Query 040188
Match_columns 117
No_of_seqs 113 out of 1102
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 09:10:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040188.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/040188hhsearch_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 2.2E-27 7.4E-32 152.2 5.4 61 24-84 2-62 (63)
2 1u3e_M HNH homing endonuclease 92.3 0.0046 1.6E-07 44.8 -4.0 54 8-66 93-146 (174)
3 3igm_B PF14_0633 protein; AP2 86.5 0.49 1.7E-05 30.8 2.7 24 20-43 3-27 (77)
4 3jtz_A Integrase; four strande 76.9 4.4 0.00015 26.2 4.7 44 28-72 28-75 (88)
5 1z1b_A Integrase; protein-DNA 74.0 4.5 0.00015 30.2 4.7 42 26-72 14-55 (356)
6 3ju0_A Phage integrase; four s 64.2 10 0.00035 25.4 4.4 44 28-72 28-75 (108)
7 1x60_A Sporulation-specific N- 51.5 9.6 0.00033 23.1 2.3 23 48-70 46-68 (79)
8 1uta_A FTSN, MSGA, cell divisi 43.6 13 0.00046 22.8 2.1 23 48-70 46-68 (81)
9 1b69_A Protein (integrase); in 39.5 36 0.0012 21.4 3.6 31 21-51 8-38 (69)
10 1x4e_A RNA binding motif, sing 31.9 37 0.0013 20.0 2.7 32 51-82 50-82 (85)
11 2dis_A Unnamed protein product 29.3 14 0.00047 23.1 0.4 19 50-68 54-72 (109)
12 2dnl_A Cytoplasmic polyadenyla 23.8 42 0.0014 21.2 2.0 25 50-75 54-78 (114)
13 2ftc_I Mitochondrial ribosomal 23.5 1.2E+02 0.004 20.5 4.3 36 35-74 79-115 (118)
14 2dgu_A Heterogeneous nuclear r 22.6 87 0.003 19.1 3.4 16 52-67 49-64 (103)
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=99.94 E-value=2.2e-27 Score=152.15 Aligned_cols=61 Identities=75% Similarity=1.086 Sum_probs=58.0
Q ss_pred ceeeeEECCCCcEEEEEeCCCCCCceeccCCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCC
Q 040188 24 HSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQAALANVRAAFKFRGRRALLNFPNF 84 (117)
Q Consensus 24 ~yrGV~~~~~GkW~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~~G~~A~~NFp~~ 84 (117)
+|+||+++++|||+|+|+++.++|+++|||+|+|+||||+|||.++++++|.++++|||++
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 6999999889999999999876789999999999999999999999999999999999975
No 2
>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=92.26 E-value=0.0046 Score=44.76 Aligned_cols=54 Identities=6% Similarity=-0.124 Sum_probs=34.3
Q ss_pred chhhhhhccCCCCCCCceeeeEECCCCcEEEEEeCCCCCCceeccCCCCCHHHHHHHHH
Q 040188 8 PVADAAALAVVPSKGNHSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQAALANV 66 (117)
Q Consensus 8 ~~~~~~~~~~~~~~~S~yrGV~~~~~GkW~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD 66 (117)
..+|+.+........ .++||.+...++|.+.|... +.++||.|+|.+||+++|.
T Consensus 93 ~~eN~~~~~~~~~~~-~~~g~~~~~~~k~~~vi~~~----~~~~~~~f~s~~eAa~~~G 146 (174)
T 1u3e_M 93 QKINVENQMSRGTLN-VSKAQQIAKIKNQKPIIVIS----PDGIEKEYPSTKCACEELG 146 (174)
T ss_dssp HHHHHHHHHHHTCCC-CHHHHHHHHHHTCCCEEEEC----TTSCEEEESCHHHHHHHHT
T ss_pred HHHHhhcccccCccc-ceeeeeeccCCCCceEEEEc----CCceEEeeCCHHHHHHHHC
Confidence 344555443333222 24676542246788888853 4577999999999999965
No 3
>3igm_B PF14_0633 protein; AP2 domain, specific transcription FA protein-DNA complex, transcription-DNA complex; 2.20A {Plasmodium falciparum}
Probab=86.46 E-value=0.49 Score=30.83 Aligned_cols=24 Identities=17% Similarity=0.029 Sum_probs=20.3
Q ss_pred CCCCceeeeEECC-CCcEEEEEeCC
Q 040188 20 SKGNHSRGVRQTP-SGKFAAEIRDP 43 (117)
Q Consensus 20 ~~~S~yrGV~~~~-~GkW~A~I~~~ 43 (117)
...|+|.||+|.+ .+.|.|.-.+.
T Consensus 3 ~~~Sg~pGVsw~kR~~~WlA~W~e~ 27 (77)
T 3igm_B 3 HMSSGYPGVSWNKRMCAWLAFFYDG 27 (77)
T ss_dssp -CCSSSTTEEEETTTTEEEEEEEET
T ss_pred CCCCCCCcEEeecCCceEEEEEecC
Confidence 3679999999987 79999998864
No 4
>3jtz_A Integrase; four stranded beta-sheet, DNA binding protein; 1.30A {Yersinia pestis} PDB: 3rmp_A
Probab=76.87 E-value=4.4 Score=26.17 Aligned_cols=44 Identities=16% Similarity=0.178 Sum_probs=30.9
Q ss_pred eEECCCC--cEEEEEeCCCCCCceeccCCCC--CHHHHHHHHHHHHHHh
Q 040188 28 VRQTPSG--KFAAEIRDPAKKGARCWLETFA--TAEQAALANVRAAFKF 72 (117)
Q Consensus 28 V~~~~~G--kW~A~I~~~~~~gk~~~LGtF~--t~EeAA~AYD~aa~~~ 72 (117)
|+..++| .|.-+.+...+ -+++.||.|+ |.+||....+.+...+
T Consensus 28 L~V~psG~K~w~~ryr~~Gk-~~~~~LG~yp~~sL~~AR~~a~~~r~~l 75 (88)
T 3jtz_A 28 LLVKPGGSRHWYLKYRISGK-ESRIALGAYPAISLSDARQQREGIRKML 75 (88)
T ss_dssp EEECTTSCEEEEEEEEETTE-EEEEEEEETTTSCHHHHHHHHHHHHHHH
T ss_pred EEEecCCCEEEEEEEEeCCe-EEEEEeECCCCCCHHHHHHHHHHHHHHH
Confidence 3445544 48888875432 3678899997 5889888887776666
No 5
>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=73.98 E-value=4.5 Score=30.20 Aligned_cols=42 Identities=12% Similarity=0.116 Sum_probs=31.1
Q ss_pred eeeEECCCCcEEEEEeCCCCCCceeccCCCCCHHHHHHHHHHHHHHh
Q 040188 26 RGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQAALANVRAAFKF 72 (117)
Q Consensus 26 rGV~~~~~GkW~A~I~~~~~~gk~~~LGtF~t~EeAA~AYD~aa~~~ 72 (117)
.||+.++.|.|..++.. +|+++.||. |..||......+...+
T Consensus 14 ~~v~~~~~g~~~~r~~~---~gk~~~~g~--t~~eA~~~a~~~~~~~ 55 (356)
T 1z1b_A 14 PNLYIRNNGYYCYRDPR---TGKEFGLGR--DRRIAITEAIQANIEL 55 (356)
T ss_dssp TTEEEETTTEEEEECTT---TCCEEEEES--CHHHHHHHHHHHHHHH
T ss_pred ccceecCCCeEEEEeec---CCeEEECCC--CHHHHHHHHHHHHHHH
Confidence 36777778899987653 467888996 8888887776655544
No 6
>3ju0_A Phage integrase; four stranded beta-sheet, DNA binding protein; 1.60A {Pectobacterium atrosepticum}
Probab=64.22 E-value=10 Score=25.37 Aligned_cols=44 Identities=16% Similarity=0.089 Sum_probs=30.0
Q ss_pred eEECCCC--cEEEEEeCCCCCCceeccCCCC--CHHHHHHHHHHHHHHh
Q 040188 28 VRQTPSG--KFAAEIRDPAKKGARCWLETFA--TAEQAALANVRAAFKF 72 (117)
Q Consensus 28 V~~~~~G--kW~A~I~~~~~~gk~~~LGtF~--t~EeAA~AYD~aa~~~ 72 (117)
|+..++| .|.-+.+...+ -+++.||.|+ |..||....+.+...+
T Consensus 28 L~V~psG~K~w~~rYr~~GK-~~~~~LG~yp~~SLa~AR~~a~~~r~~l 75 (108)
T 3ju0_A 28 LLVHPNGSKYWRLSYRFEKK-QRLLALGVYPAVSLADARQRRDEAKKLL 75 (108)
T ss_dssp EEECTTSCEEEEEEEEETTE-EEEEEEEEETTSCHHHHHHHHHHHHHHH
T ss_pred EEEEcCCCEEEEEEEEEcCc-eEEEecCCCCCCCHHHHHHHHHHHHHHH
Confidence 3444544 48888875432 3668899997 5888887777766555
No 7
>1x60_A Sporulation-specific N-acetylmuramoyl-L-alanine amidase; CWLC, CWLCR, peptidoglycan, cell WALL lytic amidase, tandem repeats, hydrolase; NMR {Bacillus subtilis}
Probab=51.49 E-value=9.6 Score=23.13 Aligned_cols=23 Identities=17% Similarity=0.234 Sum_probs=19.1
Q ss_pred ceeccCCCCCHHHHHHHHHHHHH
Q 040188 48 ARCWLETFATAEQAALANVRAAF 70 (117)
Q Consensus 48 k~~~LGtF~t~EeAA~AYD~aa~ 70 (117)
-+|++|-|.+.++|..+.+....
T Consensus 46 yRV~vGpf~~~~~A~~~~~~L~~ 68 (79)
T 1x60_A 46 YKVQIGAFSSKDNADTLAARAKN 68 (79)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHH
T ss_pred EEEEECCcCCHHHHHHHHHHHHH
Confidence 47889999999999988776554
No 8
>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=43.64 E-value=13 Score=22.76 Aligned_cols=23 Identities=17% Similarity=0.096 Sum_probs=19.2
Q ss_pred ceeccCCCCCHHHHHHHHHHHHH
Q 040188 48 ARCWLETFATAEQAALANVRAAF 70 (117)
Q Consensus 48 k~~~LGtF~t~EeAA~AYD~aa~ 70 (117)
-+|.+|-|.+.+||..+.+....
T Consensus 46 yRV~vGpf~s~~~A~~~~~~L~~ 68 (81)
T 1uta_A 46 NRVVIGPVKGKENADSTLNRLKM 68 (81)
T ss_dssp EEEEESSCBTTTHHHHHHHHHHH
T ss_pred EEEEECCcCCHHHHHHHHHHHHH
Confidence 57889999999999988776554
No 9
>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=39.55 E-value=36 Score=21.36 Aligned_cols=31 Identities=13% Similarity=0.121 Sum_probs=22.3
Q ss_pred CCCceeeeEECCCCcEEEEEeCCCCCCceec
Q 040188 21 KGNHSRGVRQTPSGKFAAEIRDPAKKGARCW 51 (117)
Q Consensus 21 ~~S~yrGV~~~~~GkW~A~I~~~~~~gk~~~ 51 (117)
+..-+.|+++++.|+|+..+.+...+-+.||
T Consensus 8 gr~L~~GesqR~dG~Y~yry~d~~Gkr~~vY 38 (69)
T 1b69_A 8 GRILKTGESQRKDGRYLYKYIDSFGEPQFVY 38 (69)
T ss_dssp SSCCCTTEEECSSSCEEEEEECTTSSEEEEE
T ss_pred CCccCCCeEEccCCcEEEEEEcCCCCEEEEE
Confidence 3445789999999999999998643323444
No 10
>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Probab=31.95 E-value=37 Score=19.99 Aligned_cols=32 Identities=19% Similarity=0.068 Sum_probs=21.3
Q ss_pred ccCCCCCHHHHHHHHHH-HHHHhcCCCCcCCCC
Q 040188 51 WLETFATAEQAALANVR-AAFKFRGRRALLNFP 82 (117)
Q Consensus 51 ~LGtF~t~EeAA~AYD~-aa~~~~G~~A~~NFp 82 (117)
-+=.|.+.++|..|.+. --..+.|......++
T Consensus 50 afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~ 82 (85)
T 1x4e_A 50 GFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP 82 (85)
T ss_dssp EEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred EEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence 34589999999999874 333455655555554
No 11
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Probab=29.30 E-value=14 Score=23.13 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=14.3
Q ss_pred eccCCCCCHHHHHHHHHHH
Q 040188 50 CWLETFATAEQAALANVRA 68 (117)
Q Consensus 50 ~~LGtF~t~EeAA~AYD~a 68 (117)
+-+=+|.+.++|..|.+..
T Consensus 54 ~afV~f~~~~~A~~A~~~l 72 (109)
T 2dis_A 54 FAFVEYESHRAAAMARRKL 72 (109)
T ss_dssp EEEEEESSHHHHHHHHTTT
T ss_pred EEEEEecCHHHHHHHHHHh
Confidence 4445799999999887643
No 12
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=23.77 E-value=42 Score=21.23 Aligned_cols=25 Identities=8% Similarity=0.014 Sum_probs=16.8
Q ss_pred eccCCCCCHHHHHHHHHHHHHHhcCC
Q 040188 50 CWLETFATAEQAALANVRAAFKFRGR 75 (117)
Q Consensus 50 ~~LGtF~t~EeAA~AYD~aa~~~~G~ 75 (117)
.-.=+|.+.++|..|.+.. ..+.|.
T Consensus 54 ~aFV~f~~~~~a~~Ai~~~-~~~~G~ 78 (114)
T 2dnl_A 54 YAFLLFQEESSVQALIDAC-LEEDGK 78 (114)
T ss_dssp EEEECCSSHHHHHHHHHHS-EEETTE
T ss_pred EEEEEECCHHHHHHHHHhh-hhcCCc
Confidence 3345799999999987643 234554
No 13
>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=23.47 E-value=1.2e+02 Score=20.50 Aligned_cols=36 Identities=11% Similarity=0.039 Sum_probs=26.9
Q ss_pred cEEEEEeCCCCCCceec-cCCCCCHHHHHHHHHHHHHHhcC
Q 040188 35 KFAAEIRDPAKKGARCW-LETFATAEQAALANVRAAFKFRG 74 (117)
Q Consensus 35 kW~A~I~~~~~~gk~~~-LGtF~t~EeAA~AYD~aa~~~~G 74 (117)
-|.|.|.. |+-++ ++...+++.|..|...|+.+|-.
T Consensus 79 ~wva~Vk~----G~ilfEi~g~~~~~~a~eAlr~a~~KlP~ 115 (118)
T 2ftc_I 79 HYVTPVKA----GRLVVEMGGRCEFEEVQGFLDQVAHKLPF 115 (118)
T ss_pred EEEEEECC----CCEEEEEeccCCHHHHHHHHHHHHhhCCC
Confidence 49999984 34443 44458899999999999988743
No 14
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Probab=22.65 E-value=87 Score=19.11 Aligned_cols=16 Identities=19% Similarity=0.123 Sum_probs=12.8
Q ss_pred cCCCCCHHHHHHHHHH
Q 040188 52 LETFATAEQAALANVR 67 (117)
Q Consensus 52 LGtF~t~EeAA~AYD~ 67 (117)
+=+|.+.|+|..|.+.
T Consensus 49 fV~f~~~~~a~~A~~~ 64 (103)
T 2dgu_A 49 FIHFDERDGAVKAMEE 64 (103)
T ss_dssp EEEESSHHHHHHHHHH
T ss_pred EEEeCCHHHHHHHHHH
Confidence 4579999999988664
Done!