Query psy2752
Match_columns 99
No_of_seqs 117 out of 1081
Neff 6.6
Searched_HMMs 46136
Date Sat Aug 17 00:18:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2752.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2752hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00385 Chromo: Chromo (CHRro 99.7 1.8E-17 3.8E-22 96.7 5.6 50 10-60 1-55 (55)
2 KOG2748|consensus 99.7 1.7E-18 3.8E-23 132.7 1.0 72 4-76 5-77 (369)
3 cd00024 CHROMO Chromatin organ 99.6 6.8E-16 1.5E-20 89.2 4.4 51 8-59 1-54 (55)
4 KOG1911|consensus 99.6 1.2E-15 2.7E-20 113.9 3.2 63 3-66 42-105 (270)
5 smart00298 CHROMO Chromatin or 99.4 1.2E-13 2.7E-18 79.4 3.0 52 9-60 1-53 (55)
6 KOG0384|consensus 98.0 1.5E-06 3.2E-11 76.0 1.3 52 11-64 287-340 (1373)
7 cd00034 ChSh Chromo Shadow Dom 97.9 1.8E-05 3.9E-10 46.3 3.6 47 12-61 2-50 (54)
8 PF01393 Chromo_shadow: Chromo 97.7 3.2E-05 7E-10 45.9 2.6 48 11-61 4-53 (58)
9 smart00300 ChSh Chromo Shadow 97.6 2.3E-05 5E-10 46.9 1.0 47 11-61 8-56 (61)
10 PF14061 Mtf2_C: Polycomb-like 97.3 0.0004 8.6E-09 40.0 3.3 23 14-36 27-49 (50)
11 PF11717 Tudor-knot: RNA bindi 96.7 0.0065 1.4E-07 35.2 4.9 40 8-48 14-53 (55)
12 KOG0384|consensus 96.3 0.002 4.4E-08 57.0 1.7 39 25-63 225-268 (1373)
13 KOG0383|consensus 90.5 0.08 1.7E-06 44.9 0.1 53 11-63 210-264 (696)
14 PF02178 AT_hook: AT hook moti 72.8 1.5 3.3E-05 18.5 0.4 10 69-78 2-11 (13)
15 smart00384 AT_hook DNA binding 62.5 4.9 0.00011 20.1 1.1 14 68-81 1-14 (26)
16 PLN00104 MYST -like histone ac 60.3 12 0.00026 30.6 3.5 42 8-49 68-112 (450)
17 PF08940 DUF1918: Domain of un 48.7 13 0.00028 22.1 1.5 20 14-34 24-43 (58)
18 PHA02096 hypothetical protein 42.3 11 0.00025 24.0 0.6 23 39-61 32-56 (103)
19 PF15010 FAM131: Putative cell 30.2 36 0.00079 26.3 1.7 24 22-45 46-69 (293)
20 PHA03158 hypothetical protein; 27.2 65 0.0014 23.9 2.6 26 38-63 77-103 (273)
21 PF12148 DUF3590: Protein of u 24.8 1.3E+02 0.0027 19.1 3.3 27 12-38 17-43 (85)
22 PHA03151 hypothetical protein; 24.4 1E+02 0.0023 23.0 3.2 29 49-77 180-208 (259)
No 1
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro []. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [].; PDB: 2H1E_B 3MWY_W 2DY8_A 1KNE_A 1KNA_A 1Q3L_A 2EE1_A 1AP0_A 1GUW_A 1X3P_A ....
Probab=99.71 E-value=1.8e-17 Score=96.67 Aligned_cols=50 Identities=46% Similarity=1.016 Sum_probs=44.9
Q ss_pred EEEEEEeeceeecCCeE---EEEEeeecCCCCCCeecccCCC-Ch-HHHHHHHHHH
Q psy2752 10 YVIEKIVDKKLTKEGKV---KYFLKWKDYPESDNTWEMAEDL-DC-DDLIRAFEEN 60 (99)
Q Consensus 10 y~Ve~Il~~r~~~~g~~---~YLVkW~gy~~~~~TWEp~~~l-~~-~~ll~~f~~~ 60 (99)
|+|++||+++. .++.. +|||+|+|++..++||||+++| +| +.+|.+|+++
T Consensus 1 ~~Ve~Il~~r~-~~~~~~~~~ylVkW~g~~~~~~tWe~~~~l~~~~~~li~~f~~r 55 (55)
T PF00385_consen 1 YEVERILDHRV-VKGGNKVYEYLVKWKGYPYSENTWEPEENLKNCFPELIEEFEKR 55 (55)
T ss_dssp EEEEEEEEEEE-ETTEESEEEEEEEETTSSGGGEEEEEGGGCSSHCHHHHHHHHHH
T ss_pred CEEEEEEEEEE-eCCCcccEEEEEEECCCCCCCCeEeeHHHHhHhhHHHHHHHhCC
Confidence 79999999999 55554 9999999999999999999999 55 9999999875
No 2
>KOG2748|consensus
Probab=99.71 E-value=1.7e-18 Score=132.68 Aligned_cols=72 Identities=35% Similarity=0.614 Sum_probs=63.7
Q ss_pred cCCcceEEEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCCChHHHHHHHHHHHHHHHHh-hhccCCCCC
Q psy2752 4 EEQEEVYVIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDLDCDDLIRAFEENWAVEQEA-KKKAGEPTE 76 (99)
Q Consensus 4 ~~~e~~y~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l~~~~ll~~f~~~~~~~~~~-~kkrg~~~~ 76 (99)
..++.+|.+|.||.+|+ ++|.++|||||+||+..+|||||++||.++.||..|+.+....+.. .+|||...+
T Consensus 5 avGe~VfAaEsIlkkRi-rKGrvEYlVKWkGWs~kyNTWEPEENILDpRLi~AFe~rErek~~~~~kKrgpkPk 77 (369)
T KOG2748|consen 5 AVGERVFAAESILKKRI-RKGRVEYLVKWKGWSQKYNTWEPEENILDPRLIAAFEQREREKELYGKKKRGPKPK 77 (369)
T ss_pred cchhhHHHHHHHHHHHh-hccceEEEEEecccccccCccCccccccCHHHHHHHHhhhHHHhhhhhhccCCCCc
Confidence 45788999999999999 9999999999999999999999999998899999999998877553 667776444
No 3
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=99.61 E-value=6.8e-16 Score=89.16 Aligned_cols=51 Identities=47% Similarity=0.984 Sum_probs=46.3
Q ss_pred ceEEEEEEeeceeecC--CeEEEEEeeecCCCCCCeecccCCC-ChHHHHHHHHH
Q psy2752 8 EVYVIEKIVDKKLTKE--GKVKYFLKWKDYPESDNTWEMAEDL-DCDDLIRAFEE 59 (99)
Q Consensus 8 ~~y~Ve~Il~~r~~~~--g~~~YLVkW~gy~~~~~TWEp~~~l-~~~~ll~~f~~ 59 (99)
++|.|++||+++. .. +..+|||+|+||+..++||||.++| .++.+|.+|..
T Consensus 1 ~e~~ve~Il~~r~-~~~~~~~~y~VkW~g~~~~~~tWe~~~~l~~~~~~i~~~~~ 54 (55)
T cd00024 1 EEYEVEKILDHRK-KKDGGEYEYLVKWKGYSYSEDTWEPEENLEDCKELIDEFKK 54 (55)
T ss_pred CCceEeeeeeeee-cCCCCcEEEEEEECCCCCccCccccHHHhCchHHHHHHHHh
Confidence 3689999999999 55 8999999999999999999999999 56789999975
No 4
>KOG1911|consensus
Probab=99.57 E-value=1.2e-15 Score=113.92 Aligned_cols=63 Identities=51% Similarity=0.991 Sum_probs=56.8
Q ss_pred ccCCcceEEEEEEeeceeecCCeEEEEEeeecCCCCCCeecccC-CCChHHHHHHHHHHHHHHHH
Q psy2752 3 EEEQEEVYVIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAE-DLDCDDLIRAFEENWAVEQE 66 (99)
Q Consensus 3 ~~~~e~~y~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~-~l~~~~ll~~f~~~~~~~~~ 66 (99)
+.+++++|+|+.|++++. .+|.++|||+|+||+..+|||||+. +++|++||.+|+..+...+.
T Consensus 42 ~~~~~~~~vvEki~~~r~-~~g~~eYlvkW~Gy~~~~ntWEPee~~~~C~~li~~~~~~~~~~k~ 105 (270)
T KOG1911|consen 42 EEEEEEEYVVEKILKRRK-KNGKIEYLVKWKGYPDPDNTWEPEEHNLDCPELIDEFEKSQKKLKK 105 (270)
T ss_pred cccccchhhhhhhhhccc-cCCCceeeeecCCCCCccccCCchhhccccHHHHHHHHHHhcccCc
Confidence 456778999999999999 8888999999999999999999999 55999999999999886554
No 5
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=99.42 E-value=1.2e-13 Score=79.40 Aligned_cols=52 Identities=37% Similarity=0.845 Sum_probs=46.3
Q ss_pred eEEEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCCC-hHHHHHHHHHH
Q psy2752 9 VYVIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDLD-CDDLIRAFEEN 60 (99)
Q Consensus 9 ~y~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l~-~~~ll~~f~~~ 60 (99)
.|.|++||+++....+..+|||+|.|++..++||+|..+|. |+.+|.+|..+
T Consensus 1 ~~~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~~l~~~~~~v~~~~~~ 53 (55)
T smart00298 1 EYEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKK 53 (55)
T ss_pred CcchheeeeeeecCCCcEEEEEEECCCCCccCceeeHHHHHHHHHHHHHHHHh
Confidence 36799999999327888999999999999999999999995 99999999875
No 6
>KOG0384|consensus
Probab=98.05 E-value=1.5e-06 Score=75.98 Aligned_cols=52 Identities=27% Similarity=0.681 Sum_probs=44.7
Q ss_pred EEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCC--ChHHHHHHHHHHHHHH
Q psy2752 11 VIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDL--DCDDLIRAFEENWAVE 64 (99)
Q Consensus 11 ~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l--~~~~ll~~f~~~~~~~ 64 (99)
.|++||++..... .+|||||+|.+.+++|||+.+.+ .++..+.+|..+....
T Consensus 287 ~VdRIia~~~~~d--~eYLvKW~~LpY~e~TWE~~~~I~~~~~~~~~~~~~Re~sk 340 (1373)
T KOG0384|consen 287 IVDRIIAEQTSKD--PEYLVKWRGLPYEECTWEDAEDIAKKAQEEIEEFQSRENSK 340 (1373)
T ss_pred hhhhhhhcccCCC--ceeEEEecCCCcccccccchhhhhhhHHHHHHHHhhhhccc
Confidence 7999999988333 99999999999999999999999 4677888888887644
No 7
>cd00034 ChSh Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)
Probab=97.89 E-value=1.8e-05 Score=46.33 Aligned_cols=47 Identities=23% Similarity=0.527 Sum_probs=37.9
Q ss_pred EEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCC--ChHHHHHHHHHHH
Q psy2752 12 IEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDL--DCDDLIRAFEENW 61 (99)
Q Consensus 12 Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l--~~~~ll~~f~~~~ 61 (99)
|+.|++.....+|.+.|||+|+| + ...+.|...+ .||.+|.+|++++
T Consensus 2 ~~~I~gat~~~~g~l~fl~kwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~ 50 (54)
T cd00034 2 VKPISGASKSDDGELTFLAKWKD-G--QASLVPNKELNVKCPLLVISFYEEH 50 (54)
T ss_pred ceEEEEEEEcCCCeEEEEEEEeC-C--eEEEEEHHHHHhhCcHHHHHHHHHh
Confidence 57788866623399999999999 4 4568888876 7999999999876
No 8
>PF01393 Chromo_shadow: Chromo shadow domain Web page maintained by Rein Aasland; InterPro: IPR008251 Chromo shadow domain is distantly related to chromo domain. It is always found in association with a chromo domain. The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain [], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.; GO: 0005634 nucleus; PDB: 3Q6S_C 2FMM_B 3P7J_B 1E0B_B 3I3C_A 1DZ1_B 1S4Z_A 3KUP_D.
Probab=97.70 E-value=3.2e-05 Score=45.89 Aligned_cols=48 Identities=23% Similarity=0.455 Sum_probs=39.9
Q ss_pred EEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCC--ChHHHHHHHHHHH
Q psy2752 11 VIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDL--DCDDLIRAFEENW 61 (99)
Q Consensus 11 ~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l--~~~~ll~~f~~~~ 61 (99)
..|.|++.-. ..|.+.|||+|+|.+ ..+..|..-+ .||.+|.+|++.+
T Consensus 4 ~~E~Ivg~~d-~~G~l~~likwk~~~--~~~~v~~~~~~~k~Pq~vI~FYE~~ 53 (58)
T PF01393_consen 4 EWEKIVGATD-TNGELMFLIKWKNSG--EKDLVPSKEANEKCPQKVIKFYESH 53 (58)
T ss_dssp TEEEEEEEEE-CTSSEEEEEEETTSS--SEEEEEHHHHHHHSHHHHHHHHHHT
T ss_pred ChHHHheeec-CCCcEEEEEEECCCC--ceEEeeHHHHHHHCcHHHHHHHHHH
Confidence 4688999866 789999999999965 4678888766 6999999999875
No 9
>smart00300 ChSh Chromo Shadow Domain.
Probab=97.60 E-value=2.3e-05 Score=46.87 Aligned_cols=47 Identities=23% Similarity=0.487 Sum_probs=38.6
Q ss_pred EEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCC--ChHHHHHHHHHHH
Q psy2752 11 VIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDL--DCDDLIRAFEENW 61 (99)
Q Consensus 11 ~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l--~~~~ll~~f~~~~ 61 (99)
..++|++.-. .+|.+.|||+|+| + ...+.|...+ .||.+|.+|++.+
T Consensus 8 ~~e~Ivg~~d-~~G~l~flikwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~ 56 (61)
T smart00300 8 SWEDIVGITK-DDGELTFLIKWKD-D--AASLVPNKEANVKCPQKVIRFYESH 56 (61)
T ss_pred CHHHHhceec-CCCeEEEEEEEeC-C--cEEEEEHHHHHHHChHHHHHHHHHh
Confidence 4566777766 7999999999999 4 4568888876 7999999999876
No 10
>PF14061 Mtf2_C: Polycomb-like MTF2 factor 2
Probab=97.27 E-value=0.0004 Score=39.99 Aligned_cols=23 Identities=26% Similarity=0.869 Sum_probs=19.8
Q ss_pred EEeeceeecCCeEEEEEeeecCC
Q psy2752 14 KIVDKKLTKEGKVKYFLKWKDYP 36 (99)
Q Consensus 14 ~Il~~r~~~~g~~~YLVkW~gy~ 36 (99)
+|+.+|+..+|+++|||.|.|.+
T Consensus 27 ~VlArRV~~dG~vQYLvEWeg~~ 49 (50)
T PF14061_consen 27 RVLARRVTPDGKVQYLVEWEGAT 49 (50)
T ss_pred EEEEEEEcCCCcEEEEEEecCcC
Confidence 57888887899999999999964
No 11
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=96.66 E-value=0.0065 Score=35.24 Aligned_cols=40 Identities=18% Similarity=0.473 Sum_probs=33.1
Q ss_pred ceEEEEEEeeceeecCCeEEEEEeeecCCCCCCeecccCCC
Q psy2752 8 EVYVIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDL 48 (99)
Q Consensus 8 ~~y~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~~l 48 (99)
..+---+|++.+. ..+..+|+|.+.||+...+-|.|.++|
T Consensus 14 ~~~y~A~I~~~r~-~~~~~~YyVHY~g~nkR~DeWV~~~~i 53 (55)
T PF11717_consen 14 GQWYEAKILDIRE-KNGEPEYYVHYQGWNKRLDEWVPESRI 53 (55)
T ss_dssp TEEEEEEEEEEEE-CTTCEEEEEEETTSTGCC-EEEETTTE
T ss_pred CcEEEEEEEEEEe-cCCCEEEEEEcCCCCCCceeeecHHHc
Confidence 3444457888888 888999999999999999999999876
No 12
>KOG0384|consensus
Probab=96.27 E-value=0.002 Score=57.01 Aligned_cols=39 Identities=21% Similarity=0.446 Sum_probs=30.5
Q ss_pred eEEEEEeeecCCCCCCeecccCCCC-----hHHHHHHHHHHHHH
Q psy2752 25 KVKYFLKWKDYPESDNTWEMAEDLD-----CDDLIRAFEENWAV 63 (99)
Q Consensus 25 ~~~YLVkW~gy~~~~~TWEp~~~l~-----~~~ll~~f~~~~~~ 63 (99)
..+|||||+|+++-+||||+++.|. --.-|..|.++...
T Consensus 225 ~~qFlIKWkg~SyLHctWet~~~L~~~~~rG~kKv~nf~kK~~e 268 (1373)
T KOG0384|consen 225 EEQFLIKWKGWSYLHCTWETESELLEMNVRGLKKVDNFKKKVIE 268 (1373)
T ss_pred hhhhheeeccccceeccccchHHHHhhhHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999962 33456677776553
No 13
>KOG0383|consensus
Probab=90.50 E-value=0.08 Score=44.91 Aligned_cols=53 Identities=19% Similarity=0.520 Sum_probs=44.0
Q ss_pred EEEEEeeceeecCCeEEEEEeeecCCCCCCeecccC-CC-ChHHHHHHHHHHHHH
Q psy2752 11 VIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAE-DL-DCDDLIRAFEENWAV 63 (99)
Q Consensus 11 ~Ve~Il~~r~~~~g~~~YLVkW~gy~~~~~TWEp~~-~l-~~~~ll~~f~~~~~~ 63 (99)
.|..|+.++....+.+.|+|+|+..+.+..+|+.+. .+ .+...+++|+.....
T Consensus 210 ~i~rii~~~~s~~~~~~~~Vk~k~l~~d~~~~e~~~~~ip~~~~~~qe~~~~~~~ 264 (696)
T KOG0383|consen 210 PIARIINRRSSQKGATDYLVKWKELSYDEQEWEVEDPDIPGYSSAGQEAWHHREK 264 (696)
T ss_pred ccchhhhhhcccccceeeEeeeccCCccccCCCcCCCCcccCcccccccccccCc
Confidence 477888888767889999999999999999999998 44 677788888765554
No 14
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=72.79 E-value=1.5 Score=18.46 Aligned_cols=10 Identities=30% Similarity=0.687 Sum_probs=3.4
Q ss_pred hccCCCCCCC
Q psy2752 69 KKAGEPTESL 78 (99)
Q Consensus 69 kkrg~~~~~~ 78 (99)
++||||++..
T Consensus 2 r~RGRP~k~~ 11 (13)
T PF02178_consen 2 RKRGRPRKNA 11 (13)
T ss_dssp --SS--TT--
T ss_pred CcCCCCcccc
Confidence 6788888753
No 15
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=62.48 E-value=4.9 Score=20.11 Aligned_cols=14 Identities=29% Similarity=0.555 Sum_probs=10.3
Q ss_pred hhccCCCCCCCCCC
Q psy2752 68 KKKAGEPTESLETG 81 (99)
Q Consensus 68 ~kkrg~~~~~~~~~ 81 (99)
.|+||||++.....
T Consensus 1 kRkRGRPrK~~~~~ 14 (26)
T smart00384 1 KRKRGRPRKAPKDX 14 (26)
T ss_pred CCCCCCCCCCCCcc
Confidence 36899999876653
No 16
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=60.33 E-value=12 Score=30.60 Aligned_cols=42 Identities=17% Similarity=0.477 Sum_probs=32.6
Q ss_pred ceEEEEEEeeceee---cCCeEEEEEeeecCCCCCCeecccCCCC
Q psy2752 8 EVYVIEKIVDKKLT---KEGKVKYFLKWKDYPESDNTWEMAEDLD 49 (99)
Q Consensus 8 ~~y~Ve~Il~~r~~---~~g~~~YLVkW~gy~~~~~TWEp~~~l~ 49 (99)
..|..-.||+.+.. ..+..+|.|.+.|+...-+.|.+.+.|+
T Consensus 68 g~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rLd 112 (450)
T PLN00104 68 GKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQLD 112 (450)
T ss_pred CCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhcc
Confidence 34444668887762 2356789999999999999999999984
No 17
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=48.70 E-value=13 Score=22.08 Aligned_cols=20 Identities=30% Similarity=0.800 Sum_probs=12.8
Q ss_pred EEeeceeecCCeEEEEEeeec
Q psy2752 14 KIVDKKLTKEGKVKYFLKWKD 34 (99)
Q Consensus 14 ~Il~~r~~~~g~~~YLVkW~g 34 (99)
.|+.-+. .+|..-|+|+|.+
T Consensus 24 eIveV~g-~dG~PPY~VRw~D 43 (58)
T PF08940_consen 24 EIVEVRG-PDGSPPYLVRWDD 43 (58)
T ss_dssp EEEE-S--SSS-S-EEEEETT
T ss_pred EEEEEEC-CCCCCCEEEEecC
Confidence 4666666 7888899999987
No 18
>PHA02096 hypothetical protein
Probab=42.35 E-value=11 Score=24.02 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=17.2
Q ss_pred CCeecccC-CC-ChHHHHHHHHHHH
Q psy2752 39 DNTWEMAE-DL-DCDDLIRAFEENW 61 (99)
Q Consensus 39 ~~TWEp~~-~l-~~~~ll~~f~~~~ 61 (99)
+++||... +| ++.+.|.+|.+--
T Consensus 32 h~swe~a~~~~~~ak~~i~eylkgt 56 (103)
T PHA02096 32 HDSWEEADVSLKNAKKSIEEYLKGT 56 (103)
T ss_pred eccHHHhhhHHHHHHHHHHHHhccc
Confidence 47898775 45 7888999987643
No 19
>PF15010 FAM131: Putative cell signalling
Probab=30.16 E-value=36 Score=26.25 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=20.7
Q ss_pred cCCeEEEEEeeecCCCCCCeeccc
Q psy2752 22 KEGKVKYFLKWKDYPESDNTWEMA 45 (99)
Q Consensus 22 ~~g~~~YLVkW~gy~~~~~TWEp~ 45 (99)
..|++--||.|+||+....+|+..
T Consensus 46 aqGrVAHlIEWkgW~~~~~~~~~~ 69 (293)
T PF15010_consen 46 AQGRVAHLIEWKGWGKPRSSPEAL 69 (293)
T ss_pred hcccceeeeeecCCCCCCCChhhh
Confidence 478899999999999988888654
No 20
>PHA03158 hypothetical protein; Provisional
Probab=27.22 E-value=65 Score=23.95 Aligned_cols=26 Identities=19% Similarity=0.369 Sum_probs=23.2
Q ss_pred CCCeecccCCC-ChHHHHHHHHHHHHH
Q psy2752 38 SDNTWEMAEDL-DCDDLIRAFEENWAV 63 (99)
Q Consensus 38 ~~~TWEp~~~l-~~~~ll~~f~~~~~~ 63 (99)
.-++-||.+|+ +|...|+.||.+.+.
T Consensus 77 ~pn~~e~se~~~ncst~ldl~wq~lg~ 103 (273)
T PHA03158 77 RPNILEPSENCKNCSTFLDLFWQQLGE 103 (273)
T ss_pred CCcccCcCccccchhHHHHHHHHHhcC
Confidence 45788999999 999999999999884
No 21
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=24.79 E-value=1.3e+02 Score=19.12 Aligned_cols=27 Identities=37% Similarity=0.722 Sum_probs=16.3
Q ss_pred EEEEeeceeecCCeEEEEEeeecCCCC
Q psy2752 12 IEKIVDKKLTKEGKVKYFLKWKDYPES 38 (99)
Q Consensus 12 Ve~Il~~r~~~~g~~~YLVkW~gy~~~ 38 (99)
|..|............|-|+|.+|+..
T Consensus 17 i~~i~~~~~~~~e~viYhIkyddype~ 43 (85)
T PF12148_consen 17 IVTITKKCMSDDEDVIYHIKYDDYPEN 43 (85)
T ss_dssp EEEEEES-SSSSTTEEEEEEETT-GGG
T ss_pred EEEeeccCCCCCCCEEEEEEeccCCCc
Confidence 444443333234578999999999853
No 22
>PHA03151 hypothetical protein; Provisional
Probab=24.37 E-value=1e+02 Score=23.00 Aligned_cols=29 Identities=24% Similarity=0.287 Sum_probs=19.3
Q ss_pred ChHHHHHHHHHHHHHHHHhhhccCCCCCC
Q psy2752 49 DCDDLIRAFEENWAVEQEAKKKAGEPTES 77 (99)
Q Consensus 49 ~~~~ll~~f~~~~~~~~~~~kkrg~~~~~ 77 (99)
...+.|+.|...+.+...+.+|-.|..+.
T Consensus 180 se~d~Ve~firqra~ma~~k~k~krsist 208 (259)
T PHA03151 180 SEEDVVEAFIRQRAQMAGKKKKGKRSIST 208 (259)
T ss_pred ccchHHHHHHHHHHHHhccccCCcccccc
Confidence 35678899998888877764444444443
Done!