Query psy4171
Match_columns 309
No_of_seqs 174 out of 1432
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 18:41:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4171.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4171hhsearch_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 5.7E-84 1.2E-88 618.8 21.7 290 1-309 118-409 (461)
2 TIGR02766 crypt_chrom_pln cryp 100.0 4.1E-81 8.8E-86 615.0 22.0 291 1-309 115-419 (475)
3 TIGR02765 crypto_DASH cryptoch 100.0 1.4E-78 3.1E-83 590.2 26.6 296 1-309 124-422 (429)
4 TIGR03556 photolyase_8HDF deox 100.0 2.1E-78 4.5E-83 594.3 23.4 297 1-309 118-420 (471)
5 PRK10674 deoxyribodipyrimidine 100.0 1.7E-77 3.7E-82 587.9 24.1 290 2-309 123-416 (472)
6 PF03441 FAD_binding_7: FAD bi 100.0 4.1E-71 8.9E-76 508.5 10.5 212 93-309 1-218 (277)
7 TIGR00591 phr2 photolyase PhrI 100.0 3.5E-67 7.5E-72 513.6 11.3 280 2-309 141-451 (454)
8 KOG0133|consensus 100.0 4.6E-58 9.9E-63 443.9 7.9 308 1-309 122-435 (531)
9 COG3046 Uncharacterized protei 100.0 6.9E-29 1.5E-33 230.2 10.4 293 1-306 116-443 (505)
10 PF04104 DNA_primase_lrg: Euka 41.7 26 0.00057 31.9 3.1 47 218-266 110-156 (260)
11 COG2219 PRI2 Eukaryotic-type D 37.2 54 0.0012 31.6 4.6 62 218-282 243-304 (363)
12 PRK02249 DNA primase large sub 36.5 70 0.0015 30.6 5.2 44 218-263 224-267 (343)
13 PF00440 TetR_N: Bacterial reg 28.8 49 0.0011 21.3 2.0 37 219-261 1-37 (47)
14 PF11994 DUF3489: Protein of u 26.9 53 0.0011 24.0 2.1 25 228-253 32-56 (72)
15 PRK09568 DNA primase large sub 26.8 93 0.002 29.2 4.2 45 223-270 218-262 (306)
16 PF05268 GP38: Phage tail fibr 21.8 43 0.00094 29.8 0.9 25 213-237 16-42 (260)
17 COG3590 PepO Predicted metallo 21.4 41 0.00089 34.2 0.8 37 266-308 476-512 (654)
No 1
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.7e-84 Score=618.77 Aligned_cols=290 Identities=26% Similarity=0.456 Sum_probs=244.1
Q ss_pred CCceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCCCCCCCCCCcccccccCCCCCCCCCccCCCCCccccC
Q psy4171 1 MSSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELG 80 (309)
Q Consensus 1 ~~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~l~~lg 80 (309)
.||.+++|+|++|++|++|.+.. |++|+|||+|++.|........|.+.|. .+........ .......|+ .+
T Consensus 118 ~gi~~~~~~d~~l~~p~~~~t~~-~~~y~vfT~F~k~~~~~~~~~~~~~~p~--~~~~~~~~~~--~~~~~~~P~--~~- 189 (461)
T COG0415 118 VGIAVHSFWDALLHEPGEVRTGS-GEPYKVFTPFYKAWRDRLRILRPVPAPD--VLDALRDEEP--PPEEISLPD--FS- 189 (461)
T ss_pred cCceEEEeccccccCHhhccCCC-CCCccccchHHHHHHHhcccCCCCCCcc--hhcccccccc--CcccccCCc--cc-
Confidence 38999999999999999998866 7999999999999877633222332221 1110000000 000112222 00
Q ss_pred CCcCCCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhccC
Q psy4171 81 FDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKKA 160 (309)
Q Consensus 81 ~~~~~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~~ 160 (309)
......|+|||++|+++|++|+.++ +.+|++.||.|. .++||+|||||++|+||||+||+++.+.... .+
T Consensus 190 ----~~~~~~~~~Ge~aA~~~l~~F~~~~--l~~Y~~~Rd~p~--~~~TS~LSpyL~~G~IS~r~v~~~~~~~~~~--~~ 259 (461)
T COG0415 190 ----KFDVLLFTGGEKAALARLQDFLAEG--LDDYERTRDFPA--LDGTSRLSPYLAFGVISPREVYAALLAAESD--AR 259 (461)
T ss_pred ----cccccCCCchHHHHHHHHHHHHHHH--HHHHHHhcCCcc--cccccccCHHHHcCCcCHHHHHHHHHHhhhc--cc
Confidence 0113468999999999999999988 799999999998 7899999999999999999999999886643 34
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCCcc-cccCCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHHHHhcccchHHHH
Q psy4171 161 PPPLSLHGQLLWREFFYCAATRNPNF-DRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARH 239 (309)
Q Consensus 161 ~~~~~~~~eL~WRef~~~~~~~~p~~-~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~ 239 (309)
+++++|++||+|||||++++.++|++ ...+..+....++|.++++.|++|++|+|||||||||||||++||||||||||
T Consensus 260 ~~~~~~~~eL~WREFy~h~~~~~p~~~~~~~~~~~~~~~~w~~~~~~f~aW~~G~TGyPIVDA~MRqL~~TG~MHNR~RM 339 (461)
T COG0415 260 EGTAALINELIWREFYQHLLYHYPSLSRFEPFAEKTLNIPWEDNPAHFQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRM 339 (461)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCCcccccccccccccCCccccCHHHHHHHhcCCCCCccccHHHHHHHHhCCcchHHHH
Confidence 67889999999999999999999998 66677888899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhcccC-CCCccccccChhhhhhhcCCCCCCC
Q psy4171 240 AVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS-FFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 240 ~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~~-~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
+||||||| +|.||||+|++||+++|||||+|+|+|||||+||++ |..||||||||++|++||||+|.||
T Consensus 340 ivAsFL~k-~L~IdWR~GE~~F~~~LiD~D~asN~ggWQW~AstG~Da~pyfRiFNp~~Q~~kfDp~g~fI 409 (461)
T COG0415 340 IVASFLTK-DLLIDWREGEKYFMRQLIDGDPASNNGGWQWAASTGTDAAPYFRIFNPVTQAEKFDPDGEFI 409 (461)
T ss_pred HHHHHHHH-hcCCCHHHHHHHHHHhccCCCcccCCCCeeEEeccCCCCCcceeccCHHHHHhhcCCCcccH
Confidence 99999999 999999999999999999999999999999999765 6779999999999999999999998
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=4.1e-81 Score=615.00 Aligned_cols=291 Identities=23% Similarity=0.349 Sum_probs=237.7
Q ss_pred CCceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCC-CCCCCCCCcccccccCCCCCCCCCccCCCCCcccc
Q psy4171 1 MSSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSP-SPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEEL 79 (309)
Q Consensus 1 ~~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p-~~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~l~~l 79 (309)
.||.++++++++||+|++|.+.. +++|++|++|++.+.+...+ +++.+.| ..++.. +. ..+.++++
T Consensus 115 ~gi~~~~~~~~~l~~p~~i~~~~-~~~~~~ft~f~~~~~~~~~~~~~~~~~p--~~~~~~--~~--------~~~~~~~~ 181 (475)
T TIGR02766 115 QGISVQSFNADLLYEPWEVYDEL-GRPFTMFAAFWERCLSMPYDPESPLLPP--KKIISG--DV--------SKCSADDL 181 (475)
T ss_pred cCCEEEEecCCEEEChhhhcccC-CCCCCeecHHHHHHHhccCCCCCCCCCc--cccCCC--cc--------ccCChhhc
Confidence 38999999999999999998754 78999999999987654322 1122211 111100 00 00111222
Q ss_pred CCCcC------CCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHH
Q psy4171 80 GFDIE------GLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKL 153 (309)
Q Consensus 80 g~~~~------~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~ 153 (309)
++... ......|+|||++|+++|+.|++++ +.+|++.||.|. .++||+|||||++||||||+|++++.+.
T Consensus 182 ~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~--~~~Y~~~Rd~p~--~~~tS~LSPyL~~G~ISpR~v~~~~~~~ 257 (475)
T TIGR02766 182 GFEDDSEKGSNALLARAWSPGWSNADKALTEFINGP--LLEYSKNRKKAD--SATTSLLSPYLHFGEVSVRKVFHLVRMK 257 (475)
T ss_pred CCCCcccccccccccccCCCccHHHHHHHHHHHHHH--HHHHhhcCCCCC--CCCCCCCCcccccCcccHHHHHHHHHhh
Confidence 22110 0011248999999999999999877 799999999987 5889999999999999999999998632
Q ss_pred H-----Hhhc-cCCCchhHHHHHHHHHHHHHHHHhCCcccccCCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q psy4171 154 Y-----KRIK-KAPPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQL 227 (309)
Q Consensus 154 ~-----~~~~-~~~~~~~~~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL 227 (309)
. +... ..++.++|++||+|||||++++.++|.+...+..+.++.++|+++++.|++|++|+||||+||||||||
T Consensus 258 ~~~~~~~~~~~~~~s~~~f~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~f~aW~~G~TG~P~VDA~MRqL 337 (475)
T TIGR02766 258 QIAWANEGNSAGEESVNLFLRSIGLREYSRYISFNHPFSHEKPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMREL 337 (475)
T ss_pred hhhhhhcccCCCcccHHHHHHHHHHHHHHHHHHHhCCcccccchhhhhhcCCCCCCHHHHHHHHcCCCCCcchhHHHHHH
Confidence 1 1111 134668899999999999999999998766666667788999999999999999999999999999999
Q ss_pred HHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhcccC-CCCccccccChhhhhhhcCCCC
Q psy4171 228 REEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS-FFQQFFHCYCPVKFGRKADPNG 306 (309)
Q Consensus 228 ~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~~-~~~~~~r~~np~~q~~~~Dp~g 306 (309)
++|||||||+|||||||||| +|+||||.|++||+++|||||+|+|+|||||+||+| |.+||||||||++|++||||+|
T Consensus 338 ~~TGwmhnR~Rm~vAsfl~k-~L~idWr~G~~~F~~~LiD~D~a~N~g~Wqw~Ag~g~d~~~~~RifnP~~q~~~~Dp~g 416 (475)
T TIGR02766 338 WATGWLHDRIRVVVSSFFVK-VLQLPWRWGMKYFWDTLLDADLESDALGWQYISGSLPDGRELDRIDNPQLEGYKFDPNG 416 (475)
T ss_pred HHHCCCcHHHHHHHHHHHHc-ccCCChHHHHHHHHHHccccchhcccccccccccCCCCCCcccccCCHHHHHhhcCCCc
Confidence 99999999999999999999 999999999999999999999999999999999765 6799999999999999999999
Q ss_pred CCC
Q psy4171 307 DFI 309 (309)
Q Consensus 307 ~yi 309 (309)
+||
T Consensus 417 ~yi 419 (475)
T TIGR02766 417 EYV 419 (475)
T ss_pred ccH
Confidence 997
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=1.4e-78 Score=590.23 Aligned_cols=296 Identities=25% Similarity=0.408 Sum_probs=233.1
Q ss_pred CCceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCCCCCCCCCCcccccccCCCCCCCCCccCCCCCccccC
Q psy4171 1 MSSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELG 80 (309)
Q Consensus 1 ~~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~l~~lg 80 (309)
.||.++++++++|++|++|++.. |++|.+|++|++++++...++.+.+.|. .++.. +... ....+|++++++
T Consensus 124 ~~i~~~~~~~~~l~~p~~v~~~~-~~~~~~ft~f~~~~~~~~~~~~~~~~p~--~~~~~--~~~~---~~~~~~~l~~~~ 195 (429)
T TIGR02765 124 LGIHVEQHWGSTLYHEDDLPFDL-EDLPDVFTQFRKQVEAKCSIRPPLPAPE--KLPPL--PSVD---DPGWIPTLEDLG 195 (429)
T ss_pred cCceEEEecCCEeECHHhcCCCC-CCCCCCchHHHHHHHhhCCCCCCCCCcc--cCCCC--cccc---cccCCCChhhcC
Confidence 38999999999999999997754 7999999999999875322222222221 11110 1000 011246666665
Q ss_pred CCcCCCC-CCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhcc
Q psy4171 81 FDIEGLL-PPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKK 159 (309)
Q Consensus 81 ~~~~~~~-~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~ 159 (309)
++..... ...|+|||.+|+++|++|+.++. +..|++.||.+.+ .++||+|||||++||||||+|++++.+.......
T Consensus 196 ~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~~-l~~Y~~~R~~~~~-~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~ 273 (429)
T TIGR02765 196 EESSEVDRGLPFVGGETAGLARLKEYFWSKD-LKSYKETRNGMLG-PDYSTKFSPWLALGCVSPRQIYEELQRYETERGA 273 (429)
T ss_pred CCcccccccCCcCchHHHHHHHHHHHHhhcc-HhhhhhccCcccC-CCCcCccCHHHhCCcccHHHHHHHHHHHHhhccc
Confidence 5432211 23589999999999999997432 7899999987642 4689999999999999999999998774322112
Q ss_pred CCCchhHHHHHHHHHHHHHHHHhCCc-ccccCCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHHHHhcccchHHH
Q psy4171 160 APPPLSLHGQLLWREFFYCAATRNPN-FDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLAR 238 (309)
Q Consensus 160 ~~~~~~~~~eL~WRef~~~~~~~~p~-~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R 238 (309)
..+++.+++||+|||||++++.++|. +...... ....++|+.+++.|++|++|+||||+||||||||++|||||||+|
T Consensus 274 ~~~~~~~~~eL~WRef~~~~~~~~~~~~~~~~~~-~~~~~~w~~~~~~~~~W~~G~TG~PivDAamrqL~~TG~mhnr~R 352 (429)
T TIGR02765 274 NDSTYWVIFELLWRDYFRFYALKYGNRLFRFGGL-RGKHPKWSFDAKRFEQWKTGTTGYPLVDANMRELNATGFMSNRGR 352 (429)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHcCCcccccCCC-ccCCCCCccCHHHHHHHhCCCCCChhhhHHHHHHHHhCCCCHHHH
Confidence 23455677899999999988878763 4432222 224678999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhcccC-CCCccccccChhhhhhhcCCCCCCC
Q psy4171 239 HAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS-FFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 239 ~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~~-~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
|+||||||| +|+||||+|++||+++|||||+|+|+|||||+||++ |..| ||||||++|++||||+|+||
T Consensus 353 m~vAsFl~k-~L~idWr~G~~~F~~~LiD~D~a~n~g~Wqw~ag~g~d~~~-~Rifnp~~q~~k~Dp~g~yi 422 (429)
T TIGR02765 353 QNVASFLVK-DLGLDWRYGAEWFETQLVDYDVCSNWGNWQYLAGVGNDPRG-SRQFNIEKQAQDYDPDGEYV 422 (429)
T ss_pred HHHHHHHHH-ccCCCHHHHHHHHHHHhhccchhcCcccchhhhcCcCCCCc-CccCCHHHHHHhcCCCCCcH
Confidence 999999999 999999999999999999999999999999999776 5577 99999999999999999998
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=2.1e-78 Score=594.27 Aligned_cols=297 Identities=28% Similarity=0.486 Sum_probs=245.1
Q ss_pred CCceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCCCCCCCCCCccccccc--CCCCCCCCCccCCCCCccc
Q psy4171 1 MSSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQA--TTPLRDDHDEKYGVPTLEE 78 (309)
Q Consensus 1 ~~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p~~p~~~~~~~~~~~~--~~~~~~~~~~~~~iP~l~~ 78 (309)
.||.|+++++|+|++|++|++.+ |++|++|++|++.+.....+ +|.+.|. .++.. ..+..........+|++++
T Consensus 118 ~~i~~~~~~~~~l~~p~~i~~~~-~~~y~~ft~f~k~~~~~~~~-~~~~~p~--~~~~~~~~~~~~~~~~~~~~~p~~~~ 193 (471)
T TIGR03556 118 AGIAVVTLWDQLLHSPDEILTGS-GNPYTVYTPFWKNWSSLPKP-TPVATPT--ELEGLTEAELEAAAPLGVIALPTAKD 193 (471)
T ss_pred CCCEEEEeCCcEEECccccccCC-CCCCcchhHHHHHHHhcccc-CCCCCcc--ccccCCccccccccccccccCCcccc
Confidence 38999999999999999997755 78999999999998765422 1222221 11100 0000001112234677766
Q ss_pred cCCCcCCCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhc
Q psy4171 79 LGFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIK 158 (309)
Q Consensus 79 lg~~~~~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~ 158 (309)
++++... ...|+|||.+|+++|+.|++++ +.+|++.|+.|. .++||+|||||++||||+|+|++++.+......
T Consensus 194 ~~~~~~~--~~~~~gGe~~A~~~L~~f~~~~--l~~Y~~~r~~p~--~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~ 267 (471)
T TIGR03556 194 LGFDWDG--DLILEPGETAAQARLEEFCDRA--IADYQEQRNFPA--LDGTSQLSPALKFGVIGIRTVWQATQEAHENSR 267 (471)
T ss_pred ccccccc--ccCCCCcHHHHHHHHHHHHHHH--HHHhhhccCCCC--CCCCCCCChhhcCCcccHHHHHHHHHHHHhhcc
Confidence 6665332 2258999999999999999876 899999999986 578999999999999999999999987543211
Q ss_pred ---cCCCchhHHHHHHHHHHHHHHHHhCCcccccCCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHHHHhcccch
Q psy4171 159 ---KAPPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHH 235 (309)
Q Consensus 159 ---~~~~~~~~~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhn 235 (309)
...+.++|++||+|||||+++++++|.+...+.++.+..++|+.+++.|++|++|+||+|+||||||||++||||||
T Consensus 268 ~~~~~~~~~~f~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~~~~W~~G~TG~P~vDAaMrqL~~tG~mhn 347 (471)
T TIGR03556 268 SEEARNSIRTWQQELAWREFYQHALYHFPELADGPYRSLFQNFPWENNEAHFQAWCEGRTGYPIVDAAMRQLNETGWMHN 347 (471)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHHHCcchhccccchhhhcCCCcCCHHHHHHHhcCCCCCCcccHHHHHHHHhCCccH
Confidence 13456789999999999999999999987767777788899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhccc-CCCCccccccChhhhhhhcCCCCCCC
Q psy4171 236 LARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCS-SFFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 236 r~R~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~-~~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
|+||+||||||| +|+||||+|++||+++|||||+|+|+|||||+||+ .+++| ||+|||++|++||||+|+||
T Consensus 348 r~Rm~vAsfl~k-~L~idWr~G~~~F~~~LlD~D~a~N~g~Wqw~a~~G~d~~p-~R~fnp~~q~~k~Dp~G~yI 420 (471)
T TIGR03556 348 RCRMIVASFLTK-DLIINWQWGEKYFMQKLIDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAQKFDPEAEYI 420 (471)
T ss_pred HHHHHHHHHHHc-ccCCCHHHHHHHHHHHhhhcChhhccccccchhcCCCCCCC-CcccCHHHHHHHhCCCCchH
Confidence 999999999999 99999999999999999999999999999999975 46677 89999999999999999997
No 5
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=100.00 E-value=1.7e-77 Score=587.88 Aligned_cols=290 Identities=22% Similarity=0.399 Sum_probs=235.2
Q ss_pred CceEEEecCCcccCCCccccccCccccccccccHHhHHhC-CCCC-CCCCCCCcccccccCCCCCCCCCccCCCCCcccc
Q psy4171 2 SSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKM-DSPS-PAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEEL 79 (309)
Q Consensus 2 ~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~-~~p~-~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~l~~l 79 (309)
||.++++++++|++|++|.+.+ +++|++|++|++.+++. ..+. .+.+.+. ..+.. + ..++.+..+
T Consensus 123 ~i~~~~~~~~~l~~~~~i~~~~-~~~y~~ft~f~~~~~~~~~~~~p~~~~~p~--~~~~~--~--------~~~~~~~~~ 189 (472)
T PRK10674 123 NVVCQGFDDSVLLPPGSVMTGN-HEMYKVFTPFKNAFLKRLREGDPECVPAPK--VRSSG--A--------IEPLPPIPF 189 (472)
T ss_pred CCEEEEecCceEeCccccccCC-CCCCCcccHHHHHHHHhhcccCCccCCCCc--ccccc--c--------cCCCCcccc
Confidence 7889999999999999998755 68999999999988663 2211 1111111 11000 0 011122223
Q ss_pred CCCcCCCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhcc
Q psy4171 80 GFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKK 159 (309)
Q Consensus 80 g~~~~~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~ 159 (309)
++.........|+|||++|+++|++|++++ +.+|++.|+.|. .++||+|||||++||||||+|++++.+.......
T Consensus 190 ~~~~~~~~~~~~~gGe~~A~~~L~~f~~~~--l~~Y~~~r~~p~--~~~tS~LSPyL~~G~iS~r~v~~~~~~~~~~~~~ 265 (472)
T PRK10674 190 NYPQQSFDTALFPVGEKAAIAQLRQFCQQG--AGEYEQQRDFPA--VDGTSRLSAYLATGVLSPRQCLHRLLAEQPQALD 265 (472)
T ss_pred cCcccccccCCCCCCHHHHHHHHHHHHHHH--HHHhccccCCCC--ccCCCCcChhhccCcCCHHHHHHHHHHHhhhhhc
Confidence 322211112358999999999999999876 799999999886 5789999999999999999999999764432111
Q ss_pred CCCchhHHHHHHHHHHHHHHHHhCCccccc-CCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHHHHhcccchHHH
Q psy4171 160 APPPLSLHGQLLWREFFYCAATRNPNFDRM-LGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLAR 238 (309)
Q Consensus 160 ~~~~~~~~~eL~WRef~~~~~~~~p~~~~~-~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R 238 (309)
..+.+.|++||+|||||+++++++|.+... ...+....++|+++++.|++|++|+||+||||||||||++|||||||+|
T Consensus 266 ~~~~~~fl~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~~w~~~~~~~~~W~~G~TG~P~vDA~mrqL~~tG~mhnr~R 345 (472)
T PRK10674 266 GGAGSVWLNELIWREFYRHLMVAYPSLCKHRPFIAWTDRVQWQSNPAHLQAWQQGKTGYPIVDAAMRQLNSTGWMHNRLR 345 (472)
T ss_pred cCchhHHHHHHHHHHHHHHHHHhCCchhhccCcchhhhccCcccCHHHHHHHHcCCCCCccHHHHHHHHHHHCCccHHHH
Confidence 234457999999999999999999987653 4445556788999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhccc-CCCCccccccChhhhhhhcCCCCCCC
Q psy4171 239 HAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCS-SFFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 239 ~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~-~~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
|+||||||| +|+||||.|++||+++|||||+|+|+|||||+||+ ++++||+|+|||++|++||||+|+||
T Consensus 346 m~vAsfL~k-~L~idWr~G~~~F~~~LlD~D~a~N~g~Wqw~ag~G~d~~py~R~fnP~~q~~k~Dp~g~yI 416 (472)
T PRK10674 346 MITASFLVK-DLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGERFDRDGEFI 416 (472)
T ss_pred HHHHHHHHc-CcccCCHhHHHHHHHHhhcCCcccchhccceeecCCCCCCcceeecCHHHHHHHhCCCCChH
Confidence 999999999 99999999999999999999999999999999974 57899999999999999999999997
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=4.1e-71 Score=508.51 Aligned_cols=212 Identities=39% Similarity=0.754 Sum_probs=184.9
Q ss_pred ccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhcc-CCCchhHHHHHH
Q psy4171 93 GGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKK-APPPLSLHGQLL 171 (309)
Q Consensus 93 gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~-~~~~~~~~~eL~ 171 (309)
|||++|+++|++|++++ +..|++.|+.|. .++||+|||||++||||||+|++++.+....... .++.++|++||+
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 89999999999999987 799999999985 6899999999999999999999999987761111 246789999999
Q ss_pred HHHHHHHHHHhCCccc-ccCCCCcCCCCCCC---CchHHHHHHhcCCCCcHHHHHHHHHHHHhcccchHHHHHHHHHHhh
Q psy4171 172 WREFFYCAATRNPNFD-RMLGNPICVQIPWD---VNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTR 247 (309)
Q Consensus 172 WRef~~~~~~~~p~~~-~~~~~~~~~~~~w~---~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~ 247 (309)
||||++++++++|++. ..++++.+..++|+ .+.+.|++|++|+||+||||||||||++|||||||+||+|||||||
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 9999999999999987 77889999999995 6778999999999999999999999999999999999999999999
Q ss_pred ccCCCCchHHHHHHHHhccccccCCcccchhhhcccC-CCCccccccChhhhhhhcCCCCCCC
Q psy4171 248 GDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS-FFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 248 ~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~~~-~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
+|+|||+.|++||+++|||||+|+|+|||||+||++ +.+||+|+|||++|++||||+|+||
T Consensus 157 -~l~i~W~~g~~~f~~~liD~d~a~n~~~wqw~ag~g~d~~~~~r~~np~~q~~~~Dp~g~~i 218 (277)
T PF03441_consen 157 -DLLIDWREGAEWFAEHLIDYDPASNYGNWQWAAGTGTDAKPYFRIFNPVKQSKKFDPDGEYI 218 (277)
T ss_dssp -TSHBHHHHHHHHHHHHHTT--HHHHHHHHHHHTTSSSTGCSTTTHHHHHHHHHHHSTTSHHH
T ss_pred -hccCCccccHHHHHHHhhccCcchHHHHHHHHHhhccccCccccccCchHHHHhhCcHHHHH
Confidence 999999999999999999999999999999999865 5689999999999999999999997
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=3.5e-67 Score=513.64 Aligned_cols=280 Identities=19% Similarity=0.192 Sum_probs=212.8
Q ss_pred CceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCCCCCCCCCCcccccccCCCCCCCCCccCCCCC-ccccC
Q psy4171 2 SSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPT-LEELG 80 (309)
Q Consensus 2 ~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~-l~~lg 80 (309)
+|.++++++++|++|+.+.++ .+|.+|+.|.+..+..+....+.+.+ ...+. +.... .....++. ++.++
T Consensus 141 ~i~~~~~~~~~l~p~~~~~~~---~~y~~ft~~~k~~~~~~~~~~~~~~~--~~~~~---~~~~~-~~~~~~~~~~~~~~ 211 (454)
T TIGR00591 141 DVPFQQVDAHNVVPCWAASKK---LEYAARTIRGKIRKLLPEYLTEFPRV--LKHPS---PLDLE-AGPVDWDAVRDSLA 211 (454)
T ss_pred CCcEEEECCceEeeCcccCCc---eeeeeecHHHHHHHhChhhccccCCC--ccCCc---ccccc-cCcCCHHHHHHhcc
Confidence 789999999999999998653 68899998887633321111100100 00000 00000 00000110 11121
Q ss_pred CCcCCCCCCCC-CccHHHHHHHHHHHHhhCccccccCCCCCCCCCCCCCCCCCchhhccCcCcHHHHHHHHHHHHHhhcc
Q psy4171 81 FDIEGLLPPTW-KGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKK 159 (309)
Q Consensus 81 ~~~~~~~~~~~-~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~~~~ 159 (309)
.... .....| +|||++|+++|++|++++ +.+|++.||.|. .++||+|||||++||||||+|++++.+.... .
T Consensus 212 ~~~~-~~~~~~~~gGe~aA~~~L~~F~~~~--l~~Y~~~Rn~p~--~~~tS~LSPyL~~G~IS~R~i~~~~~~~~~~--~ 284 (454)
T TIGR00591 212 VERS-VEEVVWAKPGTTAGLIMLESFIEKR--LCFFRTRRNDPN--NDALSMLSPWLHFGQLSAQRAARAVERARGN--A 284 (454)
T ss_pred CcCC-cCCcCCCCCcHHHHHHHHHHHHHHH--HHHHHHhcCCcc--cccccccchHHhcCcccHHHHHHHHHHhccC--C
Confidence 1111 112246 999999999999999876 799999999997 5899999999999999999999998653321 1
Q ss_pred CCCchhHHHHHHHH-HHHHHHHHhCCcccccCCCCcCCCCCCC--------Cch----HHHHHHhcCCCCcHHHHHHHHH
Q psy4171 160 APPPLSLHGQLLWR-EFFYCAATRNPNFDRMLGNPICVQIPWD--------VNM----EALAKWANAQTGFPWIDAIMTQ 226 (309)
Q Consensus 160 ~~~~~~~~~eL~WR-ef~~~~~~~~p~~~~~~~~~~~~~~~w~--------~~~----~~~~~w~~G~TG~p~vDA~mrq 226 (309)
..+.+.|++||+|| |||+++++++|++......+ .|. .+. +.|++|++|+||||+|||||||
T Consensus 285 ~~~~~~fl~EL~WR~ef~~~~~~~~p~~~~~~~~~-----~w~~~~l~~~~~d~r~~~~~~~~W~~G~Tg~pivdA~Mrq 359 (454)
T TIGR00591 285 GESVEFFEEELVVRRELADNFCFYNPYYDSLCGAY-----WWARTTLDDHAKDKREHLYSLEQLEKSTTHDYLWNAAQEQ 359 (454)
T ss_pred chHHHHHHHHHHHHHHHHhHhhhcCCCccccccch-----HHHHHHHHHHhcCCccccCCHHHHHhcCcCcHhHhHHHHH
Confidence 23457899999999 89999999999987533222 254 333 3799999999999999999999
Q ss_pred HHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHH--------hccccccCCcccchhhhcccCCCCcc-----c---
Q psy4171 227 LREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDE--------LLLDADWSVNAGMWMWLSCSSFFQQF-----F--- 290 (309)
Q Consensus 227 L~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~--------~liD~d~a~n~g~wqw~a~~~~~~~~-----~--- 290 (309)
|++|||||||+||+|| | +| |||+.|++||++ +|||||+|+|+|||||+++|.+++|| |
T Consensus 360 L~~TG~MHNr~RMi~a----K-~l-i~W~~g~~~f~~~~~~ln~~~lvDgd~a~n~~~wqW~~~G~d~~p~~~~~~fg~i 433 (454)
T TIGR00591 360 LVTEGKMHGFLRMYWA----K-KI-LEWTHSPEEALSIAIYLNDKYILDGRDPNGYVGCMWSICGIHDQGWAERIVFGKI 433 (454)
T ss_pred HHHhCccccceeeeee----e-eh-hhcCCCHHHHHHHHHHhhhhhhccCCCCCccceeeeEeccccCCCCCCCccceee
Confidence 9999999999999999 8 88 999999999999 89999999999999999557889999 9
Q ss_pred cccChhhhhhhcCCCCCCC
Q psy4171 291 HCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 291 r~~np~~q~~~~Dp~g~yi 309 (309)
|+|||++|++||||+| ||
T Consensus 434 R~~np~~q~~kfd~~~-yi 451 (454)
T TIGR00591 434 RYMNYAGCRRKFNVAY-FE 451 (454)
T ss_pred eecChhhhhccCCHHH-HH
Confidence 9999999999999999 97
No 8
>KOG0133|consensus
Probab=100.00 E-value=4.6e-58 Score=443.93 Aligned_cols=308 Identities=46% Similarity=0.797 Sum_probs=255.2
Q ss_pred CCceEEEecCCcccCCCccccccCccccccccccHHhHHhCCCCCCCCCCCCcccccccCCCCCCCCCccCCCCCccccC
Q psy4171 1 MSSSIEKKLTLSLPSSRRIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELG 80 (309)
Q Consensus 1 ~~~~~~~~~~~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~iP~l~~lg 80 (309)
+||++++...|+||+|+.++.+|++.+|.+|+.|+.....+..+..|.-......++ ..............+|+++.++
T Consensus 122 l~i~v~s~~s~~~~~~~~~i~~n~~k~pls~~~~~~~~~~~~~~~~p~~v~~~~~~~-~~~~~~~~~~~~~~v~~~e~l~ 200 (531)
T KOG0133|consen 122 LGLSVVSPVSHTLYLPDKIIEANGGKPPLSYKTFRGVCQSMSAPKIPALVLSGLAVE-KHPNFLANSKASAVVPTLELLR 200 (531)
T ss_pred hhhhhcccCchhhhcHHHHHHhcCCCCccccccccccccccccccccccccccccCC-CChhhhhhcccccccCCchhhc
Confidence 589999999999999999999999999999999999887775553331110000111 1011111123345688999888
Q ss_pred CCcCCCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCCCC-CCCCCCCchhhccCcCcHHHHHH--HHHHHHHhh
Q psy4171 81 FDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSL-LASQTGLSPFLRFGCLSTRLFYH--DLNKLYKRI 157 (309)
Q Consensus 81 ~~~~~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~~~-~~~tS~LSpyL~~G~iS~r~v~~--~~~~~~~~~ 157 (309)
+.........|+||++.|+.+|+.|+....+..++......++.. ..+++.|||||+|||||+|.+++ .+.+...+.
T Consensus 201 ~~~~~~~~~~~~~g~s~al~~l~~~l~~~~~~an~~~~~~~~~~~~~~s~~~Ls~yL~fg~~svr~~~~~~~~k~V~~~~ 280 (531)
T KOG0133|consen 201 FIPSNYGEVVWRGGESEALKRLDAHLKVPLWVANLELRYSNANSRVKISTTVLSPYLKFGCLSVRYFYRCVRLKQVKWKA 280 (531)
T ss_pred cCcccccccccCCcccchhHHHHHHhhHHHHHhhhhccccccchhcCCCccccccceeeccceeEeehhHhHHHHHHHhh
Confidence 876554445599999999999999998876667777666555532 36677999999999999999995 333443333
Q ss_pred cc-CCCchh-HHHHHHHHHHHHHHHHhCCcccccCCCCcCCCCCCCCchHHHHHHhcCCCCcHHHHHHHHHHHHhcccch
Q psy4171 158 KK-APPPLS-LHGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHH 235 (309)
Q Consensus 158 ~~-~~~~~~-~~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG~p~vDA~mrqL~~tG~mhn 235 (309)
.. +.+.+. ++.||.|||||++....+|.++.+.++..+.+|+|+.|+..+++|.+|+||||+|||+||||+++|||||
T Consensus 281 ~~~s~~~es~~~~qv~Wre~~y~~~~n~p~~~~m~~n~~~~~ipw~~n~~~~~aw~~G~tG~P~ida~m~~l~~~gw~h~ 360 (531)
T KOG0133|consen 281 KKNSLPPESLFLGQVAWREFFYTAAFNTPYFDDMPGNKILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQLLASGWEHH 360 (531)
T ss_pred hcccCCccccccceeeeechhhHhhcCCccccccccccccccCCcccChhhhHHHHcCCCCCCchhHHHHHHHHHHHHhc
Confidence 22 344554 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhc-ccCCCCccccccChhhhhhhcCCCCCCC
Q psy4171 236 LARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLS-CSSFFQQFFHCYCPVKFGRKADPNGDFI 309 (309)
Q Consensus 236 r~R~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a-~~~~~~~~~r~~np~~q~~~~Dp~g~yi 309 (309)
+.|++||||++||+|+|+|++|.++|+++|+|+|+..|.|||||.+ ++.+.++|+|||||+.+++++||+|.||
T Consensus 361 ~~R~~vasf~tr~~L~i~w~eg~~~F~~~llD~D~~~~agnW~~~S~~s~f~~~~~~~ysp~~~~kk~dP~g~yi 435 (531)
T KOG0133|consen 361 RSRTIVASFLTRGDLLISWREGLDVFMEYLLDADSSKNAGNWMWLSSTSHFFDQFDRVYSPVALGKKLDPDGLYI 435 (531)
T ss_pred ccchhhHhHhhccceeeeHHHHHHHHHHHhcchhhhcCCCccceeccccccccccccccCHHHHhCcCCcchhhH
Confidence 9999999999999999999999999999999999999999999998 6678899999999999999999999997
No 9
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=99.96 E-value=6.9e-29 Score=230.22 Aligned_cols=293 Identities=18% Similarity=0.171 Sum_probs=208.4
Q ss_pred CCceEEEecC-CcccCCCccccccCccccccccccHHhHHhC-------CCCCC---CCCCCCccccccc---CCCCCCC
Q psy4171 1 MSSSIEKKLT-LSLPSSRRIIEKNGGKTPLTYHQFQSIVAKM-------DSPSP---AEAPVTPLLVRQA---TTPLRDD 66 (309)
Q Consensus 1 ~~~~~~~~~~-~~L~~p~~i~~~~~g~~p~~fs~F~~~~~~~-------~~p~~---p~~~~~~~~~~~~---~~~~~~~ 66 (309)
+||++....+ |.|..+.++..--++..+.....|++.-++. +.|.- -......+.+++. +.|...
T Consensus 116 ~g~~i~~~~~~~Fl~s~a~f~~w~~~~k~~lme~FYr~mRkr~g~LM~~dqP~GGrWnFDaeNR~~~~pdL~~P~pl~f- 194 (505)
T COG3046 116 LGIEITEVENPHFLCSRAEFDAWAGDRKPLLMESFYRRMRKRTGILMEDDQPEGGRWNFDAENRKKLPPDLLPPKPLKF- 194 (505)
T ss_pred cCceeEEecCcceecCHHHhhhhhccCcchhhHHHHHHHHHhhceeccCCCCCCCcCCcCcccccCCCCcCCCCCCCCC-
Confidence 4777777665 5899999986655566677777887644431 11110 0000000001100 001110
Q ss_pred CCccCCCCCcc---ccCCCc--CCCCCCCCCccHHHHHHHHHHHHhhCccccccCCCCCCCC--CCCCCCCCCchhhccC
Q psy4171 67 HDEKYGVPTLE---ELGFDI--EGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQ--SLLASQTGLSPFLRFG 139 (309)
Q Consensus 67 ~~~~~~iP~l~---~lg~~~--~~~~~~~~~gGe~~A~~~L~~fl~~~~~l~~Y~~~r~~~~--~~~~~tS~LSpyL~~G 139 (309)
.....+++.. +-.|++ .....+.||..+++|+..|++|++.+ |.+|+...|... .....+|.|||+|+.|
T Consensus 195 -ppd~~vq~v~e~Ve~~f~~~~G~~e~F~wpvtr~~A~~~L~~Fi~~~--L~nFG~yQDam~~d~~~L~HSllS~alNig 271 (505)
T COG3046 195 -PPDEIVQEVKERVERLFPDNFGQVEGFGWPVTRTQALRALKHFIADR--LPNFGSYQDAMSADDPHLWHSLLSFALNIG 271 (505)
T ss_pred -CCcchhHHHHHHHHhhCCCCCCccccCCCCCCHHHHHHHHHHHHHHh--hhcCCcHHHHHhcCCchhHHHHHHHHhhcc
Confidence 0000011110 011221 11234679999999999999999988 788888776543 1235799999999999
Q ss_pred cCcHHHHHHHHHHHHHhhcc-CCCchhHHHH-HHHHHHHHHHHHh-CCcccccCCCCcCCCCCCCCchHHHHHHhcCCCC
Q psy4171 140 CLSTRLFYHDLNKLYKRIKK-APPPLSLHGQ-LLWREFFYCAATR-NPNFDRMLGNPICVQIPWDVNMEALAKWANAQTG 216 (309)
Q Consensus 140 ~iS~r~v~~~~~~~~~~~~~-~~~~~~~~~e-L~WRef~~~~~~~-~p~~~~~~~~~~~~~~~w~~~~~~~~~w~~G~TG 216 (309)
.|+|++|++++.+++...+. -.++|.|++| |+||||.+.+++. .|.|.+.|.. .++..+....++|+|+
T Consensus 272 LL~PleVi~Aa~~Ay~~g~ipLN~VEGFvRQiiGWREfmRgiY~~~~P~y~trN~f--------~~d~~Lp~~yw~g~T~ 343 (505)
T COG3046 272 LLTPLEVIRAALKAYREGDIPLNSVEGFVRQIIGWREFMRGIYWLKMPDYATRNFF--------NADRKLPPFYWTGQTK 343 (505)
T ss_pred CCCHHHHHHHHHHhhccCCCchHHHHHHHHHHhhHHHHHHHhhhhcCCchhhhhhh--------ccCCCCCCccccCCcC
Confidence 99999999999988866333 4578999999 7899999999976 5888876663 3444455677899999
Q ss_pred cHHHHHHHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHHhccc-ccc---CCcccchhhhcccCC-CCcc--
Q psy4171 217 FPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLD-ADW---SVNAGMWMWLSCSSF-FQQF-- 289 (309)
Q Consensus 217 ~p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~~liD-~d~---a~n~g~wqw~a~~~~-~~~~-- 289 (309)
+-|++-++.|-..+||.||+.|.||-+.|.- .+++|.....+||++.+|| ||| ++..|+-|++.||-. .+||
T Consensus 344 M~cl~~av~~v~d~gYAHHIqRLMV~gNfAL-l~G~dPd~v~~Wf~~~fiDAYdWV~~PNv~GM~qFADGG~iatKPYas 422 (505)
T COG3046 344 MACLAIAVGRVLDHGYAHHIQRLMVTGNFAL-LLGVDPDAVDRWFMEVFIDAYDWVELPNVRGMSQFADGGLIATKPYAS 422 (505)
T ss_pred chHHHHHHHHHhhhhHHHHHHHHHHHhhHHH-HhCCCHHHHHHHHHHHHhhHhhheecccccchhhcccCceeecCcccc
Confidence 9999999999999999999999888777777 8999999999999999999 687 577899999988743 4554
Q ss_pred ----ccccChhhhhhhcCCCC
Q psy4171 290 ----FHCYCPVKFGRKADPNG 306 (309)
Q Consensus 290 ----~r~~np~~q~~~~Dp~g 306 (309)
+-.|+-..+...|||+-
T Consensus 423 S~nYInkMSDyC~~C~yd~k~ 443 (505)
T COG3046 423 SGNYINKMSDYCSDCAYDPKS 443 (505)
T ss_pred chhHHHHHhHhhhhcccChhh
Confidence 67788889999999973
No 10
>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=41.65 E-value=26 Score=31.92 Aligned_cols=47 Identities=21% Similarity=0.412 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHHhcc
Q psy4171 218 PWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLL 266 (309)
Q Consensus 218 p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~~li 266 (309)
||+=+.+..|+..+=+.|..|+.+++||. .++++-.+...+|...+.
T Consensus 110 pCMr~l~~~L~~~~hL~h~~R~ql~lFLk--~iGl~~ee~l~f~~~~f~ 156 (260)
T PF04104_consen 110 PCMRNLHERLRKGHHLKHSGRFQLGLFLK--GIGLSLEEALEFWRSEFS 156 (260)
T ss_dssp HHHHHHHHHHHHHS---HHHHHHHHHHHH--HTTEECCCHHHCCHHHCC
T ss_pred hHHHHHHHHHhhCCCCCchhHhhHHHHHH--hcCCCHHHHHHHHHHHhc
Confidence 67888888889999999999999999997 599997777776666543
No 11
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=37.23 E-value=54 Score=31.57 Aligned_cols=62 Identities=23% Similarity=0.223 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHHhccccccCCcccchhhhcc
Q psy4171 218 PWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSC 282 (309)
Q Consensus 218 p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~~liD~d~a~n~g~wqw~a~ 282 (309)
|||=..|+.|..-.-+.|..|..++|||.+ .+++-.+..+ |.+..-|+|--+.....++.+|
T Consensus 243 PCik~iL~~l~~G~~l~h~~R~al~sFL~~--ig~~~deiv~-~fr~~pdFdee~tryqirHi~G 304 (363)
T COG2219 243 PCIKNILAGLKSGENLPHAARFALTSFLSN--IGLSVDEIVE-LFRNSPDFDEEITRYQIRHIIG 304 (363)
T ss_pred hHHHHHHHHhhcCCCchHHHHHHHHHHHHh--cCCChhHHHH-HhccCCCcchhhhhhhhheeec
Confidence 899999999999999999999999999985 8999888888 4455667777776666666665
No 12
>PRK02249 DNA primase large subunit; Validated
Probab=36.47 E-value=70 Score=30.56 Aligned_cols=44 Identities=27% Similarity=0.484 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHH
Q psy4171 218 PWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDE 263 (309)
Q Consensus 218 p~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~ 263 (309)
||+=+.+..|.+.+-+.|..|+.+++||.. .+++..+-...|..
T Consensus 224 pCm~~l~~~l~~g~~L~h~~R~~l~~FL~~--iG~~~deil~~~~~ 267 (343)
T PRK02249 224 PCMKALLSALQAGENLPHTARFAITSFLLN--IGMSVDEIVELFRN 267 (343)
T ss_pred HHHHHHHHHHHcCCCCChHHHHHHHHHHHh--cCCCHHHHHHHHhh
Confidence 677777788899999999999999999984 99999999888754
No 13
>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=28.78 E-value=49 Score=21.35 Aligned_cols=37 Identities=22% Similarity=0.214 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHH
Q psy4171 219 WIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIF 261 (309)
Q Consensus 219 ~vDA~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f 261 (309)
+++||.+.+.+.||=.-.+|.+. + .++++-.--..+|
T Consensus 1 Il~aa~~l~~~~G~~~~s~~~Ia-----~-~~gvs~~~~y~~f 37 (47)
T PF00440_consen 1 ILEAALELFAEKGYEAVSIRDIA-----R-RAGVSKGSFYRYF 37 (47)
T ss_dssp HHHHHHHHHHHHHTTTSSHHHHH-----H-HHTSCHHHHHHHC
T ss_pred CHHHHHHHHHHhCHHhCCHHHHH-----H-HHccchhhHHHHc
Confidence 68999999999999999999874 3 5666666555555
No 14
>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=26.93 E-value=53 Score=23.97 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=21.0
Q ss_pred HHhcccchHHHHHHHHHHhhccCCCC
Q psy4171 228 REEGWIHHLARHAVACFLTRGDLWVS 253 (309)
Q Consensus 228 ~~tG~mhnr~R~~vasfl~~~~l~id 253 (309)
..|||..|-+|-.++.-|-| .|+++
T Consensus 32 ~atGWq~HTvRgalsg~~kK-klGl~ 56 (72)
T PF11994_consen 32 EATGWQPHTVRGALSGLLKK-KLGLT 56 (72)
T ss_pred HhhCCchhhHHHHHHHHHHH-hcCcE
Confidence 46899999999999988877 77664
No 15
>PRK09568 DNA primase large subunit; Reviewed
Probab=26.79 E-value=93 Score=29.23 Aligned_cols=45 Identities=4% Similarity=0.012 Sum_probs=34.4
Q ss_pred HHHHHHHhcccchHHHHHHHHHHhhccCCCCchHHHHHHHHhcccccc
Q psy4171 223 IMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADW 270 (309)
Q Consensus 223 ~mrqL~~tG~mhnr~R~~vasfl~~~~l~idW~~g~~~f~~~liD~d~ 270 (309)
||+.|...-=++|-.|-++|+||.+ .|.+=..-.+.|...= |.+.
T Consensus 218 Cik~li~g~nL~H~~RFaLasFL~n--iG~~vd~Iv~lf~~~p-de~~ 262 (306)
T PRK09568 218 CIENILGKEELSEEEIRTLITYYIN--IGKGLDSIIAIMNVTN-IEDL 262 (306)
T ss_pred hHHHHhcCCCCChHHHHHHHHHHHH--cCCCHHHHHHHHhcCC-cHHH
Confidence 4555666667999999999999996 8999888888885332 4443
No 16
>PF05268 GP38: Phage tail fibre adhesin Gp38; InterPro: IPR007932 This entry is represented by Bacteriophage T2, Gp38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, Gp57, catalyses the organisation of Gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition [].
Probab=21.79 E-value=43 Score=29.82 Aligned_cols=25 Identities=36% Similarity=0.700 Sum_probs=20.3
Q ss_pred CCCCcHHHHHHHHHHHHh--cccchHH
Q psy4171 213 AQTGFPWIDAIMTQLREE--GWIHHLA 237 (309)
Q Consensus 213 G~TG~p~vDA~mrqL~~t--G~mhnr~ 237 (309)
-+||-.+++|||++|+-- +||++.+
T Consensus 16 ~eTGqrwM~aA~~~lrl~~P~wMsqm~ 42 (260)
T PF05268_consen 16 NETGQRWMSAAMRALRLGVPFWMSQMA 42 (260)
T ss_pred hhccchhHHHHHhhhccCCchHHHHhh
Confidence 479999999999999864 7776544
No 17
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=21.43 E-value=41 Score=34.19 Aligned_cols=37 Identities=24% Similarity=0.184 Sum_probs=26.0
Q ss_pred cccccCCcccchhhhcccCCCCccccccChhhhhhhcCCCCCC
Q psy4171 266 LDADWSVNAGMWMWLSCSSFFQQFFHCYCPVKFGRKADPNGDF 308 (309)
Q Consensus 266 iD~d~a~n~g~wqw~a~~~~~~~~~r~~np~~q~~~~Dp~g~y 308 (309)
.|.|.++||||..-+.|--....| -.||.+||++|..
T Consensus 476 ~ea~~a~NYGgIGaVIgHEI~HgF------DdqGakfD~~GnL 512 (654)
T COG3590 476 PEADSAANYGGIGAVIGHEIGHGF------DDQGAKFDGDGNL 512 (654)
T ss_pred CCcchhhcccCccceehhhhcccc------cCCccccCCCCcH
Confidence 468899999999866542222322 2589999999974
Done!