Query 034052
Match_columns 105
No_of_seqs 135 out of 1120
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:14:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034052.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034052hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00145 DNA_methylase: C-5 cy 99.8 5.3E-21 1.2E-25 144.7 5.7 56 15-70 280-335 (335)
2 TIGR00675 dcm DNA-methyltransf 99.8 4.3E-20 9.4E-25 144.4 5.7 53 16-68 263-315 (315)
3 cd00315 Cyt_C5_DNA_methylase C 99.8 7.6E-20 1.6E-24 140.6 6.7 69 1-69 197-274 (275)
4 COG0270 Dcm Site-specific DNA 99.7 3.8E-18 8.3E-23 133.9 7.3 71 2-75 257-327 (328)
5 PRK10458 DNA cytosine methylas 99.6 2.7E-15 5.8E-20 123.6 6.1 56 20-75 400-459 (467)
6 KOG0919 C-5 cytosine-specific 99.0 2E-10 4.3E-15 89.4 1.7 53 16-68 282-336 (338)
7 PF03078 ATHILA: ATHILA ORF-1 53.2 29 0.00063 29.3 4.8 57 18-74 137-210 (458)
8 PF03635 Vps35: Vacuolar prote 43.3 7.9 0.00017 34.4 0.0 46 31-77 251-296 (762)
9 PF00479 G6PD_N: Glucose-6-pho 35.5 29 0.00063 25.3 2.0 46 55-100 112-160 (183)
10 PF08144 CPL: CPL (NUC119) dom 35.1 1.1E+02 0.0024 21.6 4.8 59 15-73 13-71 (148)
11 COG2098 Uncharacterized protei 24.5 1.1E+02 0.0025 21.2 3.2 48 22-76 6-54 (116)
12 TIGR01764 excise DNA binding d 22.6 61 0.0013 17.1 1.4 16 23-38 1-16 (49)
13 smart00250 PLEC Plectin repeat 21.6 70 0.0015 17.1 1.5 20 12-31 10-29 (38)
No 1
>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=99.83 E-value=5.3e-21 Score=144.70 Aligned_cols=56 Identities=54% Similarity=0.837 Sum_probs=48.8
Q ss_pred cccCCCcccccHHHHhhhcCCCCCceecCChHhHHhhhcccccHHHHHHHHHHHHH
Q 034052 15 VLHPEQDRVLTIRECARLQGFPDYYRFFGTVKERYCQVGNAVPIVVARALGYALGM 70 (105)
Q Consensus 15 ~ihp~~~R~lT~rE~arLQgFPd~f~~~~s~~~~~k~iGNaVp~~v~~~I~~~l~~ 70 (105)
.+||.+.|.||+||+||||||||+|.|.|+.+++|+||||||||.|+++|+++|++
T Consensus 280 ~~hp~~~R~LT~rE~aRLqgFPd~~~f~g~~~~~~~qiGNAVpp~v~~~I~~~i~~ 335 (335)
T PF00145_consen 280 FIHPEQNRRLTPREAARLQGFPDDFKFPGSKTQQYKQIGNAVPPPVAEAIAKAIKK 335 (335)
T ss_dssp EBTTSSSCB-BHHHHHHHTTSSTTS-S-SSHHHHHHHHHCS--HHHHHHHHHHHH-
T ss_pred ccCCCCCCcCcHHHHHHhCCCCCceEccCCHHHHhceECCCcCHHHHHHHHHHhhC
Confidence 68999999999999999999999999999999999999999999999999999974
No 2
>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=99.80 E-value=4.3e-20 Score=144.35 Aligned_cols=53 Identities=47% Similarity=0.718 Sum_probs=51.2
Q ss_pred ccCCCcccccHHHHhhhcCCCCCceecCChHhHHhhhcccccHHHHHHHHHHH
Q 034052 16 LHPEQDRVLTIRECARLQGFPDYYRFFGTVKERYCQVGNAVPIVVARALGYAL 68 (105)
Q Consensus 16 ihp~~~R~lT~rE~arLQgFPd~f~~~~s~~~~~k~iGNaVp~~v~~~I~~~l 68 (105)
+||.+.|.||+||+||||||||+|.|.++.+++|+||||||||+++++|++.|
T Consensus 263 ~hp~~~R~lT~RE~aRLQ~FPd~f~f~~s~~~~~~qiGNAVPp~la~~I~~~i 315 (315)
T TIGR00675 263 VHPGRIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVVPVIEAIAKQI 315 (315)
T ss_pred ccCCceeeCCHHHHHHHcCCCcccEeCCCHHHHHhhhCCcccHHHHHHHHhhC
Confidence 79999999999999999999999999999999999999999999999999764
No 3
>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=99.80 E-value=7.6e-20 Score=140.56 Aligned_cols=69 Identities=41% Similarity=0.597 Sum_probs=58.3
Q ss_pred CceeeccCCCCCCc--------cccCCCcccccHHHHhhhcCCCCCceecC-ChHhHHhhhcccccHHHHHHHHHHHH
Q 034052 1 MTTVVTFPSLHSMA--------VLHPEQDRVLTIRECARLQGFPDYYRFFG-TVKERYCQVGNAVPIVVARALGYALG 69 (105)
Q Consensus 1 ~pTItT~~~~~~~~--------~ihp~~~R~lT~rE~arLQgFPd~f~~~~-s~~~~~k~iGNaVp~~v~~~I~~~l~ 69 (105)
++|||+....+.+. ..|+.+.|.||+||+||||||||+|.|.| +.+++|+||||||||+++++|++.|.
T Consensus 197 ~~ti~~~~~~~~~~~~~~~~~~~~~~~~~R~lT~rE~arlqgFPd~f~f~g~~~~~~~~qiGNAVp~~~~~~I~~~i~ 274 (275)
T cd00315 197 SPTLTASYGKGTGSVHPTAPDMIGKESNIRRLTPRECARLQGFPDDFEFPGKSVTQAYRQIGNSVPVPVAEAIAKAIK 274 (275)
T ss_pred ccceecCCCCCccccccCcccccccCCCCCCCCHHHHHHHcCCCCCcEEcCCCHHHHHHhhcCCcCHHHHHHHHHHHh
Confidence 46888765421112 14567899999999999999999999999 99999999999999999999999875
No 4
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=99.74 E-value=3.8e-18 Score=133.93 Aligned_cols=71 Identities=41% Similarity=0.623 Sum_probs=64.3
Q ss_pred ceeeccCCCCCCccccCCCcccccHHHHhhhcCCCCCceecCChHhHHhhhcccccHHHHHHHHHHHHHHHHhc
Q 034052 2 TTVVTFPSLHSMAVLHPEQDRVLTIRECARLQGFPDYYRFFGTVKERYCQVGNAVPIVVARALGYALGMAFQKL 75 (105)
Q Consensus 2 pTItT~~~~~~~~~ihp~~~R~lT~rE~arLQgFPd~f~~~~s~~~~~k~iGNaVp~~v~~~I~~~l~~~l~~~ 75 (105)
||+++ ......+||...|.||++|++|||||||+|.|.|+.+++|+||||||||+++++|++.|.+.|.+.
T Consensus 257 ~t~~~---~~~~~~~h~~~~r~lt~rE~arlq~fPd~~~~~gs~~~~~~qiGnsVp~~l~~~ia~~i~~~l~~~ 327 (328)
T COG0270 257 PTVRG---GGNERFIHPLEDRELTVREAARLQGFPDDFVFPGSKTDQYRQIGNSVPPLLAEAIAKAILKKLNEK 327 (328)
T ss_pred ceeec---CCCcccCCCCcCCCCCHHHHHHhcCCCCceEEeccchhhhhhccCcCCHHHHHHHHHHHHHHhhcC
Confidence 55552 245779999999999999999999999999999999999999999999999999999999998763
No 5
>PRK10458 DNA cytosine methylase; Provisional
Probab=99.57 E-value=2.7e-15 Score=123.62 Aligned_cols=56 Identities=38% Similarity=0.501 Sum_probs=49.4
Q ss_pred CcccccHHHHhhhcCC--CCCcee--cCChHhHHhhhcccccHHHHHHHHHHHHHHHHhc
Q 034052 20 QDRVLTIRECARLQGF--PDYYRF--FGTVKERYCQVGNAVPIVVARALGYALGMAFQKL 75 (105)
Q Consensus 20 ~~R~lT~rE~arLQgF--Pd~f~~--~~s~~~~~k~iGNaVp~~v~~~I~~~l~~~l~~~ 75 (105)
..|+|||||||||||| |++|.| +.+.+++|+|+||||+|+|+++|++.|...+...
T Consensus 400 ~~RrLTprE~aRLqGF~~pd~~~F~~~vSdtq~Ykq~GNSV~Vpvv~aIa~~L~~~~~~~ 459 (467)
T PRK10458 400 RPRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAKLLEPKIKQA 459 (467)
T ss_pred CcccCCHHHHHHhCCCCCCccccccCCCCHHHHHHHhCCcccHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999 555555 4589999999999999999999999999988653
No 6
>KOG0919 consensus C-5 cytosine-specific DNA methylase [Transcription]
Probab=98.96 E-value=2e-10 Score=89.40 Aligned_cols=53 Identities=40% Similarity=0.563 Sum_probs=46.8
Q ss_pred ccCCCcccccHHHHhhhcCCCCCceecC--ChHhHHhhhcccccHHHHHHHHHHH
Q 034052 16 LHPEQDRVLTIRECARLQGFPDYYRFFG--TVKERYCQVGNAVPIVVARALGYAL 68 (105)
Q Consensus 16 ihp~~~R~lT~rE~arLQgFPd~f~~~~--s~~~~~k~iGNaVp~~v~~~I~~~l 68 (105)
.|--+.|+||+||.|||||||++|.|+. +..+.|+.+|||+.+.|+..+.+-+
T Consensus 282 l~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVkVV~~LIklL 336 (338)
T KOG0919|consen 282 LHQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVKVVGELIKLL 336 (338)
T ss_pred HHHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccceeHHHHHHHh
Confidence 4556789999999999999999999997 6789999999999999988776554
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=53.15 E-value=29 Score=29.32 Aligned_cols=57 Identities=16% Similarity=0.214 Sum_probs=40.1
Q ss_pred CCCcccccHHHHhhhcCCCCCceecC-----ChHhHHhhhcccc------------cHHHHHHHHHHHHHHHHh
Q 034052 18 PEQDRVLTIRECARLQGFPDYYRFFG-----TVKERYCQVGNAV------------PIVVARALGYALGMAFQK 74 (105)
Q Consensus 18 p~~~R~lT~rE~arLQgFPd~f~~~~-----s~~~~~k~iGNaV------------p~~v~~~I~~~l~~~l~~ 74 (105)
.+..-.||+.+..++-|||.+....+ ...+.|..||+++ --|+++.+-+.|...|..
T Consensus 137 ~~~~y~lsi~~L~~i~GF~~~~~i~~~~~~~el~~~W~~ig~~~p~~~~~~ks~~Ir~PviRy~hr~iA~tlf~ 210 (458)
T PF03078_consen 137 YGVEYSLSIKHLERIFGFPSGDEIKPDFDPEELNDFWATIGGGKPFNSARSKSNQIRSPVIRYFHRLIANTLFA 210 (458)
T ss_pred cceeeeeeHHHHHHHhCCCCccccCCCCCchHHHHHHHHhcCCCcccccccccccccChHHHHHHHHHHhhhcc
Confidence 45667899999999999999865432 3477888899984 345556555555555544
No 8
>PF03635 Vps35: Vacuolar protein sorting-associated protein 35 ; InterPro: IPR005378 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35.Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains [].; PDB: 2R17_C.
Probab=43.32 E-value=7.9 Score=34.40 Aligned_cols=46 Identities=20% Similarity=0.191 Sum_probs=0.0
Q ss_pred hhcCCCCCceecCChHhHHhhhcccccHHHHHHHHHHHHHHHHhcCC
Q 034052 31 RLQGFPDYYRFFGTVKERYCQVGNAVPIVVARALGYALGMAFQKLGN 77 (105)
Q Consensus 31 rLQgFPd~f~~~~s~~~~~k~iGNaVp~~v~~~I~~~l~~~l~~~~~ 77 (105)
.+|-|||+|++. +.......+++--|-.=++.|...+++.|.....
T Consensus 251 iIQvFPDefHL~-TL~~lL~~~~~L~~~V~i~~il~~Li~RL~~y~~ 296 (762)
T PF03635_consen 251 IIQVFPDEFHLQ-TLDELLSACLQLQPGVNIKEILISLIDRLANYAE 296 (762)
T ss_dssp -----------------------------------------------
T ss_pred HHHHCCcHHHHH-HHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHH
Confidence 589999999986 6666777777777777777777777777766443
No 9
>PF00479 G6PD_N: Glucose-6-phosphate dehydrogenase, NAD binding domain; InterPro: IPR022674 Glucose-6-phosphate dehydrogenase (1.1.1.49 from EC) (G6PDH) is a ubiquitous protein, present in bacteria and all eukaryotic cell types []. The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells []. Deficiency of G6PDH is a common genetic abnormality affecting millions of people worldwide. Many sequence variants, most caused by single point mutations, are known, exhibiting a wide variety of phenotypes []. This entry represents the NAD-binding domain of glucose-6-phosphate dehydrogenase.; GO: 0004345 glucose-6-phosphate dehydrogenase activity, 0050661 NADP binding, 0006006 glucose metabolic process, 0055114 oxidation-reduction process; PDB: 4EM5_C 4E9I_A 2DPG_A 1E77_A 1E7M_A 1H9B_A 1E7Y_A 1DPG_B 1H93_A 1H9A_A ....
Probab=35.52 E-value=29 Score=25.31 Aligned_cols=46 Identities=20% Similarity=0.125 Sum_probs=34.3
Q ss_pred cccHHHHHHHHHHHHHHHHhcCC---CCCCcCCCCCCchhhhhHHHHhh
Q 034052 55 AVPIVVARALGYALGMAFQKLGN---DEPLMTLPPKFSLSTNLQLAKSL 100 (105)
Q Consensus 55 aVp~~v~~~I~~~l~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 100 (105)
||||.+...|+..|.++-..... .+-+.+=||..+.+.-+.|-+.|
T Consensus 112 AvPP~~f~~i~~~L~~~~l~~~~~g~~RiVvEKPFG~Dl~SA~~Ln~~l 160 (183)
T PF00479_consen 112 AVPPSLFGPIARNLSEAGLNEEPNGWSRIVVEKPFGRDLESARELNDQL 160 (183)
T ss_dssp -S-GGGHHHHHHHHHHHT-S-TSSS-EEEEESSTSTSSHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHHhcccccCCceEEEEeCCCCCCHHHHHHHHHHH
Confidence 89999999999999887666554 56788889999988877776654
No 10
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=35.13 E-value=1.1e+02 Score=21.64 Aligned_cols=59 Identities=12% Similarity=0.000 Sum_probs=40.9
Q ss_pred cccCCCcccccHHHHhhhcCCCCCceecCChHhHHhhhcccccHHHHHHHHHHHHHHHH
Q 034052 15 VLHPEQDRVLTIRECARLQGFPDYYRFFGTVKERYCQVGNAVPIVVARALGYALGMAFQ 73 (105)
Q Consensus 15 ~ihp~~~R~lT~rE~arLQgFPd~f~~~~s~~~~~k~iGNaVp~~v~~~I~~~l~~~l~ 73 (105)
.++|...|+|++.....|...-..-+-.-....+.+.+=+++.|.+..+|+.+..+.+.
T Consensus 13 Ll~~~d~~~f~p~~i~~L~~~d~~~tSKKd~~~Rr~ELl~~~sp~Ll~~i~~~~~~ll~ 71 (148)
T PF08144_consen 13 LLSPRDPRYFSPEIIKLLKEGDRNATSKKDPEVRRKELLEAISPPLLEAIAENAEELLS 71 (148)
T ss_pred eccCCCcccCCHHHHHHHhhhcccccccCCHHHHHHHHHHHhhHHHHHHHHHhHHHHHh
Confidence 45678889999999888876542222222345666668889999999999877655443
No 11
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.49 E-value=1.1e+02 Score=21.19 Aligned_cols=48 Identities=27% Similarity=0.189 Sum_probs=36.3
Q ss_pred ccccHHHHhhhcCCCCCceecCChHhHHhh-hcccccHHHHHHHHHHHHHHHHhcC
Q 034052 22 RVLTIRECARLQGFPDYYRFFGTVKERYCQ-VGNAVPIVVARALGYALGMAFQKLG 76 (105)
Q Consensus 22 R~lT~rE~arLQgFPd~f~~~~s~~~~~k~-iGNaVp~~v~~~I~~~l~~~l~~~~ 76 (105)
-.+|.||-|.+-+ --+....|+| +|--|.+.-+..|.++|.+.+..+.
T Consensus 6 ~~~tdrerAiFEa-------GIklGalyHqf~GtPvs~~~a~~le~aI~esi~~QP 54 (116)
T COG2098 6 KKLTDRERAIFEA-------GIKLGALYHQFVGTPVSPGTAESLEKAIEESIKVQP 54 (116)
T ss_pred cccCHHHHHHHHc-------ccchhhhhhhhcCCcCCccchHHHHHHHHHHHhcCC
Confidence 4578888876433 1156677777 8999999999999999998887654
No 12
>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=22.62 E-value=61 Score=17.14 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=12.3
Q ss_pred cccHHHHhhhcCCCCC
Q 034052 23 VLTIRECARLQGFPDY 38 (105)
Q Consensus 23 ~lT~rE~arLQgFPd~ 38 (105)
++|+.|++.+-|.+..
T Consensus 1 ~lt~~e~a~~lgis~~ 16 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKD 16 (49)
T ss_pred CCCHHHHHHHHCCCHH
Confidence 4788899888887653
No 13
>smart00250 PLEC Plectin repeat.
Probab=21.65 E-value=70 Score=17.15 Aligned_cols=20 Identities=25% Similarity=0.488 Sum_probs=17.0
Q ss_pred CCccccCCCcccccHHHHhh
Q 034052 12 SMAVLHPEQDRVLTIRECAR 31 (105)
Q Consensus 12 ~~~~ihp~~~R~lT~rE~ar 31 (105)
.+.+++|.-...||+.|+.+
T Consensus 10 ~~Giidp~t~~~lsv~eA~~ 29 (38)
T smart00250 10 IGGIIDPETGQKLSVEEALR 29 (38)
T ss_pred eeEEEcCCCCCCcCHHHHHH
Confidence 35688999999999999875
Done!