Query 026734
Match_columns 234
No_of_seqs 220 out of 1356
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 11:57:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026734.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026734hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0919 C-5 cytosine-specific 100.0 1.2E-35 2.5E-40 266.7 2.9 169 8-230 156-337 (338)
2 PRK10458 DNA cytosine methylas 99.9 1.6E-21 3.4E-26 187.9 14.2 114 117-231 322-454 (467)
3 TIGR00675 dcm DNA-methyltransf 99.7 8.8E-17 1.9E-21 146.9 10.9 53 175-229 263-315 (315)
4 PF00145 DNA_methylase: C-5 cy 99.7 8E-17 1.7E-21 141.5 6.1 56 174-231 280-335 (335)
5 cd00315 Cyt_C5_DNA_methylase C 99.6 2.1E-16 4.5E-21 141.9 7.4 86 135-231 190-275 (275)
6 COG0270 Dcm Site-specific DNA 99.4 2.5E-13 5.4E-18 124.7 7.7 79 147-231 244-322 (328)
7 PF00985 MSA_2: Merozoite Surf 27.4 23 0.00051 30.6 0.3 6 2-7 108-113 (171)
8 PF13443 HTH_26: Cro/C1-type H 19.6 2.5E+02 0.0053 18.9 4.3 41 180-230 8-51 (63)
9 TIGR01764 excise DNA binding d 16.0 1E+02 0.0022 19.3 1.5 16 182-197 1-16 (49)
10 PRK09786 endodeoxyribonuclease 15.7 74 0.0016 25.8 1.0 9 8-16 10-18 (120)
No 1
>KOG0919 consensus C-5 cytosine-specific DNA methylase [Transcription]
Probab=100.00 E-value=1.2e-35 Score=266.66 Aligned_cols=169 Identities=34% Similarity=0.523 Sum_probs=135.3
Q ss_pred CCCCCCceeEeeecCCCCccccccccccccCCCCCCCCCcccccccCCCCCcchhhcccCcchHHHhhcccCCCCCcccc
Q 026734 8 FPPHVNPTLGKAKRKPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLEFSNSGDQVNTE 87 (234)
Q Consensus 8 ~~~~~~ry~~lAk~~~~~f~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~le~~~~~~~~~~~ 87 (234)
.|-+|+||||+||.. .+|+++... .|..+|.+ .. ..+ -.+.++-|.+|||.+
T Consensus 156 iPNsR~Ryy~iArl~-~~F~~~G~~---s~d~~~qF-----se---------iaq-k~g~Vk~i~d~lE~~--------- 207 (338)
T KOG0919|consen 156 IPNSRYRYYCIARLG-ADFPFAGGK---SWDEMPQF-----SE---------IAQ-KQGLVKQIADILEEN--------- 207 (338)
T ss_pred CCCcchheeehhhhC-CCCCCCCCc---ccccccch-----HH---------HHH-hcchHHHHHHHHHhc---------
Confidence 599999999999976 467665533 45544443 01 111 133467899999952
Q ss_pred ccccccCCccccccCCccccchhcccccccccCCChhHHhhhcCcceeeccCCCCCcccccceeeeecCCcceeeecCC-
Q 026734 88 TGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPDSKRCCCFTKSYYRYVKGTGSLLATVQP- 166 (234)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~v~~~~l~k~g~~~DIV~p~s~~s~cFTksY~r~~~GtgSvl~~~~~- 166 (234)
..+.+|+||+++|.||+..||||.|.+.+|+||||+|++|.+|+||++....-
T Consensus 208 --------------------------~d~s~ylvp~~vL~k~~l~~DIv~P~~srs~CFTkGYthy~eGtGSilq~~~~i 261 (338)
T KOG0919|consen 208 --------------------------VDPSDYLVPDDVLTKRVLVMDIVHPAQSRSMCFTKGYTHYTEGTGSILQLVKEI 261 (338)
T ss_pred --------------------------CCHHHccCCHHHHHHhHhheeecccccccceEeecCccceeecchHHHHHHhhh
Confidence 12467999999999999999999999999999999999999999999865431
Q ss_pred --CC----------CCCCccccCCCcccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhcCcccHHHHHHHHHHHH
Q 026734 167 --KN----------KGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYLF 230 (234)
Q Consensus 167 --~~----------~~k~~~l~~~~lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiGNAV~v~vv~~La~~Ll 230 (234)
.+ ..+...++..++|||||||+|||||||.+|.||..++.+|+|+++|||++|.||..|++-|.
T Consensus 262 ~~eN~~~s~~~~~~~~~~~~l~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVkVV~~LIklL~ 337 (338)
T KOG0919|consen 262 DTENQDASKSEKILQQRLDLLHQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVKVVGELIKLLT 337 (338)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccceeHHHHHHHhc
Confidence 00 01124567789999999999999999999999988999999999999999999999998875
No 2
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.87 E-value=1.6e-21 Score=187.88 Aligned_cols=114 Identities=29% Similarity=0.443 Sum_probs=84.2
Q ss_pred cccCCChhHHh---hh---------cCcceeeccCCCCCcccccceeeeecCCcceeeecC-CCCCCCCcccc----CCC
Q 026734 117 DHFLVPLSLIE---RW---------GSAMDIVYPDSKRCCCFTKSYYRYVKGTGSLLATVQ-PKNKGKASSLK----EQH 179 (234)
Q Consensus 117 ~~y~v~~~~l~---k~---------g~~~DIV~p~s~~s~cFTksY~r~~~GtgSvl~~~~-~~~~~k~~~l~----~~~ 179 (234)
++|++++++.. +| |+.++++.|.+.++.|+|.+| +|.+++..+++... ....+...+.+ ..+
T Consensus 322 ~ky~ls~~~~~~l~~~~~k~~~~g~g~~~~i~~~~~~~~~~~t~~~-ry~k~gs~~~i~~~~~~~~~~~~~~~~~~~~~~ 400 (467)
T PRK10458 322 AKYILTPVLWKYLYRYAKKHQAKGNGFGYGLVYPNNPQSVTRTLSA-RYYKDGSEILIDRGWDMALGEKDFDDPENQQHR 400 (467)
T ss_pred cceeeCHHHHHHHHHHHhhccccCCCcceeeeecCCCCCccccccc-ccccCCCceeeecccccccccccccccccccCC
Confidence 45777766543 33 567899999888899999994 88888544444321 01111112222 356
Q ss_pred cccCcHHHHHHhCCC--CCCeecCCCCCHHHHHHHhcCcccHHHHHHHHHHHHh
Q 026734 180 LRYFTPREVANLHSF--PGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYLFA 231 (234)
Q Consensus 180 lR~lTprE~aRLQgF--Pddf~fp~~~s~~q~ykqiGNAV~v~vv~~La~~Ll~ 231 (234)
+|+|||||||||||| |++|.|+..++.+|+|+|+||||+|+|+++|++.|..
T Consensus 401 ~RrLTprE~aRLqGF~~pd~~~F~~~vSdtq~Ykq~GNSV~Vpvv~aIa~~L~~ 454 (467)
T PRK10458 401 PRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAKLLEP 454 (467)
T ss_pred cccCCHHHHHHhCCCCCCccccccCCCCHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 899999999999999 6667776558999999999999999999999999864
No 3
>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=99.70 E-value=8.8e-17 Score=146.89 Aligned_cols=53 Identities=36% Similarity=0.692 Sum_probs=50.4
Q ss_pred ccCCCcccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhcCcccHHHHHHHHHHH
Q 026734 175 LKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYL 229 (234)
Q Consensus 175 l~~~~lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiGNAV~v~vv~~La~~L 229 (234)
+|+.+.|.||+||+||||||||+|.|+ ++.+++|+||||||||+++++|++.|
T Consensus 263 ~hp~~~R~lT~RE~aRLQ~FPd~f~f~--~s~~~~~~qiGNAVPp~la~~I~~~i 315 (315)
T TIGR00675 263 VHPGRIRRLTPRECARLQGFPDDFKFP--VSDSQLYKQAGNAVVVPVIEAIAKQI 315 (315)
T ss_pred ccCCceeeCCHHHHHHHcCCCcccEeC--CCHHHHHhhhCCcccHHHHHHHHhhC
Confidence 788999999999999999999999997 59999999999999999999999875
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=99.66 E-value=8e-17 Score=141.54 Aligned_cols=56 Identities=34% Similarity=0.600 Sum_probs=47.6
Q ss_pred cccCCCcccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhcCcccHHHHHHHHHHHHh
Q 026734 174 SLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYLFA 231 (234)
Q Consensus 174 ~l~~~~lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiGNAV~v~vv~~La~~Ll~ 231 (234)
.+|+.+.|+|||||+||||||||+|.|+. +..++|+||||||||+|+++|++.|++
T Consensus 280 ~~hp~~~R~LT~rE~aRLqgFPd~~~f~g--~~~~~~~qiGNAVpp~v~~~I~~~i~~ 335 (335)
T PF00145_consen 280 FIHPEQNRRLTPREAARLQGFPDDFKFPG--SKTQQYKQIGNAVPPPVAEAIAKAIKK 335 (335)
T ss_dssp EBTTSSSCB-BHHHHHHHTTSSTTS-S-S--SHHHHHHHHHCS--HHHHHHHHHHHH-
T ss_pred ccCCCCCCcCcHHHHHHhCCCCCceEccC--CHHHHhceECCCcCHHHHHHHHHHhhC
Confidence 68999999999999999999999999984 888999999999999999999999874
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=99.65 E-value=2.1e-16 Score=141.87 Aligned_cols=86 Identities=38% Similarity=0.597 Sum_probs=66.9
Q ss_pred eeccCCCCCcccccceeeeecCCcceeeecCCCCCCCCccccCCCcccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhc
Q 026734 135 IVYPDSKRCCCFTKSYYRYVKGTGSLLATVQPKNKGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLG 214 (234)
Q Consensus 135 IV~p~s~~s~cFTksY~r~~~GtgSvl~~~~~~~~~k~~~l~~~~lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiG 214 (234)
++.+++ .+.|+|..|++ +++++..... ....++.+.|+||+||+||||||||+|.|+.. +.+++|+|||
T Consensus 190 ~~~~~~-~~~ti~~~~~~---~~~~~~~~~~------~~~~~~~~~R~lT~rE~arlqgFPd~f~f~g~-~~~~~~~qiG 258 (275)
T cd00315 190 IRDPDE-PSPTLTASYGK---GTGSVHPTAP------DMIGKESNIRRLTPRECARLQGFPDDFEFPGK-SVTQAYRQIG 258 (275)
T ss_pred hhcCCC-CccceecCCCC---CccccccCcc------cccccCCCCCCCCHHHHHHHcCCCCCcEEcCC-CHHHHHHhhc
Confidence 344443 56788877665 4555543211 11457788999999999999999999999732 8999999999
Q ss_pred CcccHHHHHHHHHHHHh
Q 026734 215 NSLSIAVVAPLLQYLFA 231 (234)
Q Consensus 215 NAV~v~vv~~La~~Ll~ 231 (234)
|||||+++++|++.|.+
T Consensus 259 NAVp~~~~~~I~~~i~~ 275 (275)
T cd00315 259 NSVPVPVAEAIAKAIKE 275 (275)
T ss_pred CCcCHHHHHHHHHHHhC
Confidence 99999999999999863
No 6
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.43 E-value=2.5e-13 Score=124.73 Aligned_cols=79 Identities=27% Similarity=0.393 Sum_probs=66.4
Q ss_pred ccceeeeecCCcceeeecCCCCCCCCccccCCCcccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhcCcccHHHHHHHH
Q 026734 147 TKSYYRYVKGTGSLLATVQPKNKGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLL 226 (234)
Q Consensus 147 TksY~r~~~GtgSvl~~~~~~~~~k~~~l~~~~lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiGNAV~v~vv~~La 226 (234)
...|.++.+...+..+.. ......+|+...|.||++|++|||||||+|.|.. +..++|+||||||||+++++|+
T Consensus 244 ~~~~~rl~~~~~~~t~~~----~~~~~~~h~~~~r~lt~rE~arlq~fPd~~~~~g--s~~~~~~qiGnsVp~~l~~~ia 317 (328)
T COG0270 244 KGSYIRLHPDKPAPTVRG----GGNERFIHPLEDRELTVREAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEAIA 317 (328)
T ss_pred CceeEeCCCCCCCceeec----CCCcccCCCCcCCCCCHHHHHHhcCCCCceEEec--cchhhhhhccCcCCHHHHHHHH
Confidence 456667777666655541 2335678999999999999999999999999985 9999999999999999999999
Q ss_pred HHHHh
Q 026734 227 QYLFA 231 (234)
Q Consensus 227 ~~Ll~ 231 (234)
+.|++
T Consensus 318 ~~i~~ 322 (328)
T COG0270 318 KAILK 322 (328)
T ss_pred HHHHH
Confidence 99975
No 7
>PF00985 MSA_2: Merozoite Surface Antigen 2 (MSA-2) family; InterPro: IPR001136 The merozoite surface antigen 2 (MSA-2) may play a role in the merozoite attachment to the erythrocyte. It is thought to be attached to the membrane by a GPI-anchor.; GO: 0007155 cell adhesion
Probab=27.39 E-value=23 Score=30.60 Aligned_cols=6 Identities=83% Similarity=1.481 Sum_probs=5.3
Q ss_pred CCCCcC
Q 026734 2 GHMHGF 7 (234)
Q Consensus 2 ~~~~~~ 7 (234)
|||||-
T Consensus 108 ghmhgs 113 (171)
T PF00985_consen 108 GHMHGS 113 (171)
T ss_pred cccccc
Confidence 899995
No 8
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=19.55 E-value=2.5e+02 Score=18.92 Aligned_cols=41 Identities=15% Similarity=0.143 Sum_probs=24.8
Q ss_pred cccCcHHHHHHhCCCCCCeecCCCCCHHHHHHHhcC---cccHHHHHHHHHHHH
Q 026734 180 LRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGN---SLSIAVVAPLLQYLF 230 (234)
Q Consensus 180 lR~lTprE~aRLQgFPddf~fp~~~s~~q~ykqiGN---AV~v~vv~~La~~Ll 230 (234)
-|.+|..+.|+..|++ ....++.+.+ .+....+..|++.|-
T Consensus 8 ~~~it~~~La~~~gis----------~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 8 ERGITQKDLARKTGIS----------RSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp HTT--HHHHHHHHT------------HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcC----------HHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 3677999999988764 4455554433 588888999998874
No 9
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=16.02 E-value=1e+02 Score=19.27 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=13.2
Q ss_pred cCcHHHHHHhCCCCCC
Q 026734 182 YFTPREVANLHSFPGD 197 (234)
Q Consensus 182 ~lTprE~aRLQgFPdd 197 (234)
+||+.|+|++.|.+..
T Consensus 1 ~lt~~e~a~~lgis~~ 16 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKD 16 (49)
T ss_pred CCCHHHHHHHHCCCHH
Confidence 5899999999988654
No 10
>PRK09786 endodeoxyribonuclease RUS; Reviewed
Probab=15.73 E-value=74 Score=25.77 Aligned_cols=9 Identities=33% Similarity=0.645 Sum_probs=8.6
Q ss_pred CCCCCCcee
Q 026734 8 FPPHVNPTL 16 (234)
Q Consensus 8 ~~~~~~ry~ 16 (234)
|||||+||.
T Consensus 10 ~Pps~nry~ 18 (120)
T PRK09786 10 WPPSNNRYY 18 (120)
T ss_pred CCCCCCccE
Confidence 799999999
Done!