Query 042818
Match_columns 440
No_of_seqs 210 out of 1076
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 09:49:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042818.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042818hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2748 Uncharacterized conser 99.6 4.3E-16 9.3E-21 156.4 0.5 85 97-185 3-87 (369)
2 KOG1911 Heterochromatin-associ 99.6 6.2E-15 1.3E-19 142.1 7.7 221 101-421 45-269 (270)
3 PF00385 Chromo: Chromo (CHRro 99.5 2.1E-14 4.6E-19 107.2 6.6 51 105-155 1-55 (55)
4 cd00024 CHROMO Chromatin organ 99.4 2.9E-13 6.3E-18 99.5 5.0 52 103-154 1-54 (55)
5 smart00298 CHROMO Chromatin or 99.2 1.8E-11 3.8E-16 89.6 3.6 52 104-155 1-53 (55)
6 cd00034 ChSh Chromo Shadow Dom 99.2 1.8E-11 3.9E-16 94.1 3.1 54 381-438 1-54 (54)
7 smart00300 ChSh Chromo Shadow 98.9 8.8E-10 1.9E-14 86.5 2.7 43 396-438 18-60 (61)
8 KOG0384 Chromodomain-helicase 97.3 2.2E-05 4.8E-10 90.0 -2.9 81 120-213 226-311 (1373)
9 PF01393 Chromo_shadow: Chromo 96.5 0.0012 2.6E-08 51.8 1.6 39 397-438 19-57 (58)
10 KOG0384 Chromodomain-helicase 96.5 0.0016 3.4E-08 75.5 2.7 52 106-158 287-339 (1373)
11 cd00034 ChSh Chromo Shadow Dom 96.4 0.0039 8.5E-08 48.2 3.5 47 107-156 2-50 (54)
12 PF01393 Chromo_shadow: Chromo 96.3 0.0033 7.2E-08 49.4 2.7 49 106-156 4-53 (58)
13 PF11717 Tudor-knot: RNA bindi 95.6 0.036 7.8E-07 42.5 5.9 41 102-142 13-53 (55)
14 smart00300 ChSh Chromo Shadow 95.4 0.0062 1.3E-07 48.1 0.8 48 106-156 8-56 (61)
15 PF14061 Mtf2_C: Polycomb-like 94.5 0.052 1.1E-06 42.3 3.7 22 109-130 27-49 (50)
16 KOG0383 Predicted helicase [Ge 45.7 6.3 0.00014 44.6 -0.3 52 106-157 210-263 (696)
17 PF11095 Gemin7: Gem-associate 45.2 25 0.00055 29.9 3.3 31 383-416 25-55 (80)
18 PF12733 Cadherin-like: Cadher 44.3 29 0.00063 27.9 3.4 35 386-421 15-49 (88)
19 PLN00104 MYST -like histone ac 41.5 28 0.0006 37.8 3.7 40 103-142 68-111 (450)
20 KOG1832 HIV-1 Vpr-binding prot 28.6 34 0.00074 40.6 2.0 13 30-42 1346-1358(1516)
21 PF14725 DUF4466: Domain of un 21.2 84 0.0018 32.5 2.9 29 385-413 105-135 (308)
22 PLN02967 kinase 20.8 49 0.0011 36.9 1.3 31 50-80 123-153 (581)
No 1
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=99.56 E-value=4.3e-16 Score=156.41 Aligned_cols=85 Identities=40% Similarity=0.690 Sum_probs=68.6
Q ss_pred CCCCCCceEEEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCcCChHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCc
Q 042818 97 RPKLDEGFFEIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENLQSCSDVIDAFEESLRSGKSSRKRKRKGGGSSSLP 176 (440)
Q Consensus 97 ~p~~dEeEYEVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL~dc~ELIeeFe~k~~~~K~srKRkRks~g~~s~~ 176 (440)
+..+++.+|.+|.||.+|+++|+++|||||+||+..+|||||++||.+. .||..|+++.+..+...+||| ++.+.+
T Consensus 3 l~avGe~VfAaEsIlkkRirKGrvEYlVKWkGWs~kyNTWEPEENILDp-RLi~AFe~rErek~~~~~kKr---gpkPk~ 78 (369)
T KOG2748|consen 3 LSAVGERVFAAESILKKRIRKGRVEYLVKWKGWSQKYNTWEPEENILDP-RLIAAFEQREREKELYGKKKR---GPKPKG 78 (369)
T ss_pred cccchhhHHHHHHHHHHHhhccceEEEEEecccccccCccCccccccCH-HHHHHHHhhhHHHhhhhhhcc---CCCCcc
Confidence 5678899999999999999999999999999999999999999999995 599999999776554333321 555555
Q ss_pred ccccccCCC
Q 042818 177 KKKQARTFS 185 (440)
Q Consensus 177 kKrk~rs~s 185 (440)
...+.++++
T Consensus 79 ~~~k~~a~s 87 (369)
T KOG2748|consen 79 FLLKARAAS 87 (369)
T ss_pred chhhHHHhh
Confidence 555555433
No 2
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=99.56 E-value=6.2e-15 Score=142.14 Aligned_cols=221 Identities=26% Similarity=0.366 Sum_probs=132.6
Q ss_pred CCceEEEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCcCChHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCccccc
Q 042818 101 DEGFFEIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENLQSCSDVIDAFEESLRSGKSSRKRKRKGGGSSSLPKKKQ 180 (440)
Q Consensus 101 dEeEYEVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL~dc~ELIeeFe~k~~~~K~srKRkRks~g~~s~~kKrk 180 (440)
++++|+||.|+++|..+|+++|||+|+||+..++||||++++.+|++||.+|+.++...+...++++... ..+.+++
T Consensus 45 ~~~~~vvEki~~~r~~~g~~eYlvkW~Gy~~~~ntWEPee~~~~C~~li~~~~~~~~~~k~~~~~~~~~~---~~~~~~~ 121 (270)
T KOG1911|consen 45 EEEEYVVEKILKRRKKNGKIEYLVKWKGYPDPDNTWEPEEHNLDCPELIDEFEKSQKKLKKKSKLKRTSR---SSSNKAK 121 (270)
T ss_pred ccchhhhhhhhhccccCCCceeeeecCCCCCccccCCchhhccccHHHHHHHHHHhcccCcccccccccc---ccccccc
Confidence 4478999999999999999999999999999999999999777999999999999887664443322211 1111111
Q ss_pred ccCCCCCcccccCCCCCCCCCCCCccCCCCCCCCCCcCCCCCCCCccccccccccccccccccccCCcccccCCCccccC
Q 042818 181 ARTFSAPYYVTGGVGQSLPADPLINAGLIDLSPSTQSIGSGHVGGNVGNVNNLRTAKQTNDNRLANGSKQIDGRNEEAEY 260 (440)
Q Consensus 181 ~rs~s~~ynv~~i~~~~~~s~P~~~~~~~~lp~p~~~~~~~~~g~~~~~~n~~~~~~~~~~n~s~~~s~q~~~~~e~n~~ 260 (440)
..+ + ++ + . .+...+
T Consensus 122 ~~~-~---------------------------------~S---~--~---------------------------~~~~~~ 135 (270)
T KOG1911|consen 122 EET-S---------------------------------RS---T--S---------------------------DEKSKS 135 (270)
T ss_pred ccc-c---------------------------------cc---c--c---------------------------cccccc
Confidence 100 0 00 0 0 000111
Q ss_pred CcchhhhcccccccccccccceeehhhhhcccCCCCCCCCCCCcccCCCCcCCccCccccCCccccccccccccccc---
Q 042818 261 DPKLSELKGMISNNEANADKLALHFQEARVSEGNGLTNGLSKADQVEPLHSNRRTGARRRKPSSVKRFKQDLASTKV--- 337 (440)
Q Consensus 261 dp~lsel~~~~~~~~~~~~~~~i~~q~~~~~~~n~~~ng~skv~~~~~~q~~~~tGakrRKsgsVkRFkqd~~~~~~--- 337 (440)
++..+...-...+ ....+.+.|+ ...+-+||++.....+++++.......+
T Consensus 136 ~~~~~~~~~~~~~-----------------~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 (270)
T KOG1911|consen 136 SPKKSVKKKKEKS-----------------KKSKGFPRGK---------EGKRIAGAKKSSGKLMFLMKSSKELSEPKDE 189 (270)
T ss_pred ccccccccccchh-----------------cccccccccc---------cchhhhccccCCcchhhhhcCCccccccCCc
Confidence 1111111100000 0000111111 3446778988888888888876643222
Q ss_pred -cccCCCCCCccccCCccccccCCCCCCCCCCCCCCCCccceeeeeccccccccccCCceeEEEEEEEEecCCcEEEeec
Q 042818 338 -IVTQDSTPGIAVGCDSADEQLGIGNSSHKSKHEGPINASAIVKILKPIDFSASVSDNMQDVVVTFMAVRSDGKEVMVDN 416 (440)
Q Consensus 338 -~~~~n~~~~~~v~s~~~~~~~g~g~~~~~~~~~~~~~~~~ItkIiKPv~ysasv~~~vQdV~vTF~A~RSDG~EV~VDn 416 (440)
..++...... .+-. + -.. -.--....+..+....-+.+...|+.+.+...+-.+...+++...+++|..-+...
T Consensus 190 ~~~~~~~~~~~--~~p~-~-~~~-~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 264 (270)
T KOG1911|consen 190 ADLTPAKEKSS--KCPQ-V-VID-FYEERLEDQETPKDEDKKEKRDSLKSPGAEQSDLSSRTLIHPLINRSDGLLTAKMA 264 (270)
T ss_pred ccccccccccc--cCCc-c-hhH-HHHhccccccccccccccccccCccccccccccccccccCccccccCCcccccccc
Confidence 2222211111 0000 0 000 00001123556667778888999999999999999999999999999999888777
Q ss_pred cchhc
Q 042818 417 KYLKA 421 (440)
Q Consensus 417 k~LKa 421 (440)
.+|+.
T Consensus 265 ~~~~~ 269 (270)
T KOG1911|consen 265 SFLKL 269 (270)
T ss_pred ccccc
Confidence 77764
No 3
>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=99.52 E-value=2.1e-14 Score=107.17 Aligned_cols=51 Identities=49% Similarity=1.041 Sum_probs=47.4
Q ss_pred EEEEEEEEeEEeCCeE---EEEEEecCCCCCCCceeecCCcCCh-HHHHHHHHHH
Q 042818 105 FEIEAIRRKRVRKGQL---QYLIKWRGWPENANTWEPLENLQSC-SDVIDAFEES 155 (440)
Q Consensus 105 YEVEkILd~R~~~Gkl---eYLVKWKGY~eseNTWEPeENL~dc-~ELIeeFe~k 155 (440)
|+||+||++|..++.. +|||||+||+..++||||+++|.+| +++|++|+++
T Consensus 1 ~~Ve~Il~~r~~~~~~~~~~ylVkW~g~~~~~~tWe~~~~l~~~~~~li~~f~~r 55 (55)
T PF00385_consen 1 YEVERILDHRVVKGGNKVYEYLVKWKGYPYSENTWEPEENLKNCFPELIEEFEKR 55 (55)
T ss_dssp EEEEEEEEEEEETTEESEEEEEEEETTSSGGGEEEEEGGGCSSHCHHHHHHHHHH
T ss_pred CEEEEEEEEEEeCCCcccEEEEEEECCCCCCCCeEeeHHHHhHhhHHHHHHHhCC
Confidence 8999999999987666 9999999999999999999999887 9999999875
No 4
>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=99.40 E-value=2.9e-13 Score=99.53 Aligned_cols=52 Identities=42% Similarity=0.965 Sum_probs=48.4
Q ss_pred ceEEEEEEEEeEEeC--CeEEEEEEecCCCCCCCceeecCCcCChHHHHHHHHH
Q 042818 103 GFFEIEAIRRKRVRK--GQLQYLIKWRGWPENANTWEPLENLQSCSDVIDAFEE 154 (440)
Q Consensus 103 eEYEVEkILd~R~~~--GkleYLVKWKGY~eseNTWEPeENL~dc~ELIeeFe~ 154 (440)
++|+||+||++|... |.++|||||+||+..++||||+++|..++.+|.+|..
T Consensus 1 ~e~~ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~~~l~~~~~~i~~~~~ 54 (55)
T cd00024 1 EEYEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDCKELIDEFKK 54 (55)
T ss_pred CCceEeeeeeeeecCCCCcEEEEEEECCCCCccCccccHHHhCchHHHHHHHHh
Confidence 479999999999987 8999999999999999999999999887889999975
No 5
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=99.17 E-value=1.8e-11 Score=89.64 Aligned_cols=52 Identities=42% Similarity=0.933 Sum_probs=47.5
Q ss_pred eEEEEEEEEeE-EeCCeEEEEEEecCCCCCCCceeecCCcCChHHHHHHHHHH
Q 042818 104 FFEIEAIRRKR-VRKGQLQYLIKWRGWPENANTWEPLENLQSCSDVIDAFEES 155 (440)
Q Consensus 104 EYEVEkILd~R-~~~GkleYLVKWKGY~eseNTWEPeENL~dc~ELIeeFe~k 155 (440)
+|+|++||++| ...+..+|||||+|++..++||+|.++|..|+.+|.+|..+
T Consensus 1 ~~~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~~l~~~~~~v~~~~~~ 53 (55)
T smart00298 1 EYEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKK 53 (55)
T ss_pred CcchheeeeeeecCCCcEEEEEEECCCCCccCceeeHHHHHHHHHHHHHHHHh
Confidence 47799999999 67888999999999999999999999997689999999875
No 6
>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=99.16 E-value=1.8e-11 Score=94.09 Aligned_cols=54 Identities=50% Similarity=0.765 Sum_probs=47.6
Q ss_pred eeccccccccccCCceeEEEEEEEEecCCcEEEeeccchhccCCeeehhHHHhhhccC
Q 042818 381 ILKPIDFSASVSDNMQDVVVTFMAVRSDGKEVMVDNKYLKANNPLLLINFYEQHLKYS 438 (440)
Q Consensus 381 IiKPv~ysasv~~~vQdV~vTF~A~RSDG~EV~VDnk~LKannPllLInfYEqHLrY~ 438 (440)
|+++|.+ |+..+ +..++|.+..+||+..+|+.+.++...|++||+|||+||+|+
T Consensus 1 ~~~~I~g-at~~~---~g~l~fl~kwk~~~~~lVp~~~~~~k~P~~vI~FYE~~l~~~ 54 (54)
T cd00034 1 LVKPISG-ASKSD---DGELTFLAKWKDGQASLVPNKELNVKCPLLVISFYEEHLTYN 54 (54)
T ss_pred CceEEEE-EEEcC---CCeEEEEEEEeCCeEEEEEHHHHHhhCcHHHHHHHHHhcccC
Confidence 4677777 55543 378999999999999999999999999999999999999995
No 7
>smart00300 ChSh Chromo Shadow Domain.
Probab=98.88 E-value=8.8e-10 Score=86.48 Aligned_cols=43 Identities=33% Similarity=0.516 Sum_probs=41.3
Q ss_pred eeEEEEEEEEecCCcEEEeeccchhccCCeeehhHHHhhhccC
Q 042818 396 QDVVVTFMAVRSDGKEVMVDNKYLKANNPLLLINFYEQHLKYS 438 (440)
Q Consensus 396 QdV~vTF~A~RSDG~EV~VDnk~LKannPllLInfYEqHLrY~ 438 (440)
++..++|.+..+||+..+|+.+.++...|++||+|||+||+|.
T Consensus 18 ~~G~l~flikwk~~~~~lVp~~~~~~k~P~~vI~FYE~~l~~~ 60 (61)
T smart00300 18 DDGELTFLIKWKDDAASLVPNKEANVKCPQKVIRFYESHLTFQ 60 (61)
T ss_pred CCCeEEEEEEEeCCcEEEEEHHHHHHHChHHHHHHHHHhCccC
Confidence 6778999999999999999999999999999999999999996
No 8
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=97.32 E-value=2.2e-05 Score=89.99 Aligned_cols=81 Identities=23% Similarity=0.436 Sum_probs=56.1
Q ss_pred EEEEEEecCCCCCCCceeecCCcC--Ch--HHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcccccccCCCCCc-ccccCC
Q 042818 120 LQYLIKWRGWPENANTWEPLENLQ--SC--SDVIDAFEESLRSGKSSRKRKRKGGGSSSLPKKKQARTFSAPY-YVTGGV 194 (440)
Q Consensus 120 leYLVKWKGY~eseNTWEPeENL~--dc--~ELIeeFe~k~~~~K~srKRkRks~g~~s~~kKrk~rs~s~~y-nv~~i~ 194 (440)
.+|||||+||+.-+||||+++.|. +. -.-|..|..+....+.-+++- +... +--.| .|.||+
T Consensus 226 ~qFlIKWkg~SyLHctWet~~~L~~~~~rG~kKv~nf~kK~~e~~~~~r~E------------~~~~-~~~dy~~VdRIi 292 (1373)
T KOG0384|consen 226 EQFLIKWKGWSYLHCTWETESELLEMNVRGLKKVDNFKKKVIEEDRWRRQE------------REED-LNKDYVIVDRII 292 (1373)
T ss_pred hhhheeeccccceeccccchHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhh------------hhhh-hhhhhhhhhhhh
Confidence 689999999999999999999975 32 234777877765444221110 0001 11223 568899
Q ss_pred CCCCCCCCCCccCCCCCCC
Q 042818 195 GQSLPADPLINAGLIDLSP 213 (440)
Q Consensus 195 ~~~~~s~P~~~~~~~~lp~ 213 (440)
..+.+..|.+-.+|-.||=
T Consensus 293 a~~~~~d~eYLvKW~~LpY 311 (1373)
T KOG0384|consen 293 AEQTSKDPEYLVKWRGLPY 311 (1373)
T ss_pred hcccCCCceeEEEecCCCc
Confidence 9999777999999999983
No 9
>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=96.52 E-value=0.0012 Score=51.80 Aligned_cols=39 Identities=26% Similarity=0.548 Sum_probs=32.4
Q ss_pred eEEEEEEEEecCCcEEEeeccchhccCCeeehhHHHhhhccC
Q 042818 397 DVVVTFMAVRSDGKEVMVDNKYLKANNPLLLINFYEQHLKYS 438 (440)
Q Consensus 397 dV~vTF~A~RSDG~EV~VDnk~LKannPllLInfYEqHLrY~ 438 (440)
-++|+| +.-|+-.+|..+.+...-|.++|.|||+||.+.
T Consensus 19 ~~likw---k~~~~~~~v~~~~~~~k~Pq~vI~FYE~~l~f~ 57 (58)
T PF01393_consen 19 MFLIKW---KNSGEKDLVPSKEANEKCPQKVIKFYESHLVFK 57 (58)
T ss_dssp EEEEEE---TTSSSEEEEEHHHHHHHSHHHHHHHHHHTCEEE
T ss_pred EEEEEE---CCCCceEEeeHHHHHHHCcHHHHHHHHHHeeec
Confidence 445555 333889999999999999999999999999873
No 10
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=96.47 E-value=0.0016 Score=75.48 Aligned_cols=52 Identities=31% Similarity=0.636 Sum_probs=44.7
Q ss_pred EEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCcCC-hHHHHHHHHHHhhc
Q 042818 106 EIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENLQS-CSDVIDAFEESLRS 158 (440)
Q Consensus 106 EVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL~d-c~ELIeeFe~k~~~ 158 (440)
.|++||++..... .+|||||.|.+-+++|||+++.+.- ++..+++|+.+..+
T Consensus 287 ~VdRIia~~~~~d-~eYLvKW~~LpY~e~TWE~~~~I~~~~~~~~~~~~~Re~s 339 (1373)
T KOG0384|consen 287 IVDRIIAEQTSKD-PEYLVKWRGLPYEECTWEDAEDIAKKAQEEIEEFQSRENS 339 (1373)
T ss_pred hhhhhhhcccCCC-ceeEEEecCCCcccccccchhhhhhhHHHHHHHHhhhhcc
Confidence 6999999988765 9999999999999999999999964 46678888887653
No 11
>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=96.36 E-value=0.0039 Score=48.20 Aligned_cols=47 Identities=23% Similarity=0.516 Sum_probs=37.6
Q ss_pred EEEEEEeEEeC-CeEEEEEEecCCCCCCCceeecCCcC-ChHHHHHHHHHHh
Q 042818 107 IEAIRRKRVRK-GQLQYLIKWRGWPENANTWEPLENLQ-SCSDVIDAFEESL 156 (440)
Q Consensus 107 VEkILd~R~~~-GkleYLVKWKGY~eseNTWEPeENL~-dc~ELIeeFe~k~ 156 (440)
++.|+...... |.+.||++|+| +. -.+.|..-+. .||.+|.+|++++
T Consensus 2 ~~~I~gat~~~~g~l~fl~kwk~-~~--~~lVp~~~~~~k~P~~vI~FYE~~ 50 (54)
T cd00034 2 VKPISGASKSDDGELTFLAKWKD-GQ--ASLVPNKELNVKCPLLVISFYEEH 50 (54)
T ss_pred ceEEEEEEEcCCCeEEEEEEEeC-Ce--EEEEEHHHHHhhCcHHHHHHHHHh
Confidence 57787766555 99999999999 54 4699987664 6999999999875
No 12
>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=96.27 E-value=0.0033 Score=49.36 Aligned_cols=49 Identities=31% Similarity=0.479 Sum_probs=40.5
Q ss_pred EEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCcC-ChHHHHHHHHHHh
Q 042818 106 EIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENLQ-SCSDVIDAFEESL 156 (440)
Q Consensus 106 EVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL~-dc~ELIeeFe~k~ 156 (440)
+.|+|++.-...|.+.|||||+|-+. -++.|..-+- .||.+|.+|++++
T Consensus 4 ~~E~Ivg~~d~~G~l~~likwk~~~~--~~~v~~~~~~~k~Pq~vI~FYE~~ 53 (58)
T PF01393_consen 4 EWEKIVGATDTNGELMFLIKWKNSGE--KDLVPSKEANEKCPQKVIKFYESH 53 (58)
T ss_dssp TEEEEEEEEECTSSEEEEEEETTSSS--EEEEEHHHHHHHSHHHHHHHHHHT
T ss_pred ChHHHheeecCCCcEEEEEEECCCCc--eEEeeHHHHHHHCcHHHHHHHHHH
Confidence 57899998777899999999999764 4688887553 6999999999875
No 13
>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=95.64 E-value=0.036 Score=42.50 Aligned_cols=41 Identities=22% Similarity=0.632 Sum_probs=35.6
Q ss_pred CceEEEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCc
Q 042818 102 EGFFEIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENL 142 (440)
Q Consensus 102 EeEYEVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL 142 (440)
+..+---+|++.|...|..+|+|.|.||....+.|.|.++|
T Consensus 13 ~~~~y~A~I~~~r~~~~~~~YyVHY~g~nkR~DeWV~~~~i 53 (55)
T PF11717_consen 13 DGQWYEAKILDIREKNGEPEYYVHYQGWNKRLDEWVPESRI 53 (55)
T ss_dssp TTEEEEEEEEEEEECTTCEEEEEEETTSTGCC-EEEETTTE
T ss_pred CCcEEEEEEEEEEecCCCEEEEEEcCCCCCCceeeecHHHc
Confidence 45566668999999999999999999999999999999987
No 14
>smart00300 ChSh Chromo Shadow Domain.
Probab=95.35 E-value=0.0062 Score=48.05 Aligned_cols=48 Identities=27% Similarity=0.464 Sum_probs=38.1
Q ss_pred EEEEEEEeEEeCCeEEEEEEecCCCCCCCceeecCCcC-ChHHHHHHHHHHh
Q 042818 106 EIEAIRRKRVRKGQLQYLIKWRGWPENANTWEPLENLQ-SCSDVIDAFEESL 156 (440)
Q Consensus 106 EVEkILd~R~~~GkleYLVKWKGY~eseNTWEPeENL~-dc~ELIeeFe~k~ 156 (440)
..|+|+..-..+|.+.|||+|+| +. ..+.|..-+. .||.+|.+|++++
T Consensus 8 ~~e~Ivg~~d~~G~l~flikwk~-~~--~~lVp~~~~~~k~P~~vI~FYE~~ 56 (61)
T smart00300 8 SWEDIVGITKDDGELTFLIKWKD-DA--ASLVPNKEANVKCPQKVIRFYESH 56 (61)
T ss_pred CHHHHhceecCCCeEEEEEEEeC-Cc--EEEEEHHHHHHHChHHHHHHHHHh
Confidence 45667666667899999999999 54 4699987664 6999999999875
No 15
>PF14061 Mtf2_C: Polycomb-like MTF2 factor 2
Probab=94.46 E-value=0.052 Score=42.33 Aligned_cols=22 Identities=36% Similarity=0.866 Sum_probs=18.8
Q ss_pred EEEEeEEe-CCeEEEEEEecCCC
Q 042818 109 AIRRKRVR-KGQLQYLIKWRGWP 130 (440)
Q Consensus 109 kILd~R~~-~GkleYLVKWKGY~ 130 (440)
.|+.+|+. +|++||||.|.|..
T Consensus 27 ~VlArRV~~dG~vQYLvEWeg~~ 49 (50)
T PF14061_consen 27 RVLARRVTPDGKVQYLVEWEGAT 49 (50)
T ss_pred EEEEEEEcCCCcEEEEEEecCcC
Confidence 46888876 89999999999975
No 16
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=45.70 E-value=6.3 Score=44.56 Aligned_cols=52 Identities=23% Similarity=0.434 Sum_probs=42.0
Q ss_pred EEEEEEEeEE-eCCeEEEEEEecCCCCCCCceeecC-CcCChHHHHHHHHHHhh
Q 042818 106 EIEAIRRKRV-RKGQLQYLIKWRGWPENANTWEPLE-NLQSCSDVIDAFEESLR 157 (440)
Q Consensus 106 EVEkILd~R~-~~GkleYLVKWKGY~eseNTWEPeE-NL~dc~ELIeeFe~k~~ 157 (440)
.|-.|+.++. ..+...|+|+|+.-+....+|+..+ .+.+++..+++|+.-..
T Consensus 210 ~i~rii~~~~s~~~~~~~~Vk~k~l~~d~~~~e~~~~~ip~~~~~~qe~~~~~~ 263 (696)
T KOG0383|consen 210 PIARIINRRSSQKGATDYLVKWKELSYDEQEWEVEDPDIPGYSSAGQEAWHHRE 263 (696)
T ss_pred ccchhhhhhcccccceeeEeeeccCCccccCCCcCCCCcccCcccccccccccC
Confidence 5677888885 4789999999999888899999998 66677778888775543
No 17
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=45.19 E-value=25 Score=29.91 Aligned_cols=31 Identities=32% Similarity=0.516 Sum_probs=23.4
Q ss_pred ccccccccccCCceeEEEEEEEEecCCcEEEeec
Q 042818 383 KPIDFSASVSDNMQDVVVTFMAVRSDGKEVMVDN 416 (440)
Q Consensus 383 KPv~ysasv~~~vQdV~vTF~A~RSDG~EV~VDn 416 (440)
|||.|. |-++++ |.=+|.|..+|+..+.|.|
T Consensus 25 k~v~f~--l~e~t~-V~a~F~a~d~~~~~f~Vs~ 55 (80)
T PF11095_consen 25 KPVEFT--LHENTT-VSARFGACDIDVSNFQVSN 55 (80)
T ss_dssp SEEEEE--EGGG-E-EEEEEEEE-TTS-EEEEEE
T ss_pred CceEEE--EeCCeE-EEEEEEEecCchheEEhhh
Confidence 566665 666766 9999999999999999987
No 18
>PF12733 Cadherin-like: Cadherin-like beta sandwich domain
Probab=44.27 E-value=29 Score=27.85 Aligned_cols=35 Identities=20% Similarity=0.398 Sum_probs=30.1
Q ss_pred cccccccCCceeEEEEEEEEecCCcEEEeeccchhc
Q 042818 386 DFSASVSDNMQDVVVTFMAVRSDGKEVMVDNKYLKA 421 (440)
Q Consensus 386 ~ysasv~~~vQdV~vTF~A~RSDG~EV~VDnk~LKa 421 (440)
.|.+.|..++..|.|+..+. ..+-.|.|++.-...
T Consensus 15 ~Y~~~V~~~~~~v~v~a~~~-~~~a~v~vng~~~~~ 49 (88)
T PF12733_consen 15 EYTVTVPNDVDSVTVTATPE-DSGATVTVNGVPVNS 49 (88)
T ss_pred EEEEEECCCceEEEEEEEEC-CCCEEEEEcCEEccC
Confidence 48899999999999999998 678999999976654
No 19
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=41.47 E-value=28 Score=37.79 Aligned_cols=40 Identities=18% Similarity=0.457 Sum_probs=33.1
Q ss_pred ceEEEEEEEEeEEe----CCeEEEEEEecCCCCCCCceeecCCc
Q 042818 103 GFFEIEAIRRKRVR----KGQLQYLIKWRGWPENANTWEPLENL 142 (440)
Q Consensus 103 eEYEVEkILd~R~~----~GkleYLVKWKGY~eseNTWEPeENL 142 (440)
..|-..+|++.|.. .+..+|.|.|.||...-+.|.+.+.|
T Consensus 68 g~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rL 111 (450)
T PLN00104 68 GKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQL 111 (450)
T ss_pred CCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhc
Confidence 44445778888873 36789999999999999999999998
No 20
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=28.63 E-value=34 Score=40.58 Aligned_cols=13 Identities=38% Similarity=0.680 Sum_probs=7.5
Q ss_pred ccCCCccceeech
Q 042818 30 ENINYDSIDLIDV 42 (440)
Q Consensus 30 ~~~~~~~~~~~~~ 42 (440)
+.|+|..|--|++
T Consensus 1346 ~a~dYs~iaTi~v 1358 (1516)
T KOG1832|consen 1346 DAIDYSDIATIPV 1358 (1516)
T ss_pred cccccccceeeec
Confidence 4567766654443
No 21
>PF14725 DUF4466: Domain of unknown function (DUF4466); PDB: 4EI0_A.
Probab=21.24 E-value=84 Score=32.52 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=20.7
Q ss_pred ccccccccCCc--eeEEEEEEEEecCCcEEE
Q 042818 385 IDFSASVSDNM--QDVVVTFMAVRSDGKEVM 413 (440)
Q Consensus 385 v~ysasv~~~v--QdV~vTF~A~RSDG~EV~ 413 (440)
+||.=-++... ++|++||-|--|+|++|-
T Consensus 105 LRYyYvipeeA~GK~vsFtFSa~sS~G~~vs 135 (308)
T PF14725_consen 105 LRYYYVIPEEARGKDVSFTFSAKSSNGQTVS 135 (308)
T ss_dssp EEEEEE--GGGTTSEEEEEEEEEETTS-EEE
T ss_pred EEEEEECchhhCCceEEEEEEEecCCCcEEE
Confidence 45655555554 599999999999999995
No 22
>PLN02967 kinase
Probab=20.83 E-value=49 Score=36.88 Aligned_cols=31 Identities=16% Similarity=0.253 Sum_probs=21.3
Q ss_pred hhhhhHHHhhcCccccccccccchhHhhhhh
Q 042818 50 QEKENEKEKEKGKEKVGEEKNNEEEEEEEEE 80 (440)
Q Consensus 50 ~~~~~~~~~~~~k~k~~~~k~~~~~~ee~~~ 80 (440)
..++..+++++-||+|++||-++.+|..++.
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (581)
T PLN02967 123 AASSDVEEEKTEKKVRKRRKVKKMDEDVEDQ 153 (581)
T ss_pred hcccchhhhhcchhhhhcccccchhhccccc
Confidence 4455667777778888888887776655533
Done!