Query psy8387
Match_columns 176
No_of_seqs 157 out of 1151
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 17:20:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8387hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1891|consensus 99.6 6.9E-16 1.5E-20 128.4 4.6 77 73-160 87-163 (271)
2 KOG3209|consensus 99.2 7.6E-12 1.6E-16 117.8 3.8 92 75-166 218-309 (984)
3 PF00397 WW: WW domain; Inter 99.2 1.8E-11 4E-16 72.4 4.0 30 126-155 1-31 (31)
4 KOG0940|consensus 99.2 2.9E-11 6.3E-16 107.4 6.3 118 13-158 21-146 (358)
5 smart00456 WW Domain with 2 co 99.1 1.1E-10 2.4E-15 68.9 4.4 32 126-157 1-32 (32)
6 cd00201 WW Two conserved trypt 99.0 7.7E-10 1.7E-14 64.4 4.3 31 127-157 1-31 (31)
7 PF00397 WW: WW domain; Inter 98.8 4.1E-09 8.8E-14 62.3 3.4 30 80-109 1-31 (31)
8 KOG3209|consensus 98.7 1.9E-08 4.2E-13 95.3 4.9 86 76-161 129-258 (984)
9 smart00456 WW Domain with 2 co 98.7 3E-08 6.6E-13 58.3 3.8 31 80-110 1-31 (32)
10 COG5104 PRP40 Splicing factor 98.7 3.3E-09 7.1E-14 95.9 -0.7 74 82-160 15-88 (590)
11 KOG1891|consensus 98.5 8.2E-08 1.8E-12 80.5 3.1 40 118-157 86-125 (271)
12 cd00201 WW Two conserved trypt 98.5 1.8E-07 4E-12 54.2 3.7 30 81-110 1-30 (31)
13 KOG3259|consensus 98.1 1.2E-06 2.6E-11 69.2 1.7 35 124-158 5-40 (163)
14 KOG3259|consensus 97.8 1.4E-05 3E-10 63.3 2.1 37 76-112 3-40 (163)
15 KOG0155|consensus 97.4 0.00019 4E-09 66.6 5.2 77 81-157 11-143 (617)
16 COG5104 PRP40 Splicing factor 96.0 0.0022 4.7E-08 58.8 0.4 29 127-155 14-42 (590)
17 COG5021 HUL4 Ubiquitin-protein 94.4 0.0063 1.4E-07 60.0 -1.8 87 78-164 386-485 (872)
18 KOG3552|consensus 93.9 0.014 3E-07 57.8 -0.4 48 102-156 3-50 (1298)
19 KOG0155|consensus 91.5 0.24 5.3E-06 46.5 4.2 32 82-113 114-145 (617)
20 KOG4334|consensus 89.9 0.32 7E-06 45.6 3.5 37 121-157 150-186 (650)
21 KOG4286|consensus 89.2 0.11 2.3E-06 50.8 -0.2 30 129-158 353-382 (966)
22 KOG0940|consensus 88.6 0.43 9.2E-06 42.9 3.2 37 122-158 57-97 (358)
23 KOG4334|consensus 85.7 0.87 1.9E-05 42.8 3.5 40 72-111 147-186 (650)
24 PF15238 FAM181: FAM181 82.4 1.3 2.7E-05 39.0 3.0 36 27-62 114-154 (297)
25 COG5021 HUL4 Ubiquitin-protein 78.2 0.29 6.2E-06 48.6 -2.6 89 76-164 295-426 (872)
26 smart00391 MBD Methyl-CpG bind 77.8 3 6.5E-05 29.3 3.2 34 124-158 6-47 (77)
27 cd01396 MeCP2_MBD MeCP2, MBD1, 72.6 5.5 0.00012 28.0 3.4 33 125-158 6-45 (77)
28 cd00122 MBD MeCP2, MBD1, MBD2, 71.3 5 0.00011 26.7 2.9 24 124-147 4-34 (62)
29 PF01429 MBD: Methyl-CpG bindi 67.3 7.5 0.00016 27.0 3.2 34 123-157 8-49 (77)
30 KOG4286|consensus 65.7 2.3 5E-05 41.9 0.4 31 81-111 351-381 (966)
31 cd01397 HAT_MBD Methyl-CpG bin 65.4 7.5 0.00016 27.3 2.9 26 124-149 4-36 (73)
32 KOG3552|consensus 48.8 4.9 0.00011 40.6 -0.4 40 73-112 13-52 (1298)
33 COG3828 Uncharacterized protei 33.8 50 0.0011 27.9 3.3 41 125-166 172-212 (239)
34 KOG1450|consensus 31.8 1.2E+02 0.0027 29.6 6.0 77 82-158 271-358 (650)
35 KOG0150|consensus 31.3 29 0.00063 30.9 1.6 29 130-158 153-181 (336)
36 TIGR03300 assembly_YfgL outer 26.0 1.9E+02 0.0041 24.9 5.8 63 89-157 112-174 (377)
37 PRK11138 outer membrane biogen 25.8 2.3E+02 0.0049 24.8 6.3 61 89-155 301-362 (394)
38 PRK11138 outer membrane biogen 24.9 2E+02 0.0044 25.1 5.9 62 89-156 127-188 (394)
39 smart00564 PQQ beta-propeller 23.3 1.4E+02 0.003 16.2 3.1 22 133-154 11-32 (33)
40 TIGR03300 assembly_YfgL outer 21.6 2.6E+02 0.0055 24.1 5.8 61 89-156 72-133 (377)
No 1
>KOG1891|consensus
Probab=99.60 E-value=6.9e-16 Score=128.37 Aligned_cols=77 Identities=23% Similarity=0.522 Sum_probs=70.1
Q ss_pred CCCCCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeec
Q psy8387 73 LLQQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQF 152 (176)
Q Consensus 73 a~~s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtW 152 (176)
+.+.+.+||+||...++-.||.|||||++++|.|.||-.- +.||+||+..+++.-.+||+|+.++.|++
T Consensus 87 ~~sedlPLPpgWav~~T~~grkYYIDHn~~tTHW~HPler-----------EgLppGW~rv~s~e~GtyY~~~~~k~tQy 155 (271)
T KOG1891|consen 87 DCSEDLPLPPGWAVEFTTEGRKYYIDHNNRTTHWVHPLER-----------EGLPPGWKRVFSPEKGTYYYHEEMKRTQY 155 (271)
T ss_pred CCcccCCCCCCcceeeEecCceeEeecCCCcccccChhhh-----------ccCCcchhhccccccceeeeecccchhhh
Confidence 4577889999999999999999999999999999999633 45999999999999899999999999999
Q ss_pred cCCCCcHH
Q psy8387 153 TDPRLTPA 160 (176)
Q Consensus 153 edPrl~~~ 160 (176)
+||++...
T Consensus 156 ~HPc~~s~ 163 (271)
T KOG1891|consen 156 EHPCISSP 163 (271)
T ss_pred cCCCCCCC
Confidence 99998644
No 2
>KOG3209|consensus
Probab=99.21 E-value=7.6e-12 Score=117.83 Aligned_cols=92 Identities=36% Similarity=0.649 Sum_probs=75.1
Q ss_pred CCCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccC
Q psy8387 75 QQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTD 154 (176)
Q Consensus 75 ~s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWed 154 (176)
...++||..||+.++.+|.+||++|+|++|+|.+|+..+.....+-.....||+|||..-|+-..+||++|+++.|+++.
T Consensus 218 ~~~gplp~nwemayte~gevyfiDhntkttswLdprl~kkaK~~eeckd~elPygWeki~dpiYg~yyvdHiN~~sq~en 297 (984)
T KOG3209|consen 218 DNLGPLPHNWEMAYTEQGEVYFIDHNTKTTSWLDPRLTKKAKPPEECKDQELPYGWEKIEDPIYGTYYVDHINRKSQYEN 297 (984)
T ss_pred cccCCCCccceEeEeecCeeEeeecccccceecChhhhcccCChhhcccccccccccccCCccceeEEecccchhhhhcc
Confidence 34567999999999999999999999999999999955433222212345699999999999999999999999999999
Q ss_pred CCCcHHHHhhhh
Q psy8387 155 PRLTPAIIQNLV 166 (176)
Q Consensus 155 Prl~~~~~~~~~ 166 (176)
|.+.++-..+.+
T Consensus 298 pvleakrk~Q~~ 309 (984)
T KOG3209|consen 298 PVLEAKRKKQLR 309 (984)
T ss_pred chhhcccchhhc
Confidence 998766544443
No 3
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=99.20 E-value=1.8e-11 Score=72.44 Aligned_cols=30 Identities=43% Similarity=0.936 Sum_probs=28.5
Q ss_pred CCCCceEEEcCC-CceEEeeCCCCeeeccCC
Q psy8387 126 LPPGWEVRQTAS-GRYYYVDHNNRTTQFTDP 155 (176)
Q Consensus 126 LP~GWE~~~d~~-Gr~YYiNh~tr~TtWedP 155 (176)
||+||++++|++ |++||+|+.|++|+|++|
T Consensus 1 LP~gW~~~~~~~~g~~YY~N~~t~~s~W~~P 31 (31)
T PF00397_consen 1 LPPGWEEYFDPDSGRPYYYNHETGESQWERP 31 (31)
T ss_dssp SSTTEEEEEETTTSEEEEEETTTTEEESSST
T ss_pred CCcCCEEEEcCCCCCEEEEeCCCCCEEeCCC
Confidence 799999999875 999999999999999998
No 4
>KOG0940|consensus
Probab=99.19 E-value=2.9e-11 Score=107.38 Aligned_cols=118 Identities=18% Similarity=0.193 Sum_probs=86.3
Q ss_pred cCCCCChHHHhhhcccCCCCCCCCcccCcccCCCCCCCCcceeccccCCCCCCcccCCCCCCCCCCCCCCCcEEEECCCC
Q psy8387 13 SGNYNNSNLILNNSHVNNNNTSSPALPLRSRTEDQQHNHRLLVQQPRKRGASKKCSGGNSLLQQPPDLPHGYEIRTTQQG 92 (176)
Q Consensus 13 ~~~~~~~~~lf~~v~~p~~~~~~~~~p~r~~~~~~~~~~~~sr~~~~~~~~~~~~~~~~ra~~s~~~LP~gWe~~~~~~G 92 (176)
-+-+.+|||+||.|||++.+. +|+|-+. ... +. +..+.+.||.+|+...+..|
T Consensus 21 ~~~~~~~e~~f~~iM~~~~~~------~~~~l~~---------~~~---~e---------e~ldy~glprewf~~lS~e~ 73 (358)
T KOG0940|consen 21 VDRDHLLEDSFNQIMNPKPSD------LQKRLMR---------EFK---GE---------EGLDYGGLPREWFFLLSHEG 73 (358)
T ss_pred echhhhHHHHHHHHhCCCchh------hhhccee---------ecc---cc---------cccccCCCCcceeeeecccc
Confidence 356789999999999999866 4444331 100 01 23345568999999999988
Q ss_pred ---ceEeecCCCC-eeeccCCCCCC---cCCccch-hccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCCc
Q psy8387 93 ---QVYFYHLPTG-VSTWHDPRIPK---ELRPEQA-TELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 93 ---rvYY~nh~Tr-tTsW~~P~~~~---~~~~~~~-~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
..||+++.+. .|.|++|.... ++....+ .....|| ||+++++..|.+||++|+.+.|+|.||+..
T Consensus 74 ~~p~~~~~~~~~~~~tlq~~P~sg~~p~~l~~~~~vg~~~~l~-~~h~~~~~~g~r~F~~~i~~ktt~ldd~e~ 146 (358)
T KOG0940|consen 74 FNPWYGLFQHSRKDYTLWLNPRSGVNPGHLTYFRFVGGVLALA-GWHMRFTDTGQRPFYKHILKKTTTLDDREA 146 (358)
T ss_pred CCcceeeeeecccccccccCCccCCCCCccccccccccccccc-ceeeEecCCCceehhhhhhcCccccCchhh
Confidence 9999999999 69999998762 1111111 1222343 899999999999999999999999999876
No 5
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=99.11 E-value=1.1e-10 Score=68.85 Aligned_cols=32 Identities=50% Similarity=1.065 Sum_probs=30.4
Q ss_pred CCCCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 126 LPPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 126 LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
||.||++..|++|++||+|+.|++++|++|+.
T Consensus 1 lp~gW~~~~~~~g~~yy~n~~t~~s~W~~P~~ 32 (32)
T smart00456 1 LPPGWEERKDPDGRPYYYNHETKETQWEKPRE 32 (32)
T ss_pred CCCCCEEEECCCCCEEEEECCCCCEEcCCCCC
Confidence 69999999999999999999999999999973
No 6
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=98.98 E-value=7.7e-10 Score=64.41 Aligned_cols=31 Identities=55% Similarity=1.108 Sum_probs=29.4
Q ss_pred CCCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 127 PPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 127 P~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
|.||++..|.+|++||+|+.+++++|++|+.
T Consensus 1 p~~W~~~~~~~g~~yy~n~~t~~s~W~~P~~ 31 (31)
T cd00201 1 PPGWEERWDPDGRVYYYNHNTKETQWEDPRE 31 (31)
T ss_pred CCCCEEEECCCCCEEEEECCCCCEeCCCCCC
Confidence 7899999999999999999999999999973
No 7
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=98.82 E-value=4.1e-09 Score=62.31 Aligned_cols=30 Identities=40% Similarity=0.843 Sum_probs=28.0
Q ss_pred CCCCcEEEECCC-CceEeecCCCCeeeccCC
Q psy8387 80 LPHGYEIRTTQQ-GQVYFYHLPTGVSTWHDP 109 (176)
Q Consensus 80 LP~gWe~~~~~~-GrvYY~nh~TrtTsW~~P 109 (176)
||+||+++++.+ |++||+|+.|++++|++|
T Consensus 1 LP~gW~~~~~~~~g~~YY~N~~t~~s~W~~P 31 (31)
T PF00397_consen 1 LPPGWEEYFDPDSGRPYYYNHETGESQWERP 31 (31)
T ss_dssp SSTTEEEEEETTTSEEEEEETTTTEEESSST
T ss_pred CCcCCEEEEcCCCCCEEEEeCCCCCEEeCCC
Confidence 799999999865 999999999999999987
No 8
>KOG3209|consensus
Probab=98.68 E-value=1.9e-08 Score=95.29 Aligned_cols=86 Identities=30% Similarity=0.488 Sum_probs=67.5
Q ss_pred CCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCCCC-c-----------------------CCc---------c----
Q psy8387 76 QPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPK-E-----------------------LRP---------E---- 118 (176)
Q Consensus 76 s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~-~-----------------------~~~---------~---- 118 (176)
....||++|++.+...+.-|++.++++.++|+.++... . +.. +
T Consensus 129 ~~~~~~~~~~es~~kr~~sy~~m~n~g~~~~eeeee~d~g~~n~~~~~~~~E~~e~s~~~s~~m~ssy~aPsts~s~~~~ 208 (984)
T KOG3209|consen 129 QELLLPPNSAESYRKRTKSYSIMENAGITTPEEEEEEDPGWENGSGQNYSVEMEESSYPTSSDMPSSYFAPSTSQSTTPM 208 (984)
T ss_pred ccccCCCcchhcccccCcceeehhccCCCCcccccccCccccccCCcccchhhhhccCCccCCCcccccccccCCCCCcc
Confidence 34567899999988899999999999999998776420 0 000 0
Q ss_pred -------chhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCCcHHH
Q psy8387 119 -------QATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAI 161 (176)
Q Consensus 119 -------~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~~~~ 161 (176)
.-..+++||..||+++++.|.+|||||+|++|+|-|||+..+.
T Consensus 209 ~~~~~~~~e~~~gplp~nwemayte~gevyfiDhntkttswLdprl~kka 258 (984)
T KOG3209|consen 209 DRYSPATQEDNLGPLPHNWEMAYTEQGEVYFIDHNTKTTSWLDPRLTKKA 258 (984)
T ss_pred cccCccccccccCCCCccceEeEeecCeeEeeecccccceecChhhhccc
Confidence 0134668999999999999999999999999999999976443
No 9
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=98.67 E-value=3e-08 Score=58.28 Aligned_cols=31 Identities=39% Similarity=0.879 Sum_probs=29.6
Q ss_pred CCCCcEEEECCCCceEeecCCCCeeeccCCC
Q psy8387 80 LPHGYEIRTTQQGQVYFYHLPTGVSTWHDPR 110 (176)
Q Consensus 80 LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~ 110 (176)
||.||++..+.+|++||+|+.|++++|++|.
T Consensus 1 lp~gW~~~~~~~g~~yy~n~~t~~s~W~~P~ 31 (32)
T smart00456 1 LPPGWEERKDPDGRPYYYNHETKETQWEKPR 31 (32)
T ss_pred CCCCCEEEECCCCCEEEEECCCCCEEcCCCC
Confidence 6999999999999999999999999999996
No 10
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=98.66 E-value=3.3e-09 Score=95.94 Aligned_cols=74 Identities=23% Similarity=0.481 Sum_probs=58.8
Q ss_pred CCcEEEECCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCCcHH
Q psy8387 82 HGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPA 160 (176)
Q Consensus 82 ~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~~~ 160 (176)
..|++..+++||+||||..|+.++|+.|..... ..+. . ---.||.++.+++|++||+|.+|+++.|.-|....+
T Consensus 15 s~w~e~k~~dgRiYYYN~~T~kS~weKPkell~--~~e~-~--l~~~~Wke~~TadGkvyyyN~~TREs~W~iP~e~Kk 88 (590)
T COG5104 15 SEWEELKAPDGRIYYYNKRTGKSSWEKPKELLK--GSEE-D--LDVDPWKECRTADGKVYYYNSITRESRWKIPPERKK 88 (590)
T ss_pred HHHHHhhCCCCceEEEecccccccccChHHHhc--chHh-h--hchhhHHHHhhcCCceEEecCccccccccCChhhhc
Confidence 459999999999999999999999999953211 1110 0 113579999999999999999999999999876544
No 11
>KOG1891|consensus
Probab=98.48 E-value=8.2e-08 Score=80.49 Aligned_cols=40 Identities=50% Similarity=0.853 Sum_probs=35.8
Q ss_pred cchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 118 EQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 118 ~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
+++.++.|||+||...++-.||.|||||++++|.|.||-.
T Consensus 86 ~~~sedlPLPpgWav~~T~~grkYYIDHn~~tTHW~HPle 125 (271)
T KOG1891|consen 86 CDCSEDLPLPPGWAVEFTTEGRKYYIDHNNRTTHWVHPLE 125 (271)
T ss_pred CCCcccCCCCCCcceeeEecCceeEeecCCCcccccChhh
Confidence 3456778999999999999999999999999999999954
No 12
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=98.48 E-value=1.8e-07 Score=54.22 Aligned_cols=30 Identities=43% Similarity=0.924 Sum_probs=28.5
Q ss_pred CCCcEEEECCCCceEeecCCCCeeeccCCC
Q psy8387 81 PHGYEIRTTQQGQVYFYHLPTGVSTWHDPR 110 (176)
Q Consensus 81 P~gWe~~~~~~GrvYY~nh~TrtTsW~~P~ 110 (176)
|.||+...+..|++||+|+.|++++|++|.
T Consensus 1 p~~W~~~~~~~g~~yy~n~~t~~s~W~~P~ 30 (31)
T cd00201 1 PPGWEERWDPDGRVYYYNHNTKETQWEDPR 30 (31)
T ss_pred CCCCEEEECCCCCEEEEECCCCCEeCCCCC
Confidence 689999999999999999999999999996
No 13
>KOG3259|consensus
Probab=98.11 E-value=1.2e-06 Score=69.24 Aligned_cols=35 Identities=43% Similarity=0.847 Sum_probs=31.8
Q ss_pred CCCCCCceEEEcC-CCceEEeeCCCCeeeccCCCCc
Q psy8387 124 GNLPPGWEVRQTA-SGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 124 ~~LP~GWE~~~d~-~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
..||+|||.+.+. .|++||+|+.|+.++||.|.-.
T Consensus 5 ~~LP~~Wekr~Srs~gr~YyfN~~T~~SqWe~P~~t 40 (163)
T KOG3259|consen 5 EKLPPGWEKRMSRSSGRPYYFNTETNESQWERPSGT 40 (163)
T ss_pred ccCCchhheeccccCCCcceeccccchhhccCCCcc
Confidence 4699999999985 8999999999999999999764
No 14
>KOG3259|consensus
Probab=97.76 E-value=1.4e-05 Score=63.29 Aligned_cols=37 Identities=30% Similarity=0.661 Sum_probs=33.2
Q ss_pred CCCCCCCCcEEEEC-CCCceEeecCCCCeeeccCCCCC
Q psy8387 76 QPPDLPHGYEIRTT-QQGQVYFYHLPTGVSTWHDPRIP 112 (176)
Q Consensus 76 s~~~LP~gWe~~~~-~~GrvYY~nh~TrtTsW~~P~~~ 112 (176)
+...||+||+.+++ +.|++||+|+.|..++|+.|...
T Consensus 3 ~~~~LP~~Wekr~Srs~gr~YyfN~~T~~SqWe~P~~t 40 (163)
T KOG3259|consen 3 DEEKLPPGWEKRMSRSSGRPYYFNTETNESQWERPSGT 40 (163)
T ss_pred ccccCCchhheeccccCCCcceeccccchhhccCCCcc
Confidence 45679999999998 58999999999999999999854
No 15
>KOG0155|consensus
Probab=97.45 E-value=0.00019 Score=66.61 Aligned_cols=77 Identities=21% Similarity=0.419 Sum_probs=58.2
Q ss_pred CCCcEEEECCCCceEeecCCCCeeeccCCCCCCcC-----------C-------------------c-------------
Q psy8387 81 PHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKEL-----------R-------------------P------------- 117 (176)
Q Consensus 81 P~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~~~-----------~-------------------~------------- 117 (176)
|.+|...-.++|..||+|..|...+|++|...... . .
T Consensus 11 ps~wtef~ap~G~pyy~ns~t~~st~ekP~~l~~~~s~~~~~~~p~~sp~~~~~~~~t~~~~~~e~~~~k~~~s~~~~ee 90 (617)
T KOG0155|consen 11 PSGWTEFKAPDGIPYYWNSETLESTWEKPSFLEKNESSGVTASEPSLSPAIAEAQQKTSSNAFGENPSEKLFVSENAAEE 90 (617)
T ss_pred CCCCccCCCCCCcceecccccccchhhCchhhhhccccCccccCCccCcchhhhhhhhhhccCCcchHHHHHhCcchhhc
Confidence 48999999999999999999999999999753110 0 0
Q ss_pred -cc-------h----hccCCCC-CCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 118 -EQ-------A----TELGNLP-PGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 118 -~~-------~----~~~~~LP-~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
.. + ....++| ..|-..+|.++++||+|..|+.+.|+.|--
T Consensus 91 ~~~~~~~~kk~p~rPi~~~~ipgtdWcVVwTgD~RvFFyNpktk~S~We~P~d 143 (617)
T KOG0155|consen 91 RKNSRAARKKLPDRPIFKKPIPGTDWCVVWTGDNRVFFYNPKTKLSVWERPLD 143 (617)
T ss_pred CCCcccccccCCCCCCCCCCCCCCCeEEEEeCCCceEEeCCccccccccCchh
Confidence 00 0 0011233 239999999999999999999999999954
No 16
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=95.96 E-value=0.0022 Score=58.84 Aligned_cols=29 Identities=24% Similarity=0.649 Sum_probs=27.2
Q ss_pred CCCceEEEcCCCceEEeeCCCCeeeccCC
Q psy8387 127 PPGWEVRQTASGRYYYVDHNNRTTQFTDP 155 (176)
Q Consensus 127 P~GWE~~~d~~Gr~YYiNh~tr~TtWedP 155 (176)
-.-|++..+++||+||+|..|+.++|+.|
T Consensus 14 ~s~w~e~k~~dgRiYYYN~~T~kS~weKP 42 (590)
T COG5104 14 RSEWEELKAPDGRIYYYNKRTGKSSWEKP 42 (590)
T ss_pred HHHHHHhhCCCCceEEEecccccccccCh
Confidence 34599999999999999999999999999
No 17
>COG5021 HUL4 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.36 E-value=0.0063 Score=60.01 Aligned_cols=87 Identities=31% Similarity=0.486 Sum_probs=70.7
Q ss_pred CCCCCCcEEEECCCCceEeecCCCCeeeccCCCCCCcCC-------------ccchhccCCCCCCceEEEcCCCceEEee
Q psy8387 78 PDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELR-------------PEQATELGNLPPGWEVRQTASGRYYYVD 144 (176)
Q Consensus 78 ~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~~~~-------------~~~~~~~~~LP~GWE~~~d~~Gr~YYiN 144 (176)
...|.+|+..+...++.+++++.+..++|..+....-.. .......++++.+|+++....-++||..
T Consensus 386 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~r~~~~~~~~~~~ 465 (872)
T COG5021 386 RNKPTGWSSSIEDLGQFLFSDFLTSSSTYEDLRREQLGRESDESFYVASNVQQQRASREGPLLSGWKTRLNNLYRFYFVE 465 (872)
T ss_pred hcCCccchhhhhhhHHHHHhhhhcchhhhhchhhhhhhhhhccchhhhcccccccccccccccchHHHHhhhhheeeehh
Confidence 457999999999999999999999999999987532111 1111466789999999999999999999
Q ss_pred CCCCeeeccCCCCcHHHHhh
Q psy8387 145 HNNRTTQFTDPRLTPAIIQN 164 (176)
Q Consensus 145 h~tr~TtWedPrl~~~~~~~ 164 (176)
|.+.+++|.++++...+..+
T Consensus 466 h~k~~~~~~~~~~g~~~~~~ 485 (872)
T COG5021 466 HRKKTLTKNDSRLGSFISLN 485 (872)
T ss_pred cccceeeecCCCCchhhhhc
Confidence 99999999999866555444
No 18
>KOG3552|consensus
Probab=93.91 E-value=0.014 Score=57.79 Aligned_cols=48 Identities=29% Similarity=0.567 Sum_probs=36.6
Q ss_pred CeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCC
Q psy8387 102 GVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPR 156 (176)
Q Consensus 102 rtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPr 156 (176)
..+.|..++... .....|++||+++.|..|+.|||||..+++++++|.
T Consensus 3 ~~a~~~p~~~~~-------~~~~~v~~~~~r~~dsk~r~~y~~~~~~~~~~~~~~ 50 (1298)
T KOG3552|consen 3 QSAGWLPACEDW-------SKHEELSYGWERAIDSKGRSYYINHLNKTTTYEAPE 50 (1298)
T ss_pred ccccCCCCcccc-------ccccccchHHHHhhhcccchhHHhhcCCccCcCCCc
Confidence 346676665432 123469999999999999999999999999987763
No 19
>KOG0155|consensus
Probab=91.50 E-value=0.24 Score=46.48 Aligned_cols=32 Identities=28% Similarity=0.486 Sum_probs=28.7
Q ss_pred CCcEEEECCCCceEeecCCCCeeeccCCCCCC
Q psy8387 82 HGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPK 113 (176)
Q Consensus 82 ~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~ 113 (176)
..|...++-+|++||||..|+.+.|+.|....
T Consensus 114 tdWcVVwTgD~RvFFyNpktk~S~We~P~dlk 145 (617)
T KOG0155|consen 114 TDWCVVWTGDNRVFFYNPKTKLSVWERPLDLK 145 (617)
T ss_pred CCeEEEEeCCCceEEeCCccccccccCchhhc
Confidence 35999999999999999999999999997543
No 20
>KOG4334|consensus
Probab=89.95 E-value=0.32 Score=45.56 Aligned_cols=37 Identities=27% Similarity=0.490 Sum_probs=33.4
Q ss_pred hccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 121 TELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 121 ~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
+...+||.||.+.+..+|-.-|+...||..+|..|-+
T Consensus 150 ~~~epLPeGW~~i~HnSGmPvylHr~tRVvt~SrPYf 186 (650)
T KOG4334|consen 150 DKSEPLPEGWTVISHNSGMPVYLHRFTRVVTHSRPYF 186 (650)
T ss_pred CCCCcCCCceEEEeecCCCceEEeeeeeeEeccCcee
Confidence 4567899999999999999999999999999988855
No 21
>KOG4286|consensus
Probab=89.16 E-value=0.11 Score=50.76 Aligned_cols=30 Identities=30% Similarity=0.669 Sum_probs=27.4
Q ss_pred CceEEEcCCCceEEeeCCCCeeeccCCCCc
Q psy8387 129 GWEVRQTASGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 129 GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
.|+.+..+.--+|||||.+.+|+|+||-..
T Consensus 353 pw~rais~nkvpyyinh~~q~t~wdhp~~t 382 (966)
T KOG4286|consen 353 PWERAISPNKVPYYINHETQTTCWDHPKMT 382 (966)
T ss_pred cchhccCccccchhhcccchhhhccchHHH
Confidence 399999998889999999999999999764
No 22
>KOG0940|consensus
Probab=88.57 E-value=0.43 Score=42.90 Aligned_cols=37 Identities=27% Similarity=0.536 Sum_probs=33.1
Q ss_pred ccCCCCCCceEEEcCCC---ceEEeeCCCC-eeeccCCCCc
Q psy8387 122 ELGNLPPGWEVRQTASG---RYYYVDHNNR-TTQFTDPRLT 158 (176)
Q Consensus 122 ~~~~LP~GWE~~~d~~G---r~YYiNh~tr-~TtWedPrl~ 158 (176)
+-++||.+|+...+.+| ..||++|... .|+|++|...
T Consensus 57 dy~glprewf~~lS~e~~~p~~~~~~~~~~~~tlq~~P~sg 97 (358)
T KOG0940|consen 57 DYGGLPREWFFLLSHEGFNPWYGLFQHSRKDYTLWLNPRSG 97 (358)
T ss_pred ccCCCCcceeeeeccccCCcceeeeeecccccccccCCccC
Confidence 34679999999999999 8999999999 5999999887
No 23
>KOG4334|consensus
Probab=85.66 E-value=0.87 Score=42.79 Aligned_cols=40 Identities=25% Similarity=0.375 Sum_probs=35.8
Q ss_pred CCCCCCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCC
Q psy8387 72 SLLQQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRI 111 (176)
Q Consensus 72 ra~~s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~ 111 (176)
+......+||.||.+.+-.+|-..|++..||..+|.+|=.
T Consensus 147 ~~l~~~epLPeGW~~i~HnSGmPvylHr~tRVvt~SrPYf 186 (650)
T KOG4334|consen 147 IDLDKSEPLPEGWTVISHNSGMPVYLHRFTRVVTHSRPYF 186 (650)
T ss_pred ccCCCCCcCCCceEEEeecCCCceEEeeeeeeEeccCcee
Confidence 4677788999999998888999999999999999998854
No 24
>PF15238 FAM181: FAM181
Probab=82.35 E-value=1.3 Score=39.03 Aligned_cols=36 Identities=11% Similarity=0.188 Sum_probs=23.2
Q ss_pred ccCCCCCCCCcccCcccCC-----CCCCCCcceeccccCCC
Q psy8387 27 HVNNNNTSSPALPLRSRTE-----DQQHNHRLLVQQPRKRG 62 (176)
Q Consensus 27 ~~p~~~~~~~~~p~r~~~~-----~~~~~~~~sr~~~~~~~ 62 (176)
+.-.....+.+||||+|+| .+|.+.+++++++...+
T Consensus 114 ~~~~~~~ap~qVPmRkRnLPaSFfeEP~~~ss~~~~s~~~~ 154 (297)
T PF15238_consen 114 LQEQDPEAPDQVPMRKRNLPASFFEEPRPSSSSGSASCSSG 154 (297)
T ss_pred ccccCCCCCCCCchhhccCCccccCCCCcCCccCccccCCc
Confidence 3333344589999999999 66655566555433443
No 25
>COG5021 HUL4 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.18 E-value=0.29 Score=48.65 Aligned_cols=89 Identities=15% Similarity=0.332 Sum_probs=67.0
Q ss_pred CCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCCCC---------cC---C------------------c----cc--
Q psy8387 76 QPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPK---------EL---R------------------P----EQ-- 119 (176)
Q Consensus 76 s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~~---------~~---~------------------~----~~-- 119 (176)
+...++++|+...+.-|+.||+.|.+..+.|..|-... .. . . ..
T Consensus 295 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~~~~~~~~~~~~~~~~~~~~~ 374 (872)
T COG5021 295 SLLRLNSLFSTRADSFGRTYYLDHDRILTQYSRPLLEETLGESTSFLVVNNDDSSSIKDLPHQVGSNPFLEAHPEFSELL 374 (872)
T ss_pred hcccccccccchhhhcchhhhhhhhhhhhhhhhccchhhhhhhhhhccccccchhhhhhcccccCCcccccccHHHHHHH
Confidence 44567899999999999999999999999998773210 00 0 0 00
Q ss_pred -------hhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCCcHHHHhh
Q psy8387 120 -------ATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAIIQN 164 (176)
Q Consensus 120 -------~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~~~~~~~ 164 (176)
..+....|.||+..+...++.+++++.+..+.|++|+-...+...
T Consensus 375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 426 (872)
T COG5021 375 KNQSRGTTRDFRNKPTGWSSSIEDLGQFLFSDFLTSSSTYEDLRREQLGRES 426 (872)
T ss_pred hhhcccccchhhcCCccchhhhhhhHHHHHhhhhcchhhhhchhhhhhhhhh
Confidence 012235799999999999999999999999999999986555443
No 26
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=77.75 E-value=3 Score=29.34 Aligned_cols=34 Identities=21% Similarity=0.384 Sum_probs=21.8
Q ss_pred CCCCCCceEEEc--------CCCceEEeeCCCCeeeccCCCCc
Q psy8387 124 GNLPPGWEVRQT--------ASGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 124 ~~LP~GWE~~~d--------~~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
.|||.||+.... ..+.+||+...-+ .--..+.+.
T Consensus 6 ~Plp~GW~R~~~~r~~g~~~~~~dV~Y~sP~Gk-klRs~~ev~ 47 (77)
T smart00391 6 LPLPCGWRRETKQRKSGRSAGKFDVYYISPCGK-KLRSKSELA 47 (77)
T ss_pred CCCCCCcEEEEEEecCCCCCCcccEEEECCCCC-eeeCHHHHH
Confidence 369999987764 2568999988543 343333333
No 27
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=72.61 E-value=5.5 Score=28.02 Aligned_cols=33 Identities=24% Similarity=0.513 Sum_probs=20.3
Q ss_pred CCCCCceEEEcC-------CCceEEeeCCCCeeeccCCCCc
Q psy8387 125 NLPPGWEVRQTA-------SGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 125 ~LP~GWE~~~d~-------~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
.||+||+..+-. .+.+||+.... ..--..+.+.
T Consensus 6 ~lp~GW~r~~~~R~~gs~~k~DvyY~sP~G-kk~RS~~ev~ 45 (77)
T cd01396 6 RLPPGWKRELVPRKSGSAGKFDVYYISPTG-KKFRSKVELA 45 (77)
T ss_pred CCCCCCEEEEEEecCCCCCcceEEEECCCC-CEEECHHHHH
Confidence 499999776521 33589998875 3333334433
No 28
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=71.29 E-value=5 Score=26.73 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=17.7
Q ss_pred CCCCCCceEEEc-------CCCceEEeeCCC
Q psy8387 124 GNLPPGWEVRQT-------ASGRYYYVDHNN 147 (176)
Q Consensus 124 ~~LP~GWE~~~d-------~~Gr~YYiNh~t 147 (176)
.|||.||+.... ..+.+||+....
T Consensus 4 ~P~p~GW~R~~~~r~~g~~~k~dv~Y~sP~G 34 (62)
T cd00122 4 DPLPPGWKRELVIRKSGSAGKGDVYYYSPCG 34 (62)
T ss_pred CCCCCCeEEEEEEcCCCCCCcceEEEECCCC
Confidence 468999987764 245689998874
No 29
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=67.30 E-value=7.5 Score=27.01 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=21.7
Q ss_pred cCCCCCCceEEEc--CC------CceEEeeCCCCeeeccCCCC
Q psy8387 123 LGNLPPGWEVRQT--AS------GRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 123 ~~~LP~GWE~~~d--~~------Gr~YYiNh~tr~TtWedPrl 157 (176)
..+||.||....- .+ ..+||+.+ ++..-.....+
T Consensus 8 ~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP-~Gk~~RS~~eV 49 (77)
T PF01429_consen 8 DPPLPDGWKREVVVRKSGSSAGKKDVYYYSP-CGKRFRSKKEV 49 (77)
T ss_dssp BTTSTTT-EEEEEESSSSTTTTSEEEEEEET-TSEEESSHHHH
T ss_pred cCCCCCCCEEEEEEecCCCcCCceEEEEECC-CCCEEeCHHHH
Confidence 4579999977653 22 35799998 67666544443
No 30
>KOG4286|consensus
Probab=65.66 E-value=2.3 Score=41.86 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=27.1
Q ss_pred CCCcEEEECCCCceEeecCCCCeeeccCCCC
Q psy8387 81 PHGYEIRTTQQGQVYFYHLPTGVSTWHDPRI 111 (176)
Q Consensus 81 P~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~ 111 (176)
...|+..++++--.|||||.|.+|.|.||-.
T Consensus 351 q~pw~rais~nkvpyyinh~~q~t~wdhp~~ 381 (966)
T KOG4286|consen 351 QGPWERAISPNKVPYYINHETQTTCWDHPKM 381 (966)
T ss_pred cccchhccCccccchhhcccchhhhccchHH
Confidence 3448889998889999999999999999964
No 31
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
Probab=65.40 E-value=7.5 Score=27.33 Aligned_cols=26 Identities=19% Similarity=0.337 Sum_probs=18.8
Q ss_pred CCCCCCceEEE-------cCCCceEEeeCCCCe
Q psy8387 124 GNLPPGWEVRQ-------TASGRYYYVDHNNRT 149 (176)
Q Consensus 124 ~~LP~GWE~~~-------d~~Gr~YYiNh~tr~ 149 (176)
.||+.||+... ...|.+||+.+.-+.
T Consensus 4 ~Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKk 36 (73)
T cd01397 4 VPLELGWRRETRIRGLGGRIQGEVAYYAPCGKK 36 (73)
T ss_pred CCCCCCceeEEEeccCCCCccceEEEECCCCcc
Confidence 47999998776 235679999776444
No 32
>KOG3552|consensus
Probab=48.80 E-value=4.9 Score=40.63 Aligned_cols=40 Identities=18% Similarity=0.342 Sum_probs=32.0
Q ss_pred CCCCCCCCCCCcEEEECCCCceEeecCCCCeeeccCCCCC
Q psy8387 73 LLQQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIP 112 (176)
Q Consensus 73 a~~s~~~LP~gWe~~~~~~GrvYY~nh~TrtTsW~~P~~~ 112 (176)
+......|+++|+..++..|+.||++|...+++.+.|...
T Consensus 13 ~~~~~~~v~~~~~r~~dsk~r~~y~~~~~~~~~~~~~~~i 52 (1298)
T KOG3552|consen 13 DWSKHEELSYGWERAIDSKGRSYYINHLNKTTTYEAPECI 52 (1298)
T ss_pred ccccccccchHHHHhhhcccchhHHhhcCCccCcCCCccc
Confidence 4455667999999999999999999998888777666543
No 33
>COG3828 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.77 E-value=50 Score=27.90 Aligned_cols=41 Identities=22% Similarity=0.536 Sum_probs=30.7
Q ss_pred CCCCCceEEEcCCCceEEeeCCCCeeeccCCCCcHHHHhhhh
Q psy8387 125 NLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAIIQNLV 166 (176)
Q Consensus 125 ~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl~~~~~~~~~ 166 (176)
.+|.-|..+.- .||+||-+---....|.+|++...+..-|.
T Consensus 172 ~mPVvWtR~~G-kGRvFYssLGHta~~~~~pe~~~i~~rg~~ 212 (239)
T COG3828 172 VMPVVWTRRYG-KGRVFYSSLGHTASEFAVPEMRTIIRRGIL 212 (239)
T ss_pred eeeeEEEeeec-CceEEEeccCCCccccccHHHHHHHHHHHH
Confidence 35666766655 699999887777889999998776655544
No 34
>KOG1450|consensus
Probab=31.80 E-value=1.2e+02 Score=29.59 Aligned_cols=77 Identities=17% Similarity=0.199 Sum_probs=51.7
Q ss_pred CCcEEEEC-CCCceEeecCCCCeeeccC-CCCCC---cCCcc-----chhccCCCCCCceEEEcC-CCceEEeeCCCCee
Q psy8387 82 HGYEIRTT-QQGQVYFYHLPTGVSTWHD-PRIPK---ELRPE-----QATELGNLPPGWEVRQTA-SGRYYYVDHNNRTT 150 (176)
Q Consensus 82 ~gWe~~~~-~~GrvYY~nh~TrtTsW~~-P~~~~---~~~~~-----~~~~~~~LP~GWE~~~d~-~Gr~YYiNh~tr~T 150 (176)
.-|+..+. ..|..+|+...++.++|.. +.... ..... .......++.-|...... .+...|+|.....|
T Consensus 271 ~~~~~~~~~~t~~~~~~~~~~~~~~~s~~~~~~~~~~~~~sps~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~net 350 (650)
T KOG1450|consen 271 TVWETSTDALTGNPLYYYSDTGSTTWSGHHSPPEKAEIAQSPSLSPAMVSASKNKSTRKNTLWLTTNRTSKVLNRSHNET 350 (650)
T ss_pred cccccchhhcccccceeecccCcccccCCCCccccccCCCCcccchhhhccccccCCccceeeeeecCCceeeecCCCCc
Confidence 34777776 4788888888899888873 32221 11111 112234577888888754 77888999999999
Q ss_pred eccCCCCc
Q psy8387 151 QFTDPRLT 158 (176)
Q Consensus 151 tWedPrl~ 158 (176)
.|+|.-..
T Consensus 351 ~~~d~~~~ 358 (650)
T KOG1450|consen 351 SFEDWSSN 358 (650)
T ss_pred cccchhhc
Confidence 99997553
No 35
>KOG0150|consensus
Probab=31.30 E-value=29 Score=30.93 Aligned_cols=29 Identities=24% Similarity=0.637 Sum_probs=25.9
Q ss_pred ceEEEcCCCceEEeeCCCCeeeccCCCCc
Q psy8387 130 WEVRQTASGRYYYVDHNNRTTQFTDPRLT 158 (176)
Q Consensus 130 WE~~~d~~Gr~YYiNh~tr~TtWedPrl~ 158 (176)
|-....++|..||.|..++.+.|.-|+..
T Consensus 153 wv~~Knes~~~yy~n~~t~esvwk~P~~~ 181 (336)
T KOG0150|consen 153 WVEGKNESGPTYYSNKRTNESVWKPPRIS 181 (336)
T ss_pred cccccCCCCCCcceecCCCccccCCCCcc
Confidence 67777889999999999999999999864
No 36
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=26.02 E-value=1.9e+02 Score=24.86 Aligned_cols=63 Identities=24% Similarity=0.348 Sum_probs=41.5
Q ss_pred CCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCCC
Q psy8387 89 TQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157 (176)
Q Consensus 89 ~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPrl 157 (176)
+.+|.+|-+|..|+..-|............ -+-.+.-...+.+|.+|-+|..+++..|+....
T Consensus 112 ~~~g~l~ald~~tG~~~W~~~~~~~~~~~p------~v~~~~v~v~~~~g~l~a~d~~tG~~~W~~~~~ 174 (377)
T TIGR03300 112 TEKGEVIALDAEDGKELWRAKLSSEVLSPP------LVANGLVVVRTNDGRLTALDAATGERLWTYSRV 174 (377)
T ss_pred cCCCEEEEEECCCCcEeeeeccCceeecCC------EEECCEEEEECCCCeEEEEEcCCCceeeEEccC
Confidence 457888989999999999765422111000 011344444466899999999999999986543
No 37
>PRK11138 outer membrane biogenesis protein BamB; Provisional
Probab=25.81 E-value=2.3e+02 Score=24.81 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=36.7
Q ss_pred CCCCceEeecCCCCeeeccCCCCCCcCCccchhccCC-CCCCceEEEcCCCceEEeeCCCCeeeccCC
Q psy8387 89 TQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGN-LPPGWEVRQTASGRYYYVDHNNRTTQFTDP 155 (176)
Q Consensus 89 ~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~-LP~GWE~~~d~~Gr~YYiNh~tr~TtWedP 155 (176)
+.+|.+|-++..++..-|..+........ .+ +-.|.-...+.+|.+|.+|..+++..|...
T Consensus 301 ~~~g~l~ald~~tG~~~W~~~~~~~~~~~------sp~v~~g~l~v~~~~G~l~~ld~~tG~~~~~~~ 362 (394)
T PRK11138 301 DQNDRVYALDTRGGVELWSQSDLLHRLLT------APVLYNGYLVVGDSEGYLHWINREDGRFVAQQK 362 (394)
T ss_pred cCCCeEEEEECCCCcEEEcccccCCCccc------CCEEECCEEEEEeCCCEEEEEECCCCCEEEEEE
Confidence 44566666777777777754432110000 01 113444455778999999999999999654
No 38
>PRK11138 outer membrane biogenesis protein BamB; Provisional
Probab=24.88 E-value=2e+02 Score=25.08 Aligned_cols=62 Identities=18% Similarity=0.334 Sum_probs=41.6
Q ss_pred CCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCCCCCceEEEcCCCceEEeeCCCCeeeccCCC
Q psy8387 89 TQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPR 156 (176)
Q Consensus 89 ~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~LP~GWE~~~d~~Gr~YYiNh~tr~TtWedPr 156 (176)
+.+|.+|-+|..|+..-|........... .. +-.|--...+.+|.+|-+|..|++..|..+.
T Consensus 127 ~~~g~l~ald~~tG~~~W~~~~~~~~~ss-P~-----v~~~~v~v~~~~g~l~ald~~tG~~~W~~~~ 188 (394)
T PRK11138 127 SEKGQVYALNAEDGEVAWQTKVAGEALSR-PV-----VSDGLVLVHTSNGMLQALNESDGAVKWTVNL 188 (394)
T ss_pred cCCCEEEEEECCCCCCcccccCCCceecC-CE-----EECCEEEEECCCCEEEEEEccCCCEeeeecC
Confidence 45788999999999999976643211100 00 1123333346688999999999999998764
No 39
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=23.32 E-value=1.4e+02 Score=16.16 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=18.1
Q ss_pred EEcCCCceEEeeCCCCeeeccC
Q psy8387 133 RQTASGRYYYVDHNNRTTQFTD 154 (176)
Q Consensus 133 ~~d~~Gr~YYiNh~tr~TtWed 154 (176)
..+.+|.+|-+|-.+++..|+-
T Consensus 11 ~~~~~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 11 VGSTDGTLYALDAKTGEILWTY 32 (33)
T ss_pred EEcCCCEEEEEEcccCcEEEEc
Confidence 4466899999999999999974
No 40
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=21.57 E-value=2.6e+02 Score=24.06 Aligned_cols=61 Identities=16% Similarity=0.135 Sum_probs=41.1
Q ss_pred CCCCceEeecCCCCeeeccCCCCCCcCCccchhccCCC-CCCceEEEcCCCceEEeeCCCCeeeccCCC
Q psy8387 89 TQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNL-PPGWEVRQTASGRYYYVDHNNRTTQFTDPR 156 (176)
Q Consensus 89 ~~~GrvYY~nh~TrtTsW~~P~~~~~~~~~~~~~~~~L-P~GWE~~~d~~Gr~YYiNh~tr~TtWedPr 156 (176)
+.+|.+|-+|..++..-|...-...... .+. -.+.-...+.+|.+|-+|..+++..|....
T Consensus 72 ~~~g~v~a~d~~tG~~~W~~~~~~~~~~-------~p~v~~~~v~v~~~~g~l~ald~~tG~~~W~~~~ 133 (377)
T TIGR03300 72 DADGTVVALDAETGKRLWRVDLDERLSG-------GVGADGGLVFVGTEKGEVIALDAEDGKELWRAKL 133 (377)
T ss_pred CCCCeEEEEEccCCcEeeeecCCCCccc-------ceEEcCCEEEEEcCCCEEEEEECCCCcEeeeecc
Confidence 4578999999999999996543321111 111 123333446789999999999999997654
Done!