Query 036667
Match_columns 96
No_of_seqs 118 out of 1070
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 04:19:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036667hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03441 FAD_binding_7: FAD bi 99.2 8.3E-12 1.8E-16 93.6 2.4 50 1-50 228-277 (277)
2 TIGR02766 crypt_chrom_pln cryp 99.1 6.4E-11 1.4E-15 94.1 4.1 44 1-44 429-472 (475)
3 PRK10674 deoxyribodipyrimidine 98.5 6.7E-08 1.4E-12 77.2 3.9 43 1-53 426-468 (472)
4 COG0415 PhrB Deoxyribodipyrimi 98.4 1E-07 2.2E-12 76.7 2.6 41 1-52 419-459 (461)
5 KOG0133 Deoxyribodipyrimidine 98.4 2.6E-07 5.6E-12 75.4 4.2 53 1-53 445-497 (531)
6 TIGR03556 photolyase_8HDF deox 98.1 2.3E-06 4.9E-11 68.5 3.8 41 1-52 430-470 (471)
7 PF10281 Ish1: Putative stress 29.2 35 0.00077 17.9 1.2 10 87-96 7-16 (38)
8 PF07533 BRK: BRK domain; Int 21.5 34 0.00074 19.2 0.2 13 84-96 25-37 (46)
9 PF07966 A1_Propeptide: A1 Pro 20.4 48 0.001 16.6 0.6 13 84-96 17-29 (29)
10 PLN00078 photosystem I reactio 16.2 1.1E+02 0.0023 20.6 1.6 34 59-95 52-86 (122)
No 1
>PF03441 FAD_binding_7: FAD binding domain of DNA photolyase from Prosite.; InterPro: IPR005101 This entry represents a multi-helical domain composed of two all-alpha subdomains that is found as the C-terminal domain in cryptochrome proteins, as well as at the N-terminal of DNA photolyase where it acts as a FAD-binding domain (the N-terminal of DNA photolyase binds a light-harvesting cofactor). Photolyases and cryptochromes are related flavoproteins that bind FAD. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes (CRY1 and CRY2) are blue light photoreceptors that mediate blue light-induced gene expression [, ]. DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [, ].; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 3ZXS_A 1DNP_A 2XRZ_B 2XRY_A 2VTB_A 2J4D_B 2IJG_X 3TVS_A 2E0I_D ....
Probab=99.19 E-value=8.3e-12 Score=93.64 Aligned_cols=50 Identities=46% Similarity=0.989 Sum_probs=44.0
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 228 ~~~~~ih~p~~~~~~~~~~~~~~~~~~YP~pivd~~~~r~~~~~~~~~~~ 277 (277)
T PF03441_consen 228 LPDEYIHEPWKAPPAVQKAAGCVLGNDYPKPIVDHKEARKRALKRYKAAY 277 (277)
T ss_dssp STHHHHTSCHGSHHHHHHHCT-CTTTSSBTSSSHHHHHHHHHHHHHHHH-
T ss_pred CChhheeChhccChHHHHHhCCccCCCCCcccCCHHHHHHHHHHHHHhcC
Confidence 58899999999999999999999999999999999999998877776654
No 2
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=99.10 E-value=6.4e-11 Score=94.14 Aligned_cols=44 Identities=34% Similarity=0.721 Sum_probs=39.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKR 44 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~ 44 (96)
||+++||+||+++..++...||.+|.+||.|||||+.+|++|+.
T Consensus 429 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~~~~ 472 (475)
T TIGR02766 429 LPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVGLDEARARLHE 472 (475)
T ss_pred CCHHHhcCcccCCHHHHHHcCCccCCCCCcccCCHHHHHHHHHH
Confidence 68999999999998887788999999999999999999996653
No 3
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=98.54 E-value=6.7e-08 Score=77.24 Aligned_cols=43 Identities=33% Similarity=0.556 Sum_probs=32.6
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALN 53 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~ 53 (96)
||+++||+||+++.. .++ +.+||.|||||+.+|++|+ ++|+..
T Consensus 426 ~p~~~ih~Pw~~~~~----~~~--~~~YP~PiVd~~~~r~~~~----~~~~~~ 468 (472)
T PRK10674 426 VPGKAIHQPWRWAEK----AGV--TLDYPQPIVDHKQARLATL----AAYEAA 468 (472)
T ss_pred CCHHhhcCccccchh----cCC--CCCCCcCCcCHHHHHHHHH----HHHHHH
Confidence 689999999988732 244 3479999999999999654 555443
No 4
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=98.45 E-value=1e-07 Score=76.65 Aligned_cols=41 Identities=37% Similarity=0.844 Sum_probs=34.0
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL 52 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~ 52 (96)
||.++||+||.++. +.+|.+||.|||||..+|++| +.+|+.
T Consensus 419 ~~~~~ih~p~~~~~-------~~~~~~YP~piVd~~~~r~~a----~~~y~~ 459 (461)
T COG0415 419 LPDKYIHEPWELSE-------VVLGVDYPKPIVDHKESREQA----LAAYEA 459 (461)
T ss_pred CChhhccChhhccc-------ccccCCCCccccccHHHHHHH----HHHHHh
Confidence 68899999999885 456889999999999999965 455654
No 5
>KOG0133 consensus Deoxyribodipyrimidine photolyase/cryptochrome [Replication, recombination and repair; Signal transduction mechanisms]
Probab=98.41 E-value=2.6e-07 Score=75.35 Aligned_cols=53 Identities=40% Similarity=0.756 Sum_probs=47.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALN 53 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~ 53 (96)
.|..+||.||.++..++..++|.+|.+||.|||++..+++.+.+++..+|+..
T Consensus 445 ~p~~~i~~pW~~p~~~~~~~~~~lg~~Yp~~iv~~~~a~k~~~e~~~~~~~~~ 497 (531)
T KOG0133|consen 445 GPMHFIYEPWAAPEGVQTAAGELLGVDYPKPIVKLASAAKRNMEAMGCMWSIG 497 (531)
T ss_pred CCcceeccCCCCcHHHhhhhhhhhhcccchhhhhhHHhhHhHHHHHHHHHhhc
Confidence 36789999999999999999999999999999999999999888888777643
No 6
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=98.13 E-value=2.3e-06 Score=68.48 Aligned_cols=41 Identities=20% Similarity=0.397 Sum_probs=30.8
Q ss_pred CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 036667 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL 52 (96)
Q Consensus 1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~ 52 (96)
||+++||+||..+. .+. ..+||.|||||+.+|+ +++.+|+.
T Consensus 430 ~p~~~ih~p~~~~~-~~~------~~~YP~Pivd~~~~r~----~~~~~~~~ 470 (471)
T TIGR03556 430 VDTKDLVTGKITPL-ERR------AVGYPLPIVDHNQQQQ----LFKQLYQQ 470 (471)
T ss_pred CCHhhhcCcccCch-hhh------ccCCCCCCCCHHHHHH----HHHHHHhh
Confidence 68999999987662 222 2369999999999999 45666653
No 7
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=29.23 E-value=35 Score=17.88 Aligned_cols=10 Identities=50% Similarity=1.076 Sum_probs=8.0
Q ss_pred HHHHHHhhhC
Q 036667 87 KRLTDWLKDH 96 (96)
Q Consensus 87 ~~~~~~~~~~ 96 (96)
.+|.+||++|
T Consensus 7 ~~L~~wL~~~ 16 (38)
T PF10281_consen 7 SDLKSWLKSH 16 (38)
T ss_pred HHHHHHHHHc
Confidence 5788999876
No 8
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=21.53 E-value=34 Score=19.19 Aligned_cols=13 Identities=46% Similarity=1.017 Sum_probs=8.3
Q ss_pred HHHHHHHHHhhhC
Q 036667 84 QKQKRLTDWLKDH 96 (96)
Q Consensus 84 ~~~~~~~~~~~~~ 96 (96)
-+-+.|++||+.|
T Consensus 25 P~~~~L~~WL~~~ 37 (46)
T PF07533_consen 25 PKLKELEEWLEEH 37 (46)
T ss_dssp -BCCCHHHHHHH-
T ss_pred cCHHHHHHHHHHC
Confidence 4456788888876
No 9
>PF07966 A1_Propeptide: A1 Propeptide ; InterPro: IPR012848 Most eukaryotic endopeptidases (MEROPS peptidase family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residue in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions [, ]. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1AVF_Q 1HTR_P 3PSG_A 2PSG_A 3VCM_Q 1TZS_P.
Probab=20.35 E-value=48 Score=16.61 Aligned_cols=13 Identities=31% Similarity=0.744 Sum_probs=6.5
Q ss_pred HHHHHHHHHhhhC
Q 036667 84 QKQKRLTDWLKDH 96 (96)
Q Consensus 84 ~~~~~~~~~~~~~ 96 (96)
.....|.+||+.|
T Consensus 17 ~e~g~~~~flk~~ 29 (29)
T PF07966_consen 17 REKGTLEEFLKEH 29 (29)
T ss_dssp HHTT-HHHHHCC-
T ss_pred HHcCchHHHHHhC
Confidence 3444566777665
No 10
>PLN00078 photosystem I reaction center subunit N (PsaN); Provisional
Probab=16.22 E-value=1.1e+02 Score=20.61 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=19.7
Q ss_pred CccHHHHHHHhHhhccccccchhHH-HHHHHHHHHhhh
Q 036667 59 QVSEDDLKNLRRKFEGEENQESGRR-QKQKRLTDWLKD 95 (96)
Q Consensus 59 ~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~~~ 95 (96)
++.+.-..-+++-+..+ +.+++ +||.+|.||-|.
T Consensus 52 ~~~~Sr~~liq~llkkS---eeNKakndkERLDdYYKR 86 (122)
T PLN00078 52 AGSESRKALLQEYLKKS---EENKEKNDKERLDDYYKR 86 (122)
T ss_pred CcCchHHHHHHHHHHHh---HHhHHHhHHHHHHHHHHH
Confidence 33443334444443322 34666 899999999763
Done!