHHHHHHhhCCCc
Confidence 3999999 4444444444 268999999999999887543
No 15
>2bn8_A CEDA, cell division activator CEDA; cell division activator protein, cell cycle protein; NMR {Escherichia coli} PDB: 2d35_A
Probab=24.91 E-value=29 Score=24.45 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=24.4
Q ss_pred CCceeeEEeCCCCcEEEEEeeCCCCeEEeeccCccHHHHHH
Q 029068 14 DSRYKGVRKRKWGKYVSEIRLPNSRARIWLGSYDTAEKAAR 54 (199)
Q Consensus 14 ~S~yrGV~~r~~gkW~A~I~~~~~~kri~LGtf~t~eeAA~ 54 (199)
--+||-|+.-+ |||+|.+. .+-.-.---.|..+|.|.+
T Consensus 37 md~frdvw~lr-gkyvafvl--~ge~frrspafsvpesaqr 74 (87)
T 2bn8_A 37 MDSFRDVWMLR-GKYVAFVL--MGESFLRSPAFTVPESAQR 74 (87)
T ss_dssp TTTCTTEEEET-TEEEEBCC--SSSCCCBCCCBSSHHHHHH
T ss_pred cccchhheeec-cceEEEEE--echhhccCCccCCcHHHHH
Confidence 34788887655 99999987 3222222356777777655
Done!