Query 036667
Match_columns 96
No_of_seqs 118 out of 1070
Neff 6.4
Searched_HMMs 29240
Date Mon Mar 25 06:41:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036667.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/036667hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3fy4_A 6-4 photolyase; DNA rep 99.6 7.5E-16 2.6E-20 123.4 7.7 80 1-80 448-527 (537)
2 1u3d_A Cryptochrome 1 apoprote 99.2 9.7E-12 3.3E-16 98.4 5.2 50 1-50 443-492 (509)
3 2wq7_A RE11660P; lyase-DNA com 99.2 1.5E-11 5.2E-16 98.2 4.7 50 1-50 472-521 (543)
4 3tvs_A Cryptochrome-1; circadi 99.2 3.8E-12 1.3E-16 101.9 0.4 47 1-47 463-509 (538)
5 1np7_A DNA photolyase; protein 99.1 3.9E-11 1.3E-15 94.5 3.3 45 1-45 438-482 (489)
6 1dnp_A DNA photolyase; DNA rep 98.6 1.1E-08 3.8E-13 80.4 2.4 44 1-54 425-468 (471)
7 2e0i_A 432AA long hypothetical 98.6 2.2E-08 7.5E-13 78.3 2.9 39 1-54 391-429 (440)
8 1owl_A Photolyase, deoxyribodi 98.5 8.7E-08 3E-12 75.4 3.6 39 1-48 432-470 (484)
9 2j4d_A Cryptochrome 3, cryptoc 98.2 1.4E-07 4.7E-12 75.0 -0.5 37 1-42 474-510 (525)
10 2j07_A Deoxyribodipyrimidine p 96.1 0.0039 1.3E-07 48.1 3.4 22 28-53 396-417 (420)
11 2ckc_A Chromodomain-helicase-D 58.5 3.9 0.00013 25.0 1.2 13 84-96 44-56 (80)
12 2cka_A Chromodomain-helicase-D 35.6 14 0.00047 23.2 1.1 14 83-96 62-75 (95)
13 2dl6_A Chromodomain-helicase-D 34.6 12 0.0004 22.9 0.7 14 83-96 36-49 (83)
No 1
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}
Probab=99.62 E-value=7.5e-16 Score=123.39 Aligned_cols=80 Identities=68% Similarity=1.272 Sum_probs=70.4
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhhhccCCccHHHHHHHhHhhccccccch
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKFEGEENQES 80 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~ 80 (96)
||+++||+||.++..++..+||.+|.+||.|||||+++|++|++++.++|+..+..++.+...+.+.+++.++.....++
T Consensus 448 lp~~~Ih~Pw~~~~~~~~~~g~~~g~~YP~PIVdh~~ar~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 527 (537)
T 3fy4_A 448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKVDEENLRDLRRKLQKDEHEES 527 (537)
T ss_dssp CCTTTTTCGGGSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHTTC--
T ss_pred CCHHhhCCcccCCHHHHHhcCCccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccccCCCCccc
Confidence 68999999999999888889999999999999999999999999999999999998888888888888887765544444
No 2
>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A*
Probab=99.21 E-value=9.7e-12 Score=98.38 Aligned_cols=50 Identities=30% Similarity=0.688 Sum_probs=42.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~ 50 (96)
+|+++||+||.++...+..++|.+|.+||.|||||+.+|++|++++..++
T Consensus 443 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~a~~~~~~~~ 492 (509)
T 1u3d_A 443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMW 492 (509)
T ss_dssp CCHHHHTCTTTSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHHHH
T ss_pred cccccccCcccCChHHHHHhccccCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 58899999999998888888999999999999999999997654444433
No 3
>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
Probab=99.17 E-value=1.5e-11 Score=98.17 Aligned_cols=50 Identities=42% Similarity=0.859 Sum_probs=43.2
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~ 50 (96)
+|+++||+||.++..++..++|.+|.+||.|||||+.+|++|++++..++
T Consensus 472 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~al~~~~~~~ 521 (543)
T 2wq7_A 472 YPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAY 521 (543)
T ss_dssp SCHHHHTSGGGSCHHHHHHTTCCBTTTBCCCSSCHHHHHHHHHHHHHHHH
T ss_pred cccccccCcccCChHHHHhhcccccCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 58899999999998888889999999999999999999997665554443
No 4
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag, phosphorylation, gene regulation, signaling protein; HET: TPO FAD; 2.30A {Drosophila melanogaster} PDB: 4gu5_A*
Probab=99.16 E-value=3.8e-12 Score=101.91 Aligned_cols=47 Identities=30% Similarity=0.634 Sum_probs=41.3
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLG 47 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~ 47 (96)
||+++||+||.++..++..+||.+|.+||.|||||+++|++|++++.
T Consensus 463 lp~~~Ih~Pw~~~~~~~~~~~~~~g~~YP~PIVdh~~ar~~al~~~~ 509 (538)
T 3tvs_A 463 VPKEFVHEPWRMSAEQQEQYECLIGVHYPERIIDLSMAVKRNMLAMK 509 (538)
T ss_dssp SCCSSCCSHHHHHTTHHHHSSCCSSSSSCCCSSCSHHHHHHHHHHHH
T ss_pred CCHHhhcCcccCCHHHHHHcCCccCCCCCCCCCCHHHHHHHHHHHHH
Confidence 68999999999988888889999999999999999999996654433
No 5
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1
Probab=99.09 E-value=3.9e-11 Score=94.45 Aligned_cols=45 Identities=27% Similarity=0.527 Sum_probs=40.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRK 45 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r 45 (96)
+|+++||+||.++..++..++|.+|.+||.|||||+++|++|+++
T Consensus 438 ~p~~~ih~pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~a~~~ 482 (489)
T 1np7_A 438 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKI 482 (489)
T ss_dssp CCSGGGGCGGGCCHHHHHHTTCCBTTTBCCCSSCHHHHHHHHHTC
T ss_pred cCcccccCCccCCHHHHHHhccccCCCCCCCCCCHHHHHHHHHHH
Confidence 589999999999998888899999999999999999999976543
No 6
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1
Probab=98.62 E-value=1.1e-08 Score=80.38 Aligned_cols=44 Identities=32% Similarity=0.647 Sum_probs=33.7
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQ 54 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~ 54 (96)
+|+++||+||.+ +...+|.+ +||.|||||+++|++| +++|+..+
T Consensus 425 ~p~~~ih~Pw~~----~~~~~~~~--~YP~PiVd~~~~r~~a----l~~~~~~~ 468 (471)
T 1dnp_A 425 VPGKVVHEPWKW----AQKAGVTL--DYPQPIVEHKEARVQT----LAAYEAAR 468 (471)
T ss_dssp SCTTGGGSHHHH----HHTTTCCC--SSCCCSSCHHHHHHHH----HHHHHHHT
T ss_pred CChhhcCCchhh----HHhcCCCC--CCCCCCCCHHHHHHHH----HHHHHHhh
Confidence 589999999986 23456655 7999999999999965 55665543
No 7
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}
Probab=98.57 E-value=2.2e-08 Score=78.33 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=30.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQ 54 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~ 54 (96)
+|+++||+||.+ +|.+||.|||||+++|++| +++|+..+
T Consensus 391 ~p~~~ih~pw~~-----------~~~~YP~PiVd~~~~r~~a----~~~~~~~~ 429 (440)
T 2e0i_A 391 VPPSIIHSIYKT-----------KVPGYPSPIVNWLERVNYV----KSEYKNVK 429 (440)
T ss_dssp SCHHHHTTTTTS-----------CCTTSCCCSSCHHHHHHHH----HHHHHHC-
T ss_pred cCcccccCchhh-----------cCCCCCCCCCCHHHHHHHH----HHHHHHHH
Confidence 588999999985 2678999999999999965 45565543
No 8
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*
Probab=98.46 E-value=8.7e-08 Score=75.40 Aligned_cols=39 Identities=23% Similarity=0.422 Sum_probs=29.9
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGE 48 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~ 48 (96)
+|+++||+||.++. .. | +||.|||||+.+|++|++++..
T Consensus 432 ~p~~~ih~Pw~~~~----~~----~-~YP~PiVd~~~~r~~a~~~~~~ 470 (484)
T 1owl_A 432 VHPKDLISGEITPI----ER----R-GYPAPIVNHNLRQKQFKALYNQ 470 (484)
T ss_dssp SCHHHHHHTCCCHH----HH----T-TSCCCSSCHHHHHHHHHHHHHH
T ss_pred CChhhcCCcccchh----hh----c-CCCCCCCCHHHHHHHHHHHHHH
Confidence 58899999999832 12 3 7999999999999966544443
No 9
>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*
Probab=98.21 E-value=1.4e-07 Score=75.05 Aligned_cols=37 Identities=16% Similarity=0.006 Sum_probs=21.5
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKEC 42 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a 42 (96)
+|+++||+||.++ ..+|.+|.+||.|||||..+|+++
T Consensus 474 ~p~~~ih~Pw~~~-----~~~~~~g~~Yp~Pi~~~~~~~~~~ 510 (525)
T 2j4d_A 474 LPKEKRHWPGRLM-----YMDTVVPLKHGNGPMAGGSKSGGG 510 (525)
T ss_dssp SCTTTTTSCHHHH-----TCCCSSCCSCCC------------
T ss_pred CChhcccCCccCc-----ccccccCCCCCCCcccchhhhhcc
Confidence 5899999999863 357889999999999999999853
No 10
>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A*
Probab=96.08 E-value=0.0039 Score=48.08 Aligned_cols=22 Identities=18% Similarity=0.028 Sum_probs=17.7
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667 28 YPAPVVSHDSASKECKRKLGEAYALN 53 (96)
Q Consensus 28 YP~PIVDh~~ar~~a~~r~~~a~~~~ 53 (96)
||.|||||+.+|++| +++|+..
T Consensus 396 YP~Pivd~~~~r~~a----~~~~~~~ 417 (420)
T 2j07_A 396 PKDPVVDLEEARRRY----LRLARDL 417 (420)
T ss_dssp CSSCSSCHHHHHHHH----HHHHHHH
T ss_pred CCCCccCHHHHHHHH----HHHHHHh
Confidence 999999999999965 4555544
No 11
>2ckc_A Chromodomain-helicase-DNA-binding protein 7; protein-protein interaction, phosphorylation, disease mutation, nucleotide-binding; NMR {Homo sapiens} SCOP: d.76.2.1 PDB: 2v0e_A
Probab=58.48 E-value=3.9 Score=24.97 Aligned_cols=13 Identities=54% Similarity=0.940 Sum_probs=10.6
Q ss_pred HHHHHHHHHhhhC
Q 036667 84 QKQKRLTDWLKDH 96 (96)
Q Consensus 84 ~~~~~~~~~~~~~ 96 (96)
-+-|.|.|||+.|
T Consensus 44 P~~KdL~dWLrqh 56 (80)
T 2ckc_A 44 PKNKDLVEWLKLH 56 (80)
T ss_dssp CBHHHHHHHHHHC
T ss_pred ccccCHHHHHHHC
Confidence 4568899999976
No 12
>2cka_A Chromodomain-helicase-DNA-binding protein 8; BRK domain, transcription elongation, chromatin remodeling, protein-protein interaction, transcription; NMR {Homo sapiens} SCOP: d.76.2.1
Probab=35.55 E-value=14 Score=23.20 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.6
Q ss_pred HHHHHHHHHHhhhC
Q 036667 83 RQKQKRLTDWLKDH 96 (96)
Q Consensus 83 ~~~~~~~~~~~~~~ 96 (96)
|-+.++|.+||+.|
T Consensus 62 Ap~~K~L~~WLk~n 75 (95)
T 2cka_A 62 APRRAELEMWLQGH 75 (95)
T ss_dssp SCBHHHHHHHHHHC
T ss_pred CchHhHHHHHHHHC
Confidence 36699999999875
No 13
>2dl6_A Chromodomain-helicase-DNA-binding protein 8; BRK, CHD8, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.76.2.1
Probab=34.63 E-value=12 Score=22.92 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.2
Q ss_pred HHHHHHHHHHhhhC
Q 036667 83 RQKQKRLTDWLKDH 96 (96)
Q Consensus 83 ~~~~~~~~~~~~~~ 96 (96)
|-+.++|.+||+.|
T Consensus 36 AP~~k~L~~WLk~n 49 (83)
T 2dl6_A 36 APRRAELEMWLQGH 49 (83)
T ss_dssp SCBSTTHHHHHHHC
T ss_pred chhHhHHHHHHhHC
Confidence 35588999999875
Done!