Query 046713
Match_columns 216
No_of_seqs 141 out of 1590
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 03:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046713.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046713hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00675 dcm DNA-methyltransf 99.9 3.5E-24 7.6E-29 190.7 8.0 106 91-216 199-314 (315)
2 cd00315 Cyt_C5_DNA_methylase C 99.8 1E-20 2.2E-25 165.5 7.0 77 137-215 186-271 (275)
3 PF00145 DNA_methylase: C-5 cy 99.8 3.3E-20 7.2E-25 162.5 7.5 52 164-215 280-331 (335)
4 COG0270 Dcm Site-specific DNA 99.8 8.3E-20 1.8E-24 163.4 6.5 75 136-215 244-318 (328)
5 PRK10458 DNA cytosine methylas 99.4 2.8E-13 6.1E-18 126.5 6.1 52 164-215 391-450 (467)
6 KOG0919 C-5 cytosine-specific 97.7 2.6E-05 5.5E-10 67.4 2.5 43 166-208 283-327 (338)
7 PF03078 ATHILA: ATHILA ORF-1 23.5 65 0.0014 30.7 2.5 40 168-207 138-182 (458)
8 PF08624 CRC_subunit: Chromati 22.8 17 0.00037 28.9 -1.2 25 174-198 50-74 (139)
9 PF14744 WASH-7_mid: WASH comp 21.1 43 0.00094 30.6 0.8 31 175-205 289-319 (350)
10 PRK00014 ribB 3,4-dihydroxy-2- 17.2 30 0.00065 29.9 -1.0 25 169-193 117-141 (230)
No 1
>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=99.90 E-value=3.5e-24 Score=190.67 Aligned_cols=106 Identities=21% Similarity=0.152 Sum_probs=78.8
Q ss_pred CHHHHHHHhcCCCCCCCCCCCCCchhhhccccCCCCCccccCCCCCCccccccCCCCCCceecCCC---CCCC-------
Q 046713 91 SELNLIRCQKIPKQPGSDWRVLPSEKVVDLIPWCLPNTAEKHNQWKGLFGRLDWEGNFPTSVTDPH---PMGM------- 160 (216)
Q Consensus 91 s~~~~~r~~~ip~~~G~~~~dlp~~~~~~l~~~~~~~~~~~~~~~~~~y~Rl~~~~p~~Ti~~~~~---~~~~------- 160 (216)
++..++++..++ +|.+|.+... ..+...|+|+.|+.+++|+++... ..+.
T Consensus 199 ~~~~~~~~~~~~--~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~t~~~~~~ 258 (315)
T TIGR00675 199 SEEKKNGLLLLL--ENMRKKEGTG------------------EQIGSFYNRESKSSIIRTLSARGYTFVKGGKSVLIVPH 258 (315)
T ss_pred CHHHHHHHHHHh--hccccccccc------------------cccceeeccCCccceeeeeeccccccCCCCcceeeccc
Confidence 556788888888 6776654111 112235667777777777765221 0000
Q ss_pred CceeeCCCCCccCcHHHHHHhcCCCCCceecCCHHhHHhhcccccchHHHHHhhcC
Q 046713 161 VGTCFHPNQDRIITVRECARSQGFSDSYKFVGDIQHIIGRLEMLFHLLWRLHWGEN 216 (216)
Q Consensus 161 ~~~~~Hp~~~R~lTvrE~aRlQsFPD~~~f~g~~~~~~~qIGNAVpp~la~aig~~ 216 (216)
.+..+||.++|.||+|||||||||||+|+|.|+.+++|+||||||||+|+++||+.
T Consensus 259 ~~~~~hp~~~R~lT~RE~aRLQ~FPd~f~f~~s~~~~~~qiGNAVPp~la~~I~~~ 314 (315)
T TIGR00675 259 KSTVVHPGRIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVVPVIEAIAKQ 314 (315)
T ss_pred cceeccCCceeeCCHHHHHHHcCCCcccEeCCCHHHHHhhhCCcccHHHHHHHHhh
Confidence 01127999999999999999999999999999999999999999999999999973
No 2
>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=99.82 E-value=1e-20 Score=165.53 Aligned_cols=77 Identities=23% Similarity=0.314 Sum_probs=66.2
Q ss_pred CccccccCCCCCCceecCCCCCCCCcee--------eCCCCCccCcHHHHHHhcCCCCCceecC-CHHhHHhhcccccch
Q 046713 137 GLFGRLDWEGNFPTSVTDPHPMGMVGTC--------FHPNQDRIITVRECARSQGFSDSYKFVG-DIQHIIGRLEMLFHL 207 (216)
Q Consensus 137 ~~y~Rl~~~~p~~Ti~~~~~~~~~~~~~--------~Hp~~~R~lTvrE~aRlQsFPD~~~f~g-~~~~~~~qIGNAVpp 207 (216)
+..+++.|++|++||++..+. + .+.+ .||.+.|.||+||+||||||||+|.|.| +.+++|+||||||||
T Consensus 186 d~l~~~~~~~~~~ti~~~~~~-~-~~~~~~~~~~~~~~~~~~R~lT~rE~arlqgFPd~f~f~g~~~~~~~~qiGNAVp~ 263 (275)
T cd00315 186 DILRIRDPDEPSPTLTASYGK-G-TGSVHPTAPDMIGKESNIRRLTPRECARLQGFPDDFEFPGKSVTQAYRQIGNSVPV 263 (275)
T ss_pred HHHhhhcCCCCccceecCCCC-C-ccccccCcccccccCCCCCCCCHHHHHHHcCCCCCcEEcCCCHHHHHHhhcCCcCH
Confidence 344789999999999987753 1 1221 4667899999999999999999999999 999999999999999
Q ss_pred HHHHHhhc
Q 046713 208 LWRLHWGE 215 (216)
Q Consensus 208 ~la~aig~ 215 (216)
+++++||+
T Consensus 264 ~~~~~I~~ 271 (275)
T cd00315 264 PVAEAIAK 271 (275)
T ss_pred HHHHHHHH
Confidence 99999986
No 3
>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=99.81 E-value=3.3e-20 Score=162.50 Aligned_cols=52 Identities=31% Similarity=0.416 Sum_probs=45.9
Q ss_pred eeCCCCCccCcHHHHHHhcCCCCCceecCCHHhHHhhcccccchHHHHHhhc
Q 046713 164 CFHPNQDRIITVRECARSQGFSDSYKFVGDIQHIIGRLEMLFHLLWRLHWGE 215 (216)
Q Consensus 164 ~~Hp~~~R~lTvrE~aRlQsFPD~~~f~g~~~~~~~qIGNAVpp~la~aig~ 215 (216)
.+||.+.|.||+|||||||||||+|.|.|+.+++|+||||||||+|+++||+
T Consensus 280 ~~hp~~~R~LT~rE~aRLqgFPd~~~f~g~~~~~~~qiGNAVpp~v~~~I~~ 331 (335)
T PF00145_consen 280 FIHPEQNRRLTPREAARLQGFPDDFKFPGSKTQQYKQIGNAVPPPVAEAIAK 331 (335)
T ss_dssp EBTTSSSCB-BHHHHHHHTTSSTTS-S-SSHHHHHHHHHCS--HHHHHHHHH
T ss_pred ccCCCCCCcCcHHHHHHhCCCCCceEccCCHHHHhceECCCcCHHHHHHHHH
Confidence 6899999999999999999999999999999999999999999999999986
No 4
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.79 E-value=8.3e-20 Score=163.41 Aligned_cols=75 Identities=31% Similarity=0.361 Sum_probs=69.3
Q ss_pred CCccccccCCCCCCceecCCCCCCCCceeeCCCCCccCcHHHHHHhcCCCCCceecCCHHhHHhhcccccchHHHHHhhc
Q 046713 136 KGLFGRLDWEGNFPTSVTDPHPMGMVGTCFHPNQDRIITVRECARSQGFSDSYKFVGDIQHIIGRLEMLFHLLWRLHWGE 215 (216)
Q Consensus 136 ~~~y~Rl~~~~p~~Ti~~~~~~~~~~~~~~Hp~~~R~lTvrE~aRlQsFPD~~~f~g~~~~~~~qIGNAVpp~la~aig~ 215 (216)
...|.||.|+.|++|+.... ....+||...|.||+||+||||||||+|.|.|+.+++|+||||||||+++++||+
T Consensus 244 ~~~~~rl~~~~~~~t~~~~~-----~~~~~h~~~~r~lt~rE~arlq~fPd~~~~~gs~~~~~~qiGnsVp~~l~~~ia~ 318 (328)
T COG0270 244 KGSYIRLHPDKPAPTVRGGG-----NERFIHPLEDRELTVREAARLQGFPDDFVFPGSKTDQYRQIGNSVPPLLAEAIAK 318 (328)
T ss_pred CceeEeCCCCCCCceeecCC-----CcccCCCCcCCCCCHHHHHHhcCCCCceEEeccchhhhhhccCcCCHHHHHHHHH
Confidence 57899999999999998432 2468999999999999999999999999999999999999999999999999997
No 5
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.40 E-value=2.8e-13 Score=126.48 Aligned_cols=52 Identities=23% Similarity=0.218 Sum_probs=44.5
Q ss_pred eeCCC----CCccCcHHHHHHhcCC--CCCceec--CCHHhHHhhcccccchHHHHHhhc
Q 046713 164 CFHPN----QDRIITVRECARSQGF--SDSYKFV--GDIQHIIGRLEMLFHLLWRLHWGE 215 (216)
Q Consensus 164 ~~Hp~----~~R~lTvrE~aRlQsF--PD~~~f~--g~~~~~~~qIGNAVpp~la~aig~ 215 (216)
+.||. ..|.||+||||||||| ||+|.|. .+.+++|+|+||||+++++++||+
T Consensus 391 ~~~~~~~~~~~RrLTprE~aRLqGF~~pd~~~F~~~vSdtq~Ykq~GNSV~Vpvv~aIa~ 450 (467)
T PRK10458 391 FDDPENQQHRPRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAK 450 (467)
T ss_pred ccccccccCCcccCCHHHHHHhCCCCCCccccccCCCCHHHHHHHhCCcccHHHHHHHHH
Confidence 45554 3699999999999999 6666664 578999999999999999999986
No 6
>KOG0919 consensus C-5 cytosine-specific DNA methylase [Transcription]
Probab=97.66 E-value=2.6e-05 Score=67.42 Aligned_cols=43 Identities=26% Similarity=0.336 Sum_probs=35.9
Q ss_pred CCCCCccCcHHHHHHhcCCCCCceecCC--HHhHHhhcccccchH
Q 046713 166 HPNQDRIITVRECARSQGFSDSYKFVGD--IQHIIGRLEMLFHLL 208 (216)
Q Consensus 166 Hp~~~R~lTvrE~aRlQsFPD~~~f~g~--~~~~~~qIGNAVpp~ 208 (216)
|-.+-|-+|+||.|||+|||.+|.|... ..+.|+.+||++=..
T Consensus 283 ~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVk 327 (338)
T KOG0919|consen 283 HQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVK 327 (338)
T ss_pred HHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccce
Confidence 3346799999999999999999999854 457899999998543
No 7
>PF03078 ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 ATHILA is a group of Arabidopsis thaliana retrotransposons [] belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons[, ]. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.
Probab=23.51 E-value=65 Score=30.65 Aligned_cols=40 Identities=10% Similarity=0.153 Sum_probs=30.3
Q ss_pred CCCccCcHHHHHHhcCCCCCceecCC-----HHhHHhhcccccch
Q 046713 168 NQDRIITVRECARSQGFSDSYKFVGD-----IQHIIGRLEMLFHL 207 (216)
Q Consensus 168 ~~~R~lTvrE~aRlQsFPD~~~f~g~-----~~~~~~qIGNAVpp 207 (216)
...=.||+.+..++=|||++...... ...-+..||+++|-
T Consensus 138 ~~~y~lsi~~L~~i~GF~~~~~i~~~~~~~el~~~W~~ig~~~p~ 182 (458)
T PF03078_consen 138 GVEYSLSIKHLERIFGFPSGDEIKPDFDPEELNDFWATIGGGKPF 182 (458)
T ss_pred ceeeeeeHHHHHHHhCCCCccccCCCCCchHHHHHHHHhcCCCcc
Confidence 34556999999999999999766432 35667889998654
No 8
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=22.77 E-value=17 Score=28.91 Aligned_cols=25 Identities=32% Similarity=0.483 Sum_probs=19.3
Q ss_pred cHHHHHHhcCCCCCceecCCHHhHH
Q 046713 174 TVRECARSQGFSDSYKFVGDIQHII 198 (216)
Q Consensus 174 TvrE~aRlQsFPD~~~f~g~~~~~~ 198 (216)
-+.|+||+.||-|+|.|.....+.|
T Consensus 50 L~td~ar~lg~rDs~~ff~~~~~l~ 74 (139)
T PF08624_consen 50 LSTDPARCLGFRDSYLFFRKHPQLY 74 (139)
T ss_pred EeHHHHHHhccccHHHHHHhCCcee
Confidence 4789999999999999975433333
No 9
>PF14744 WASH-7_mid: WASH complex subunit 7
Probab=21.06 E-value=43 Score=30.64 Aligned_cols=31 Identities=6% Similarity=0.146 Sum_probs=22.7
Q ss_pred HHHHHHhcCCCCCceecCCHHhHHhhccccc
Q 046713 175 VRECARSQGFSDSYKFVGDIQHIIGRLEMLF 205 (216)
Q Consensus 175 vrE~aRlQsFPD~~~f~g~~~~~~~qIGNAV 205 (216)
.|+..+|.--+|...|...-.....|||||+
T Consensus 289 ~k~irkLG~~~dG~sylD~FR~LItqIGNA~ 319 (350)
T PF14744_consen 289 NKGIRKLGLSDDGQSYLDQFRQLITQIGNAM 319 (350)
T ss_pred HHHHHHcCCCCCcchHHHHHHHHHHHHhHHH
Confidence 4556666666777777766677778999997
No 10
>PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=17.24 E-value=30 Score=29.87 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=22.7
Q ss_pred CCccCcHHHHHHhcCCCCCceecCC
Q 046713 169 QDRIITVRECARSQGFSDSYKFVGD 193 (216)
Q Consensus 169 ~~R~lTvrE~aRlQsFPD~~~f~g~ 193 (216)
.+|..|+|++|--+++|+||.-.|-
T Consensus 117 ~DRa~Tir~La~~~~~~~DF~rPGH 141 (230)
T PRK00014 117 VDRVTTIRAAIAPGARSGDVVSPGH 141 (230)
T ss_pred HHHHHHHHHHhCCCCCHHHcCCCCc
Confidence 4799999999999999999998873
Done!