Query psy4735
Match_columns 1232
No_of_seqs 473 out of 875
Neff 2.6
Searched_HMMs 46136
Date Sat Aug 17 00:39:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4735hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0919|consensus 100.0 1E-53 2.2E-58 447.1 5.1 241 259-649 93-337 (338)
2 KOG0919|consensus 100.0 5.3E-39 1.1E-43 336.9 3.9 140 912-1226 199-338 (338)
3 PRK10458 DNA cytosine methylas 100.0 8E-35 1.7E-39 326.3 18.0 150 259-431 202-377 (467)
4 PF00145 DNA_methylase: C-5 cy 100.0 2.7E-30 5.9E-35 262.1 12.8 77 258-334 84-165 (335)
5 cd00315 Cyt_C5_DNA_methylase C 100.0 6.5E-30 1.4E-34 267.3 13.0 76 259-334 86-166 (275)
6 TIGR00675 dcm DNA-methyltransf 99.9 1.2E-27 2.6E-32 254.8 13.5 117 259-397 83-205 (315)
7 COG0270 Dcm Site-specific DNA 99.9 1.7E-25 3.6E-30 239.3 10.7 77 257-333 89-169 (328)
8 PRK10458 DNA cytosine methylas 99.7 2.7E-17 5.8E-22 186.0 7.4 55 1172-1226 398-454 (467)
9 PF00145 DNA_methylase: C-5 cy 99.4 1.6E-13 3.5E-18 140.2 4.9 56 1169-1226 280-335 (335)
10 cd00315 Cyt_C5_DNA_methylase C 99.2 7.4E-12 1.6E-16 132.2 5.5 55 1171-1226 221-275 (275)
11 TIGR00675 dcm DNA-methyltransf 99.2 1.6E-11 3.5E-16 132.1 4.8 52 1171-1224 264-315 (315)
12 COG0270 Dcm Site-specific DNA 98.9 7.6E-10 1.6E-14 119.7 4.6 54 1171-1226 269-322 (328)
13 COG3091 SprT Zn-dependent meta 34.1 7.5 0.00016 40.9 -1.8 13 38-50 64-76 (156)
14 PF13443 HTH_26: Cro/C1-type H 30.0 66 0.0014 27.2 3.5 51 837-897 9-62 (63)
15 KOG0031|consensus 29.4 37 0.0008 36.3 2.2 68 966-1042 17-84 (171)
16 PRK04351 hypothetical protein; 26.5 13 0.00028 38.4 -1.6 13 38-50 64-76 (149)
17 PRK04860 hypothetical protein; 22.3 16 0.00036 38.1 -1.8 13 38-50 66-78 (160)
No 1
>KOG0919|consensus
Probab=100.00 E-value=1e-53 Score=447.10 Aligned_cols=241 Identities=36% Similarity=0.560 Sum_probs=192.3
Q ss_pred hccCCCcccchhhhhc--cCCcEEEEEEccc--CCchHHHHHHHHHhCCCeeEEEEeCCCCCCCCcccceEEEEEEeCCC
Q psy4735 259 ESRTHAPCTVEPYVNC--LHQTMICFINVLK--NQLPYVCTTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKRSPA 334 (1232)
Q Consensus 259 ~~R~~l~~~~v~~V~a--lrPr~~VfENV~K--~~~~fkeIietLeslGY~VqEfILNPaDFGVPQSR~RYFLIAkRk~l 334 (1232)
.+|..+|-++...+-. .-|..|++|||++ ....-+.++++|++|||+++||||+|++|||||+|.||||||+..-
T Consensus 93 D~Rs~aflhil~~lP~~q~LPeYIL~ENVkGFE~S~ar~~~i~~lencGf~~~EfiLsPtqfniPNsR~Ryy~iArl~~- 171 (338)
T KOG0919|consen 93 DKRSDAFLHILGLLPECQELPEYILMENVKGFESSQARNQFIESLENCGFHWREFILSPTQFNIPNSRYRYYCIARLGA- 171 (338)
T ss_pred CchhHHHHHHHhhhhhhhhhhHHHHHhhcccchhhhHHHHHHHHHHhcCchhhheeccccccCCCCcchheeehhhhCC-
Confidence 4555555444444333 4589999999974 6678899999999999999999999999999999999999998863
Q ss_pred CCCCCCcccccCCccccccccccccccCCCCccccchhhhccCCCCCcccccccccCHHHHhhhcccceEeeCCCCcccc
Q psy4735 335 AHSSEASFCFETSSELMTELPKLKSKTCNPLLSRMTLHSILDSTDPSDDLYRRYLVSDKDLLRRFHVFDIVNGKASSTNC 414 (1232)
Q Consensus 335 ~~sd~ndF~Fp~psqIl~e~Pk~~sksC~PIlsvkpLsDFLEedVDs~E~~eKYLLPDKLLeRyG~lfDIVtPsSrRScC 414 (1232)
+|+|+. +..|..+|.++..- ..--.++.|+||||++.+ +++|+||+++|.||+.+||||.|.++||||
T Consensus 172 ------~F~~~G-~~s~d~~~qFseia-qk~g~Vk~i~d~lE~~~d----~s~ylvp~~vL~k~~l~~DIv~P~~srs~C 239 (338)
T KOG0919|consen 172 ------DFPFAG-GKSWDEMPQFSEIA-QKQGLVKQIADILEENVD----PSDYLVPDDVLTKRVLVMDIVHPAQSRSMC 239 (338)
T ss_pred ------CCCCCC-CcccccccchHHHH-HhcchHHHHHHHHHhcCC----HHHccCCHHHHHHhHhheeecccccccceE
Confidence 677753 33566677643100 001136789999999987 679999999999999999999999999999
Q ss_pred ccccceeeeeeccceeeccCCCchhHHHHHHHhhhcccccccchhhhHHHhhhhhHHHhhhccCCCcccchhhhhhhhhh
Q psy4735 415 FTKAYTHYAEGTGSVLSNLGDMTHIEDIIEKCKHLKQQTDISSTHETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDAQN 494 (1232)
Q Consensus 415 FTKGYGhYVEGTGSVLQ~~~d~t~~e~~~~~~~~~~~~~~~sS~~~~~~~~~~~~~~~q~~~s~~~~~~~~~~~~~~~~~ 494 (1232)
||||||||+||||||||..++.. .. -++.+
T Consensus 240 FTkGYthy~eGtGSilq~~~~i~----~e-------------N~~~s--------------------------------- 269 (338)
T KOG0919|consen 240 FTKGYTHYTEGTGSILQLVKEID----TE-------------NQDAS--------------------------------- 269 (338)
T ss_pred eecCccceeecchHHHHHHhhhc----cc-------------chhHH---------------------------------
Confidence 99999999999999998665411 00 00000
Q ss_pred hhhHHHHHHHHHHhhhhccccccCCCcccccccCCCcccccccccccccccccccccccchhhhhhhccCcccccccccc
Q psy4735 495 RADLEKKILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETKSKHIARTNESEAKREEIAPNATGAYQNQ 574 (1232)
Q Consensus 495 ~~d~ek~~l~~~~k~a~~~~D~~~~~~d~~~d~~~~~~~~~~~~e~~~~e~~s~~~ar~~e~~a~~~~~~~~~~~~~~~~ 574 (1232)
++
T Consensus 270 ---~~--------------------------------------------------------------------------- 271 (338)
T KOG0919|consen 270 ---KS--------------------------------------------------------------------------- 271 (338)
T ss_pred ---HH---------------------------------------------------------------------------
Confidence 00
Q ss_pred cccchhhhhcchhhhhhhhhcCCCcccccHHHHHhhCCCCCCCCCCCCCCHHHHHHHhCCcccHHHHHHHHHHHh
Q psy4735 575 ENSVNTLLANQNEATLLQELKRLNLRYFSPDEIRKLMCFPDECQFPPDCSDKARYKLLGNSINVHVVAYCICLML 649 (1232)
Q Consensus 575 ~n~Vs~tl~~~~e~~~l~~LhplkLRyFTPREvARLQGFPDdF~FP~~IS~KQrYKLLGNSVnV~VVa~Lak~LL 649 (1232)
+...+.++..+|.++||||||||+|||||||++|.||++++.+|+||++|||+||+||++|++.|.
T Consensus 272 ---------~~~~~~~~~~l~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVkVV~~LIklL~ 337 (338)
T KOG0919|consen 272 ---------EKILQQRLDLLHQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVKVVGELIKLLT 337 (338)
T ss_pred ---------HHHHHHHHHHHHHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccceeHHHHHHHhc
Confidence 111234567788899999999999999999999999999999999999999999999999999885
No 2
>KOG0919|consensus
Probab=100.00 E-value=5.3e-39 Score=336.92 Aligned_cols=140 Identities=44% Similarity=0.731 Sum_probs=118.7
Q ss_pred cccccccCCCCCcccccccccChHHhhhcceeeeeeccCCCCccccccccceeeeccccccccCCchhHHHHHHHHHhhh
Q psy4735 912 TLHGILDSTHPSGDLYRRYLVSDKDLLRRFHVFDIVNRKASSTNCFTKAYTHYAEGTGSVLSNLGDMTQIEEIIEKCKHL 991 (1232)
Q Consensus 912 ~~~~~Ld~~~~~~~~y~~yllpdk~L~r~~~vlDIv~~~s~rS~CFTKgY~hYvEGTGSVl~~~~~~~~~~~~~~~~~~~ 991 (1232)
.+.+|||++++. .+|+|||++|.||+++||||+|.++||||||||||||+|||||+|.-. +|+
T Consensus 199 ~i~d~lE~~~d~----s~ylvp~~vL~k~~l~~DIv~P~~srs~CFTkGYthy~eGtGSilq~~-------------~~i 261 (338)
T KOG0919|consen 199 QIADILEENVDP----SDYLVPDDVLTKRVLVMDIVHPAQSRSMCFTKGYTHYTEGTGSILQLV-------------KEI 261 (338)
T ss_pred HHHHHHHhcCCH----HHccCCHHHHHHhHhheeecccccccceEeecCccceeecchHHHHHH-------------hhh
Confidence 579999999985 899999999999999999999999999999999999999999977221 111
Q ss_pred hhcccCCCchhhhhhhhcccccccccccCCcchhHHHHHHHHhhhhhhhhhhhchhhhhcccccchhHHHHHHhhhhhhh
Q psy4735 992 KQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRVNLEKKTLDEKVNDTLNQDDLVEKELLNEKVND 1071 (1232)
Q Consensus 992 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1071 (1232)
. -+ ||+.
T Consensus 262 ~----~e--------------------------------------------------------N~~~------------- 268 (338)
T KOG0919|consen 262 D----TE--------------------------------------------------------NQDA------------- 268 (338)
T ss_pred c----cc--------------------------------------------------------chhH-------------
Confidence 1 00 1110
Q ss_pred hccccCCCccccccccCCcccccccchhhhhhhhhhhhhhccCCCCCcCCccCCCcccccCCccCCCCcccccccccccc
Q psy4735 1072 TLNKANSKDITTNVTGTNQNEAKSKHVTEIARTNEREAKREDISPNVTGANQRDGSVNALGTNENAGNSVTTTRTNQNEE 1151 (1232)
Q Consensus 1072 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Trr~rv~~ 1151 (1232)
T Consensus 269 -------------------------------------------------------------------------------- 268 (338)
T KOG0919|consen 269 -------------------------------------------------------------------------------- 268 (338)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccccccccccHHHHHHHHhcCCcccCCHHHHHhhcCCCCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHHhc
Q psy4735 1152 SSVNTLETNQNEATLLQELKRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLMLC 1226 (1232)
Q Consensus 1152 ~~a~tl~t~~~ee~~l~~L~~lkLR~FTPRE~ARLqGFPddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~Ll~ 1226 (1232)
-+++...++++..|+.+++|||||||+|||||||++|.||+.++.+|+||+||||+||+||++|++.|.+
T Consensus 269 -----s~~~~~~~~~~~~l~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVkVV~~LIklL~e 338 (338)
T KOG0919|consen 269 -----SKSEKILQQRLDLLHQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVKVVGELIKLLTE 338 (338)
T ss_pred -----HHHHHHHHHHHHHHHHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccceeHHHHHHHhcC
Confidence 0123345677888899999999999999999999999999999999999999999999999999999864
No 3
>PRK10458 DNA cytosine methylase; Provisional
Probab=100.00 E-value=8e-35 Score=326.34 Aligned_cols=150 Identities=18% Similarity=0.244 Sum_probs=121.2
Q ss_pred hccCCCcccchhhhhccCCcEEEEEEcc-----cCCchHHHHHHHHHhCCCeeE---------EEEeCCCCCCCCcccce
Q psy4735 259 ESRTHAPCTVEPYVNCLHQTMICFINVL-----KNQLPYVCTTSMLTRAGFRFQ---------EFLLSPTQFGVPNSRTR 324 (1232)
Q Consensus 259 ~~R~~l~~~~v~~V~alrPr~~VfENV~-----K~~~~fkeIietLeslGY~Vq---------EfILNPaDFGVPQSR~R 324 (1232)
+.||+||.+|+++|+.++|+|||+|||. +++.+|+.|++.|+++||.+. +.|||+.+| |||+|+|
T Consensus 202 d~rg~Lf~~~~rii~~~kPk~fvlENV~gl~s~~~g~~f~~i~~~L~~lGY~v~~~~~~g~~~~~vlna~~f-VPQ~R~R 280 (467)
T PRK10458 202 ETQGTLFFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFRIIMQTLDELGYDVADAEDNGPDDPKIIDGKHF-LPQHRER 280 (467)
T ss_pred CccccHHHHHHHHHHHhCCCEEEEeCcHhhhcccccHHHHHHHHHHHHcCCeEEeccccCcccceEeehhhC-CCccCcE
Confidence 4699999999999999999999999994 466799999999999999996 489999999 9999999
Q ss_pred EEEEEEeCCCCCCCCCcccccCCccccccccccccccCCCCccccchhhhccCCCCCcccccccccCHHHHh---hh---
Q psy4735 325 YYLIAKRSPAAHSSEASFCFETSSELMTELPKLKSKTCNPLLSRMTLHSILDSTDPSDDLYRRYLVSDKDLL---RR--- 398 (1232)
Q Consensus 325 YFLIAkRk~l~~sd~ndF~Fp~psqIl~e~Pk~~sksC~PIlsvkpLsDFLEedVDs~E~~eKYLLPDKLLe---Ry--- 398 (1232)
+||||+|++.. ...+|.|+.. ...+|. ...+|++||+..++ ++|++|++++. +|
T Consensus 281 vfiVg~r~~~~--~~~~f~~~~~---~~~~p~----------~~~~l~diL~~~~~-----~ky~ls~~~~~~l~~~~~k 340 (467)
T PRK10458 281 IVLVGFRRDLN--LKADFTLRDI---SECYPA----------QRPTLAELLDPVVD-----AKYILTPVLWKYLYRYAKK 340 (467)
T ss_pred EEEEEEeCCcc--cccCcccccc---cccCCC----------CCCCHHHhcCCCCC-----cceeeCHHHHHHHHHHHhh
Confidence 99999998861 1123554321 111221 12369999997765 68999998876 44
Q ss_pred ------cccceEeeCCCCccccccccceeeeeeccceee
Q psy4735 399 ------FHVFDIVNGKASSTNCFTKAYTHYAEGTGSVLS 431 (1232)
Q Consensus 399 ------G~lfDIVtPsSrRScCFTKGYGhYVEGTGSVLQ 431 (1232)
|+.++||+|.+.+|+|+|.+| +|.++ ||.+.
T Consensus 341 ~~~~g~g~~~~i~~~~~~~~~~~t~~~-ry~k~-gs~~~ 377 (467)
T PRK10458 341 HQAKGNGFGYGLVYPNNPQSVTRTLSA-RYYKD-GSEIL 377 (467)
T ss_pred ccccCCCcceeeeecCCCCCccccccc-ccccC-CCcee
Confidence 678999999999999999998 88888 66653
No 4
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=99.97 E-value=2.7e-30 Score=262.15 Aligned_cols=77 Identities=22% Similarity=0.287 Sum_probs=70.1
Q ss_pred HhccCCCcccchhhhhccCCcEEEEEEcc-----cCCchHHHHHHHHHhCCCeeEEEEeCCCCCCCCcccceEEEEEEeC
Q psy4735 258 VESRTHAPCTVEPYVNCLHQTMICFINVL-----KNQLPYVCTTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKRS 332 (1232)
Q Consensus 258 ~~~R~~l~~~~v~~V~alrPr~~VfENV~-----K~~~~fkeIietLeslGY~VqEfILNPaDFGVPQSR~RYFLIAkRk 332 (1232)
-..|++||..|+++|+.++|++|++|||. +++..|+.|++.|+++||.+++++|||.+|||||+|+|+||||.|+
T Consensus 84 ~d~r~~L~~~~~~~v~~~~Pk~~~~ENV~~l~~~~~~~~~~~i~~~l~~lGY~v~~~vlna~~yGvPQ~R~R~fivg~r~ 163 (335)
T PF00145_consen 84 DDPRNSLFFEFLRIVKELKPKYFLLENVPGLLSSKNGEVFKEILEELEELGYNVQWRVLNAADYGVPQNRERVFIVGIRK 163 (335)
T ss_dssp CCHTTSHHHHHHHHHHHHS-SEEEEEEEGGGGTGGGHHHHHHHHHHHHHTTEEEEEEEEEGGGGTSSBE-EEEEEEEEEG
T ss_pred ccccchhhHHHHHHHhhccceEEEecccceeeccccccccccccccccccceeehhccccHhhCCCCCceeeEEEEEECC
Confidence 35799999999999999999999999994 3457899999999999999999999999999999999999999999
Q ss_pred CC
Q psy4735 333 PA 334 (1232)
Q Consensus 333 ~l 334 (1232)
+.
T Consensus 164 ~~ 165 (335)
T PF00145_consen 164 DL 165 (335)
T ss_dssp GG
T ss_pred CC
Confidence 86
No 5
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=99.96 E-value=6.5e-30 Score=267.31 Aligned_cols=76 Identities=20% Similarity=0.275 Sum_probs=71.1
Q ss_pred hccCCCcccchhhhhccCCcEEEEEEcc-----cCCchHHHHHHHHHhCCCeeEEEEeCCCCCCCCcccceEEEEEEeCC
Q psy4735 259 ESRTHAPCTVEPYVNCLHQTMICFINVL-----KNQLPYVCTTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKRSP 333 (1232)
Q Consensus 259 ~~R~~l~~~~v~~V~alrPr~~VfENV~-----K~~~~fkeIietLeslGY~VqEfILNPaDFGVPQSR~RYFLIAkRk~ 333 (1232)
..|+.||.+|+++|+.++|+||++|||. +++..|+.|++.|+++||++.+.+|++.+||+||+|+|+|+||.|++
T Consensus 86 d~r~~L~~~~~~~i~~~~P~~~v~ENV~g~~~~~~~~~~~~i~~~l~~~GY~~~~~~l~a~~~GvPQ~R~R~~~ia~~~~ 165 (275)
T cd00315 86 DTRGTLFFEIIRILKEKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVYWKLLNASDYGVPQNRERVFIIGIRKD 165 (275)
T ss_pred CchHHHHHHHHHHHHhcCCCEEEEEcCcchhccCchHHHHHHHHHHHhCCcEEEEEEEEHHHcCCCCCCcEEEEEEEeCC
Confidence 3488899999999999999999999994 35778999999999999999999999999999999999999999988
Q ss_pred C
Q psy4735 334 A 334 (1232)
Q Consensus 334 l 334 (1232)
.
T Consensus 166 ~ 166 (275)
T cd00315 166 L 166 (275)
T ss_pred C
Confidence 6
No 6
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.95 E-value=1.2e-27 Score=254.81 Aligned_cols=117 Identities=17% Similarity=0.265 Sum_probs=90.0
Q ss_pred hccCCCcccchhhhhccCCcEEEEEEcc-----cCCchHHHHHHHHHhCCCeeEEEEeCCCCCCCCcccceEEEEEEe-C
Q psy4735 259 ESRTHAPCTVEPYVNCLHQTMICFINVL-----KNQLPYVCTTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKR-S 332 (1232)
Q Consensus 259 ~~R~~l~~~~v~~V~alrPr~~VfENV~-----K~~~~fkeIietLeslGY~VqEfILNPaDFGVPQSR~RYFLIAkR-k 332 (1232)
..|+.||..++++|+.++|++||+|||. +++..|+.|+..|+++||.+.+++|++.+|||||+|+|+|+||.| .
T Consensus 83 d~r~~L~~~~~r~i~~~~P~~~v~ENV~~l~~~~~~~~~~~i~~~l~~~GY~v~~~~l~a~dyGvPQ~R~R~f~ia~r~~ 162 (315)
T TIGR00675 83 DTRGTLFFEIVRILKEKKPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYYKVLNAKDFGVPQNRERIYIVGFRDF 162 (315)
T ss_pred CchhhHHHHHHHHHhhcCCCEEEeeccHHHHhcccchHHHHHHHHHHhCCCEEEEEEEcHHHCCCCCCccEEEEEEEeCC
Confidence 5699999999999999999999999994 466789999999999999999999999999999999999999999 3
Q ss_pred CCCCCCCCcccccCCccccccccccccccCCCCccccchhhhccCCCCCcccccccccCHHHHhh
Q psy4735 333 PAAHSSEASFCFETSSELMTELPKLKSKTCNPLLSRMTLHSILDSTDPSDDLYRRYLVSDKDLLR 397 (1232)
Q Consensus 333 ~l~~sd~ndF~Fp~psqIl~e~Pk~~sksC~PIlsvkpLsDFLEedVDs~E~~eKYLLPDKLLeR 397 (1232)
+. ...|.||.+.. + ....+|+++++..... ...|.+++..+.+
T Consensus 163 ~~----~~~~~~p~~~~-----~----------~~~~~l~d~~~~~~~~---~~~~~~~~~~~~~ 205 (315)
T TIGR00675 163 DD----KLNFEFPKPIY-----V----------AKKKRIGDLLDLSVDL---EEKYYLSEEKKNG 205 (315)
T ss_pred Cc----CcCCCCCCCcc-----c----------ccccchHHhcccccCc---CCcEEeCHHHHHH
Confidence 32 12466654311 0 0123688888744321 1356777765544
No 7
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.92 E-value=1.7e-25 Score=239.31 Aligned_cols=77 Identities=18% Similarity=0.286 Sum_probs=72.2
Q ss_pred HHhccCCCcccchhhhhccCCcEEEEEEcc----cCCchHHHHHHHHHhCCCeeEEEEeCCCCCCCCcccceEEEEEEeC
Q psy4735 257 LVESRTHAPCTVEPYVNCLHQTMICFINVL----KNQLPYVCTTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKRS 332 (1232)
Q Consensus 257 ~~~~R~~l~~~~v~~V~alrPr~~VfENV~----K~~~~fkeIietLeslGY~VqEfILNPaDFGVPQSR~RYFLIAkRk 332 (1232)
+-..||+||.+|+++|+.++|++||+|||+ .++.+|+.|++.|+++||.+.+.|||+++|||||+|+|+|+||.++
T Consensus 89 ~~D~R~~L~~~~~r~I~~~~P~~fv~ENV~gl~~~~~~~~~~i~~~L~~~GY~~~~~ilna~dyGvPQ~ReRvfiig~~~ 168 (328)
T COG0270 89 YDDPRGSLFLEFIRLIEQLRPKFFVLENVKGLLSSKGQTFDEIKKELEELGYGVEFNILNAADYGVPQSRERVFIVGFRR 168 (328)
T ss_pred CcCccceeeHHHHHHHHhhCCCEEEEecCchHHhcCchHHHHHHHHHHHcCCcchHheeeHHhcCCCCCccEEEEEEecC
Confidence 457899999999999999999999999994 2467999999999999999999999999999999999999999998
Q ss_pred C
Q psy4735 333 P 333 (1232)
Q Consensus 333 ~ 333 (1232)
+
T Consensus 169 ~ 169 (328)
T COG0270 169 D 169 (328)
T ss_pred c
Confidence 4
No 8
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.69 E-value=2.7e-17 Score=185.99 Aligned_cols=55 Identities=35% Similarity=0.491 Sum_probs=48.9
Q ss_pred cCCcccCCHHHHHhhcCC--CCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHHhc
Q psy4735 1172 RLNLRYFSPDEIRKLMCF--PDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLMLC 1226 (1232)
Q Consensus 1172 ~lkLR~FTPRE~ARLqGF--PddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~Ll~ 1226 (1232)
+.++|+|||||||||||| |++|.|+..+|++|+|||+||||+|+||++|++.|..
T Consensus 398 ~~~~RrLTprE~aRLqGF~~pd~~~F~~~vSdtq~Ykq~GNSV~Vpvv~aIa~~L~~ 454 (467)
T PRK10458 398 QHRPRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAKLLEP 454 (467)
T ss_pred cCCcccCCHHHHHHhCCCCCCccccccCCCCHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 457899999999999999 5667776558999999999999999999999999864
No 9
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=99.40 E-value=1.6e-13 Score=140.24 Aligned_cols=56 Identities=27% Similarity=0.418 Sum_probs=46.3
Q ss_pred HHhcCCcccCCHHHHHhhcCCCCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHHhc
Q psy4735 1169 ELKRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLMLC 1226 (1232)
Q Consensus 1169 ~L~~lkLR~FTPRE~ARLqGFPddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~Ll~ 1226 (1232)
.++..+.|+||||||||||||||+|.|+ .+..++|||+||||+|+|+++|++.|..
T Consensus 280 ~~hp~~~R~LT~rE~aRLqgFPd~~~f~--g~~~~~~~qiGNAVpp~v~~~I~~~i~~ 335 (335)
T PF00145_consen 280 FIHPEQNRRLTPREAARLQGFPDDFKFP--GSKTQQYKQIGNAVPPPVAEAIAKAIKK 335 (335)
T ss_dssp EBTTSSSCB-BHHHHHHHTTSSTTS-S---SSHHHHHHHHHCS--HHHHHHHHHHHH-
T ss_pred ccCCCCCCcCcHHHHHHhCCCCCceEcc--CCHHHHhceECCCcCHHHHHHHHHHhhC
Confidence 4577889999999999999999999999 5777999999999999999999999863
No 10
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=99.23 E-value=7.4e-12 Score=132.19 Aligned_cols=55 Identities=33% Similarity=0.504 Sum_probs=49.9
Q ss_pred hcCCcccCCHHHHHhhcCCCCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHHhc
Q psy4735 1171 KRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLMLC 1226 (1232)
Q Consensus 1171 ~~lkLR~FTPRE~ARLqGFPddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~Ll~ 1226 (1232)
+....|+||+||+|||||||++|.|+.. +.+++|||+||||+|+|+++|++.|.+
T Consensus 221 ~~~~~R~lT~rE~arlqgFPd~f~f~g~-~~~~~~~qiGNAVp~~~~~~I~~~i~~ 275 (275)
T cd00315 221 KESNIRRLTPRECARLQGFPDDFEFPGK-SVTQAYRQIGNSVPVPVAEAIAKAIKE 275 (275)
T ss_pred cCCCCCCCCHHHHHHHcCCCCCcEEcCC-CHHHHHHhhcCCcCHHHHHHHHHHHhC
Confidence 4567899999999999999999999832 899999999999999999999998763
No 11
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.17 E-value=1.6e-11 Score=132.05 Aligned_cols=52 Identities=33% Similarity=0.543 Sum_probs=47.9
Q ss_pred hcCCcccCCHHHHHhhcCCCCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHH
Q psy4735 1171 KRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLM 1224 (1232)
Q Consensus 1171 ~~lkLR~FTPRE~ARLqGFPddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~L 1224 (1232)
+....|.||+||+||||||||+|.|+ .+.+++|||+||||+|+++++|++.|
T Consensus 264 hp~~~R~lT~RE~aRLQ~FPd~f~f~--~s~~~~~~qiGNAVPp~la~~I~~~i 315 (315)
T TIGR00675 264 HPGRIRRLTPRECARLQGFPDDFKFP--VSDSQLYKQAGNAVVVPVIEAIAKQI 315 (315)
T ss_pred cCCceeeCCHHHHHHHcCCCcccEeC--CCHHHHHhhhCCcccHHHHHHHHhhC
Confidence 45567999999999999999999998 69999999999999999999999764
No 12
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=98.92 E-value=7.6e-10 Score=119.73 Aligned_cols=54 Identities=28% Similarity=0.416 Sum_probs=50.7
Q ss_pred hcCCcccCCHHHHHhhcCCCCCCcCCCCCChhhHHHHhCCceehHHHHHHHHHHhc
Q psy4735 1171 KRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAYCICLMLC 1226 (1232)
Q Consensus 1171 ~~lkLR~FTPRE~ARLqGFPddF~FPe~vS~kQ~YKQLGNSVnV~VV~~Lak~Ll~ 1226 (1232)
+....|.||+||+||||||||+|.|+. |..++|+|+||||+|.++++|++.|++
T Consensus 269 h~~~~r~lt~rE~arlq~fPd~~~~~g--s~~~~~~qiGnsVp~~l~~~ia~~i~~ 322 (328)
T COG0270 269 HPLEDRELTVREAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEAIAKAILK 322 (328)
T ss_pred CCCcCCCCCHHHHHHhcCCCCceEEec--cchhhhhhccCcCCHHHHHHHHHHHHH
Confidence 666789999999999999999999994 999999999999999999999999875
No 13
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.09 E-value=7.5 Score=40.87 Aligned_cols=13 Identities=54% Similarity=0.925 Sum_probs=11.3
Q ss_pred eeccccccccccc
Q psy4735 38 LIPHEYAHYHLDL 50 (1232)
Q Consensus 38 ~~~~~~~~~~~~~ 50 (1232)
+||||.||||+-+
T Consensus 64 vV~HELaHl~ly~ 76 (156)
T COG3091 64 VVPHELAHLHLYQ 76 (156)
T ss_pred HHHHHHHHHHHHH
Confidence 5899999999854
No 14
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=29.97 E-value=66 Score=27.21 Aligned_cols=51 Identities=14% Similarity=0.288 Sum_probs=32.9
Q ss_pred cccCHHHHHhhcCCCCCCCCCCCCChhHHHHHh-CC--ceehHHHHHHHHHhccCCccccccCc
Q psy4735 837 RYFSPDEIRKLMCFPDDCRFPPDCSDKSRYKLL-GN--SINVHVVAYCICLMLCEPAPMMTELP 897 (1232)
Q Consensus 837 R~LTPREcaRLqGFPddF~fP~~iS~~Q~Ykql-GN--SVsVpVV~~la~~l~~~~~pMmteLp 897 (1232)
|.+|..++++-.|+ |....++.+ |+ ++++..+..||..|-+.|+.++..-|
T Consensus 9 ~~it~~~La~~~gi----------s~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~~~~~ 62 (63)
T PF13443_consen 9 RGITQKDLARKTGI----------SRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEELFEYEP 62 (63)
T ss_dssp TT--HHHHHHHHT------------HHHHHHHHTTT-----HHHHHHHHHHHT--HHHCTECCE
T ss_pred cCCCHHHHHHHHCc----------CHHHHHHHHhcccccccHHHHHHHHHHcCCCHHHHhhcCC
Confidence 34599999999885 455566664 33 69999999999999999998886543
No 15
>KOG0031|consensus
Probab=29.40 E-value=37 Score=36.34 Aligned_cols=68 Identities=26% Similarity=0.382 Sum_probs=54.7
Q ss_pred eccccccccCCchhHHHHHHHHHhhhhhcccCCCchhhhhhhhcccccccccccCCcchhHHHHHHHHhhhhhhhhh
Q psy4735 966 EGTGSVLSNLGDMTQIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRVNLE 1042 (1232)
Q Consensus 966 EGTGSVl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1042 (1232)
.++++|++.+.. .||.|.-|.+.-+.|--|-.-. |=|+.|+-+..|..---+-||+|++.|-.-+|+-
T Consensus 17 rasSnvFamf~q-~QIqEfKEAF~~mDqnrDG~Id--------keDL~d~~aSlGk~~~d~elDaM~~Ea~gPINft 84 (171)
T KOG0031|consen 17 RASSNVFAMFDQ-SQIQEFKEAFNLMDQNRDGFID--------KEDLRDMLASLGKIASDEELDAMMKEAPGPINFT 84 (171)
T ss_pred cccchHHHHhhH-HHHHHHHHHHHHHhccCCCccc--------HHHHHHHHHHcCCCCCHHHHHHHHHhCCCCeeHH
Confidence 467788887766 9999999999988886555532 2377888888898888889999999999888764
No 16
>PRK04351 hypothetical protein; Provisional
Probab=26.54 E-value=13 Score=38.40 Aligned_cols=13 Identities=62% Similarity=1.140 Sum_probs=10.8
Q ss_pred eeccccccccccc
Q psy4735 38 LIPHEYAHYHLDL 50 (1232)
Q Consensus 38 ~~~~~~~~~~~~~ 50 (1232)
.||||++|||+-+
T Consensus 64 vv~HElcH~~~~~ 76 (149)
T PRK04351 64 IIKHELCHYHLHL 76 (149)
T ss_pred hHHHHHHHHHHHH
Confidence 5899999998653
No 17
>PRK04860 hypothetical protein; Provisional
Probab=22.34 E-value=16 Score=38.05 Aligned_cols=13 Identities=38% Similarity=0.667 Sum_probs=11.4
Q ss_pred eeccccccccccc
Q psy4735 38 LIPHEYAHYHLDL 50 (1232)
Q Consensus 38 ~~~~~~~~~~~~~ 50 (1232)
+||||.||||+-+
T Consensus 66 ~v~HEl~H~~~~~ 78 (160)
T PRK04860 66 VVPHELAHLLVYQ 78 (160)
T ss_pred HHHHHHHHHHHHH
Confidence 5799999999875
Done!