Query 012907
Match_columns 453
No_of_seqs 160 out of 346
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 07:33:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012907hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2267 Eukaryotic-type DNA pr 100.0 5E-133 1E-137 994.8 34.4 430 14-449 23-462 (475)
2 cd07322 PriL_PriS_Eukaryotic E 100.0 2E-121 3E-126 944.4 38.2 388 23-441 1-390 (390)
3 PF04104 DNA_primase_lrg: Euka 100.0 5.9E-80 1.3E-84 607.4 9.4 256 172-438 1-260 (260)
4 PRK02249 DNA primase large sub 100.0 3.3E-54 7.1E-59 437.1 19.0 231 83-365 61-303 (343)
5 COG2219 PRI2 Eukaryotic-type D 100.0 5.7E-47 1.2E-51 387.2 18.9 354 19-449 3-359 (363)
6 PRK09568 DNA primase large sub 100.0 2.4E-28 5.1E-33 244.0 16.2 213 86-365 61-285 (306)
7 cd06560 PriL Archaeal/eukaryot 99.8 2E-20 4.4E-25 172.4 11.1 121 83-221 35-165 (166)
8 PRK03968 DNA primase large sub 99.5 1.2E-12 2.6E-17 132.2 17.5 259 88-367 66-368 (399)
9 PF10281 Ish1: Putative stress 79.9 2.9 6.2E-05 29.3 3.6 32 377-408 1-36 (38)
10 PRK02249 DNA primase large sub 40.7 43 0.00093 34.9 4.9 82 357-444 223-329 (343)
11 COG1851 Uncharacterized conser 40.4 25 0.00054 33.5 2.8 62 238-305 130-191 (229)
12 PF09278 MerR-DNA-bind: MerR, 39.5 28 0.00061 26.5 2.6 23 298-320 2-24 (65)
13 PRK00117 recX recombination re 38.5 31 0.00066 31.3 3.1 37 375-411 21-57 (157)
14 PRK14136 recX recombination re 36.8 33 0.00072 35.2 3.3 46 375-420 172-219 (309)
15 COG2137 OraA Uncharacterized p 35.3 51 0.0011 31.1 4.0 43 381-423 86-129 (174)
16 TIGR03556 photolyase_8HDF deox 31.7 1.1E+02 0.0023 33.2 6.3 48 276-324 328-376 (471)
17 PRK14137 recX recombination re 30.9 47 0.001 31.8 3.1 43 378-420 53-97 (195)
18 PHA02046 hypothetical protein 28.7 2.7E+02 0.0058 23.8 6.7 32 127-158 41-72 (99)
19 PF13645 YkuD_2: L,D-transpept 27.2 89 0.0019 29.6 4.2 60 331-410 99-171 (176)
20 PF03441 FAD_binding_7: FAD bi 25.0 39 0.00085 33.8 1.5 72 276-357 125-198 (277)
21 PF12672 DUF3793: Protein of u 23.2 95 0.0021 29.2 3.6 38 277-322 89-126 (176)
22 cd07178 terB_like_YebE telluri 23.0 1.7E+02 0.0036 24.6 4.8 50 281-331 3-52 (95)
23 KOG3347 Predicted nucleotide k 22.2 98 0.0021 29.0 3.4 51 369-419 79-140 (176)
24 cd04777 HTH_MerR-like_sg1 Heli 21.8 91 0.002 26.4 3.0 24 298-321 43-66 (107)
No 1
>KOG2267 consensus Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
Probab=100.00 E-value=4.5e-133 Score=994.76 Aligned_cols=430 Identities=40% Similarity=0.756 Sum_probs=402.1
Q ss_pred CCCCCcccCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCC------Cccchhhhh
Q 012907 14 PNDSVSTLPLYRYAPQLEVRLEDFEVFAMDRLRVLKGISDALARGKRPEEMENLVRDLWKANMRH------PEASEDVNK 87 (453)
Q Consensus 14 ~~~~~~~l~fY~~pP~~~i~leefe~~a~dRLkvL~~ie~~~~~~~~~~e~~~~i~~~~~~~~~~------~~~~~~~~k 87 (453)
...+|+.|+||..||.++|||+|||.||||||++|+.||++.++++..+|+++.|++.+.|.+.- ....+.+++
T Consensus 23 ~~~yp~~L~fY~~pp~~~IsleeFe~~AidRlklL~~~E~~~s~~k~~de~~~ii~k~ldk~l~f~~~~k~e~~ye~rrr 102 (475)
T KOG2267|consen 23 KESYPPGLQFYTAPPKSEISLEEFEKWAIDRLKLLKSIENKDSRNKYNDEFKGIIKKCLDKLLPFSDQKKQESLYESRRR 102 (475)
T ss_pred hccCCcceeeeccCCCCcccHHHHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHHHhhcCCcchhhhhhhhhhHhh
Confidence 55679999999999999999999999999999999999999999999999999999999877622 224588999
Q ss_pred hhHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCCCC
Q 012907 88 DIISHFVLRLVYCRTEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVARSFDQPLP 167 (453)
Q Consensus 88 D~iSHfiLRLa~c~s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~~~~~~~~ 167 (453)
|||||||||||||||+|+|.||+++|+.|||+||..+....+..||++.++.|+.|+.+|++.+.+.|.+.+... ..
T Consensus 103 D~~sHFilRLafcrs~elr~wfv~aE~~llRfRf~~~~~~~~~~fl~~v~~~~e~is~eEk~~~~e~l~As~q~~---l~ 179 (475)
T KOG2267|consen 103 DHISHFILRLAFCRSAELRVWFVQAEVDLLRFRFSKEPGGARQFFLSSVDFQMEGISTEEKQVLYEGLRASSQRN---LV 179 (475)
T ss_pred hhHHHHHhhhhhcCCHHHHHHHHHhhhhheeeEeecCcchHHHHHHHhhhHHHhhccchhhHHHHHHHHHhhccC---cc
Confidence 999999999999999999999999999999999999999999999999999999999999999999988764321 22
Q ss_pred CCCCceEeecccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhchHHHHHHHH
Q 012907 168 TADAIFYKVPFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALS 247 (453)
Q Consensus 168 ~~~~~~~kVpF~~v~~LV~~R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~~i~~de~~RL~p~l~~L~ 247 (453)
+..+.||||||++|++||++|.|+|++||||||.+++++||+++|+++|+++|+.+++.+|. +.+| +||.|+|++|+
T Consensus 180 ~~~esf~kvpF~~vidLi~~r~V~l~~Gyay~p~~~~vsllv~Ef~~~L~~al~~t~k~Lp~-leeD--eRLlpllnhLs 256 (475)
T KOG2267|consen 180 SANESFYKVPFTKVIDLIGRRAVFLEKGYAYLPFEDIVSLLVNEFRRNLSKALAETAKSLPR-LEED--ERLLPLLNHLS 256 (475)
T ss_pred cccceeEeechhhHHHHHhcceeeeeCCeEeccHHHHHHHHHHHHHHHHHHHHHHHHhhccc-CCcc--chHHHHHHHhh
Confidence 56789999999999999999999999999999999999999999999999999999999997 5544 59999999999
Q ss_pred hhhcCCCCCC-ccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhcc
Q 012907 248 MSYLGPDYSQ-TKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQ 326 (453)
Q Consensus 248 ~~~~~~~~~~-~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~~F~k 326 (453)
..|.|.||+. +.+.+.|++..|+.++..+|||||++||+.||+||||+|+||+||||||||||||+||||+|||.+|||
T Consensus 257 ~~ytg~d~~~~q~~~~~i~~~~v~sls~r~FppCmk~lhe~LrkNhHLry~gR~qygLFLKgiGLS~deal~fwr~sFtk 336 (475)
T KOG2267|consen 257 AGYTGYDYNGEQPDGGNIVARSVDSLSERSFPPCMKQLHERLRKNHHLRYGGRQQYGLFLKGIGLSVDEALAFWRGSFTK 336 (475)
T ss_pred cCCccccccCcCCCCCeeehhhHhhhhhhcCcHHHHHHHHHHhhcccccccchhhhhhhhhccCcCHHHHHHHHHHHHhc
Confidence 9999999984 447789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCccccccccceeeeeeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHH
Q 012907 327 KVGAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDK 405 (453)
Q Consensus 327 ~~~~~~F~Key~YnIrH~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~ 405 (453)
+|+.|+|||||+|||||+||+||+|+||+|+||.||++. +||+||+|||||||+|++.|++.|+++||+.++|..|+++
T Consensus 337 ~~t~dkFdKEY~YnIRh~YGlEGkR~nyt~~sC~~Ii~~~~p~~gd~hgCPFr~~~~e~L~qkL~s~~i~~~~I~~i~e~ 416 (475)
T KOG2267|consen 337 KMTRDKFDKEYRYNIRHNYGLEGKRANYTPFSCSKIILMNPPSEGDYHGCPFRHSDPEHLKQKLKSMGIDIEQIMGILEL 416 (475)
T ss_pred cCChhHhchhhceeheeccccccccccCCcccHHHHhcCCCCCCCccCCCCCCCCCHHHHHHHHHhcccCHHHHHHHHHh
Confidence 999999999999999999999999999999999999999 8899999999999999999999999999999999999999
Q ss_pred hhccchHHHHHHHHHHHcCCCC--CCcccCchHHHHHHHcccCccC
Q 012907 406 VRNRHYQLACTLTFEAVHSSSC--DAGINHPNQYFSDSHKILQPKN 449 (453)
Q Consensus 406 ~~~~~yq~AC~~~Fe~~h~~~~--~~~i~HPN~Yf~~S~~~~~~~~ 449 (453)
++.+||++|||||||.||+... +.+|+||||||++|+.....+.
T Consensus 417 ~~~~~Y~iaCTr~fE~~hn~~~~~g~~i~hPnqyf~esqq~e~~~~ 462 (475)
T KOG2267|consen 417 VKLNHYDIACTRYFEMTHNRKQSIGESIAHPNQYFEESQQPERNQQ 462 (475)
T ss_pred hcccchhHHHHHHHHHHhcchhccchhccChHHHHHHhcccccccC
Confidence 9999999999999999998754 4789999999999987766554
No 2
>cd07322 PriL_PriS_Eukaryotic Eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of
Probab=100.00 E-value=1.6e-121 Score=944.42 Aligned_cols=388 Identities=52% Similarity=0.938 Sum_probs=364.2
Q ss_pred CCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCCCccchhhhhhhHHHHHHHHHhcCC
Q 012907 23 LYRYAPQLEVRLEDFEVFAMDRLRVLKGISDALARGKRPEEMENLVRDLWKANMRHPEASEDVNKDIISHFVLRLVYCRT 102 (453)
Q Consensus 23 fY~~pP~~~i~leefe~~a~dRLkvL~~ie~~~~~~~~~~e~~~~i~~~~~~~~~~~~~~~~~~kD~iSHfiLRLa~c~s 102 (453)
||..||.++|||+|||+||+|||+||++||++ .++++||++||||||||||+|
T Consensus 1 ~Y~~pP~~~isl~efe~~a~dRlkvL~~ie~~---------------------------~~~~~kD~lSHfiLRLa~c~s 53 (390)
T cd07322 1 FYDTPPTGNISLEEFEEIAIDRLKLLREIEQL---------------------------EEERRKDHISHFILRLAYCRS 53 (390)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhh---------------------------hhhhhhhHHHHHHHHHHHhCC
Confidence 89999999999999999999999999999987 277999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCCCCCCCCceEeecccchH
Q 012907 103 EDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVARSFDQPLPTADAIFYKVPFEEVP 182 (453)
Q Consensus 103 ~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~~~~~~~~~~~~~~~kVpF~~v~ 182 (453)
+++|+||+++|++||++||+.++.+++..|++++|++|++|+++|+..+.++|...... .....+..++||+|||++|+
T Consensus 54 eelr~wFv~~E~~Lfr~Rl~~~~~~~~~~fl~~~~l~~~~i~~~e~~~~~~~l~~~~~~-~~~~~~~~~~~~kVpF~~v~ 132 (390)
T cd07322 54 EELRRWFVRQETELFRYRLELLSLEGLKQFLKSNGLDYQPVSDEEKEELREELLKSASS-LKQIKIEATNFYKVPFEEVL 132 (390)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHcCCCccccCHHHHHHHHHHHHHhhcc-ccccccccCCEEEeehhhhH
Confidence 99999999999999999999999999999999999999999999999999999754322 23344567889999999999
Q ss_pred hhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhchHHHHHHHHhhhcCCCCCCccccc
Q 012907 183 ELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALSMSYLGPDYSQTKEFG 262 (453)
Q Consensus 183 ~LV~~R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~~i~~de~~RL~p~l~~L~~~~~~~~~~~~~~~~ 262 (453)
+||.+|+|+|++|+||||.+++.+||+++|+.+|+++|+.+.+.++. +. +++||.|+|++|++.|.+.+|+...+.+
T Consensus 133 ~Lv~~R~V~L~~G~ayVp~~el~~ll~~~Fr~~L~~~L~~~~~~l~~-l~--~ddRL~p~l~~L~~~~~~~~~~~~~~~~ 209 (390)
T cd07322 133 DLVRKRRVFLKKGFAYVPQDELVSLVLSKFRSRLSKALALTARSLPR-LE--EDDRLLPLLKSLSKSYTGKDYSKNGNGG 209 (390)
T ss_pred HHHhcCeEEEeCcEEEEcHHHHHHHHHHHHHHHHHHHHHHHHhhccc-cC--cchhHHHHHHHHHHhhcccccccccccc
Confidence 99999999999999999999999999999999999999988777665 33 4469999999999999999887665667
Q ss_pred cccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhccccCccccccccceeee
Q 012907 263 EISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAERFDKEYAYSIR 342 (453)
Q Consensus 263 ~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~~F~k~~~~~~F~Key~YnIr 342 (453)
.+++.+++.+++++|||||++||+.|+++|||||+||||||||||||||++||+|.||+++|+++|++|+|+|+|+||||
T Consensus 210 ~l~~~~i~~l~~~~fP~Cm~~l~~~l~~~~hL~h~gR~ql~lFLk~iGl~~~e~l~~~~~~ftk~~~~~~f~k~~~Y~ir 289 (390)
T cd07322 210 GLTLSSIDELSKKSFPLCMRQLHEALRKNHHLKHGGRLQLGLFLKGIGLSLEEALKFWRSEFTKKMDADKFDKEYAYNIR 289 (390)
T ss_pred cccccchhhhhhhcCCHHHHHHHHHHhcCCCCCchhHHHHHHHHHhCCCCHHHHHHHHHHhhcccCCcchhhhhhHhhhh
Confidence 78889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccchHHHHHHHHHH
Q 012907 343 HNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHYQLACTLTFEA 421 (453)
Q Consensus 343 H~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~yq~AC~~~Fe~ 421 (453)
|+||+||+|++|+||||+||++. +||+||+|||||||||.++|+++|+++|++.+++++|+++++++|||+|||+|||.
T Consensus 290 H~yG~eG~~~~Y~p~sC~~i~~~~~p~~g~~HGCPfr~~~~~~L~~~L~~~~~~~~~i~~I~~~~~~~~yq~AC~~~Fe~ 369 (390)
T cd07322 290 HNYGKEGKRANYTPYSCSKIISQNPPGPGDCHGCPFRHFDSDSLKQLLQSYGLSDSDIEEIIDLVKSGHYQLACTKYFEL 369 (390)
T ss_pred hhccccCCCCCCCCCCHHHHHcCCCCCCCCcCCCCCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHhcCCccHHHHHHHHH
Confidence 99999999999999999999999 69999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCC-CCcccCchHHHHHH
Q 012907 422 VHSSSC-DAGINHPNQYFSDS 441 (453)
Q Consensus 422 ~h~~~~-~~~i~HPN~Yf~~S 441 (453)
||+... +.+|+||||||++|
T Consensus 370 ~h~~~~~~~~i~HPN~Yf~~S 390 (390)
T cd07322 370 THPGAESDTGINHPNQYFEES 390 (390)
T ss_pred HcCCCCCCCcccChHHHHhcC
Confidence 997654 78899999999987
No 3
>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=100.00 E-value=5.9e-80 Score=607.44 Aligned_cols=256 Identities=53% Similarity=0.958 Sum_probs=198.9
Q ss_pred ceEeecccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhh---hhhhhhhhchHHHHHHHHh
Q 012907 172 IFYKVPFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTS---TIREQERDRLTPIVEALSM 248 (453)
Q Consensus 172 ~~~kVpF~~v~~LV~~R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~---~i~~de~~RL~p~l~~L~~ 248 (453)
.||+|||+++++||++|+|+|++|+||||.+++.+||+++|+++|.++|+.+....+. .+.+|+.++|.++++.|++
T Consensus 1 ~~y~Vpf~~~~~lv~~r~v~l~~G~a~v~~~~l~~ll~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~r~~l~~~l~~l~~ 80 (260)
T PF04104_consen 1 TFYKVPFEDYLDLVRRRNVFLKNGYAYVPREELSSLLEEAFRSRLEEGLPSLKKALPRLPEEIEEDERPELSPILRELSN 80 (260)
T ss_dssp -EEEEEHHHHHHHTTTCCSEECTTEEEE-HHHHHHHHHHHHHHHHHHHCCCCHCCGGGS-HHHHCHHHHHHHHHHHHHH-
T ss_pred CeEEEeHHHHHHHHhcCcEEEECCEEEECHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccchhHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999999999999999999999865554443 1345553349999999999
Q ss_pred hhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhcccc
Q 012907 249 SYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKV 328 (453)
Q Consensus 249 ~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~~F~k~~ 328 (453)
.|++.+.+. ...+.+++.+++.+++.+|||||++||+.|+++|||+|+|||||++|||||||++||+|.||+++|++
T Consensus 81 ~~~~~~~~~-~~~~~i~~~~i~~l~~~~FPpCMr~l~~~L~~~~hL~h~~R~ql~lFLk~iGl~~ee~l~f~~~~f~~-- 157 (260)
T PF04104_consen 81 SYLGKDSSF-ESDGKISAENIDELAPESFPPCMRNLHERLRKGHHLKHSGRFQLGLFLKGIGLSLEEALEFWRSEFSK-- 157 (260)
T ss_dssp -------------CCCCCCGHCHHHHCCS-HHHHHHHHHHHHHS---HHHHHHHHHHHHHTTEECCCHHHCCHHHCCT--
T ss_pred hcccccccc-ccccccccccccccccccCChHHHHHHHHHhhCCCCCchhHhhHHHHHHhcCCCHHHHHHHHHHHhcc--
Confidence 999888433 36788999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CccccccccceeeeeeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhh
Q 012907 329 GAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVR 407 (453)
Q Consensus 329 ~~~~F~Key~YnIrH~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~ 407 (453)
++++|+|+|+|||||+||+||+|++|+||||.|||++ +||+|++||||||| |.+.|++.|+ ++.++|++|++
T Consensus 158 ~~~~F~k~~~Y~IrH~yG~eG~r~~Y~p~sC~kii~~~~~~~g~~hGCPfk~-~~d~L~~~L~---~~~~~i~~I~~--- 230 (260)
T PF04104_consen 158 SAPDFDKEYRYNIRHIYGLEGKRTNYTPYSCEKIISQSPPGPGQYHGCPFKH-DPDSLKQLLQ---ISEEQIEEILD--- 230 (260)
T ss_dssp -HHHHHHHTHCCCCCHTT-STT--------HHHHHHSS---TT---S-HHHH--HHHHHHHHH-----HHHHHHHHH---
T ss_pred CcHhHHHHhHhhhhhhccCCCCCeeeCCCchHHHHcCCCCCCCcccCcCCCC-ChHHHHHHhc---ccHHHHHHHHH---
Confidence 7899999999999999999999999999999999999 88999999999999 9999999999 89999999999
Q ss_pred ccchHHHHHHHHHHHcCCCCCCcccCchHHH
Q 012907 408 NRHYQLACTLTFEAVHSSSCDAGINHPNQYF 438 (453)
Q Consensus 408 ~~~yq~AC~~~Fe~~h~~~~~~~i~HPN~Yf 438 (453)
++|||+||++|||++|+ ..+.+|+|||+||
T Consensus 231 ~~~y~~AC~~~f~~~h~-~~~~~I~HPn~Yf 260 (260)
T PF04104_consen 231 SGHYQLACTKYFEATHP-CRGDGINHPNQYF 260 (260)
T ss_dssp TT-HHHHHHHHHHHHHT--TTT---SHHHHH
T ss_pred cCCccHHHHHHHHHHcc-CCCCCCCCchhcC
Confidence 89999999999999999 5567899999998
No 4
>PRK02249 DNA primase large subunit; Validated
Probab=100.00 E-value=3.3e-54 Score=437.14 Aligned_cols=231 Identities=22% Similarity=0.407 Sum_probs=205.7
Q ss_pred hhhhhhhHHHHHHHH-HhcCCh-HHHHHHHHHHHHHHHHHHccCCHHH-HHHHHHhcCCCCccCCHHHHHHHHHHHHHHh
Q 012907 83 EDVNKDIISHFVLRL-VYCRTE-DLRKWFLSMETALYRYRFLLGSSEA-KRALMEEFDLPCKAISRTEFENAKEKLEQVA 159 (453)
Q Consensus 83 ~~~~kD~iSHfiLRL-a~c~s~-elrrwFi~~E~~LF~~R~~~~~~~~-~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~ 159 (453)
...+.+++|++++|+ |+|.++ .+++||+.+|+++|+.||..+++++ +..|++++|+++..
T Consensus 61 ~~~~~evlsy~~a~~Lv~~~~d~~l~~rfa~~Ea~~~~~~l~~e~~e~~~~~~~~~lgl~~~~----------------- 123 (343)
T PRK02249 61 DRPEVELLSYPVARVLVSCVDDPYLTRRYARAEAKAAYDLLRAEEPDDDLRELARDLGIPARV----------------- 123 (343)
T ss_pred cchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcCchhHHHHHHHHcCCCccc-----------------
Confidence 346679999999996 999776 9999999999999999999999999 99999999987521
Q ss_pred hhcCCCCCCCCCceEeecccchHhhhcccce--------EEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 012907 160 RSFDQPLPTADAIFYKVPFEEVPELVAGRRV--------YIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTI 231 (453)
Q Consensus 160 ~~~~~~~~~~~~~~~kVpF~~v~~LV~~R~v--------~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~~i 231 (453)
...+|+|||+++++|++++++ .|.+|+||||.+++.+||.++|+.+|+++|+. .+|.
T Consensus 124 ----------~~~~~kv~~~dyl~la~~~~~~~wrLvNR~l~~G~Vyv~~~el~~Ll~e~~r~~l~~~l~~---~vp~-- 188 (343)
T PRK02249 124 ----------EGDGFAVHVTDYLRLAARLKDPKWRLVNRPVVKGYVYVTREEFARLLREAIRERILDGLPL---AVPE-- 188 (343)
T ss_pred ----------cCceeEEeHHHHHHHhcccCCcccccceeeeeCCEEEECHHHHHHHHHHHHHHHHHHHHHH---hcCH--
Confidence 136899999999999998654 79999999999999999999999999999976 3553
Q ss_pred hhhhhhchHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCC
Q 012907 232 REQERDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGL 311 (453)
Q Consensus 232 ~~de~~RL~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGl 311 (453)
++++||.|++++|++.|.+.+++ ..++.+.+.+|||||++|++.|++|+||+|+|||||++|||||||
T Consensus 189 --~~~drl~~~l~~L~~~~~~~~~~----------~~~~~i~~~~fPpCm~~l~~~l~~g~~L~h~~R~~l~~FL~~iG~ 256 (343)
T PRK02249 189 --EIAEALLPLLEEIREELEELDLE----------TEFGTVDPELFPPCMKALLSALQAGENLPHTARFAITSFLLNIGM 256 (343)
T ss_pred --hhHHhHHHHHHHHHHHhcccccc----------ccccccccccCCHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCC
Confidence 34569999999999988765543 335667788999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHhccccCccccccc-cceeeeeeccCCCCCcccCCccchhhhcc
Q 012907 312 RMEDALAFWKAEFSQKVGAERFDKE-YAYSIRHNYGKEGKRTDYTPYSCQKIISS 365 (453)
Q Consensus 312 s~eeal~fwr~~F~k~~~~~~F~Ke-y~YnIrH~YG~eGkr~~Y~p~sC~kiis~ 365 (453)
++||++.||++ +++|+++ |+|||||+||++|+ ++|+||||+||++.
T Consensus 257 ~~deil~~~~~-------~~~f~e~~~~Y~irH~~G~~G~-~~Y~p~sC~~m~s~ 303 (343)
T PRK02249 257 SVDEIVELFRN-------APDFDEEKTRYQVEHIAGETGG-TEYTPPSCETMRTY 303 (343)
T ss_pred CHHHHHHHHhh-------CCCccHHHHHHHHHHHhcccCC-CCCCCccHHHHHHc
Confidence 99999999987 4789954 99999999999999 99999999999994
No 5
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.7e-47 Score=387.18 Aligned_cols=354 Identities=26% Similarity=0.422 Sum_probs=276.2
Q ss_pred cccCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCCCccchhhhhhhHHHHHHHHH
Q 012907 19 STLPLYRYAPQLEVRLEDFEVFAMDRLRVLKGISDALARGKRPEEMENLVRDLWKANMRHPEASEDVNKDIISHFVLRLV 98 (453)
Q Consensus 19 ~~l~fY~~pP~~~i~leefe~~a~dRLkvL~~ie~~~~~~~~~~e~~~~i~~~~~~~~~~~~~~~~~~kD~iSHfiLRLa 98 (453)
.++.+|.-||.....+++|+. +|+|..+++.|..+..+++ |++........+..... ...+..+|+++||.+|.|
T Consensus 3 ~~~~~~pf~~~~~~~l~~~~~-~I~r~~~~~~~~~~~~r~~---eieri~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~ 77 (363)
T COG2219 3 SRLMLYPFSEEAREALRDFGI-DIDRSVDLLEIRGRVERDK---EIERIRKASLDKILEAP-VSGDIVKDLYEHLALRFA 77 (363)
T ss_pred ccccccCCCchHHHHHHHHHh-HHHHHHHHHhhhhhhhHhh---HHHHHHHHHhccccccc-ccchHHHHHHHHHHhhhh
Confidence 478899999999999999999 9999999999998887765 44433333333333211 125788999999999999
Q ss_pred hcCChHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhc--CCCCccCCHHHHHHHHHHHHHHhhhcCCCCCCCCCceEee
Q 012907 99 YCRTEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEF--DLPCKAISRTEFENAKEKLEQVARSFDQPLPTADAIFYKV 176 (453)
Q Consensus 99 ~c~s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~--~l~~~~is~~e~~~~~~~L~~~~~~~~~~~~~~~~~~~kV 176 (453)
++....+..||+..++.|++.|........+..+.... +..+..|+.+.+.+ ....... .....+..+.|+++
T Consensus 78 ~~~~~~~~~~~~~~~~~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~i~~~~l~~-~~~~~~~----~~~~~~~~~~~~~~ 152 (363)
T COG2219 78 LSVVKELDENFLRAETALREARAVENRLGAIEIFRDSLLIASEAEEISFEVLVE-GAEKYER----LVISKIDVWTFIRV 152 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHhhhhhcchhhhhhhhhccccccccHHHHhh-cccccee----eeeecccceEEEEe
Confidence 99999999999999999999999876665555555533 33677777766643 1111110 01111345789999
Q ss_pred cccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhchHHHHHHHHhhhcCCCCC
Q 012907 177 PFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALSMSYLGPDYS 256 (453)
Q Consensus 177 pF~~v~~LV~~R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~~i~~de~~RL~p~l~~L~~~~~~~~~~ 256 (453)
+|....+..+.+.+++.+|+||+|.+++.+++++.|++++.+++......++. +++..++.+.++++...+......
T Consensus 153 ~~~~~~~~~~l~~~~~~~G~v~l~~~~~~~ll~e~~~~~i~~~~~~~~~~~~~---~~~~~~~~~~i~e~~e~~~~~~~~ 229 (363)
T COG2219 153 AFRDLIDDWRLSNRVLRKGYVYLTKEELIRLLEEAFRENIEESLNMLREILEV---PDEVSELLEEISELAERYKKLFGA 229 (363)
T ss_pred eeeecCcchhheeeeccCCeEecCHHHHHHHHHHHHHHHHHhhhhhhhhcccc---chhhHhhhHHHHHHHHHHhhhhcc
Confidence 99999999999999999999999999999999999999999999876544332 234457777777777776433221
Q ss_pred CccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhccccCccccccc
Q 012907 257 QTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAERFDKE 336 (453)
Q Consensus 257 ~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~~F~k~~~~~~F~Ke 336 (453)
.+++..++ +..|||||+++++.|++|+||+|.+||++++||++|||++||++.||+. +++||++
T Consensus 230 ------~~~~g~~~---~e~fPPCik~iL~~l~~G~~l~h~~R~al~sFL~~ig~~~deiv~~fr~-------~pdFdee 293 (363)
T COG2219 230 ------RIRAGKVD---PEAFPPCIKNILAGLKSGENLPHAARFALTSFLSNIGLSVDEIVELFRN-------SPDFDEE 293 (363)
T ss_pred ------cccccccC---cCcCChHHHHHHHHhhcCCCchHHHHHHHHHHHHhcCCChhHHHHHhcc-------CCCcchh
Confidence 13444444 5789999999999999999999999999999999999999999999998 4779999
Q ss_pred c-ceeeeeeccCCCCCcccCCccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccchHHHH
Q 012907 337 Y-AYSIRHNYGKEGKRTDYTPYSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHYQLAC 415 (453)
Q Consensus 337 y-~YnIrH~YG~eGkr~~Y~p~sC~kiis~~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~yq~AC 415 (453)
+ +|||||+||.+|+|++|+||+|+||.+++ |+| |++... +|
T Consensus 294 ~tryqirHi~G~~~~~~ey~~p~C~~m~~~g------~lC--------------------------~~~~~~------lC 335 (363)
T COG2219 294 ITRYQIRHIIGEEGNRTEYTPPSCDTMRSYG------HLC--------------------------IVDNDP------LC 335 (363)
T ss_pred hhhhhhheeecccCCCCCCCCCCchhHhhcC------Ccc--------------------------cccCcc------cc
Confidence 5 99999999999999999999999999963 999 222211 88
Q ss_pred HHHHHHHcCCCCCCcccCchHHHHHHHcccCccC
Q 012907 416 TLTFEAVHSSSCDAGINHPNQYFSDSHKILQPKN 449 (453)
Q Consensus 416 ~~~Fe~~h~~~~~~~i~HPN~Yf~~S~~~~~~~~ 449 (453)
| |. ..|.||.+||..++.....+.
T Consensus 336 ~------~~----~~v~hPL~Yy~r~~~~~~~~~ 359 (363)
T COG2219 336 T------HC----KAVSHPLTYYERSRDKEGKRG 359 (363)
T ss_pred c------ch----hhcCCcHHHHHHHhhcccccc
Confidence 8 63 357799999999987655543
No 6
>PRK09568 DNA primase large subunit; Reviewed
Probab=99.96 E-value=2.4e-28 Score=244.05 Aligned_cols=213 Identities=14% Similarity=0.222 Sum_probs=160.6
Q ss_pred hhhhHHHHHHHH-Hhc-CChHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcC
Q 012907 86 NKDIISHFVLRL-VYC-RTEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVARSFD 163 (453)
Q Consensus 86 ~kD~iSHfiLRL-a~c-~s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~~~~ 163 (453)
..+.+|++++|+ +.| .+..+.++|+..|++.|...|..++++.+..+.+.+|++...-+...+ .. ..+
T Consensus 61 ~~~vlsy~~a~~lvs~~~d~~l~~R~A~~Eak~~~~~L~~e~~e~l~~i~~~lGi~~~~~~~~~~----~~------~~~ 130 (306)
T PRK09568 61 NEPVLVFYTTLLSLAILNDLRLIRKYAHKEAKQFKSLLQNENEENLLEITKLLGLNINKCDLKIK----FS------LEK 130 (306)
T ss_pred chhHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHcCCceeecccccc----cc------ccc
Confidence 456999999995 444 788999999999999999999999999999999999987543211100 00 011
Q ss_pred CCCCCCCCceEeecccchHhhhc---------ccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhhhhhh-hhhh
Q 012907 164 QPLPTADAIFYKVPFEEVPELVA---------GRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTS-TIRE 233 (453)
Q Consensus 164 ~~~~~~~~~~~kVpF~~v~~LV~---------~R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~~~~~-~i~~ 233 (453)
.... ....|.|||.+++.+.+ ||. |.+|+|||+.+++.+||.++++.++.+.+.. +|. .+.
T Consensus 131 ~~~~--~~~~~~i~~~dYl~~a~~~~~~WkLvNR~--v~~G~V~l~~~e~~rLl~Eai~~ri~~~i~~----l~~~~i~- 201 (306)
T PRK09568 131 KRRI--VQLEFSVNFIDYLKYTKGLREDFKLSKQI--LYKGYVYLDKNQLTDLLAENIKNKIVEMIRP----LNLKEIP- 201 (306)
T ss_pred cccc--cCcceeEeHHHHHHhccCCccceeeecee--ccCCEEEeCHHHHHHHHHHHHHHHHHhcccc----CChHHHH-
Confidence 1111 12568889888776543 465 8999999999999999999999999877421 111 121
Q ss_pred hhhhchHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCCh
Q 012907 234 QERDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRM 313 (453)
Q Consensus 234 de~~RL~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~ 313 (453)
+.|..+++. ....|||||++|+ ++.||+|.|||+++.||.+|||++
T Consensus 202 ---e~ik~~~~~---------------------------~~~~fPPCik~li----~g~nL~H~~RFaLasFL~niG~~v 247 (306)
T PRK09568 202 ---EKLKSLIEE---------------------------KGGKTPPCIENIL----GKEELSEEEIRTLITYYINIGKGL 247 (306)
T ss_pred ---HHHHHHHHH---------------------------ccCCCCchHHHHh----cCCCCChHHHHHHHHHHHHcCCCH
Confidence 134333331 0126999999998 788999999999999999999999
Q ss_pred HHHHHHHHHHhccccCccccccccceeeeeeccCCCCCcccCCccchhhhcc
Q 012907 314 EDALAFWKAEFSQKVGAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISS 365 (453)
Q Consensus 314 eeal~fwr~~F~k~~~~~~F~Key~YnIrH~YG~eGkr~~Y~p~sC~kiis~ 365 (453)
||++.+|+. ++++++ ++|+-| |+++.|+||||+||.+.
T Consensus 248 d~Iv~lf~~-------~pde~~-----~~~i~G--~~gteY~~PSC~tMks~ 285 (306)
T PRK09568 248 DSIIAIMNV-------TNIEDL-----YKKYRG--DKKTRYIVYSCARMKQL 285 (306)
T ss_pred HHHHHHHhc-------CCcHHH-----HHHhhc--CCCceeCCCchHHHHHc
Confidence 999999976 356665 348777 57899999999999994
No 7
>cd06560 PriL Archaeal/eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. The DNA replication machinery of archaeal organisms contains only the core primase, a simpler arrangement compared to eukaryotes. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL, such as the stabilization of PriS, involvement in the initiation of synthesis, the improvement of primase processivity, and the determination of product size.
Probab=99.83 E-value=2e-20 Score=172.40 Aligned_cols=121 Identities=19% Similarity=0.301 Sum_probs=102.2
Q ss_pred hhhhhhhHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhh
Q 012907 83 EDVNKDIISHFVLRLVYCR--TEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVAR 160 (453)
Q Consensus 83 ~~~~kD~iSHfiLRLa~c~--s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~ 160 (453)
.+.++|++|||+||+++|. ++++++||+.+|+++|+.||..+++++...|+..+|.. . ..+.+.
T Consensus 35 ~~~~~d~~s~~ilr~~~~~~~~~~l~~rf~~~Ea~~~~~rl~~~~~~~~~~~~~~~~~~----~------~~~~~~---- 100 (166)
T cd06560 35 DSVENEVLSFYIARVLVAALDDSILTRRFARAEAKIAEERLRKESEEDLLEIAIELGYL----K------PDELIG---- 100 (166)
T ss_pred cchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhCChhHHHHHHHHhccc----h------hhhhhc----
Confidence 5678899999999999998 59999999999999999999999999999999887721 0 001110
Q ss_pred hcCCCCCCCCCceEeecccchHhhhcccc--------eEEeccEEEEehhhHHHHHHHHHHHHHHHHHH
Q 012907 161 SFDQPLPTADAIFYKVPFEEVPELVAGRR--------VYIHKGHAYVAMHQVVSLVVTQFRSNLSKALI 221 (453)
Q Consensus 161 ~~~~~~~~~~~~~~kVpF~~v~~LV~~R~--------v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~ 221 (453)
........+|+|||.++++|+++|+ ++|++|+||||.+++.+||.++|+++|.++|+
T Consensus 101 ----~~~~~~~~~~kv~~~d~l~l~~~~~~~~~rLvn~~l~~G~vyl~~~e~~~ll~e~~~~~l~~~l~ 165 (166)
T cd06560 101 ----IEVGIEDLPYKIPVSDYLKLAARLRGDKWRLVNRILRNGYVYLTKEELLRLLREAIRERLLDGLP 165 (166)
T ss_pred ----ccccccCCceeeeHHHHHHHhcCCCCCccccccccccCCEEEECHHHHHHHHHHHHHHHHHhhCC
Confidence 0112246799999999999999998 99999999999999999999999999998763
No 8
>PRK03968 DNA primase large subunit; Validated
Probab=99.48 E-value=1.2e-12 Score=132.18 Aligned_cols=259 Identities=19% Similarity=0.346 Sum_probs=152.6
Q ss_pred hhHHHHHHH--HHhcCChHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCC
Q 012907 88 DIISHFVLR--LVYCRTEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVARSFDQP 165 (453)
Q Consensus 88 D~iSHfiLR--La~c~s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~~~~~~ 165 (453)
|.+|.|+|- +||+..--=.+-++.....++.-|+..... +.+.-++.+.+.+.|+-.- ++...-+..+.-
T Consensus 66 Dl~~Fy~L~~A~af~~~~~E~~lv~e~~~~i~~~Rl~~~~~------~~~~~~~~~~~~~~e~p~~--d~~~l~~~~~~e 137 (399)
T PRK03968 66 DLLSFYALLGALAFSPYGREAELVVESNGKIYEERLRRAKE------IEETEIPVKVVNAIEIPEK--DRKILERVRGRE 137 (399)
T ss_pred HHHHHHHHHHHhccCCCCcchhHHHHhhhHHHHHHHHHhcc------cccccccccccccccccch--hhhhhhhhcccc
Confidence 999999998 677753222344888888999888875321 1111222333322221100 000000000000
Q ss_pred CC----CCCCceEeecccchHhhhcc---cceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhh---hhhhhhhhhh
Q 012907 166 LP----TADAIFYKVPFEEVPELVAG---RRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNR---KWTSTIREQE 235 (453)
Q Consensus 166 ~~----~~~~~~~kVpF~~v~~LV~~---R~v~L~~G~ayVp~~~l~~lv~~~fr~~L~~~L~~~~~---~~~~~i~~de 235 (453)
.. ..-..-|+|.|.+..+|+.. -.++|++|+||+..+++..++.++|++++.++...... .++. +..+.
T Consensus 138 l~~e~~~~~~~~y~i~~~df~~l~gs~sLt~~iL~nG~VYLdkee~iki~~eaf~knleR~vn~lYeIrdEl~~-~i~~l 216 (399)
T PRK03968 138 LPPEELEDLLPEYKIKWKDLLDLIGSGSLTDLYIRNGRVYLRREEFLKLWSKAFEKNLERAVNRLYEIRDELPE-FYLEL 216 (399)
T ss_pred cCHHHHHHHhhhccccHHHHHHhcCCcchhhhhhcCcEEEecHHHHHHHHHHHHHHHhhccHHHHHHHhhhhHH-HHHHH
Confidence 00 00011289999999998887 34789999999999999999999999999766543211 1121 11111
Q ss_pred hhchHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHh--------
Q 012907 236 RDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLK-------- 307 (453)
Q Consensus 236 ~~RL~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLK-------- 307 (453)
.++|..+. ..+.... ....+..++. .+-...|||||+.+++.+..|.. .+.+|+.+++||.
T Consensus 217 ~ekI~E~~----~E~fkk~---~~~~~s~~~g---~l~~e~fPPCik~~l~gv~sG~r-n~ai~lll~sFl~yar~~p~~ 285 (399)
T PRK03968 217 AEEIRETA----EEEFSER---GGAYGSAGAG---KLRPEAFPPCIRNTLEGVPSGGR-NYAITVLLTSFLSYARLCPNP 285 (399)
T ss_pred HHHHHHHH----HHHHHhh---ccccccCCCC---CCChhhCChhHHHHHhccccccc-cchHHHHHHHHHHHHhcCCCC
Confidence 12333222 1221110 0011122222 33356799999999999999963 3448899999999
Q ss_pred ------------hcCCChHHHHHHHHHHhccccCccccc------cccceeeeeecc------CCCCCcccCCccchhhh
Q 012907 308 ------------GVGLRMEDALAFWKAEFSQKVGAERFD------KEYAYSIRHNYG------KEGKRTDYTPYSCQKII 363 (453)
Q Consensus 308 ------------giGls~eeal~fwr~~F~k~~~~~~F~------Key~YnIrH~YG------~eGkr~~Y~p~sC~kii 363 (453)
.++.+.+|++-+-=.. ..+.+++-|+ |..-|.+-.-|- -+|+.+-|+||||.||.
T Consensus 286 ~~~~vkv~D~~~~l~~~~~ei~p~i~ea-~~~c~pplf~DqP~E~~ni~~~lgfG~~~~p~le~~g~~~~y~p~~c~ki~ 364 (399)
T PRK03968 286 PRRDVKVSDCDPDLRIIEEEILPLIIEA-ANRCSPPLFEDQPQEIKNIWYHLGFGMTDEPELEDSGNSTWYFPPNCEKIK 364 (399)
T ss_pred cccCcchhhccchhHHHHHHHHHHHHHH-hhcCCCCccccCchHHHHHHHHhccCccCCCcccccCCccccCCCCHHHHh
Confidence 9999999999876543 2345566675 223343322111 27999999999999998
Q ss_pred ccCC
Q 012907 364 SSTP 367 (453)
Q Consensus 364 s~~p 367 (453)
...|
T Consensus 365 ~~~p 368 (399)
T PRK03968 365 AHAP 368 (399)
T ss_pred hccc
Confidence 7644
No 9
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=79.87 E-value=2.9 Score=29.25 Aligned_cols=32 Identities=13% Similarity=0.388 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHHHhCCCCch----hHHHHHHHhhc
Q 012907 377 YRHFSEENLRAALGRMGVGSR----AMEDVVDKVRN 408 (453)
Q Consensus 377 fr~~~~~~L~~~L~~~gi~~~----~i~~I~~~~~~ 408 (453)
|-.|+.+.|+..|.+.||..+ ..+++++.|+.
T Consensus 1 fdtWs~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 1 FDTWSDSDLKSWLKSHGIPVPKSAKTRDELLKLAKK 36 (38)
T ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHH
Confidence 668999999999999999643 57899988864
No 10
>PRK02249 DNA primase large subunit; Validated
Probab=40.70 E-value=43 Score=34.92 Aligned_cols=82 Identities=17% Similarity=0.315 Sum_probs=48.0
Q ss_pred ccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhc-----cchHH---------------HHH
Q 012907 357 YSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRN-----RHYQL---------------ACT 416 (453)
Q Consensus 357 ~sC~kiis~~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~-----~~yq~---------------AC~ 416 (453)
|-|++-+-..-..| .| -+|...-.|...|.+.|++.++|-++...... -.||+ .|.
T Consensus 223 PpCm~~l~~~l~~g-~~---L~h~~R~~l~~FL~~iG~~~deil~~~~~~~~f~e~~~~Y~irH~~G~~G~~~Y~p~sC~ 298 (343)
T PRK02249 223 PPCMKALLSALQAG-EN---LPHTARFAITSFLLNIGMSVDEIVELFRNAPDFDEEKTRYQVEHIAGETGGTEYTPPSCE 298 (343)
T ss_pred CHHHHHHHHHHHcC-CC---CChHHHHHHHHHHHhcCCCHHHHHHHHhhCCCccHHHHHHHHHHHhcccCCCCCCCccHH
Confidence 45877664311111 12 45788889999999999988777666533211 11222 355
Q ss_pred HHHHHHcCC-C-CC---CcccCchHHHHHHHcc
Q 012907 417 LTFEAVHSS-S-CD---AGINHPNQYFSDSHKI 444 (453)
Q Consensus 417 ~~Fe~~h~~-~-~~---~~i~HPN~Yf~~S~~~ 444 (453)
+.-. .|. . .+ .+|.||-|||.....-
T Consensus 299 ~m~s--~g~C~~~d~lC~~i~hPL~yY~~~~~~ 329 (343)
T PRK02249 299 TMRT--YGLCVGKDDLCEKVKHPLSYYRRKLRD 329 (343)
T ss_pred HHHH--cCCCCCchhhhhccCChHHHHHHHHHh
Confidence 5432 221 1 11 3799999999887553
No 11
>COG1851 Uncharacterized conserved protein [Function unknown]
Probab=40.44 E-value=25 Score=33.47 Aligned_cols=62 Identities=18% Similarity=0.368 Sum_probs=45.8
Q ss_pred chHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHH
Q 012907 238 RLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLF 305 (453)
Q Consensus 238 RL~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lF 305 (453)
+|..+++++.+--+..++..+...+.+. |.=..+||-.|..+...++-|.|.-+||+.++-|
T Consensus 130 kL~~l~k~vk~vGlttefykqng~~~~P------LpYeelP~vaRrflr~akkvek~tGFGR~~faYf 191 (229)
T COG1851 130 KLNQLLKHVKAVGLTTEFYKQNGFESIP------LPYEELPPVARRFLREAKKVEKLTGFGRFVFAYF 191 (229)
T ss_pred HHHHHHHHHHhccchhhhhhhcCcCCCC------CChhhCCHHHHHHHHHHHHHHHhcCceeeeeehh
Confidence 8888888888766555554443333332 2234599999999999999999999999987655
No 12
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=39.46 E-value=28 Score=26.47 Aligned_cols=23 Identities=22% Similarity=0.364 Sum_probs=18.9
Q ss_pred hhhHHHHHHhhcCCChHHHHHHH
Q 012907 298 GRMQLGLFLKGVGLRMEDALAFW 320 (453)
Q Consensus 298 gR~Ql~lFLKgiGls~eeal~fw 320 (453)
.|+++-..+|.+|||++|+=.+.
T Consensus 2 ~rL~~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 2 ERLQFIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHH
T ss_pred hHHHHHHHHHHcCCCHHHHHHHH
Confidence 47889999999999999998887
No 13
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=38.45 E-value=31 Score=31.26 Aligned_cols=37 Identities=24% Similarity=0.418 Sum_probs=32.5
Q ss_pred CCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch
Q 012907 375 CPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY 411 (453)
Q Consensus 375 CPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y 411 (453)
|=++..+...|++.|...|++++.|+++++..+..+|
T Consensus 21 L~~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ 57 (157)
T PRK00117 21 LARREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGL 57 (157)
T ss_pred HccchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC
Confidence 5567778899999999999999999999998888776
No 14
>PRK14136 recX recombination regulator RecX; Provisional
Probab=36.76 E-value=33 Score=35.21 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=37.7
Q ss_pred CCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch--HHHHHHHHH
Q 012907 375 CPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY--QLACTLTFE 420 (453)
Q Consensus 375 CPfr~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y--q~AC~~~Fe 420 (453)
|=++..+...|+++|...|++++.|++||+..+..+| -....+.|-
T Consensus 172 LSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyV 219 (309)
T PRK14136 172 LSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLV 219 (309)
T ss_pred hhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHH
Confidence 5567788999999999999999999999999999998 344444444
No 15
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=35.30 E-value=51 Score=31.10 Aligned_cols=43 Identities=12% Similarity=0.206 Sum_probs=36.8
Q ss_pred CHHHHHHHHHhCCCCchhHHHHHH-HhhccchHHHHHHHHHHHc
Q 012907 381 SEENLRAALGRMGVGSRAMEDVVD-KVRNRHYQLACTLTFEAVH 423 (453)
Q Consensus 381 ~~~~L~~~L~~~gi~~~~i~~I~~-~~~~~~yq~AC~~~Fe~~h 423 (453)
.+..|++.|...||+.+.|+++++ .......+.||...+...-
T Consensus 86 G~~rl~qeL~qkGi~~~~Ie~aL~~~~~~~~~~~a~~~~~kk~~ 129 (174)
T COG2137 86 GPARLKQELKQKGIDDEIIEEALELIDEEDEQERARKVLRKKFK 129 (174)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHHhccchHHHHHHHHHHHHHHhC
Confidence 366899999999999999999998 6667778999999888654
No 16
>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=31.71 E-value=1.1e+02 Score=33.18 Aligned_cols=48 Identities=15% Similarity=0.303 Sum_probs=38.0
Q ss_pred cCcHHHHHHHHHHhccCCCCCchhhHHHHHHh-hcCCChHHHHHHHHHHh
Q 012907 276 SFPLCMRHLFDKLREDHHLKHGGRMQLGLFLK-GVGLRMEDALAFWKAEF 324 (453)
Q Consensus 276 ~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLK-giGls~eeal~fwr~~F 324 (453)
.|| |+-+.+..|+.+.-+-|.+||-.+.||- ..|++=.+.-++|.+.+
T Consensus 328 G~P-~vDAaMrqL~~tG~mhnr~Rm~vAsfl~k~L~idWr~G~~~F~~~L 376 (471)
T TIGR03556 328 GYP-IVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYFMQKL 376 (471)
T ss_pred CCC-cccHHHHHHHHhCCccHHHHHHHHHHHHcccCCCHHHHHHHHHHHh
Confidence 465 5666667788889999999999999997 58888777777776644
No 17
>PRK14137 recX recombination regulator RecX; Provisional
Probab=30.89 E-value=47 Score=31.81 Aligned_cols=43 Identities=21% Similarity=0.328 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch--HHHHHHHHH
Q 012907 378 RHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY--QLACTLTFE 420 (453)
Q Consensus 378 r~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y--q~AC~~~Fe 420 (453)
+..+...|+++|...|++++.|+.|++..+..+| ..+..+.|.
T Consensus 53 R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~ 97 (195)
T PRK14137 53 RAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAEN 97 (195)
T ss_pred chhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 4467788999999999999999999999999988 333334453
No 18
>PHA02046 hypothetical protein
Probab=28.73 E-value=2.7e+02 Score=23.82 Aligned_cols=32 Identities=13% Similarity=0.398 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCCCccCCHHHHHHHHHHHHHH
Q 012907 127 EAKRALMEEFDLPCKAISRTEFENAKEKLEQV 158 (453)
Q Consensus 127 ~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~ 158 (453)
..+.+||++|++.+.+-+.++.+.+++++...
T Consensus 41 aa~~KFLKDNnItcdpaD~~~m~~Lr~e~~~~ 72 (99)
T PHA02046 41 AAIAKFLKDNEITCDPADTINIDRLREEFRQA 72 (99)
T ss_pred HHHHHHhhcCCcccCcccHHHHHHHHHHHHHH
Confidence 46789999999999999999999998888754
No 19
>PF13645 YkuD_2: L,D-transpeptidase catalytic domain
Probab=27.22 E-value=89 Score=29.58 Aligned_cols=60 Identities=27% Similarity=0.518 Sum_probs=37.9
Q ss_pred cccccccceeeeeeccCCCC-------------CcccCCccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCch
Q 012907 331 ERFDKEYAYSIRHNYGKEGK-------------RTDYTPYSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSR 397 (453)
Q Consensus 331 ~~F~Key~YnIrH~YG~eGk-------------r~~Y~p~sC~kiis~~p~~g~~HGCPfr~~~~~~L~~~L~~~gi~~~ 397 (453)
+.+.-.+-|++| ++|+|-. ..+|-+ ...+....--|...|||= |+++
T Consensus 99 ~~Y~G~~G~slr-L~GLe~~~NdnA~~R~IViH~a~Yv~---~~~i~~~grlGrS~GCpA----------------v~~~ 158 (176)
T PF13645_consen 99 ETYYGKHGYSLR-LDGLEKGINDNARKRAIVIHGADYVS---EDFIKKYGRLGRSWGCPA----------------VSPE 158 (176)
T ss_pred CEecCCCcceEE-EeCCCCCCCcCcccccEEEechhcCC---HHHHHhcCCCcccCCCCc----------------CCHH
Confidence 445555778888 9999954 234444 445543223377899993 4556
Q ss_pred hHHHHHHHhhccc
Q 012907 398 AMEDVVDKVRNRH 410 (453)
Q Consensus 398 ~i~~I~~~~~~~~ 410 (453)
.+++|++..|+|.
T Consensus 159 ~~~~ii~~ik~g~ 171 (176)
T PF13645_consen 159 LMKKIIDTIKGGS 171 (176)
T ss_pred HHHHHHHHhcCCe
Confidence 6777777777664
No 20
>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=25.00 E-value=39 Score=33.78 Aligned_cols=72 Identities=18% Similarity=0.329 Sum_probs=49.0
Q ss_pred cCcHHHHHHHHHHhccCCCCCchhhHHHHHHh-hcCCChHHHHHHHHHHhccccCcccccc-ccceeeeeeccCCCCCcc
Q 012907 276 SFPLCMRHLFDKLREDHHLKHGGRMQLGLFLK-GVGLRMEDALAFWKAEFSQKVGAERFDK-EYAYSIRHNYGKEGKRTD 353 (453)
Q Consensus 276 ~FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLK-giGls~eeal~fwr~~F~k~~~~~~F~K-ey~YnIrH~YG~eGkr~~ 353 (453)
.| ||+-+.+..|+.+.-+-|..|+-++.||- .+|++-.+.-++|.+.+. |+|- -...+..+..| .| ++
T Consensus 125 G~-p~vDAamrqL~~tG~mHn~~R~~vasfl~k~l~i~W~~g~~~f~~~li------D~d~a~n~~~wqw~ag-~g--~d 194 (277)
T PF03441_consen 125 GY-PLVDAAMRQLRQTGWMHNRLRMIVASFLTKDLLIDWREGAEWFAEHLI------DYDPASNYGNWQWAAG-TG--TD 194 (277)
T ss_dssp S--HHHHHHHHHHHHHS---HHHHHHHHHHHHHTSHBHHHHHHHHHHHHHT------T--HHHHHHHHHHHTT-SS--ST
T ss_pred CC-hHHHHHHHHHHHhCcccHHHHHHHHHHHHHhccCCccccHHHHHHHhh------ccCcchHHHHHHHHHh-hc--cc
Confidence 35 57888888899999999999999999885 466677778887777553 2442 25677788888 55 66
Q ss_pred cCCc
Q 012907 354 YTPY 357 (453)
Q Consensus 354 Y~p~ 357 (453)
..||
T Consensus 195 ~~~~ 198 (277)
T PF03441_consen 195 AKPY 198 (277)
T ss_dssp GCST
T ss_pred cCcc
Confidence 6554
No 21
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=23.24 E-value=95 Score=29.18 Aligned_cols=38 Identities=32% Similarity=0.688 Sum_probs=29.3
Q ss_pred CcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHH
Q 012907 277 FPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKA 322 (453)
Q Consensus 277 FPpCMr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~ 322 (453)
.-.|+.+|..++ ....-+|. +|+|| |.|+||+..|-..
T Consensus 89 ~~~~L~~L~~R~-~~~~FPHE----IGiFL---GYPleDV~GFI~~ 126 (176)
T PF12672_consen 89 LEDCLEHLKKRF-ESGEFPHE----IGIFL---GYPLEDVKGFIEN 126 (176)
T ss_pred HHHHHHHHHHHh-cCCCCCch----hHhcc---CCCHHHHHHHHhC
Confidence 445677777777 55557776 89997 9999999999854
No 22
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=23.03 E-value=1.7e+02 Score=24.56 Aligned_cols=50 Identities=22% Similarity=0.373 Sum_probs=43.6
Q ss_pred HHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhccccCcc
Q 012907 281 MRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAE 331 (453)
Q Consensus 281 Mr~L~~~L~~~~hLkH~gR~Ql~lFLKgiGls~eeal~fwr~~F~k~~~~~ 331 (453)
+|.|+..-+.+.|+.-.-|..+.-++...|++ ++.-.+...+|.+.++.+
T Consensus 3 lrami~aAkADG~id~~E~~~I~~~~~~~~~~-~~~~~~~~~~l~~p~~~~ 52 (95)
T cd07178 3 LRAMIAAAKADGHIDEAERARILGELGEAGLD-AEERAFLEAELAAPLDPD 52 (95)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHCCCCHH
Confidence 68899999999999999999999999999998 566777778888777654
No 23
>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]
Probab=22.23 E-value=98 Score=29.02 Aligned_cols=51 Identities=14% Similarity=0.196 Sum_probs=32.9
Q ss_pred CCCCCCCCCCC-----------CCHHHHHHHHHhCCCCchhHHHHHHHhhccchHHHHHHHH
Q 012907 369 VGDHHGCPYRH-----------FSEENLRAALGRMGVGSRAMEDVVDKVRNRHYQLACTLTF 419 (453)
Q Consensus 369 ~g~~HGCPfr~-----------~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~yq~AC~~~F 419 (453)
.-|+|||-|-- .+...|-..|++-|.+...|.+.++.--=|-..--|.+.|
T Consensus 79 IVDyHgCd~FperwfdlVvVLr~~~s~LY~RL~sRgY~e~Ki~eNiecEIfgv~~eea~eSy 140 (176)
T KOG3347|consen 79 IVDYHGCDFFPERWFDLVVVLRTPNSVLYDRLKSRGYSEKKIKENIECEIFGVVLEEARESY 140 (176)
T ss_pred EEeecccCccchhheeEEEEEecCchHHHHHHHHcCCCHHHHhhhcchHHHHHHHHHHHHHc
Confidence 35899997721 4678999999998988777766554422222233444444
No 24
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.82 E-value=91 Score=26.38 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=20.8
Q ss_pred hhhHHHHHHhhcCCChHHHHHHHH
Q 012907 298 GRMQLGLFLKGVGLRMEDALAFWK 321 (453)
Q Consensus 298 gR~Ql~lFLKgiGls~eeal~fwr 321 (453)
.|++.-..||.+|||++|+-.+..
T Consensus 43 ~~l~~I~~lr~~G~sL~eI~~~l~ 66 (107)
T cd04777 43 DDLEFILELKGLGFSLIEIQKIFS 66 (107)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHH
Confidence 377788999999999999988774
Done!