Query psy11420
Match_columns 315
No_of_seqs 217 out of 1759
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 17:58:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11420hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0415 PhrB Deoxyribodipyrimi 100.0 5.3E-76 1.1E-80 565.8 19.7 271 2-287 146-418 (461)
2 TIGR02766 crypt_chrom_pln cryp 100.0 2.8E-73 6E-78 561.6 21.1 273 1-287 142-428 (475)
3 TIGR02765 crypto_DASH cryptoch 100.0 1.6E-71 3.4E-76 542.9 25.6 275 2-285 152-429 (429)
4 TIGR03556 photolyase_8HDF deox 100.0 5.8E-71 1.3E-75 543.6 22.8 278 1-287 145-429 (471)
5 PRK10674 deoxyribodipyrimidine 100.0 1.8E-69 4E-74 533.1 21.8 273 1-287 149-425 (472)
6 PF03441 FAD_binding_7: FAD bi 100.0 3.1E-68 6.7E-73 491.2 15.7 221 61-287 1-227 (277)
7 TIGR00591 phr2 photolyase PhrI 100.0 2.7E-58 6E-63 452.5 8.8 208 58-279 220-453 (454)
8 KOG0133|consensus 100.0 3E-49 6.5E-54 383.9 9.3 282 1-284 150-441 (531)
9 COG3046 Uncharacterized protei 99.9 6.9E-28 1.5E-32 224.3 8.3 225 56-292 220-461 (505)
10 TIGR02766 crypt_chrom_pln cryp 99.5 1.7E-15 3.8E-20 150.1 -0.9 94 219-315 317-414 (475)
11 COG0415 PhrB Deoxyribodipyrimi 99.4 9.5E-15 2.1E-19 141.8 -0.7 92 221-315 309-404 (461)
12 TIGR02765 crypto_DASH cryptoch 99.4 1.1E-14 2.3E-19 142.7 -1.3 94 218-315 320-417 (429)
13 PRK10674 deoxyribodipyrimidine 99.3 1.5E-13 3.2E-18 136.1 -1.5 94 219-315 314-411 (472)
14 TIGR03556 photolyase_8HDF deox 99.3 2.7E-13 5.9E-18 134.2 -1.1 95 218-315 318-415 (471)
15 PF03441 FAD_binding_7: FAD bi 99.2 6.9E-13 1.5E-17 122.7 -4.0 93 220-315 117-213 (277)
16 TIGR00591 phr2 photolyase PhrI 98.9 1.3E-10 2.9E-15 114.7 -0.7 93 218-315 339-447 (454)
17 KOG0133|consensus 98.6 9.7E-09 2.1E-13 101.3 0.5 96 217-315 330-430 (531)
18 PF11994 DUF3489: Protein of u 46.7 22 0.00048 26.0 2.8 30 188-221 27-56 (72)
19 PRK02249 DNA primase large sub 42.6 64 0.0014 30.9 6.0 63 185-250 223-285 (343)
20 COG2219 PRI2 Eukaryotic-type D 37.3 63 0.0014 31.2 5.1 63 185-250 242-304 (363)
21 PF04104 DNA_primase_lrg: Euka 35.3 25 0.00053 32.2 1.9 49 185-235 109-157 (260)
22 PRK09568 DNA primase large sub 28.0 84 0.0018 29.6 4.2 38 191-230 218-255 (306)
23 COG3590 PepO Predicted metallo 27.7 17 0.00036 37.0 -0.6 42 234-282 476-517 (654)
24 PF10440 WIYLD: Ubiquitin-bind 22.8 1.6E+02 0.0035 21.1 3.8 52 183-236 6-57 (65)
25 PF00440 TetR_N: Bacterial reg 22.2 1.1E+02 0.0024 19.7 2.8 38 187-230 1-38 (47)
No 1
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.3e-76 Score=565.78 Aligned_cols=271 Identities=31% Similarity=0.537 Sum_probs=234.4
Q ss_pred ChHhHHHHHhcCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccHHHHHHHHHHHHhcCcccc
Q psy11420 2 TYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLANKEWVR 81 (315)
Q Consensus 2 tf~~F~~~~~~~~~p~~Pl~~P~~l~~~~~p~~~~~~~~ip~l~~lg~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~~~~~ 81 (315)
+||+|+++++....+.+|.+.|..+...............|+ .+-+ ....|.|||.+|+++|++|+.++ +.
T Consensus 146 vfT~F~k~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~P~--~~~~-----~~~~~~~Ge~aA~~~l~~F~~~~--l~ 216 (461)
T COG0415 146 VFTPFYKAWRDRLRILRPVPAPDVLDALRDEEPPPEEISLPD--FSKF-----DVLLFTGGEKAALARLQDFLAEG--LD 216 (461)
T ss_pred ccchHHHHHHHhcccCCCCCCcchhccccccccCcccccCCc--cccc-----cccCCCchHHHHHHHHHHHHHHH--HH
Confidence 799999999988666678888875443211100012222333 1101 13568999999999999999986 89
Q ss_pred cccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcCCCCCChHhHHHhHHHHHHHHHHhhcCCCc-ccccCC
Q psy11420 82 KFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNF-DKMKGN 160 (315)
Q Consensus 82 ~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~~~~~~~~~~~eL~WRef~~~~~~~~p~~-~~~~~~ 160 (315)
+|++.|+.|. .++||+|||||++|+||||+||+++.+.... ..+++++|+.||+|||||++++.++|+. ...+..
T Consensus 217 ~Y~~~Rd~p~--~~~TS~LSpyL~~G~IS~r~v~~~~~~~~~~--~~~~~~~~~~eL~WREFy~h~~~~~p~~~~~~~~~ 292 (461)
T COG0415 217 DYERTRDFPA--LDGTSRLSPYLAFGVISPREVYAALLAAESD--AREGTAALINELIWREFYQHLLYHYPSLSRFEPFA 292 (461)
T ss_pred HHHHhcCCcc--cccccccCHHHHcCCcCHHHHHHHHHHhhhc--ccchHHHHHHHHHHHHHHHHHHHhCCccccccccc
Confidence 9999999887 7899999999999999999999999887642 4567889999999999999999999988 566778
Q ss_pred ccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcchhhhh
Q psy11420 161 KICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAM 240 (315)
Q Consensus 161 ~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~d~a~ 240 (315)
.....++|..++..|++|++|+|||||||||||||++|||||||+||+||||||| +|.||||.|++||+++|||||+++
T Consensus 293 ~~~~~~~w~~~~~~f~aW~~G~TGyPIVDA~MRqL~~TG~MHNR~RMivAsFL~k-~L~IdWR~GE~~F~~~LiD~D~as 371 (461)
T COG0415 293 EKTLNIPWEDNPAHFQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRMIVASFLTK-DLLIDWREGEKYFMRQLIDGDPAS 371 (461)
T ss_pred ccccCCccccCHHHHHHHhcCCCCCccccHHHHHHHHhCCcchHHHHHHHHHHHH-hcCCCHHHHHHHHHHhccCCCccc
Confidence 8889999999999999999999999999999999999999999999999999998 999999999999999999999999
Q ss_pred hhhhHhhhhccccc-cccccccCHHHHHHhcCcccchhhhhhhcccCC
Q psy11420 241 NAGNWMWLSASAFF-HQFFRVYSPVAFGKKTDKFELLLDADWAMNAGN 287 (315)
Q Consensus 241 n~~~W~~~ag~g~~-~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~ 287 (315)
|+|||||+||+|++ .+|||||||++|+++|||+|+|||+ |+|++.+
T Consensus 372 N~ggWQW~AstG~Da~pyfRiFNp~~Q~~kfDp~g~fIr~-wvPeL~~ 418 (461)
T COG0415 372 NNGGWQWAASTGTDAAPYFRIFNPVTQAEKFDPDGEFIRR-WVPELRN 418 (461)
T ss_pred CCCCeeEEeccCCCCCcceeccCHHHHHhhcCCCcccHHh-hCHHhhC
Confidence 99999999999995 4899999999999999999999997 9988765
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=100.00 E-value=2.8e-73 Score=561.56 Aligned_cols=273 Identities=25% Similarity=0.405 Sum_probs=224.1
Q ss_pred CChHhHHHHHhcCCC-CCCCCCCCCCCCCCcCCCCCCCCCCCCCcccCCCCCC------CCCCCCCCccHHHHHHHHHHH
Q psy11420 1 MTYQKLVSVLESLPK-PKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDES------SIPLCKFPGGETEALKRLEKS 73 (315)
Q Consensus 1 ~tf~~F~~~~~~~~~-p~~Pl~~P~~l~~~~~p~~~~~~~~ip~l~~lg~~~~------~~~~~~~~gGe~~A~~~L~~F 73 (315)
.+||+|++++.+... |..|+++|..++..+.+ .+.++++++... ......|+|||++|+++|+.|
T Consensus 142 ~~ft~f~~~~~~~~~~~~~~~~~p~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~F 213 (475)
T TIGR02766 142 TMFAAFWERCLSMPYDPESPLLPPKKIISGDVS--------KCSADDLGFEDDSEKGSNALLARAWSPGWSNADKALTEF 213 (475)
T ss_pred CeecHHHHHHHhccCCCCCCCCCccccCCCccc--------cCChhhcCCCCcccccccccccccCCCccHHHHHHHHHH
Confidence 379999999876543 23345555544321010 011222332211 000124899999999999999
Q ss_pred HhcCcccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHH-----hc-CCCCCChHhHHHhHHHHHHHHHH
Q psy11420 74 LANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKIL-----AT-GPHAKPPVSLLGQIYWREFYYVV 147 (315)
Q Consensus 74 l~~~~~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~-----~~-~~~~~~~~~~~~eL~WRef~~~~ 147 (315)
++++ +..|++.|+.|. ..+||+|||||++||||||+|++++.+.. .. ....+++++|++||+|||||+++
T Consensus 214 l~~~--~~~Y~~~Rd~p~--~~~tS~LSPyL~~G~ISpR~v~~~~~~~~~~~~~~~~~~~~~s~~~f~~eL~WRef~~~~ 289 (475)
T TIGR02766 214 INGP--LLEYSKNRKKAD--SATTSLLSPYLHFGEVSVRKVFHLVRMKQIAWANEGNSAGEESVNLFLRSIGLREYSRYI 289 (475)
T ss_pred HHHH--HHHHhhcCCCCC--CCCCCCCCcccccCcccHHHHHHHHHhhhhhhhhcccCCCcccHHHHHHHHHHHHHHHHH
Confidence 9875 789999999986 58999999999999999999999986321 11 11245678899999999999999
Q ss_pred hhcCCCcccccCCccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHH
Q psy11420 148 GSDTPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQS 227 (315)
Q Consensus 148 ~~~~p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~ 227 (315)
+.++|.+...+..+.+..++|+.+++.|++|++|+||+|+||||||||++|||||||+|||||||||| +|+||||.|++
T Consensus 290 ~~~~p~~~~~~~~~~~~~~~w~~~~~~f~aW~~G~TG~P~VDA~MRqL~~TGwmhnR~Rm~vAsfl~k-~L~idWr~G~~ 368 (475)
T TIGR02766 290 SFNHPFSHEKPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVK-VLQLPWRWGMK 368 (475)
T ss_pred HHhCCcccccchhhhhhcCCCCCCHHHHHHHHcCCCCCcchhHHHHHHHHHCCCcHHHHHHHHHHHHc-ccCCChHHHHH
Confidence 99999776666666677899999999999999999999999999999999999999999999999998 99999999999
Q ss_pred HHHhhhcchhhhhhhhhHhhhhcccc-ccccccccCHHHHHHhcCcccchhhhhhhcccCC
Q psy11420 228 VFEELLLDADWAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTDKFELLLDADWAMNAGN 287 (315)
Q Consensus 228 ~f~~~liD~d~a~n~~~W~~~ag~g~-~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~ 287 (315)
||+++|||||+++|+|||||+||+|+ ..+|+|+|||++|+++|||+|+|||+ |+|++.+
T Consensus 369 ~F~~~LiD~D~a~N~g~Wqw~Ag~g~d~~~~~RifnP~~q~~~~Dp~g~yir~-wvPeL~~ 428 (475)
T TIGR02766 369 YFWDTLLDADLESDALGWQYISGSLPDGRELDRIDNPQLEGYKFDPNGEYVRR-WLPELAR 428 (475)
T ss_pred HHHHHccccchhcccccccccccCCCCCCcccccCCHHHHHhhcCCCcccHHH-hChhhcc
Confidence 99999999999999999999999999 58999999999999999999999997 9998654
No 3
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=100.00 E-value=1.6e-71 Score=542.93 Aligned_cols=275 Identities=26% Similarity=0.461 Sum_probs=220.1
Q ss_pred ChHhHHHHHhcCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCcccCCCCCCCCC-CCCCCccHHHHHHHHHHHHhcCccc
Q psy11420 2 TYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIP-LCKFPGGETEALKRLEKSLANKEWV 80 (315)
Q Consensus 2 tf~~F~~~~~~~~~p~~Pl~~P~~l~~~~~p~~~~~~~~ip~l~~lg~~~~~~~-~~~~~gGe~~A~~~L~~Fl~~~~~~ 80 (315)
+|++|++++++...++.|+++|..++..+.. .....+|+++++++...... ...|+|||++|+++|++|++++ .+
T Consensus 152 ~ft~f~~~~~~~~~~~~~~~~p~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~-~l 227 (429)
T TIGR02765 152 VFTQFRKQVEAKCSIRPPLPAPEKLPPLPSV---DDPGWIPTLEDLGEESSEVDRGLPFVGGETAGLARLKEYFWSK-DL 227 (429)
T ss_pred CchHHHHHHHhhCCCCCCCCCcccCCCCccc---ccccCCCChhhcCCCcccccccCCcCchHHHHHHHHHHHHhhc-cH
Confidence 7999999998744445667766655432110 11122566666665432211 2348999999999999999753 37
Q ss_pred ccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcCCCCCChHhHHHhHHHHHHHHHHhhcCC-CcccccC
Q psy11420 81 RKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTP-NFDKMKG 159 (315)
Q Consensus 81 ~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~~~~~~~~~~~eL~WRef~~~~~~~~p-~~~~~~~ 159 (315)
..|++.|+.+.. ..+||+|||||++||||||+|++++.+........++.+++++||+|||||++++.++| .+.....
T Consensus 228 ~~Y~~~R~~~~~-~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~~~~~~~~~~eL~WRef~~~~~~~~~~~~~~~~~ 306 (429)
T TIGR02765 228 KSYKETRNGMLG-PDYSTKFSPWLALGCVSPRQIYEELQRYETERGANDSTYWVIFELLWRDYFRFYALKYGNRLFRFGG 306 (429)
T ss_pred hhhhhccCcccC-CCCcCccCHHHhCCcccHHHHHHHHHHHHhhcccCCCcHHHHHHHHHHHHHHHHHHHcCCcccccCC
Confidence 899998887542 56899999999999999999999997743221122345567789999999998887776 3333222
Q ss_pred CccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcchhhh
Q psy11420 160 NKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWA 239 (315)
Q Consensus 160 ~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~d~a 239 (315)
. ....++|+.+++.|++|++|+||+|+||||||||++|||||||+||+||||||| +|+||||.|++||+++|||||++
T Consensus 307 ~-~~~~~~w~~~~~~~~~W~~G~TG~PivDAamrqL~~TG~mhnr~Rm~vAsFl~k-~L~idWr~G~~~F~~~LiD~D~a 384 (429)
T TIGR02765 307 L-RGKHPKWSFDAKRFEQWKTGTTGYPLVDANMRELNATGFMSNRGRQNVASFLVK-DLGLDWRYGAEWFETQLVDYDVC 384 (429)
T ss_pred C-ccCCCCCccCHHHHHHHhCCCCCChhhhHHHHHHHHhCCCCHHHHHHHHHHHHH-ccCCCHHHHHHHHHHHhhccchh
Confidence 1 123578999999999999999999999999999999999999999999999998 99999999999999999999999
Q ss_pred hhhhhHhhhhccccc-cccccccCHHHHHHhcCcccchhhhhhhccc
Q psy11420 240 MNAGNWMWLSASAFF-HQFFRVYSPVAFGKKTDKFELLLDADWAMNA 285 (315)
Q Consensus 240 ~n~~~W~~~ag~g~~-~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~ 285 (315)
+|+|||||+||+|++ .+ +|+|||++|+++|||+|+|||+ |+|++
T Consensus 385 ~n~g~Wqw~ag~g~d~~~-~Rifnp~~q~~k~Dp~g~yir~-wvPeL 429 (429)
T TIGR02765 385 SNWGNWQYLAGVGNDPRG-SRQFNIEKQAQDYDPDGEYVAT-WVPEL 429 (429)
T ss_pred cCcccchhhhcCcCCCCc-CccCCHHHHHHhcCCCCCcHHH-hcCCC
Confidence 999999999999996 55 9999999999999999999997 99874
No 4
>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=100.00 E-value=5.8e-71 Score=543.61 Aligned_cols=278 Identities=29% Similarity=0.502 Sum_probs=233.9
Q ss_pred CChHhHHHHHhcCCCCCCCCCCCCCCCCCc-C-C--CCCCCCCCCCCcccCCCCCCCCCCCCCCccHHHHHHHHHHHHhc
Q psy11420 1 MTYQKLVSVLESLPKPKPADDAPTSLPREC-Q-G--ILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLAN 76 (315)
Q Consensus 1 ~tf~~F~~~~~~~~~p~~Pl~~P~~l~~~~-~-p--~~~~~~~~ip~l~~lg~~~~~~~~~~~~gGe~~A~~~L~~Fl~~ 76 (315)
.+||+|++++++... ++|+++|..++..+ . + ........+|+++++++.... ...|+|||++|+++|+.|+++
T Consensus 145 ~~ft~f~k~~~~~~~-~~~~~~p~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~--~~~~~gGe~~A~~~L~~f~~~ 221 (471)
T TIGR03556 145 TVYTPFWKNWSSLPK-PTPVATPTELEGLTEAELEAAAPLGVIALPTAKDLGFDWDG--DLILEPGETAAQARLEEFCDR 221 (471)
T ss_pred cchhHHHHHHHhccc-cCCCCCccccccCCccccccccccccccCCccccccccccc--ccCCCCcHHHHHHHHHHHHHH
Confidence 379999999987654 34677776543210 0 0 012233456777777665332 235899999999999999987
Q ss_pred CcccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcC---CCCCChHhHHHhHHHHHHHHHHhhcCCC
Q psy11420 77 KEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATG---PHAKPPVSLLGQIYWREFYYVVGSDTPN 153 (315)
Q Consensus 77 ~~~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~---~~~~~~~~~~~eL~WRef~~~~~~~~p~ 153 (315)
+ +.+|++.|+.|. .++||+|||||++||||+|+|++++.+..... ....+.+.|++||+|||||+++++++|.
T Consensus 222 ~--l~~Y~~~r~~p~--~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~~~~~~~~~~f~~eL~WRef~~~~~~~~p~ 297 (471)
T TIGR03556 222 A--IADYQEQRNFPA--LDGTSQLSPALKFGVIGIRTVWQATQEAHENSRSEEARNSIRTWQQELAWREFYQHALYHFPE 297 (471)
T ss_pred H--HHHhhhccCCCC--CCCCCCCChhhcCCcccHHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHHHHHHHCcc
Confidence 4 899999999875 67899999999999999999999998754321 1234567899999999999999999998
Q ss_pred cccccCCccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhh
Q psy11420 154 FDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELL 233 (315)
Q Consensus 154 ~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~l 233 (315)
+...+.++.+..++|+.+++.|++|++|+||+|+||||||||++|||||||+||+||||||| +|+|||+.|++||+++|
T Consensus 298 ~~~~~~~~~~~~~~w~~~~~~~~~W~~G~TG~P~vDAaMrqL~~tG~mhnr~Rm~vAsfl~k-~L~idWr~G~~~F~~~L 376 (471)
T TIGR03556 298 LADGPYRSLFQNFPWENNEAHFQAWCEGRTGYPIVDAAMRQLNETGWMHNRCRMIVASFLTK-DLIINWQWGEKYFMQKL 376 (471)
T ss_pred hhccccchhhhcCCCcCCHHHHHHHhcCCCCCCcccHHHHHHHHhCCccHHHHHHHHHHHHc-ccCCCHHHHHHHHHHHh
Confidence 87777777788889999999999999999999999999999999999999999999999998 99999999999999999
Q ss_pred cchhhhhhhhhHhhhhccccccccccccCHHHHHHhcCcccchhhhhhhcccCC
Q psy11420 234 LDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDKFELLLDADWAMNAGN 287 (315)
Q Consensus 234 iD~d~a~n~~~W~~~ag~g~~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~ 287 (315)
||||+++|+|||||+||+|++...+|+|||++|++||||+|.|||+ |+|++.+
T Consensus 377 lD~D~a~N~g~Wqw~a~~G~d~~p~R~fnp~~q~~k~Dp~G~yIr~-w~PeL~~ 429 (471)
T TIGR03556 377 IDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAQKFDPEAEYIRR-WLPELRS 429 (471)
T ss_pred hhcChhhccccccchhcCCCCCCCCcccCHHHHHHHhCCCCchHHH-hCHhhcc
Confidence 9999999999999999999965447999999999999999999997 9998554
No 5
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=100.00 E-value=1.8e-69 Score=533.09 Aligned_cols=273 Identities=27% Similarity=0.480 Sum_probs=220.7
Q ss_pred CChHhHHHHHhcCC-CC-CCCCCCCCCCCCCcCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccHHHHHHHHHHHHhcCc
Q psy11420 1 MTYQKLVSVLESLP-KP-KPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLANKE 78 (315)
Q Consensus 1 ~tf~~F~~~~~~~~-~p-~~Pl~~P~~l~~~~~p~~~~~~~~ip~l~~lg~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~~ 78 (315)
.+||+|++++++.. .+ +++++.|...+.. + ..++.+..++..........|+|||++|+++|++|++++
T Consensus 149 ~~ft~f~~~~~~~~~~~~p~~~~~p~~~~~~--~------~~~~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~f~~~~- 219 (472)
T PRK10674 149 KVFTPFKNAFLKRLREGDPECVPAPKVRSSG--A------IEPLPPIPFNYPQQSFDTALFPVGEKAAIAQLRQFCQQG- 219 (472)
T ss_pred CcccHHHHHHHHhhcccCCccCCCCcccccc--c------cCCCCcccccCcccccccCCCCCCHHHHHHHHHHHHHHH-
Confidence 37999999998742 21 1224333322110 0 011222233332222212358999999999999999875
Q ss_pred ccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcCCCCCChHhHHHhHHHHHHHHHHhhcCCCcccc-
Q psy11420 79 WVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKM- 157 (315)
Q Consensus 79 ~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~~~~~~~~~~~eL~WRef~~~~~~~~p~~~~~- 157 (315)
+.+|.+.|+.|. .++||+|||||+|||||+|+|++++.+.........+.+.|++||+|||||+++++++|.+...
T Consensus 220 -l~~Y~~~r~~p~--~~~tS~LSPyL~~G~iS~r~v~~~~~~~~~~~~~~~~~~~fl~eL~WRef~~~~~~~~p~~~~~~ 296 (472)
T PRK10674 220 -AGEYEQQRDFPA--VDGTSRLSAYLATGVLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLMVAYPSLCKHR 296 (472)
T ss_pred -HHHhccccCCCC--ccCCCCcChhhccCcCCHHHHHHHHHHHhhhhhccCchhHHHHHHHHHHHHHHHHHhCCchhhcc
Confidence 899999999876 6799999999999999999999999764332112223457899999999999999999987653
Q ss_pred cCCccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcchh
Q psy11420 158 KGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDAD 237 (315)
Q Consensus 158 ~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~d 237 (315)
...+....++|+.+++.|++|++|+||+|+|||+||||++|||||||+||+||||||| +|+|||+.|++||+++|||||
T Consensus 297 ~~~~~~~~~~w~~~~~~~~~W~~G~TG~P~vDA~mrqL~~tG~mhnr~Rm~vAsfL~k-~L~idWr~G~~~F~~~LlD~D 375 (472)
T PRK10674 297 PFIAWTDRVQWQSNPAHLQAWQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVK-DLLIDWREGERYFMSQLIDGD 375 (472)
T ss_pred CcchhhhccCcccCHHHHHHHHcCCCCCccHHHHHHHHHHHCCccHHHHHHHHHHHHc-CcccCCHhHHHHHHHHhhcCC
Confidence 4445556678999999999999999999999999999999999999999999999998 999999999999999999999
Q ss_pred hhhhhhhHhhhhcccc-ccccccccCHHHHHHhcCcccchhhhhhhcccCC
Q psy11420 238 WAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTDKFELLLDADWAMNAGN 287 (315)
Q Consensus 238 ~a~n~~~W~~~ag~g~-~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~ 287 (315)
+++|++||||+||+|+ ..+|+|+|||++|+++|||+|+|||+ |+|++.+
T Consensus 376 ~a~N~g~Wqw~ag~G~d~~py~R~fnP~~q~~k~Dp~g~yIr~-w~PeL~~ 425 (472)
T PRK10674 376 LAANNGGWQWAASTGTDAAPYFRIFNPTTQGERFDRDGEFIRR-WLPELRD 425 (472)
T ss_pred cccchhccceeecCCCCCCcceeecCHHHHHHHhCCCCChHHH-hChhhcc
Confidence 9999999999999998 57899999999999999999999997 9998654
No 6
>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=100.00 E-value=3.1e-68 Score=491.22 Aligned_cols=221 Identities=40% Similarity=0.744 Sum_probs=192.3
Q ss_pred ccHHHHHHHHHHHHhcCcccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHh-cCCCCCChHhHHHhHH
Q psy11420 61 GGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILA-TGPHAKPPVSLLGQIY 139 (315)
Q Consensus 61 gGe~~A~~~L~~Fl~~~~~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~-~~~~~~~~~~~~~eL~ 139 (315)
|||++|+++|+.||+++ +..|.+.|+.|. .++||+|||||++||||||+|++++.+... ......+.++|++||+
T Consensus 1 GGe~~A~~~L~~Fl~~~--l~~Y~~~r~~p~--~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~~~~~~~~~f~~eL~ 76 (277)
T PF03441_consen 1 GGETAALKRLEEFLKER--LADYGEQRDDPA--ADGTSRLSPYLNFGCLSPREVYRAVKKAQEANDAHSESAEKFIRELI 76 (277)
T ss_dssp SSHHHHHHHHHHHHHHC--GGGHHHHTT-TT--STTS---HHHHHTTSS-HHHHHHHHHHHHHCHTCHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHH--HHhhchhccCCC--cCCcCcccHHHhCCCcCHHHHHHHHHHHhhhcccccchHHHHHHHHH
Confidence 89999999999999875 899999999985 789999999999999999999999998765 1111256889999999
Q ss_pred HHHHHHHHhhcCCCcc-cccCCccccCCCCC---CChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhh
Q psy11420 140 WREFYYVVGSDTPNFD-KMKGNKICCQVDWD---TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTR 215 (315)
Q Consensus 140 WRef~~~~~~~~p~~~-~~~~~~~~~~~~w~---~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~ 215 (315)
||||++++++++|++. ..++++.+..++|. .+.+.|++|++|+||+|||||+||||++|||||||+||+|||||||
T Consensus 77 WRef~~~~~~~~p~~~~~~~~~~~~~~~~w~~~~~~~~~~~~w~~G~TG~p~vDAamrqL~~tG~mHn~~R~~vasfl~k 156 (277)
T PF03441_consen 77 WREFYRQLLYHNPNLDMFENFNPKFRQIPWEDDRENPELFEAWCEGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTK 156 (277)
T ss_dssp HHHHHHHHHHHSGGCTCSSTSSTTCCCSHCBTSBSTHHHHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCcchhhhhccHHHHhhhhcccccCHHHHHHHHcCCCCChHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence 9999999999999988 77888899999995 5678999999999999999999999999999999999999999998
Q ss_pred hccCCChHHHHHHHHhhhcchhhhhhhhhHhhhhcccc-ccccccccCHHHHHHhcCcccchhhhhhhcccCC
Q psy11420 216 GDLYLSWEEGQSVFEELLLDADWAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTDKFELLLDADWAMNAGN 287 (315)
Q Consensus 216 ~~l~~~W~~G~~~f~~~liD~d~a~n~~~W~~~ag~g~-~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~ 287 (315)
+|+|+|+.|++||+++|||||+++|++||||+||+|+ ..+|+|+|||++|++++||+|+|||+ |+|++.+
T Consensus 157 -~l~i~W~~g~~~f~~~liD~d~a~n~~~wqw~ag~g~d~~~~~r~~np~~q~~~~Dp~g~~ir~-w~PeL~~ 227 (277)
T PF03441_consen 157 -DLLIDWREGAEWFAEHLIDYDPASNYGNWQWAAGTGTDAKPYFRIFNPVKQSKKFDPDGEYIRR-WVPELAD 227 (277)
T ss_dssp -TSHBHHHHHHHHHHHHHTT--HHHHHHHHHHHTTSSSTGCSTTTHHHHHHHHHHHSTTSHHHHH-HSGGGTT
T ss_pred -hccCCccccHHHHHHHhhccCcchHHHHHHHHHhhccccCccccccCchHHHHhhCcHHHHHHH-HHHHHhc
Confidence 9999999999999999999999999999999999987 56899999999999999999999997 9998765
No 7
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=2.7e-58 Score=452.51 Aligned_cols=208 Identities=20% Similarity=0.231 Sum_probs=178.9
Q ss_pred CC-CccHHHHHHHHHHHHhcCcccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcCCCCCChHhHHH
Q psy11420 58 KF-PGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLG 136 (315)
Q Consensus 58 ~~-~gGe~~A~~~L~~Fl~~~~~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~~~~~~~~~~~ 136 (315)
.| +|||++|+++|++|++++ +.+|++.|+.|. .++||+|||||++|+||||+|++++.+... ....+.+.|++
T Consensus 220 ~~~~gGe~aA~~~L~~F~~~~--l~~Y~~~Rn~p~--~~~tS~LSPyL~~G~IS~R~i~~~~~~~~~--~~~~~~~~fl~ 293 (454)
T TIGR00591 220 VWAKPGTTAGLIMLESFIEKR--LCFFRTRRNDPN--NDALSMLSPWLHFGQLSAQRAARAVERARG--NAGESVEFFEE 293 (454)
T ss_pred CCCCCcHHHHHHHHHHHHHHH--HHHHHHhcCCcc--cccccccchHHhcCcccHHHHHHHHHHhcc--CCchHHHHHHH
Confidence 47 999999999999999875 899999999987 589999999999999999999999865332 11234578999
Q ss_pred hHHHH-HHHHHHhhcCCCcccccCCccccC-------CCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHH
Q psy11420 137 QIYWR-EFYYVVGSDTPNFDKMKGNKICCQ-------VDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHA 208 (315)
Q Consensus 137 eL~WR-ef~~~~~~~~p~~~~~~~~~~~~~-------~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~ 208 (315)
||+|| |||+++++++|++......+.+.. ..++.+...|++|++|+||+|+||||||||++|||||||+||+
T Consensus 294 EL~WR~ef~~~~~~~~p~~~~~~~~~~w~~~~l~~~~~d~r~~~~~~~~W~~G~Tg~pivdA~MrqL~~TG~MHNr~RMi 373 (454)
T TIGR00591 294 ELVVRRELADNFCFYNPYYDSLCGAYWWARTTLDDHAKDKREHLYSLEQLEKSTTHDYLWNAAQEQLVTEGKMHGFLRMY 373 (454)
T ss_pred HHHHHHHHHhHhhhcCCCccccccchHHHHHHHHHHhcCCccccCCHHHHHhcCcCcHhHhHHHHHHHHhCccccceeee
Confidence 99999 899999999998876332222220 1122222369999999999999999999999999999999999
Q ss_pred HHHHhhhhccCCChHHHHHHHHh--------hhcchhhhhhhhhHhhhhcccc-cccc-----c---cccCHHHHHHhcC
Q psy11420 209 VACFLTRGDLYLSWEEGQSVFEE--------LLLDADWAMNAGNWMWLSASAF-FHQF-----F---RVYSPVAFGKKTD 271 (315)
Q Consensus 209 vasfl~~~~l~~~W~~G~~~f~~--------~liD~d~a~n~~~W~~~ag~g~-~~~~-----~---r~~~p~~~~~~~d 271 (315)
|| | +| |+|+.|++||.+ +|||||+|+|++||||+ |+|+ +.|| | |+|||..|++|||
T Consensus 374 ~a----K-~l-i~W~~g~~~f~~~~~~ln~~~lvDgd~a~n~~~wqW~-~~G~d~~p~~~~~~fg~iR~~np~~q~~kfd 446 (454)
T TIGR00591 374 WA----K-KI-LEWTHSPEEALSIAIYLNDKYILDGRDPNGYVGCMWS-ICGIHDQGWAERIVFGKIRYMNYAGCRRKFN 446 (454)
T ss_pred ee----e-eh-hhcCCCHHHHHHHHHHhhhhhhccCCCCCccceeeeE-eccccCCCCCCCccceeeeecChhhhhccCC
Confidence 99 7 78 999999999999 89999999999999999 8888 6788 8 9999999999999
Q ss_pred cccchhhh
Q psy11420 272 KFELLLDA 279 (315)
Q Consensus 272 p~g~~Ir~ 279 (315)
|+| |||+
T Consensus 447 ~~~-yi~~ 453 (454)
T TIGR00591 447 VAY-FERK 453 (454)
T ss_pred HHH-HHhh
Confidence 999 9996
No 8
>KOG0133|consensus
Probab=100.00 E-value=3e-49 Score=383.95 Aligned_cols=282 Identities=48% Similarity=0.784 Sum_probs=227.7
Q ss_pred CChHhHHHHHhcCCCCCCCC-CCCCCCCCCcCCC---CCCCCCCCCCcccCCCCCCCCCCCCCCccHHHHHHHHHHHHhc
Q psy11420 1 MTYQKLVSVLESLPKPKPAD-DAPTSLPRECQGI---LHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLAN 76 (315)
Q Consensus 1 ~tf~~F~~~~~~~~~p~~Pl-~~P~~l~~~~~p~---~~~~~~~ip~l~~lg~~~~~~~~~~~~gGe~~A~~~L~~Fl~~ 76 (315)
+||+.|+..+.++..|..|. ........+ .|. .......+|+++.+++..+......|+||++.|+.+|+.||..
T Consensus 150 ls~~~~~~~~~~~~~~~~p~~v~~~~~~~~-~~~~~~~~~~~~~v~~~e~l~~~~~~~~~~~~~~g~s~al~~l~~~l~~ 228 (531)
T KOG0133|consen 150 LSYKTFRGVCQSMSAPKIPALVLSGLAVEK-HPNFLANSKASAVVPTLELLRFIPSNYGEVVWRGGESEALKRLDAHLKV 228 (531)
T ss_pred cccccccccccccccccccccccccccCCC-ChhhhhhcccccccCCchhhccCcccccccccCCcccchhHHHHHHhhH
Confidence 57888998888886554431 111111111 111 2333456788999988766544455999999999999999987
Q ss_pred CcccccccccCCCCCCC-CCCCCCCchhhhcCCCCHHHHHH--HHHHHHhcCC-CCCChHh-HHHhHHHHHHHHHHhhcC
Q psy11420 77 KEWVRKFEKPNTAPNSL-EPSTTVLSPYLKFGCLSVRLFYH--ELKKILATGP-HAKPPVS-LLGQIYWREFYYVVGSDT 151 (315)
Q Consensus 77 ~~~~~~Y~~~r~~~~~~-~~~~S~LSpyL~~G~lS~r~v~~--~~~~~~~~~~-~~~~~~~-~~~eL~WRef~~~~~~~~ 151 (315)
.....+++.....++.. ..+++.|||||+|||||+|.+++ .+.+...+.+ .....+. ++.||.||||||++...+
T Consensus 229 ~~~~an~~~~~~~~~~~~~~s~~~Ls~yL~fg~~svr~~~~~~~~k~V~~~~~~~s~~~es~~~~qv~Wre~~y~~~~n~ 308 (531)
T KOG0133|consen 229 PLWVANLELRYSNANSRVKISTTVLSPYLKFGCLSVRYFYRCVRLKQVKWKAKKNSLPPESLFLGQVAWREFFYTAAFNT 308 (531)
T ss_pred HHHHhhhhccccccchhcCCCccccccceeeccceeEeehhHhHHHHHHHhhhcccCCccccccceeeeechhhHhhcCC
Confidence 64456666655555432 35677999999999999999995 2333222222 2334454 999999999999999999
Q ss_pred CCcccccCCccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHh
Q psy11420 152 PNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEE 231 (315)
Q Consensus 152 p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~ 231 (315)
|.++.+.++..+.+++|+.|+..+++|.+|+||+|+|||+||||+++||+||+.|+++|||++++.|+|+|++|.++|.+
T Consensus 309 p~~~~m~~n~~~~~ipw~~n~~~~~aw~~G~tG~P~ida~m~~l~~~gw~h~~~R~~vasf~tr~~L~i~w~eg~~~F~~ 388 (531)
T KOG0133|consen 309 PYFDDMPGNKILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQLLASGWEHHRSRTIVASFLTRGDLLISWREGLDVFME 388 (531)
T ss_pred ccccccccccccccCCcccChhhhHHHHcCCCCCCchhHHHHHHHHHHHHhcccchhhHhHhhccceeeeHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcchhhhhhhhhHhhhhcccc-ccccccccCHHHHHHhcCcccchhhhhhhcc
Q psy11420 232 LLLDADWAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTDKFELLLDADWAMN 284 (315)
Q Consensus 232 ~liD~d~a~n~~~W~~~ag~g~-~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~ 284 (315)
+|+|+|+..|.|||||.+++.. ..+++++|||+.+++++||+|.||+. |.+.
T Consensus 389 ~llD~D~~~~agnW~~~S~~s~f~~~~~~~ysp~~~~kk~dP~g~yir~-~lp~ 441 (531)
T KOG0133|consen 389 YLLDADSSKNAGNWMWLSSTSHFFDQFDRVYSPVALGKKLDPDGLYIRQ-WLPE 441 (531)
T ss_pred HhcchhhhcCCCccceeccccccccccccccCHHHHhCcCCcchhhHHH-HhHH
Confidence 9999999999999999995444 78889999999999999999999997 7543
No 9
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=99.94 E-value=6.9e-28 Score=224.34 Aligned_cols=225 Identities=21% Similarity=0.243 Sum_probs=177.7
Q ss_pred CCCCCccHHHHHHHHHHHHhcC-cccccccccCCCCCCCCCCCCCCchhhhcCCCCHHHHHHHHHHHHhcCC-CCCChHh
Q psy11420 56 LCKFPGGETEALKRLEKSLANK-EWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGP-HAKPPVS 133 (315)
Q Consensus 56 ~~~~~gGe~~A~~~L~~Fl~~~-~~~~~Y~~~r~~~~~~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~~~~-~~~~~~~ 133 (315)
...|+..+++|+..|+.||+.+ ..++.|++.+.... ....+|.||++|+.|.|+|++|+.++.+++.+.. ..+++|.
T Consensus 220 ~F~wpvtr~~A~~~L~~Fi~~~L~nFG~yQDam~~d~-~~L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ipLN~VEG 298 (505)
T COG3046 220 GFGWPVTRTQALRALKHFIADRLPNFGSYQDAMSADD-PHLWHSLLSFALNIGLLTPLEVIRAALKAYREGDIPLNSVEG 298 (505)
T ss_pred cCCCCCCHHHHHHHHHHHHHHhhhcCCcHHHHHhcCC-chhHHHHHHHHhhccCCCHHHHHHHHHHhhccCCCchHHHHH
Confidence 4679999999999999999986 56889998876543 3578999999999999999999999999887532 2467899
Q ss_pred HHHhHH-HHHHHHHHhhcC-CCcccccCCccccCCCCCCChHHHHHHHcCCCCChHHHHHHHHHHHhcccCchhHHHHHH
Q psy11420 134 LLGQIY-WREFYYVVGSDT-PNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVAC 211 (315)
Q Consensus 134 ~~~eL~-WRef~~~~~~~~-p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vas 211 (315)
|++||+ ||||.+.+++.. |.|.+.|... .+.++.....+|+|++.|++.++.+...+||.||+.|.||.+
T Consensus 299 FvRQiiGWREfmRgiY~~~~P~y~trN~f~--------~d~~Lp~~yw~g~T~M~cl~~av~~v~d~gYAHHIqRLMV~g 370 (505)
T COG3046 299 FVRQIIGWREFMRGIYWLKMPDYATRNFFN--------ADRKLPPFYWTGQTKMACLAIAVGRVLDHGYAHHIQRLMVTG 370 (505)
T ss_pred HHHHHhhHHHHHHHhhhhcCCchhhhhhhc--------cCCCCCCccccCCcCchHHHHHHHHHhhhhHHHHHHHHHHHh
Confidence 999999 999999999876 8887766532 232333445799999999999999999999999999999999
Q ss_pred HhhhhccCCChHHHHHHHHhhhcch-hhh--hhh-hhHhhhhcccc--ccccc------cccCHHHHHHhcCcccchhhh
Q psy11420 212 FLTRGDLYLSWEEGQSVFEELLLDA-DWA--MNA-GNWMWLSASAF--FHQFF------RVYSPVAFGKKTDKFELLLDA 279 (315)
Q Consensus 212 fl~~~~l~~~W~~G~~~f~~~liD~-d~a--~n~-~~W~~~ag~g~--~~~~~------r~~~p~~~~~~~dp~g~~Ir~ 279 (315)
.|.. .++++.+...+||...+||+ ||. .|. |+-|.+.| |+ .+||. .-++..-++=.|||+.+.=+
T Consensus 371 NfAL-l~G~dPd~v~~Wf~~~fiDAYdWV~~PNv~GM~qFADG-G~iatKPYasS~nYInkMSDyC~~C~yd~k~r~Gd- 447 (505)
T COG3046 371 NFAL-LLGVDPDAVDRWFMEVFIDAYDWVELPNVRGMSQFADG-GLIATKPYASSGNYINKMSDYCSDCAYDPKSRLGD- 447 (505)
T ss_pred hHHH-HhCCCHHHHHHHHHHHHhhHhhheecccccchhhcccC-ceeecCccccchhHHHHHhHhhhhcccChhhccCc-
Confidence 9997 89999999999999999999 773 455 44455444 44 56664 33344444455666554444
Q ss_pred hhh-cccCCceeec
Q psy11420 280 DWA-MNAGNWMWLS 292 (315)
Q Consensus 280 ~w~-~~~~~w~~~s 292 (315)
+|| -|+++|-+++
T Consensus 448 ~aCpfNaLYWdFl~ 461 (505)
T COG3046 448 DACPFNALYWDFLA 461 (505)
T ss_pred ccCchHHHHHHHHH
Confidence 488 4889998776
No 10
>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=99.50 E-value=1.7e-15 Score=150.05 Aligned_cols=94 Identities=28% Similarity=0.462 Sum_probs=81.8
Q ss_pred CCChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeecccC
Q psy11420 219 YLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSASA 295 (315)
Q Consensus 219 ~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~~ 295 (315)
...|+.|.+.|+ +||+-| .++.+|||+.........+. .+..+|+.|++|+ ...+||+|+++|+|||||+||+|
T Consensus 317 f~aW~~G~TG~P--~VDA~MRqL~~TGwmhnR~Rm~vAsfl~k~L~idWr~G~~~F-~~~LiD~D~a~N~g~Wqw~Ag~g 393 (475)
T TIGR02766 317 FKAWRQGRTGYP--LVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYF-WDTLLDADLESDALGWQYISGSL 393 (475)
T ss_pred HHHHHcCCCCCc--chhHHHHHHHHHCCCcHHHHHHHHHHHHcccCCChHHHHHHH-HHHccccchhcccccccccccCC
Confidence 345888899999 999999 89999999987654322221 6889999999999 78999999999999999999997
Q ss_pred C-CCCcccccChhhhhhhcCC
Q psy11420 296 F-FHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 296 ~-~~~~~~~~~p~~~~~~~d~ 315 (315)
. ..+++|+|||++|++|+||
T Consensus 394 ~d~~~~~RifnP~~q~~~~Dp 414 (475)
T TIGR02766 394 PDGRELDRIDNPQLEGYKFDP 414 (475)
T ss_pred CCCCcccccCCHHHHHhhcCC
Confidence 6 6889999999999999998
No 11
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=99.44 E-value=9.5e-15 Score=141.79 Aligned_cols=92 Identities=26% Similarity=0.531 Sum_probs=78.5
Q ss_pred ChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeecccCC-
Q psy11420 221 SWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSASAF- 296 (315)
Q Consensus 221 ~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~~~- 296 (315)
.|++|.+.|. +|||.| .+|.+|||+.........++ .+..+|+.|++|+ +..+||+|.+.|+|||||++|+|.
T Consensus 309 aW~~G~TGyP--IVDA~MRqL~~TG~MHNR~RMivAsFL~k~L~IdWR~GE~~F-~~~LiD~D~asN~ggWQW~AstG~D 385 (461)
T COG0415 309 AWQEGKTGYP--IVDAAMRQLNQTGYMHNRMRMIVASFLTKDLLIDWREGEKYF-MRQLIDGDPASNNGGWQWAASTGTD 385 (461)
T ss_pred HHhcCCCCCc--cccHHHHHHHHhCCcchHHHHHHHHHHHHhcCCCHHHHHHHH-HHhccCCCcccCCCCeeEEeccCCC
Confidence 4556666667 999999 89999999987654323332 6889999999999 789999999999999999999976
Q ss_pred CCCcccccChhhhhhhcCC
Q psy11420 297 FHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 297 ~~~~~~~~~p~~~~~~~d~ 315 (315)
..+++|||||++|++|+||
T Consensus 386 a~pyfRiFNp~~Q~~kfDp 404 (461)
T COG0415 386 AAPYFRIFNPVTQAEKFDP 404 (461)
T ss_pred CCcceeccCHHHHHhhcCC
Confidence 4589999999999999998
No 12
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=99.43 E-value=1.1e-14 Score=142.67 Aligned_cols=94 Identities=21% Similarity=0.295 Sum_probs=80.1
Q ss_pred cCCChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeeccc
Q psy11420 218 LYLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSAS 294 (315)
Q Consensus 218 l~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~ 294 (315)
+...|+.|.++|+ +|||-| .++.+|||+.........+. .+..+|+.|++|+ ...+||+|+++|+|||||+||+
T Consensus 320 ~~~~W~~G~TG~P--ivDAamrqL~~TG~mhnr~Rm~vAsFl~k~L~idWr~G~~~F-~~~LiD~D~a~n~g~Wqw~ag~ 396 (429)
T TIGR02765 320 RFEQWKTGTTGYP--LVDANMRELNATGFMSNRGRQNVASFLVKDLGLDWRYGAEWF-ETQLVDYDVCSNWGNWQYLAGV 396 (429)
T ss_pred HHHHHhCCCCCCh--hhhHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCHHHHHHHH-HHHhhccchhcCcccchhhhcC
Confidence 3445777888888 999999 89999999986643322221 6889999999999 7899999999999999999999
Q ss_pred CCC-CCcccccChhhhhhhcCC
Q psy11420 295 AFF-HQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 295 ~~~-~~~~~~~~p~~~~~~~d~ 315 (315)
|.. .+ +|+|||++|++|+||
T Consensus 397 g~d~~~-~Rifnp~~q~~k~Dp 417 (429)
T TIGR02765 397 GNDPRG-SRQFNIEKQAQDYDP 417 (429)
T ss_pred cCCCCc-CccCCHHHHHHhcCC
Confidence 875 55 999999999999998
No 13
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=99.32 E-value=1.5e-13 Score=136.07 Aligned_cols=94 Identities=23% Similarity=0.573 Sum_probs=80.6
Q ss_pred CCChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeecccC
Q psy11420 219 YLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSASA 295 (315)
Q Consensus 219 ~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~~ 295 (315)
.-.|+.|.+.|. +||+-+ .++.+|||+.........+. .+..+|+.|.+|+ ...+||+|+++|++||||++|+|
T Consensus 314 ~~~W~~G~TG~P--~vDA~mrqL~~tG~mhnr~Rm~vAsfL~k~L~idWr~G~~~F-~~~LlD~D~a~N~g~Wqw~ag~G 390 (472)
T PRK10674 314 LQAWQQGKTGYP--IVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYF-MSQLIDGDLAANNGGWQWAASTG 390 (472)
T ss_pred HHHHHcCCCCCc--cHHHHHHHHHHHCCccHHHHHHHHHHHHcCcccCCHhHHHHH-HHHhhcCCcccchhccceeecCC
Confidence 445888888888 999998 89999999987653322221 6789999999999 78999999999999999999986
Q ss_pred C-CCCcccccChhhhhhhcCC
Q psy11420 296 F-FHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 296 ~-~~~~~~~~~p~~~~~~~d~ 315 (315)
. ..+++|+|||++|++|+||
T Consensus 391 ~d~~py~R~fnP~~q~~k~Dp 411 (472)
T PRK10674 391 TDAAPYFRIFNPTTQGERFDR 411 (472)
T ss_pred CCCCcceeecCHHHHHHHhCC
Confidence 5 6788999999999999998
No 14
>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=99.29 E-value=2.7e-13 Score=134.17 Aligned_cols=95 Identities=25% Similarity=0.541 Sum_probs=79.6
Q ss_pred cCCChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeeccc
Q psy11420 218 LYLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSAS 294 (315)
Q Consensus 218 l~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~ 294 (315)
+...|+.|.+.|+ +||+-| .++.+|||+.........+. .+..+|+.|.+|+ ...+||+|+++|++||||++|+
T Consensus 318 ~~~~W~~G~TG~P--~vDAaMrqL~~tG~mhnr~Rm~vAsfl~k~L~idWr~G~~~F-~~~LlD~D~a~N~g~Wqw~a~~ 394 (471)
T TIGR03556 318 HFQAWCEGRTGYP--IVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYF-MQKLIDGDLAANNGGWQWSASS 394 (471)
T ss_pred HHHHHhcCCCCCC--cccHHHHHHHHhCCccHHHHHHHHHHHHcccCCCHHHHHHHH-HHHhhhcChhhccccccchhcC
Confidence 3456778888888 999999 89999999987653322221 5889999999999 7899999999999999999998
Q ss_pred CCCCCcccccChhhhhhhcCC
Q psy11420 295 AFFHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 295 ~~~~~~~~~~~p~~~~~~~d~ 315 (315)
|....-+|+|||++|++|+||
T Consensus 395 G~d~~p~R~fnp~~q~~k~Dp 415 (471)
T TIGR03556 395 GMDPKPLRIFNPASQAQKFDP 415 (471)
T ss_pred CCCCCCCcccCHHHHHHHhCC
Confidence 764333899999999999998
No 15
>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=6.9e-13 Score=122.70 Aligned_cols=93 Identities=29% Similarity=0.504 Sum_probs=71.8
Q ss_pred CChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccc--cccCHHHHHHhcCcccchhhhhhhcccCCceeecccCC
Q psy11420 220 LSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFF--RVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLSASAF 296 (315)
Q Consensus 220 ~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~--r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s~~~~ 296 (315)
..|+.|.+.|. +||+-+ .++..||++.........+. .+..+|+.|.+++ ...+||.|+++|.+||||++|++.
T Consensus 117 ~~w~~G~TG~p--~vDAamrqL~~tG~mHn~~R~~vasfl~k~l~i~W~~g~~~f-~~~liD~d~a~n~~~wqw~ag~g~ 193 (277)
T PF03441_consen 117 EAWCEGRTGYP--LVDAAMRQLRQTGWMHNRLRMIVASFLTKDLLIDWREGAEWF-AEHLIDYDPASNYGNWQWAAGTGT 193 (277)
T ss_dssp HHHHTT-SS-H--HHHHHHHHHHHHS---HHHHHHHHHHHHHTSHBHHHHHHHHH-HHHHTT--HHHHHHHHHHHTTSSS
T ss_pred HHHHcCCCCCh--HHHHHHHHHHHhCcccHHHHHHHHHHHHHhccCCccccHHHH-HHHhhccCcchHHHHHHHHHhhcc
Confidence 34678888888 999998 89999999987653211121 5778999999999 789999999999999999999764
Q ss_pred -CCCcccccChhhhhhhcCC
Q psy11420 297 -FHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 297 -~~~~~~~~~p~~~~~~~d~ 315 (315)
..+++|+|||++|++++||
T Consensus 194 d~~~~~r~~np~~q~~~~Dp 213 (277)
T PF03441_consen 194 DAKPYFRIFNPVKQSKKFDP 213 (277)
T ss_dssp TGCSTTTHHHHHHHHHHHST
T ss_pred ccCccccccCchHHHHhhCc
Confidence 5688999999999999998
No 16
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.93 E-value=1.3e-10 Score=114.68 Aligned_cols=93 Identities=12% Similarity=0.059 Sum_probs=78.6
Q ss_pred cCCChHHHHHHHHhhhcchhh-hhhhhhHhhhhccccccccccccCHHHHHHhcCccc-------chhhhhhhcccCCce
Q psy11420 218 LYLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDKFE-------LLLDADWAMNAGNWM 289 (315)
Q Consensus 218 l~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~~~~~~r~~~p~~~~~~~dp~g-------~~Ir~~w~~~~~~w~ 289 (315)
.+-.|+.|.+.|. +|||-| .++.+|||+..+...... .+ .+|+.|.+++-+- ..||+|.+.|++|||
T Consensus 339 ~~~~W~~G~Tg~p--ivdA~MrqL~~TG~MHNr~RMi~aK--~l-i~W~~g~~~f~~~~~~ln~~~lvDgd~a~n~~~wq 413 (454)
T TIGR00591 339 SLEQLEKSTTHDY--LWNAAQEQLVTEGKMHGFLRMYWAK--KI-LEWTHSPEEALSIAIYLNDKYILDGRDPNGYVGCM 413 (454)
T ss_pred CHHHHHhcCcCcH--hHhHHHHHHHHhCccccceeeeeee--eh-hhcCCCHHHHHHHHHHhhhhhhccCCCCCccceee
Confidence 4678999999999 999999 999999999988654332 34 9999999998332 799999999999999
Q ss_pred eecccCCCCCc-----c---cccChhhhhhhcCC
Q psy11420 290 WLSASAFFHQF-----F---RVYSPVAFGKKTDK 315 (315)
Q Consensus 290 ~~s~~~~~~~~-----~---~~~~p~~~~~~~d~ 315 (315)
|++++++..++ + |+|||+.|++|+||
T Consensus 414 W~~~G~d~~p~~~~~~fg~iR~~np~~q~~kfd~ 447 (454)
T TIGR00591 414 WSICGIHDQGWAERIVFGKIRYMNYAGCRRKFNV 447 (454)
T ss_pred eEeccccCCCCCCCccceeeeecChhhhhccCCH
Confidence 99334557777 8 99999999999997
No 17
>KOG0133|consensus
Probab=98.60 E-value=9.7e-09 Score=101.28 Aligned_cols=96 Identities=42% Similarity=0.632 Sum_probs=79.6
Q ss_pred ccCCChHHHHHHHHhhhcchhh-hhhhhhHhhhhcccc---ccccccccCHHHHHHhcCcccchhhhhhhcccCCceeec
Q psy11420 217 DLYLSWEEGQSVFEELLLDADW-AMNAGNWMWLSASAF---FHQFFRVYSPVAFGKKTDKFELLLDADWAMNAGNWMWLS 292 (315)
Q Consensus 217 ~l~~~W~~G~~~f~~~liD~d~-a~n~~~W~~~ag~g~---~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~~~~~~w~~~s 292 (315)
....+|+.|.+.|+ +||+-+ ..-..||++.-.... ......+..+|++|.+++ ....+++||..|.+||||+|
T Consensus 330 ~~~~aw~~G~tG~P--~ida~m~~l~~~gw~h~~~R~~vasf~tr~~L~i~w~eg~~~F-~~~llD~D~~~~agnW~~~S 406 (531)
T KOG0133|consen 330 PKLAAWLEGLTGYP--WLDAGMRQLLASGWEHHRSRTIVASFLTRGDLLISWREGLDVF-MEYLLDADSSKNAGNWMWLS 406 (531)
T ss_pred hhhHHHHcCCCCCC--chhHHHHHHHHHHHHhcccchhhHhHhhccceeeeHHHHHHHH-HHHhcchhhhcCCCccceec
Confidence 34567778888888 999977 888999998755422 222336889999999999 67899999999999999999
Q ss_pred cc-CCCCCcccccChhhhhhhcCC
Q psy11420 293 AS-AFFHQFFRVYSPVAFGKKTDK 315 (315)
Q Consensus 293 ~~-~~~~~~~~~~~p~~~~~~~d~ 315 (315)
++ .++++++++|||+.++|++||
T Consensus 407 ~~s~f~~~~~~~ysp~~~~kk~dP 430 (531)
T KOG0133|consen 407 STSHFFDQFDRVYSPVALGKKLDP 430 (531)
T ss_pred cccccccccccccCHHHHhCcCCc
Confidence 65 458999999999999999998
No 18
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=46.71 E-value=22 Score=26.01 Aligned_cols=30 Identities=33% Similarity=0.555 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhcccCchhHHHHHHHhhhhccCCC
Q psy11420 188 IDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLS 221 (315)
Q Consensus 188 vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~ 221 (315)
|++.| .+|||..|-+|-.++..|-| .+++.
T Consensus 27 i~ei~---~atGWq~HTvRgalsg~~kK-klGl~ 56 (72)
T PF11994_consen 27 IAEIC---EATGWQPHTVRGALSGLLKK-KLGLT 56 (72)
T ss_pred HHHHH---HhhCCchhhHHHHHHHHHHH-hcCcE
Confidence 45554 67999999999999998877 67654
No 19
>PRK02249 DNA primase large subunit; Validated
Probab=42.60 E-value=64 Score=30.94 Aligned_cols=63 Identities=22% Similarity=0.267 Sum_probs=47.9
Q ss_pred ChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcchhhhhhhhhHhhhhc
Q psy11420 185 YPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWLSA 250 (315)
Q Consensus 185 ~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~d~a~n~~~W~~~ag 250 (315)
-||+-+.+..|.+.+-+.|.+|+.+++||. ..+++..+....|... -|.|--.-..+..|..|
T Consensus 223 PpCm~~l~~~l~~g~~L~h~~R~~l~~FL~--~iG~~~deil~~~~~~-~~f~e~~~~Y~irH~~G 285 (343)
T PRK02249 223 PPCMKALLSALQAGENLPHTARFAITSFLL--NIGMSVDEIVELFRNA-PDFDEEKTRYQVEHIAG 285 (343)
T ss_pred CHHHHHHHHHHHcCCCCChHHHHHHHHHHH--hcCCCHHHHHHHHhhC-CCccHHHHHHHHHHHhc
Confidence 467777777789999999999999999999 4899999999988653 24443333455667776
No 20
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=37.32 E-value=63 Score=31.24 Aligned_cols=63 Identities=25% Similarity=0.253 Sum_probs=53.5
Q ss_pred ChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcchhhhhhhhhHhhhhc
Q psy11420 185 YPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWLSA 250 (315)
Q Consensus 185 ~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~d~a~n~~~W~~~ag 250 (315)
-|||=.+|+.|..-.-+.|.+|..++|||.+ .++.-.+..+.| +..-|.|--.-....++.+|
T Consensus 242 PPCik~iL~~l~~G~~l~h~~R~al~sFL~~--ig~~~deiv~~f-r~~pdFdee~tryqirHi~G 304 (363)
T COG2219 242 PPCIKNILAGLKSGENLPHAARFALTSFLSN--IGLSVDEIVELF-RNSPDFDEEITRYQIRHIIG 304 (363)
T ss_pred ChHHHHHHHHhhcCCCchHHHHHHHHHHHHh--cCCChhHHHHHh-ccCCCcchhhhhhhhheeec
Confidence 4899999999999999999999999999994 788888888844 45677887787888899888
No 21
>PF04104 DNA_primase_lrg: Eukaryotic and archaeal DNA primase, large subunit; InterPro: IPR007238 DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast Saccharomyces cerevisiae) []. Both subunits participate in the formation of the active site, but the ATP binding site is located on the small subunit []. Primase function has also been demonstrated for human and mouse primase subunits [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 1ZT2_B 3Q36_A 3L9Q_B 2DLA_B 3LGB_B.
Probab=35.34 E-value=25 Score=32.21 Aligned_cols=49 Identities=22% Similarity=0.337 Sum_probs=37.4
Q ss_pred ChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcc
Q psy11420 185 YPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLD 235 (315)
Q Consensus 185 ~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD 235 (315)
-||+-+.+..|.+.+-+.|.+|+.+++||. .++++-.+..++|...+..
T Consensus 109 PpCMr~l~~~L~~~~hL~h~~R~ql~lFLk--~iGl~~ee~l~f~~~~f~~ 157 (260)
T PF04104_consen 109 PPCMRNLHERLRKGHHLKHSGRFQLGLFLK--GIGLSLEEALEFWRSEFSK 157 (260)
T ss_dssp -HHHHHHHHHHHHHS---HHHHHHHHHHHH--HTTEECCCHHHCCHHHCCT
T ss_pred ChHHHHHHHHHhhCCCCCchhHhhHHHHHH--hcCCCHHHHHHHHHHHhcc
Confidence 578888888899999999999999999998 4888877777766666544
No 22
>PRK09568 DNA primase large subunit; Reviewed
Probab=28.04 E-value=84 Score=29.63 Aligned_cols=38 Identities=0% Similarity=-0.009 Sum_probs=32.5
Q ss_pred HHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHH
Q psy11420 191 IMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFE 230 (315)
Q Consensus 191 ~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~ 230 (315)
||+.|++.--++|.+|-++|+||.+ .+.+=.+-.+.|.
T Consensus 218 Cik~li~g~nL~H~~RFaLasFL~n--iG~~vd~Iv~lf~ 255 (306)
T PRK09568 218 CIENILGKEELSEEEIRTLITYYIN--IGKGLDSIIAIMN 255 (306)
T ss_pred hHHHHhcCCCCChHHHHHHHHHHHH--cCCCHHHHHHHHh
Confidence 6777777777999999999999995 7888888888885
No 23
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=27.74 E-value=17 Score=37.02 Aligned_cols=42 Identities=31% Similarity=0.218 Sum_probs=29.0
Q ss_pred cchhhhhhhhhHhhhhccccccccccccCHHHHHHhcCcccchhhhhhh
Q psy11420 234 LDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDKFELLLDADWA 282 (315)
Q Consensus 234 iD~d~a~n~~~W~~~ag~g~~~~~~r~~~p~~~~~~~dp~g~~Ir~~w~ 282 (315)
.|+|.+.|+||.--+.|--.+..| -.||.+||++|.+.+- |.
T Consensus 476 ~ea~~a~NYGgIGaVIgHEI~HgF------DdqGakfD~~GnL~dW-WT 517 (654)
T COG3590 476 PEADSAANYGGIGAVIGHEIGHGF------DDQGAKFDGDGNLNDW-WT 517 (654)
T ss_pred CCcchhhcccCccceehhhhcccc------cCCccccCCCCcHHhh-cC
Confidence 677889999997544442112222 2479999999999986 54
No 24
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=22.81 E-value=1.6e+02 Score=21.11 Aligned_cols=52 Identities=25% Similarity=0.272 Sum_probs=40.7
Q ss_pred CCChHHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHHhhhcch
Q psy11420 183 TGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDA 236 (315)
Q Consensus 183 TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~~~liD~ 236 (315)
-|.+=+|||...+..-|+--..+|-++-..|-. .+-+|..-++--.+.|+|+
T Consensus 6 ~~~~R~daA~dam~~lG~~~~~v~~vl~~LL~l--Y~~nW~lIEed~Y~~L~da 57 (65)
T PF10440_consen 6 KGNERIDAALDAMRQLGFSKKQVRPVLKNLLKL--YDGNWELIEEDNYRVLADA 57 (65)
T ss_pred cCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH--HcCCchhhhcccHHHHHHH
Confidence 456789999999999999999999998876664 4566887776555556665
No 25
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=22.18 E-value=1.1e+02 Score=19.66 Aligned_cols=38 Identities=13% Similarity=0.075 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhcccCchhHHHHHHHhhhhccCCChHHHHHHHH
Q psy11420 187 FIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFE 230 (315)
Q Consensus 187 ~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~~~W~~G~~~f~ 230 (315)
+++|+.+.+.+.||-.-.+|.+.. .++++-..-..+|.
T Consensus 1 Il~aa~~l~~~~G~~~~s~~~Ia~------~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 1 ILEAALELFAEKGYEAVSIRDIAR------RAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHHHHHHTTTSSHHHHHH------HHTSCHHHHHHHCS
T ss_pred CHHHHHHHHHHhCHHhCCHHHHHH------HHccchhhHHHHcC
Confidence 689999999999999999999874 56666555444443
Done!