Query 012939
Match_columns 453
No_of_seqs 158 out of 347
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 07:52:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012939hhsearch_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 2E-132 3E-137 990.7 34.1 432 14-451 23-464 (475)
2 cd07322 PriL_PriS_Eukaryotic E 100.0 5E-121 1E-125 940.7 38.2 388 23-441 1-390 (390)
3 PF04104 DNA_primase_lrg: Euka 100.0 7.9E-80 1.7E-84 606.5 9.3 256 172-438 1-260 (260)
4 PRK02249 DNA primase large sub 100.0 1.1E-54 2.4E-59 440.5 19.6 236 83-377 61-308 (343)
5 COG2219 PRI2 Eukaryotic-type D 100.0 4.8E-47 1E-51 387.7 18.9 355 19-450 3-360 (363)
6 PRK09568 DNA primase large sub 100.0 5E-29 1.1E-33 248.9 16.2 217 86-376 61-289 (306)
7 cd06560 PriL Archaeal/eukaryot 99.8 2.9E-20 6.2E-25 171.4 11.2 121 83-221 35-165 (166)
8 PRK03968 DNA primase large sub 99.5 3.2E-13 6.8E-18 136.3 17.7 259 88-367 66-368 (399)
9 PF10281 Ish1: Putative stress 78.0 3.5 7.7E-05 28.8 3.6 32 377-408 1-36 (38)
10 PRK00117 recX recombination re 41.4 26 0.00056 31.8 3.1 38 374-411 20-57 (157)
11 PRK02249 DNA primase large sub 41.1 40 0.00087 35.1 4.8 82 357-444 223-329 (343)
12 COG1851 Uncharacterized conser 40.6 25 0.00055 33.4 2.9 62 238-305 130-191 (229)
13 PF09278 MerR-DNA-bind: MerR, 39.2 30 0.00066 26.3 2.8 23 298-320 2-24 (65)
14 PRK14136 recX recombination re 38.1 30 0.00066 35.5 3.2 46 375-420 172-219 (309)
15 COG2137 OraA Uncharacterized p 34.1 54 0.0012 30.9 4.0 43 381-423 86-129 (174)
16 TIGR03556 photolyase_8HDF deox 33.3 95 0.0021 33.5 6.3 48 276-324 328-376 (471)
17 PRK14137 recX recombination re 32.2 43 0.00093 32.1 3.1 44 377-420 52-97 (195)
18 PF13645 YkuD_2: L,D-transpept 30.8 72 0.0016 30.2 4.2 60 331-410 99-171 (176)
19 PHA02046 hypothetical protein 29.8 2.6E+02 0.0056 23.9 6.8 32 127-158 41-72 (99)
20 PF03441 FAD_binding_7: FAD bi 27.0 34 0.00075 34.2 1.5 72 276-357 125-198 (277)
21 cd07178 terB_like_YebE telluri 26.1 1.3E+02 0.0029 25.2 4.7 50 281-331 3-52 (95)
22 PF12672 DUF3793: Protein of u 23.2 95 0.0021 29.2 3.6 38 277-322 89-126 (176)
23 cd04777 HTH_MerR-like_sg1 Heli 21.8 90 0.002 26.4 2.9 24 298-321 43-66 (107)
24 PRK14134 recX recombination re 20.7 1E+02 0.0022 31.1 3.5 45 377-421 73-119 (283)
25 PF06342 DUF1057: Alpha/beta h 20.2 71 0.0015 32.6 2.2 23 372-394 41-63 (297)
No 1
>KOG2267 consensus Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
Probab=100.00 E-value=1.6e-132 Score=990.68 Aligned_cols=432 Identities=41% Similarity=0.758 Sum_probs=404.0
Q ss_pred CCCCCcccCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCC------Cccchhhhh
Q 012939 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 234588999
Q ss_pred hhHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCCCC
Q 012939 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 DHISHFILRLAFCRSAELRVWFVQAEVDLLRFRFSKEPGGARQFFLSSVDFQMEGISTEEKQVLYEGLRASSQR---NLV 179 (475)
T ss_pred hhHHHHHhhhhhcCCHHHHHHHHHhhhhheeeEeecCcchHHHHHHHhhhHHHhhccchhhHHHHHHHHHhhcc---Ccc
Confidence 99999999999999999999999999999999999999999999999999999999999999998888876422 112
Q ss_pred CCCCceEeecccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhhhhhhhhhhchHHHHHHHH
Q 012939 168 TADAIFYKVPFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALS 247 (453)
Q Consensus 168 ~~~~~~ykVpF~~v~~LV~~R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 012939 248 MSYLGPDYSQ-TKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQ 326 (453)
Q Consensus 248 ~~~~~~~~~~-~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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 446788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCccccccccceeeeeeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHH
Q 012939 327 KVGAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDK 405 (453)
Q Consensus 327 ~~~~~~FdKey~YnIrH~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~hGCPfk~~~~~~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--CCcccCchHHHHHHHcccCCcccc
Q 012939 406 VRNRHYQLACTLTFEAVHSSSC--DAGINHPNQYFSDSHKILQPKVEI 451 (453)
Q Consensus 406 ~~~~~yq~AC~~~Fe~~h~~~~--~~~i~HPNqYf~~S~~~~~~~~~~ 451 (453)
++.+||++|||||||.||+... +.+|+||||||++|+....++.++
T Consensus 417 ~~~~~Y~iaCTr~fE~~hn~~~~~g~~i~hPnqyf~esqq~e~~~~e~ 464 (475)
T KOG2267|consen 417 VKLNHYDIACTRYFEMTHNRKQSIGESIAHPNQYFEESQQPERNQQEI 464 (475)
T ss_pred hcccchhHHHHHHHHHHhcchhccchhccChHHHHHHhcccccccCCC
Confidence 9999999999999999997653 478999999999999887777654
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=4.9e-121 Score=940.68 Aligned_cols=388 Identities=52% Similarity=0.944 Sum_probs=364.1
Q ss_pred CCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCCCccchhhhhhhHHHHHHHHHhcCC
Q 012939 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 267999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCCCCCCCCceEeecccchH
Q 012939 103 EDLRKWFLSMETALYRYRFLLGSSEAKRALMEEFDLPCKAISRTEFENAKEKLEQVARSFDQPLPTADAIFYKVPFEEVP 182 (453)
Q Consensus 103 ~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~~l~~~~is~~e~~~~~~~L~~~~~~~~~~~~~~~~~~ykVpF~~v~ 182 (453)
+++|+||+++|++||++||+.++.+++..|++++|++|++++++|+..+.++|....... .......++||+|||++|+
T Consensus 54 eelr~wFv~~E~~Lfr~Rl~~~~~~~~~~fl~~~~l~~~~i~~~e~~~~~~~l~~~~~~~-~~~~~~~~~~~kVpF~~v~ 132 (390)
T cd07322 54 EELRRWFVRQETELFRYRLELLSLEGLKQFLKSNGLDYQPVSDEEKEELREELLKSASSL-KQIKIEATNFYKVPFEEVL 132 (390)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHcCCCccccCHHHHHHHHHHHHHhhccc-cccccccCCEEEeehhhhH
Confidence 999999999999999999999999999999999999999999999999999987543222 3344567889999999999
Q ss_pred hhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhhhhhhhhhhchHHHHHHHHhhhcCCCCCCccccc
Q 012939 183 ELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALSMSYLGPDYSQTKEFG 262 (453)
Q Consensus 183 ~LV~~R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 012939 263 EISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAERFDKEYAYSIR 342 (453)
Q Consensus 263 ~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~hLkH~gR~ql~lFLKgiGls~eeal~fwr~~F~k~~~~~~FdKey~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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccchHHHHHHHHHH
Q 012939 343 HNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHYQLACTLTFEA 421 (453)
Q Consensus 343 H~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~hGCPfk~~~~~~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 012939 422 VHSSSC-DAGINHPNQYFSDS 441 (453)
Q Consensus 422 ~h~~~~-~~~i~HPNqYf~~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=7.9e-80 Score=606.51 Aligned_cols=256 Identities=53% Similarity=0.958 Sum_probs=198.7
Q ss_pred ceEeecccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhh---hhhhhhhhchHHHHHHHHh
Q 012939 172 IFYKVPFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTS---TIREQERDRLTPIVEALSM 248 (453)
Q Consensus 172 ~~ykVpF~~v~~LV~~R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 012939 249 SYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKV 328 (453)
Q Consensus 249 ~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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 999887333 36788999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CccccccccceeeeeeccCCCCCcccCCccchhhhcc-CCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhh
Q 012939 329 GAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISS-TPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVR 407 (453)
Q Consensus 329 ~~~~FdKey~YnIrH~YG~eGkr~~Y~p~sC~kiis~-~p~~g~~hGCPfk~~~~~~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 88999999999
Q ss_pred ccchHHHHHHHHHHHcCCCCCCcccCchHHH
Q 012939 408 NRHYQLACTLTFEAVHSSSCDAGINHPNQYF 438 (453)
Q Consensus 408 ~~~yq~AC~~~Fe~~h~~~~~~~i~HPNqYf 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=1.1e-54 Score=440.55 Aligned_cols=236 Identities=22% Similarity=0.398 Sum_probs=209.6
Q ss_pred hhhhhhhHHHHHHHH-HhcCCh-HHHHHHHHHHHHHHHHHHhcCCHHH-HHHHHHhcCCCCccCCHHHHHHHHHHHHHHh
Q 012939 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 999766 9999999999999999999999999 99999999987521
Q ss_pred hhcCCCCCCCCCceEeecccchHhhhcccce--------EEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhhhh
Q 012939 160 RSFDQPLPTADAIFYKVPFEEVPELVAGRRV--------YIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTI 231 (453)
Q Consensus 160 ~~~~~~~~~~~~~~ykVpF~~v~~LV~~R~v--------~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 3554
Q ss_pred hhhhhhchHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCC
Q 012939 232 REQERDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGL 311 (453)
Q Consensus 232 ~~de~~Rl~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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 34469999999999988765543 335667788999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHhccccCccccccc-cceeeeeeccCCCCCcccCCccchhhhccCCCCCCCCCCCC
Q 012939 312 RMEDALAFWKAEFSQKVGAERFDKE-YAYSIRHNYGKEGKRTDYTPYSCQKIISSTPGVGDHHGCPY 377 (453)
Q Consensus 312 s~eeal~fwr~~F~k~~~~~~FdKe-y~YnIrH~YG~eGkr~~Y~p~sC~kiis~~p~~g~~hGCPf 377 (453)
++||++.||+. +++|+++ |+|||||+||++|+ ++|+||||+||++ ++-||-
T Consensus 257 ~~deil~~~~~-------~~~f~e~~~~Y~irH~~G~~G~-~~Y~p~sC~~m~s-------~g~C~~ 308 (343)
T PRK02249 257 SVDEIVELFRN-------APDFDEEKTRYQVEHIAGETGG-TEYTPPSCETMRT-------YGLCVG 308 (343)
T ss_pred CHHHHHHHHhh-------CCCccHHHHHHHHHHHhcccCC-CCCCCccHHHHHH-------cCCCCC
Confidence 99999999987 4789954 99999999999999 9999999999999 577984
No 5
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.8e-47 Score=387.66 Aligned_cols=355 Identities=26% Similarity=0.420 Sum_probs=276.7
Q ss_pred cccCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHhcCCCccchhhhhhhHHHHHHHHH
Q 012939 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 468899999999999999999 9999999999998887754 44433333333322221 125788999999999999
Q ss_pred hcCChHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhc--CCCCccCCHHHHHHHHHHHHHHhhhcCCCCCCCCCceEee
Q 012939 99 YCRTEDLRKWFLSMETALYRYRFLLGSSEAKRALMEEF--DLPCKAISRTEFENAKEKLEQVARSFDQPLPTADAIFYKV 176 (453)
Q Consensus 99 ~c~s~elrrwFi~~E~~LF~~R~~~~~~~~~~~fl~~~--~l~~~~is~~e~~~~~~~L~~~~~~~~~~~~~~~~~~ykV 176 (453)
++....++.||+..++.|++.|...........+.... +..+..++.+.+.. ........ ....+..+.|+++
T Consensus 78 ~~~~~~~~~~~~~~~~~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~i~~~~l~~-~~~~~~~~----~~~~~~~~~~~~~ 152 (363)
T COG2219 78 LSVVKELDENFLRAETALREARAVENRLGAIEIFRDSLLIASEAEEISFEVLVE-GAEKYERL----VISKIDVWTFIRV 152 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHhhhhhcchhhhhhhhhccccccccHHHHhh-ccccceee----eeecccceEEEEe
Confidence 99999999999999999999999877666555555533 33566677665543 11111110 1111345789999
Q ss_pred cccchHhhhcccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhhhhhhhhhhchHHHHHHHHhhhcCCCCC
Q 012939 177 PFEEVPELVAGRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTSTIREQERDRLTPIVEALSMSYLGPDYS 256 (453)
Q Consensus 177 pF~~v~~LV~~R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 99999999999999999999999999999999999999999999876554332 234457777777777776433221
Q ss_pred CccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhccccCccccccc
Q 012939 257 QTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAERFDKE 336 (453)
Q Consensus 257 ~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~hLkH~gR~ql~lFLKgiGls~eeal~fwr~~F~k~~~~~~FdKe 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 5889999999999999999999999999999999999999999999998 5779999
Q ss_pred c-ceeeeeeccCCCCCcccCCccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccchHHHH
Q 012939 337 Y-AYSIRHNYGKEGKRTDYTPYSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHYQLAC 415 (453)
Q Consensus 337 y-~YnIrH~YG~eGkr~~Y~p~sC~kiis~~p~~g~~hGCPfk~~~~~~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 99999999999999999999999999852 899 222211 88
Q ss_pred HHHHHHHcCCCCCCcccCchHHHHHHHcccCCccc
Q 012939 416 TLTFEAVHSSSCDAGINHPNQYFSDSHKILQPKVE 450 (453)
Q Consensus 416 ~~~Fe~~h~~~~~~~i~HPNqYf~~S~~~~~~~~~ 450 (453)
| |. ..|.||.+||..++.....++.
T Consensus 336 ~------~~----~~v~hPL~Yy~r~~~~~~~~~~ 360 (363)
T COG2219 336 T------HC----KAVSHPLTYYERSRDKEGKRGA 360 (363)
T ss_pred c------ch----hhcCCcHHHHHHHhhccccccc
Confidence 8 63 4578999999999887666543
No 6
>PRK09568 DNA primase large subunit; Reviewed
Probab=99.96 E-value=5e-29 Score=248.89 Aligned_cols=217 Identities=14% Similarity=0.225 Sum_probs=163.4
Q ss_pred hhhhHHHHHHHH-Hhc-CChHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcC
Q 012939 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 788999999999999999999999999999999999987553211100 00 001
Q ss_pred CCCCCCCCceEeecccchHhhhc---------ccceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhHhhhh-hhhh
Q 012939 164 QPLPTADAIFYKVPFEEVPELVA---------GRRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNRKWTS-TIRE 233 (453)
Q Consensus 164 ~~~~~~~~~~ykVpF~~v~~LV~---------~R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 012939 234 QERDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRM 313 (453)
Q Consensus 234 de~~Rl~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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 133333321 0126999999998 788999999999999999999999
Q ss_pred HHHHHHHHHHhccccCccccccccceeeeeeccCCCCCcccCCccchhhhccCCCCCCCCCCC
Q 012939 314 EDALAFWKAEFSQKVGAERFDKEYAYSIRHNYGKEGKRTDYTPYSCQKIISSTPGVGDHHGCP 376 (453)
Q Consensus 314 eeal~fwr~~F~k~~~~~~FdKey~YnIrH~YG~eGkr~~Y~p~sC~kiis~~p~~g~~hGCP 376 (453)
||++.+|+. ++++++ ++|+-| |+++.|+||||.||.+ +|-||
T Consensus 248 d~Iv~lf~~-------~pde~~-----~~~i~G--~~gteY~~PSC~tMks-------~GlC~ 289 (306)
T PRK09568 248 DSIIAIMNV-------TNIEDL-----YKKYRG--DKKTRYIVYSCARMKQ-------LGLCV 289 (306)
T ss_pred HHHHHHHhc-------CCcHHH-----HHHhhc--CCCceeCCCchHHHHH-------cCCCC
Confidence 999999976 456665 348877 5779999999999999 57787
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=2.9e-20 Score=171.40 Aligned_cols=121 Identities=19% Similarity=0.298 Sum_probs=102.2
Q ss_pred hhhhhhhHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhh
Q 012939 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----KP------DELIG---- 100 (166)
T ss_pred cchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhCChhHHHHHHHHhccc----hh------hhhhc----
Confidence 5678899999999999998 59999999999999999999999999999999887721 00 00110
Q ss_pred hcCCCCCCCCCceEeecccchHhhhcccc--------eEEeccEEEEehhhHHHHHHHHHHHHHHHHHH
Q 012939 161 SFDQPLPTADAIFYKVPFEEVPELVAGRR--------VYIHKGHAYVAMHQVVSLVVTQFRSNLSKALI 221 (453)
Q Consensus 161 ~~~~~~~~~~~~~ykVpF~~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=99.53 E-value=3.2e-13 Score=136.30 Aligned_cols=259 Identities=18% Similarity=0.321 Sum_probs=153.3
Q ss_pred hhHHHHHHH--HHhcCChHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCccCCHHHHHHHHHHHHHHhhhcCCC
Q 012939 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 677753222344888888888888875322 1111222333322222110 000000000000
Q ss_pred C----CCCCCceEeecccchHhhhcc---cceEEeccEEEEehhhHHHHHHHHHHHHHHHHHHHHhH---hhhhhhhhhh
Q 012939 166 L----PTADAIFYKVPFEEVPELVAG---RRVYIHKGHAYVAMHQVVSLVVTQFRSNLSKALILTNR---KWTSTIREQE 235 (453)
Q Consensus 166 ~----~~~~~~~ykVpF~~v~~LV~~---R~v~l~~G~ayVp~~~l~~lv~~~fr~~L~~~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 LPPEELEDLLPEYKIKWKDLLDLIGSGSLTDLYIRNGRVYLRREEFLKLWSKAFEKNLERAVNRLYEIRDELPEFY-LEL 216 (399)
T ss_pred cCHHHHHHHhhhccccHHHHHHhcCCcchhhhhhcCcEEEecHHHHHHHHHHHHHHHhhccHHHHHHHhhhhHHHH-HHH
Confidence 0 000011289999999998887 34789999999999999999999999999766643211 122211 111
Q ss_pred hhchHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHHHh--------
Q 012939 236 RDRLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLFLK-------- 307 (453)
Q Consensus 236 ~~Rl~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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---GGAYGSAGAGK---LRPEAFPPCIRNTLEGVPSGGR-NYAITVLLTSFLSYARLCPNP 285 (399)
T ss_pred HHHHHHHH----HHHHHhh---ccccccCCCCC---CChhhCChhHHHHHhccccccc-cchHHHHHHHHHHHHhcCCCC
Confidence 22333222 2222110 00112223333 3356899999999999999963 3448899999999
Q ss_pred ------------hcCCChHHHHHHHHHHhccccCccccccc--cceeeeeeccC----------CCCCcccCCccchhhh
Q 012939 308 ------------GVGLRMEDALAFWKAEFSQKVGAERFDKE--YAYSIRHNYGK----------EGKRTDYTPYSCQKII 363 (453)
Q Consensus 308 ------------giGls~eeal~fwr~~F~k~~~~~~FdKe--y~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 9999999999875432 234556777521 22233222233 8999999999999998
Q ss_pred ccCC
Q 012939 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=77.97 E-value=3.5 Score=28.78 Aligned_cols=32 Identities=13% Similarity=0.388 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHHHhCCCCch----hHHHHHHHhhc
Q 012939 377 YRHFSEENLRAALGRMGVGSR----AMEDVVDKVRN 408 (453)
Q Consensus 377 fk~~~~~~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 668999999999999999633 58899988864
No 10
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=41.35 E-value=26 Score=31.76 Aligned_cols=38 Identities=24% Similarity=0.369 Sum_probs=33.4
Q ss_pred CCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch
Q 012939 374 GCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY 411 (453)
Q Consensus 374 GCPfk~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y 411 (453)
-|-++..+...|++.|...|++++.|+++++.....+|
T Consensus 20 ~L~~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ 57 (157)
T PRK00117 20 LLARREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGL 57 (157)
T ss_pred HHccchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC
Confidence 36677788999999999999999999999998888776
No 11
>PRK02249 DNA primase large subunit; Validated
Probab=41.07 E-value=40 Score=35.12 Aligned_cols=82 Identities=17% Similarity=0.315 Sum_probs=47.6
Q ss_pred ccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhc-----cchHH---------------HHH
Q 012939 357 YSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRN-----RHYQL---------------ACT 416 (453)
Q Consensus 357 ~sC~kiis~~p~~g~~hGCPfk~~~~~~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 44877663311111 12 45778889999999999987777666533211 11322 355
Q ss_pred HHHHHHcCC-C-CC---CcccCchHHHHHHHcc
Q 012939 417 LTFEAVHSS-S-CD---AGINHPNQYFSDSHKI 444 (453)
Q Consensus 417 ~~Fe~~h~~-~-~~---~~i~HPNqYf~~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 12
>COG1851 Uncharacterized conserved protein [Function unknown]
Probab=40.57 E-value=25 Score=33.43 Aligned_cols=62 Identities=18% Similarity=0.368 Sum_probs=45.8
Q ss_pred chHHHHHHHHhhhcCCCCCCccccccccccchhhhhhccCcHHHHHHHHHHhccCCCCCchhhHHHHH
Q 012939 238 RLTPIVEALSMSYLGPDYSQTKEFGEISIKDLDQLARSSFPLCMRHLFDKLREDHHLKHGGRMQLGLF 305 (453)
Q Consensus 238 Rl~p~l~~L~~~~~~~~~~~~~~~~~i~~~~id~l~~~~FPpCMr~L~~~Lr~~~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 8888888888766655555443333332 2234599999999999999999999999987655
No 13
>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=39.23 E-value=30 Score=26.27 Aligned_cols=23 Identities=22% Similarity=0.364 Sum_probs=19.0
Q ss_pred hhhHHHHHHhhcCCChHHHHHHH
Q 012939 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 14
>PRK14136 recX recombination regulator RecX; Provisional
Probab=38.13 E-value=30 Score=35.46 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=37.9
Q ss_pred CCCCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch--HHHHHHHHH
Q 012939 375 CPYRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY--QLACTLTFE 420 (453)
Q Consensus 375 CPfk~~~~~~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 6677889999999999999999999999999999998 334444443
No 15
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=34.13 E-value=54 Score=30.91 Aligned_cols=43 Identities=12% Similarity=0.206 Sum_probs=36.9
Q ss_pred CHHHHHHHHHhCCCCchhHHHHHH-HhhccchHHHHHHHHHHHc
Q 012939 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 467899999999999999999998 7777778999999888654
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=33.31 E-value=95 Score=33.51 Aligned_cols=48 Identities=15% Similarity=0.295 Sum_probs=38.2
Q ss_pred cCcHHHHHHHHHHhccCCCCCchhhHHHHHHhh-cCCChHHHHHHHHHHh
Q 012939 276 SFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKG-VGLRMEDALAFWKAEF 324 (453)
Q Consensus 276 ~FPpCMr~L~~~Lr~~~hLkH~gR~ql~lFLKg-iGls~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 66777777888899999999999999974 7888777777776643
No 17
>PRK14137 recX recombination regulator RecX; Provisional
Probab=32.20 E-value=43 Score=32.09 Aligned_cols=44 Identities=20% Similarity=0.304 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch--HHHHHHHHH
Q 012939 377 YRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY--QLACTLTFE 420 (453)
Q Consensus 377 fk~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y--q~AC~~~Fe 420 (453)
++..+...|+++|...|++++.|+.|++..+..+| ..+..+.|.
T Consensus 52 ~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~ 97 (195)
T PRK14137 52 ARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAEN 97 (195)
T ss_pred cchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 34567888999999999999999999999999988 333334443
No 18
>PF13645 YkuD_2: L,D-transpeptidase catalytic domain
Probab=30.77 E-value=72 Score=30.21 Aligned_cols=60 Identities=27% Similarity=0.494 Sum_probs=38.3
Q ss_pred cccccccceeeeeeccCCCC-------------CcccCCccchhhhccCCCCCCCCCCCCCCCCHHHHHHHHHhCCCCch
Q 012939 331 ERFDKEYAYSIRHNYGKEGK-------------RTDYTPYSCQKIISSTPGVGDHHGCPYRHFSEENLRAALGRMGVGSR 397 (453)
Q Consensus 331 ~~FdKey~YnIrH~YG~eGk-------------r~~Y~p~sC~kiis~~p~~g~~hGCPfk~~~~~~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-LDGLEKGINDNARKRAIVIHGADYVSE---DFIKKYGRLGRSWGCPA----------------VSPE 158 (176)
T ss_pred CEecCCCcceEE-EeCCCCCCCcCcccccEEEechhcCCH---HHHHhcCCCcccCCCCc----------------CCHH
Confidence 455556788888 9999943 2345443 34442223377899993 5566
Q ss_pred hHHHHHHHhhccc
Q 012939 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 19
>PHA02046 hypothetical protein
Probab=29.75 E-value=2.6e+02 Score=23.88 Aligned_cols=32 Identities=13% Similarity=0.398 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCCCccCCHHHHHHHHHHHHHH
Q 012939 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 45789999999999999999999998888754
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=27.05 E-value=34 Score=34.19 Aligned_cols=72 Identities=18% Similarity=0.324 Sum_probs=49.0
Q ss_pred cCcHHHHHHHHHHhccCCCCCchhhHHHHHHhh-cCCChHHHHHHHHHHhccccCcccccc-ccceeeeeeccCCCCCcc
Q 012939 276 SFPLCMRHLFDKLREDHHLKHGGRMQLGLFLKG-VGLRMEDALAFWKAEFSQKVGAERFDK-EYAYSIRHNYGKEGKRTD 353 (453)
Q Consensus 276 ~FPpCMr~L~~~Lr~~~hLkH~gR~ql~lFLKg-iGls~eeal~fwr~~F~k~~~~~~FdK-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 588888899999999999999999999855 66677777777776553 2442 24677788888 55 66
Q ss_pred cCCc
Q 012939 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 6664
No 21
>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=26.12 E-value=1.3e+02 Score=25.18 Aligned_cols=50 Identities=22% Similarity=0.373 Sum_probs=43.7
Q ss_pred HHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHHHhccccCcc
Q 012939 281 MRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKAEFSQKVGAE 331 (453)
Q Consensus 281 Mr~L~~~Lr~~~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 567777778888777654
No 22
>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=23.17 E-value=95 Score=29.16 Aligned_cols=38 Identities=32% Similarity=0.688 Sum_probs=29.3
Q ss_pred CcHHHHHHHHHHhccCCCCCchhhHHHHHHhhcCCChHHHHHHHHH
Q 012939 277 FPLCMRHLFDKLREDHHLKHGGRMQLGLFLKGVGLRMEDALAFWKA 322 (453)
Q Consensus 277 FPpCMr~L~~~Lr~~~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 23
>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=90 Score=26.39 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=21.0
Q ss_pred hhhHHHHHHhhcCCChHHHHHHHH
Q 012939 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 377888999999999999988874
No 24
>PRK14134 recX recombination regulator RecX; Provisional
Probab=20.72 E-value=1e+02 Score=31.11 Aligned_cols=45 Identities=9% Similarity=0.068 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHhCCCCchhHHHHHHHhhccch--HHHHHHHHHH
Q 012939 377 YRHFSEENLRAALGRMGVGSRAMEDVVDKVRNRHY--QLACTLTFEA 421 (453)
Q Consensus 377 fk~~~~~~L~~~L~~~gi~~~~i~~I~~~~~~~~y--q~AC~~~Fe~ 421 (453)
++..+...|++.|...|.+++.|+.|++..+..+| -.+..+.|-.
T Consensus 73 ~r~rSe~Elr~KL~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~ 119 (283)
T PRK14134 73 KSYKTEKQIKEKLYLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIR 119 (283)
T ss_pred cCcchHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 34567889999999899999999999999999998 3444444433
No 25
>PF06342 DUF1057: Alpha/beta hydrolase of unknown function (DUF1057); InterPro: IPR010463 This entry consists of proteins of unknown function which have an alpha/beta hydrolase fold.
Probab=20.25 E-value=71 Score=32.65 Aligned_cols=23 Identities=30% Similarity=0.535 Sum_probs=20.9
Q ss_pred CCCCCCCCCCHHHHHHHHHhCCC
Q 012939 372 HHGCPYRHFSEENLRAALGRMGV 394 (453)
Q Consensus 372 ~hGCPfk~~~~~~L~~~L~~~gi 394 (453)
.||||-.|.|-..++..|..+||
T Consensus 41 ~hGsPGSH~DFkYi~~~l~~~~i 63 (297)
T PF06342_consen 41 FHGSPGSHNDFKYIRPPLDEAGI 63 (297)
T ss_pred ecCCCCCccchhhhhhHHHHcCe
Confidence 89999999999999999998754
Done!