Query psy1165
Match_columns 461
No_of_seqs 133 out of 167
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 15:26:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08782 c-SKI_SMAD_bind: c-SK 100.0 1E-44 2.2E-49 308.3 2.4 93 196-288 1-96 (96)
2 PF02437 Ski_Sno: SKI/SNO/DAC 100.0 1.2E-43 2.6E-48 310.0 8.1 112 69-180 3-114 (114)
3 PF08782 c-SKI_SMAD_bind: c-SK 100.0 2.5E-42 5.5E-47 293.7 2.1 91 359-449 1-94 (96)
4 KOG3915|consensus 99.9 5.9E-25 1.3E-29 227.2 15.1 137 74-216 165-307 (641)
5 PF02437 Ski_Sno: SKI/SNO/DAC 99.2 8.4E-13 1.8E-17 116.4 -0.7 49 295-343 66-114 (114)
6 PF01342 SAND: SAND domain; I 93.5 0.014 3.1E-07 49.1 -1.1 50 205-267 16-68 (82)
7 smart00258 SAND SAND domain. 90.8 0.1 2.2E-06 43.6 0.9 52 205-268 8-60 (73)
8 PF01342 SAND: SAND domain; I 90.1 0.035 7.5E-07 46.7 -2.4 49 368-429 16-67 (82)
9 smart00258 SAND SAND domain. 71.8 1.5 3.3E-05 36.7 0.5 51 368-430 8-59 (73)
10 PF14122 YokU: YokU-like prote 49.7 16 0.00034 31.8 2.8 39 192-236 10-48 (87)
11 KOG3915|consensus 41.2 18 0.00039 39.9 2.3 46 293-338 221-266 (641)
12 PF13878 zf-C2H2_3: zinc-finge 38.6 14 0.00031 27.3 0.8 13 224-236 14-26 (41)
13 PF08624 CRC_subunit: Chromati 32.7 1.7E+02 0.0038 27.5 6.9 80 97-178 34-117 (139)
14 PRK14751 tetracycline resistan 31.8 20 0.00044 25.0 0.6 14 406-419 9-23 (28)
15 cd05171 PIKKc_ATM Ataxia telan 29.3 49 0.0011 33.3 3.0 85 232-330 3-87 (279)
16 PF13913 zf-C2HC_2: zinc-finge 27.5 9.2 0.0002 25.5 -1.6 18 224-241 3-20 (25)
17 cd05169 PIKKc_TOR TOR (Target 24.4 75 0.0016 31.7 3.3 85 232-330 3-87 (280)
18 cd03742 SOCS_Rab40 SOCS (suppr 24.3 18 0.00039 27.6 -0.8 25 101-125 18-42 (43)
19 PF14001 YdfZ: YdfZ protein 23.1 41 0.00089 27.9 1.0 21 219-239 41-61 (64)
20 PF04810 zf-Sec23_Sec24: Sec23 22.5 34 0.00073 25.1 0.4 25 387-425 3-27 (40)
21 PF04236 Transp_Tc5_C: Tc5 tra 21.8 64 0.0014 26.3 1.9 26 219-244 36-62 (63)
22 PRK00766 hypothetical protein; 20.8 4.9E+02 0.011 25.6 7.9 82 86-184 70-173 (194)
No 1
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=100.00 E-value=1e-44 Score=308.30 Aligned_cols=93 Identities=48% Similarity=1.065 Sum_probs=64.6
Q ss_pred cceeeecccCceeeeeeccccCCCCCCceeccccccccCCCceeEeeccCCCCCccccCCCCcCcccceeecccc---cC
Q psy1165 196 SFKVYHECFGKCKGVCMPELFTDGESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAVEEQ---QN 272 (461)
Q Consensus 196 ~f~V~HeCfggc~G~f~P~ly~~~~a~CI~C~~C~~~FsP~kFV~HsH~~~e~r~cHwGfDSanWr~yl~l~~~~---~~ 272 (461)
+|+|||||||||+|+|+|+||++++|+||+|.+|+++|||+|||+|+|+++|++||||||||+|||+||+|++|+ +.
T Consensus 1 sf~V~HeC~g~c~G~f~P~lY~~~~a~CI~C~~C~~~FsP~kFV~HsHr~~e~~t~hwgfds~nWr~yL~l~~d~~~~~~ 80 (96)
T PF08782_consen 1 SFDVYHECFGGCRGSFIPELYSSPNAKCIECLECRGMFSPQKFVFHSHRPQEKRTCHWGFDSANWRRYLHLSQDYRDKEE 80 (96)
T ss_dssp --EEEE-STT-EEEEE-GGG--STT---EEETTT--EE-HHHHTT--SS---TTEEEES--GGGHHHC-EE-TT---TTC
T ss_pred CceeEEeecCccceEechhhcCCCCCCceEcccCCCEeCCcCEEEecCCCCCCccCCCccCHhHhhHHheecccccCcch
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999653 34
Q ss_pred hHHHHHHHHHHHHhhh
Q psy1165 273 YDQCLKILQIFKEQHI 288 (461)
Q Consensus 273 ~~~~~~~l~~~k~~~~ 288 (461)
.++++++||+|||||+
T Consensus 81 ~~~l~~~le~~k~~f~ 96 (96)
T PF08782_consen 81 QERLKQALEDVKAKFN 96 (96)
T ss_dssp HHHHHHHHHHHHCC--
T ss_pred HHHHHHHHHHHHHhhC
Confidence 5778899999999984
No 2
>PF02437 Ski_Sno: SKI/SNO/DAC family; InterPro: IPR003380 The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation []. It may play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli.; GO: 0005634 nucleus; PDB: 1L8R_B 3EQ5_F 1SBX_A.
Probab=100.00 E-value=1.2e-43 Score=310.05 Aligned_cols=112 Identities=63% Similarity=1.068 Sum_probs=89.3
Q ss_pred CCCCCCCCeeecCCCCCCceeeeeEcCeeEEEEEECCeeecchHHHHHHHhhcCChHHHHhhhcccceeeccCCHHHHHH
Q psy1165 69 PPPIQQLPILTTSDQSRSELSETLLEGETISCFVVGGEKRLCLPQILNSVLRDFSLPQINQVCDDLQIFCSRCNPEQLEI 148 (461)
Q Consensus 69 ppp~~~~Pil~~~D~~~~e~~~t~l~G~~I~~F~VgGe~rLCLpQi~~~vLk~fsl~~I~~~~~~L~I~c~~Ctp~QL~~ 148 (461)
+||+++.|+++++|.+++++.+|+++|++|+||+||||+|||||||+|+|||||++++||+++++|+|+|++||++||++
T Consensus 3 ~p~~~~~p~~~~~~~~~~~~~~~~l~G~~i~~f~v~Ge~rlCLpQi~~~vLk~~~~~~I~~~~~~L~I~~~~Ct~eQL~~ 82 (114)
T PF02437_consen 3 SPPVYSSPILSPSDPSSNECRMTELEGEPIACFVVGGEERLCLPQIFNSVLKDFSLHTINTKCKRLQIYCSRCTPEQLRI 82 (114)
T ss_dssp ---------G-GGG-GCCSEEEEEETTEEEEEEEETTEEEEEHHHHHHTTTTTSHHHHHHHHHHHTT---EE--HHHHHH
T ss_pred CCCcCCCCCCCCCCCCCceEEEEEECCEEEEEEEECCEEEEEHHHHHHHHHhcCCHHHHHHHHHhcceeEeeCCHHHHHH
Confidence 57778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCCCccccccchhHHHHHHHHhcCC
Q psy1165 149 LKLSGILPLTAASCGLMTKTDAERLCSTLLHQ 180 (461)
Q Consensus 149 Lk~~gilP~~a~sCgLITktDAERLc~~ll~~ 180 (461)
||.+||||++|+|||||||+||||||++|++.
T Consensus 83 Lk~~gaip~~~~~C~LItk~DaerL~~~~~~~ 114 (114)
T PF02437_consen 83 LKGLGAIPPSANRCGLITKTDAERLCKSCLHA 114 (114)
T ss_dssp HHHTTSS-TT----EEEEHHHHHHHHHHHHS-
T ss_pred HHhcCCCCCCCCcccceeHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999873
No 3
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=100.00 E-value=2.5e-42 Score=293.71 Aligned_cols=91 Identities=49% Similarity=1.099 Sum_probs=62.6
Q ss_pred cceEEEeeccccccccccccccCCCCCccccccccccccCCceeeeccCCCCCccccCCCCCcccccceeccccc---cc
Q psy1165 359 SFKVYHECFGKCKGVCMPELFTDGESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAVEEQ---QN 435 (461)
Q Consensus 359 ~f~V~HeCfgkc~G~f~pelY~~~~a~CI~C~~C~~~fSP~kFV~HsHr~~e~rtcHwGFds~nWr~yl~l~~~~---~~ 435 (461)
+|+|||||||||+|+|+|+||++++|+||+|.+|++||||+|||+|+|+++|+|||||||||+|||+||+|++++ +.
T Consensus 1 sf~V~HeC~g~c~G~f~P~lY~~~~a~CI~C~~C~~~FsP~kFV~HsHr~~e~~t~hwgfds~nWr~yL~l~~d~~~~~~ 80 (96)
T PF08782_consen 1 SFDVYHECFGGCRGSFIPELYSSPNAKCIECLECRGMFSPQKFVFHSHRPQEKRTCHWGFDSANWRRYLHLSQDYRDKEE 80 (96)
T ss_dssp --EEEE-STT-EEEEE-GGG--STT---EEETTT--EE-HHHHTT--SS---TTEEEES--GGGHHHC-EE-TT---TTC
T ss_pred CceeEEeecCccceEechhhcCCCCCCceEcccCCCEeCCcCEEEecCCCCCCccCCCccCHhHhhHHheecccccCcch
Confidence 599999999999999999999999999999999999999999999999999999999999999999999999654 34
Q ss_pred HHHHHHHHHHHhhh
Q psy1165 436 YDQCLKILQIFKEQ 449 (461)
Q Consensus 436 ~~~~~~~l~~~ke~ 449 (461)
.+++..+||++|+.
T Consensus 81 ~~~l~~~le~~k~~ 94 (96)
T PF08782_consen 81 QERLKQALEDVKAK 94 (96)
T ss_dssp HHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHh
Confidence 56677888888874
No 4
>KOG3915|consensus
Probab=99.92 E-value=5.9e-25 Score=227.21 Aligned_cols=137 Identities=21% Similarity=0.348 Sum_probs=116.2
Q ss_pred CCCeeecCCCCCCceeeeeEcCeeEEEEEECCeeecchHHHHHHHhhcCC--hHHHHhhhcccceeeccCCHHHHHHHHH
Q psy1165 74 QLPILTTSDQSRSELSETLLEGETISCFVVGGEKRLCLPQILNSVLRDFS--LPQINQVCDDLQIFCSRCNPEQLEILKL 151 (461)
Q Consensus 74 ~~Pil~~~D~~~~e~~~t~l~G~~I~~F~VgGe~rLCLpQi~~~vLk~fs--l~~I~~~~~~L~I~c~~Ctp~QL~~Lk~ 151 (461)
|.|| .+|....|++++.+.|.+|++|.|+|+++|||||+|+.|||+++ ||+||+++++|.|+.++||+||+||||.
T Consensus 165 p~pv--~~~p~~necKmVd~rG~kVAsF~i~g~emiCLPQafdlFLKhlVGGLHTVYTKLKRLdI~PvVCnVEQVRiLRg 242 (641)
T KOG3915|consen 165 PSPV--ENTPQNNECKMVDLRGAKVASFTIEGCELICLPQAFDLFLKHLVGGLHTVYTKLKRLDITPVVCNVEQVRILRG 242 (641)
T ss_pred CCcc--cCCCcccceeeeeecCceeeEEEecCceEEecHHHHHHHHHHHhchHHHHHHHhhccceeeeeechHHHHHHhc
Confidence 3444 67888899999999999999999999999999999999999997 9999999999999999999999999999
Q ss_pred cCCCCCCCccccccchhHHHHHHHHhc----CCCCCCCCccccccccccceeeecccCceeeeeecccc
Q psy1165 152 SGILPLTAASCGLMTKTDAERLCSTLL----HQRPGPTPRHIDKIVTFSFKVYHECFGKCKGVCMPELF 216 (461)
Q Consensus 152 ~gilP~~a~sCgLITktDAERLc~~ll----~~~~~pk~~~~~~~~~~~f~V~HeCfggc~G~f~P~ly 216 (461)
+|+|+++++||+||++.|||.|++++. ++++|||+...... .+.-++... ...|++.|.+.
T Consensus 243 LGAIQPGVNRCKLi~~kDFe~Ly~DCTnasSRPGRPpKR~~gv~~-pen~hi~~~---~~PgLmsPgm~ 307 (641)
T KOG3915|consen 243 LGAIQPGVNRCKLISRKDFETLYNDCTNASSRPGRPPKRTQGVTS-PENSHIMPH---SVPGLMSPGMI 307 (641)
T ss_pred cccccCCccceeeeecccHHHHHhhhcccccCCCCCCCCCccccc-ccccccccc---cCccccCCCCC
Confidence 999999999999999999999999988 47889988543211 111122211 33478888873
No 5
>PF02437 Ski_Sno: SKI/SNO/DAC family; InterPro: IPR003380 The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation []. It may play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli.; GO: 0005634 nucleus; PDB: 1L8R_B 3EQ5_F 1SBX_A.
Probab=99.24 E-value=8.4e-13 Score=116.42 Aligned_cols=49 Identities=57% Similarity=0.859 Sum_probs=35.2
Q ss_pred CccccCCCCCChhhHHHHHhcCCCCCCCCccCCCCCCchHHHHHHhccC
Q psy1165 295 KRKQTHRLPCNPEQLEILKLSGILPLTAASCGLMTKTDAERLCSTLLHQ 343 (461)
Q Consensus 295 KRKq~~rv~ctp~QLe~LK~~giLP~sa~sCGLITKtdAERLc~aLL~~ 343 (461)
||-+..+++|+++||++||..|+||.++++||||||+||||||++++++
T Consensus 66 ~~L~I~~~~Ct~eQL~~Lk~~gaip~~~~~C~LItk~DaerL~~~~~~~ 114 (114)
T PF02437_consen 66 KRLQIYCSRCTPEQLRILKGLGAIPPSANRCGLITKTDAERLCKSCLHA 114 (114)
T ss_dssp HHTT---EE--HHHHHHHHHTTSS-TT----EEEEHHHHHHHHHHHHS-
T ss_pred HhcceeEeeCCHHHHHHHHhcCCCCCCCCcccceeHHHHHHHHHHHhcC
Confidence 4455567899999999999999999999999999999999999999863
No 6
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=93.46 E-value=0.014 Score=49.07 Aligned_cols=50 Identities=30% Similarity=0.563 Sum_probs=38.3
Q ss_pred CceeeeeeccccC--CCCCCceeccccccccCCCceeEeeccCCCCCccccCCCCc-Ccccceeec
Q psy1165 205 GKCKGVCMPELFT--DGESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESV-KWRSYLLAV 267 (461)
Q Consensus 205 ggc~G~f~P~ly~--~~~a~CI~C~~C~~~FsP~kFV~HsH~~~e~r~cHwGfDSa-nWr~yl~l~ 267 (461)
|.-.|+|++++|. -...+||++. +.+|||..|..|. |-.++ ||++-|.+.
T Consensus 16 G~~~G~L~~~k~~~~g~~~kCI~~~--g~~~TP~eFE~~~-----------G~~~sK~WK~SIr~~ 68 (82)
T PF01342_consen 16 GDVKGTLYKKKFVKQGICGKCIQCE--GRWFTPSEFERHG-----------GKGSSKDWKRSIRCG 68 (82)
T ss_dssp TTEEEEEEHHHH-TTGTTSS-EEET--TEEE-HHHHHHHH-----------TTCTCS-HHHHSEET
T ss_pred CCeEEEEEHHHhhcccccCceEeeC--CcEECHHHHHhhc-----------CcccCCCCCccEEEC
Confidence 4569999999993 3478999999 9999999998765 45555 499999993
No 7
>smart00258 SAND SAND domain.
Probab=90.80 E-value=0.1 Score=43.63 Aligned_cols=52 Identities=23% Similarity=0.405 Sum_probs=43.1
Q ss_pred CceeeeeeccccCC-CCCCceeccccccccCCCceeEeeccCCCCCccccCCCCcCcccceeecc
Q psy1165 205 GKCKGVCMPELFTD-GESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAVE 268 (461)
Q Consensus 205 ggc~G~f~P~ly~~-~~a~CI~C~~C~~~FsP~kFV~HsH~~~e~r~cHwGfDSanWr~yl~l~~ 268 (461)
|...|+++-++|.+ ..-+||++.. .+|||..|..+.=+ -.+-+|++-|....
T Consensus 8 G~~~g~L~~~kf~~G~~~kCI~~~~--~~~TP~eFe~~~g~----------~~~K~WK~sIR~~g 60 (73)
T smart00258 8 GTVKGILYKKKFKCGISVKCIQYED--KWFTPKEFEIEGGK----------GKSKDWKRSIRCGG 60 (73)
T ss_pred CCeeeeeeHhhhhcCcccCCccCCC--EEEChHHHHhhcCC----------cccCCcchheeECC
Confidence 56789999999886 6778999987 89999999988755 35677999998875
No 8
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=90.14 E-value=0.035 Score=46.74 Aligned_cols=49 Identities=31% Similarity=0.597 Sum_probs=37.6
Q ss_pred cccccccccccc--cCCCCCccccccccccccCCceeeeccCCCCCccccCCCCCc-ccccceec
Q psy1165 368 GKCKGVCMPELF--TDGESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESV-KWRSYLLA 429 (461)
Q Consensus 368 gkc~G~f~pelY--~~~~a~CI~C~~C~~~fSP~kFV~HsHr~~e~rtcHwGFds~-nWr~yl~l 429 (461)
|.-+|+|+++.| .....+||++. +.+|||..|..|. |-.++ ||++-|.+
T Consensus 16 G~~~G~L~~~k~~~~g~~~kCI~~~--g~~~TP~eFE~~~-----------G~~~sK~WK~SIr~ 67 (82)
T PF01342_consen 16 GDVKGTLYKKKFVKQGICGKCIQCE--GRWFTPSEFERHG-----------GKGSSKDWKRSIRC 67 (82)
T ss_dssp TTEEEEEEHHHH-TTGTTSS-EEET--TEEE-HHHHHHHH-----------TTCTCS-HHHHSEE
T ss_pred CCeEEEEEHHHhhcccccCceEeeC--CcEECHHHHHhhc-----------CcccCCCCCccEEE
Confidence 556899999999 33467899997 9999999999776 54554 59999998
No 9
>smart00258 SAND SAND domain.
Probab=71.81 E-value=1.5 Score=36.74 Aligned_cols=51 Identities=24% Similarity=0.447 Sum_probs=37.9
Q ss_pred cccccccccccccC-CCCCccccccccccccCCceeeeccCCCCCccccCCCCCcccccceecc
Q psy1165 368 GKCKGVCMPELFTD-GESRCIQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAV 430 (461)
Q Consensus 368 gkc~G~f~pelY~~-~~a~CI~C~~C~~~fSP~kFV~HsHr~~e~rtcHwGFds~nWr~yl~l~ 430 (461)
|.-.|+++-+.|.. ..-+||++.+ .+|+|..|..+.=+.. +-+|++-|...
T Consensus 8 G~~~g~L~~~kf~~G~~~kCI~~~~--~~~TP~eFe~~~g~~~----------~K~WK~sIR~~ 59 (73)
T smart00258 8 GTVKGILYKKKFKCGISVKCIQYED--KWFTPKEFEIEGGKGK----------SKDWKRSIRCG 59 (73)
T ss_pred CCeeeeeeHhhhhcCcccCCccCCC--EEEChHHHHhhcCCcc----------cCCcchheeEC
Confidence 44567767677754 5678999976 8999999998876532 45799988873
No 10
>PF14122 YokU: YokU-like protein
Probab=49.66 E-value=16 Score=31.82 Aligned_cols=39 Identities=15% Similarity=0.271 Sum_probs=31.2
Q ss_pred cccccceeeecccCceeeeeeccccCCCCCCceeccccccccCCC
Q psy1165 192 IVTFSFKVYHECFGKCKGVCMPELFTDGESRCIQCLECHGFFSPQ 236 (461)
Q Consensus 192 ~~~~~f~V~HeCfggc~G~f~P~ly~~~~a~CI~C~~C~~~FsP~ 236 (461)
..+..-.||+|=-.|-+.+-+++- ++|.|..|+|.|-..
T Consensus 10 a~~~~~tvyWeLpdGtraIeI~~t------P~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 10 ASESESTVYWELPDGTRAIEITDT------PAIICSNCGMVYQDD 48 (87)
T ss_pred cccccceEEEEcCCCceEEEecCC------ceeeecCCCcEEehh
Confidence 344556799998889999988876 899999999987543
No 11
>KOG3915|consensus
Probab=41.22 E-value=18 Score=39.95 Aligned_cols=46 Identities=30% Similarity=0.456 Sum_probs=41.4
Q ss_pred CCCccccCCCCCChhhHHHHHhcCCCCCCCCccCCCCCCchHHHHH
Q psy1165 293 SGKRKQTHRLPCNPEQLEILKLSGILPLTAASCGLMTKTDAERLCS 338 (461)
Q Consensus 293 ggKRKq~~rv~ctp~QLe~LK~~giLP~sa~sCGLITKtdAERLc~ 338 (461)
.-||--...+-|+-+|-.|||-.|+|....-+|-||++.|=|.|-.
T Consensus 221 KLKRLdI~PvVCnVEQVRiLRgLGAIQPGVNRCKLi~~kDFe~Ly~ 266 (641)
T KOG3915|consen 221 KLKRLDITPVVCNVEQVRILRGLGAIQPGVNRCKLISRKDFETLYN 266 (641)
T ss_pred HhhccceeeeeechHHHHHHhccccccCCccceeeeecccHHHHHh
Confidence 3577777789999999999999999999999999999999988754
No 12
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=38.59 E-value=14 Score=27.34 Aligned_cols=13 Identities=31% Similarity=0.794 Sum_probs=12.0
Q ss_pred eeccccccccCCC
Q psy1165 224 IQCLECHGFFSPQ 236 (461)
Q Consensus 224 I~C~~C~~~FsP~ 236 (461)
+.|..|+|.|+|.
T Consensus 14 ~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 14 TTCPTCGMLYSPG 26 (41)
T ss_pred cCCCCCCCEECCC
Confidence 7999999999986
No 13
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=32.74 E-value=1.7e+02 Score=27.48 Aligned_cols=80 Identities=18% Similarity=0.203 Sum_probs=56.9
Q ss_pred eEEEEEEC--CeeecchHHHHHHHhhcCChHHHHhhhcccceeeccCCHHHHHHHHHcCCCC--CCCccccccchhHHHH
Q psy1165 97 TISCFVVG--GEKRLCLPQILNSVLRDFSLPQINQVCDDLQIFCSRCNPEQLEILKLSGILP--LTAASCGLMTKTDAER 172 (461)
Q Consensus 97 ~I~~F~Vg--Ge~rLCLpQi~~~vLk~fsl~~I~~~~~~L~I~c~~Ctp~QL~~Lk~~gilP--~~a~sCgLITktDAER 172 (461)
++.-|.+- |+...=|-+=.-.+| .| .++-.-+.+--+++-..||.+|.+-|...|+|| -..++.+++|=+-|-+
T Consensus 34 ~~~TFtl~~rg~~lymL~td~ar~l-g~-rDs~~ff~~~~~l~ki~~t~~ek~~Li~~~ll~~s~~~r~i~~VTARS~F~ 111 (139)
T PF08624_consen 34 RFRTFTLPGRGNRLYMLSTDPARCL-GF-RDSYLFFRKHPQLYKIIATQEEKDFLIERGLLPSSYRSRQITIVTARSAFR 111 (139)
T ss_pred EEEEEEeCCCCCeEEEEeHHHHHHh-cc-ccHHHHHHhCCceeeeeCCHHHHHHHHHcCCCCcccCCCceEEEEhHHHHH
Confidence 45566663 334444433333333 33 255566667889999999999999999999999 6678899999888887
Q ss_pred HHHHhc
Q psy1165 173 LCSTLL 178 (461)
Q Consensus 173 Lc~~ll 178 (461)
.-+|-.
T Consensus 112 ~FGA~i 117 (139)
T PF08624_consen 112 EFGARI 117 (139)
T ss_pred HhCcHh
Confidence 766643
No 14
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=31.83 E-value=20 Score=25.01 Aligned_cols=14 Identities=36% Similarity=0.805 Sum_probs=10.2
Q ss_pred cCC-CCCccccCCCC
Q psy1165 406 HLS-SENRTCHWGFE 419 (461)
Q Consensus 406 Hr~-~e~rtcHwGFd 419 (461)
|.. .++..|||.|-
T Consensus 9 h~~psdksi~hwdf~ 23 (28)
T PRK14751 9 HKNPSDKSIYHWDFY 23 (28)
T ss_pred ecCCCcCceeeeeeh
Confidence 444 67889999873
No 15
>cd05171 PIKKc_ATM Ataxia telangiectasia mutated (ATM), catalytic domain; The ATM catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. ATM is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). ATM contains a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. ATM is critical in the response to DNA double strand breaks (DSBs) caused by radiation. It is activated at the site of a DSB and phosphorylates key substrates that trigger pathways that regulate DNA repair and cell cycle checkpoints at the G1/S, S phase, and G2/M transi
Probab=29.30 E-value=49 Score=33.29 Aligned_cols=85 Identities=14% Similarity=0.182 Sum_probs=44.6
Q ss_pred ccCCCceeEeeccCCCCCccccCCCCcCcccceeecccccChHHHHHHHHHHHHhhhccccCCCccccCCCCCChhhHHH
Q psy1165 232 FFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAVEEQQNYDQCLKILQIFKEQHIETTTSGKRKQTHRLPCNPEQLEI 311 (461)
Q Consensus 232 ~FsP~kFV~HsH~~~e~r~cHwGfDSanWr~yl~l~~~~~~~~~~~~~l~~~k~~~~~lN~ggKRKq~~rv~ctp~QLe~ 311 (461)
.|.|+-.|+.|+.. ..++.=-|=|...+.-.++-.+|-..++..++++.-+...+....+..+|. ..
T Consensus 3 ~f~~~v~v~~s~~~-Pkri~~~gsdG~~y~fl~K~~dDlR~D~rimQl~~~~n~il~~~~e~~~r~--l~---------- 69 (279)
T cd05171 3 KFKDVFTTAGGINA-PKIITCVGSDGKKYKQLLKGGDDDRQDAVMEQVFQLVNTLLERNKETRKRK--LR---------- 69 (279)
T ss_pred CccCeEEEecCCCC-CEEEEEECCCCCEEEEEecCCCcccHHHHHHHHHHHHHHHHhhChhhhhcC--ce----------
Confidence 48899999999987 566654455544343333333443333444444443333322111112222 22
Q ss_pred HHhcCCCCCCCCccCCCCC
Q psy1165 312 LKLSGILPLTAASCGLMTK 330 (461)
Q Consensus 312 LK~~giLP~sa~sCGLITK 330 (461)
++.+.|+|.+ +.||||.=
T Consensus 70 i~~y~vipls-~~~GLIe~ 87 (279)
T cd05171 70 IRTYKVVPLS-PRAGILEW 87 (279)
T ss_pred eecceEEecC-CCceEEEE
Confidence 2237888884 88998753
No 16
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.53 E-value=9.2 Score=25.53 Aligned_cols=18 Identities=28% Similarity=0.696 Sum_probs=15.6
Q ss_pred eeccccccccCCCceeEe
Q psy1165 224 IQCLECHGFFSPQKFVCH 241 (461)
Q Consensus 224 I~C~~C~~~FsP~kFV~H 241 (461)
++|..|+..|.|..+.-|
T Consensus 3 ~~C~~CgR~F~~~~l~~H 20 (25)
T PF13913_consen 3 VPCPICGRKFNPDRLEKH 20 (25)
T ss_pred CcCCCCCCEECHHHHHHH
Confidence 689999999999887766
No 17
>cd05169 PIKKc_TOR TOR (Target of rapamycin), catalytic domain; The TOR catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. TOR is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). TOR contains a rapamycin binding domain, a catalytic domain, and a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. It is also called FRAP (FK506 binding protein 12-rapamycin associated protein). TOR is a central component of the eukaryotic growth regulatory network. It controls the expression of many genes transcribed by all three RNA polymerases. It associates with
Probab=24.45 E-value=75 Score=31.72 Aligned_cols=85 Identities=14% Similarity=0.239 Sum_probs=45.2
Q ss_pred ccCCCceeEeeccCCCCCccccCCCCcCcccceeecccccChHHHHHHHHHHHHhhhccccCCCccccCCCCCChhhHHH
Q psy1165 232 FFSPQKFVCHVHLSSENRTCHWGFESVKWRSYLLAVEEQQNYDQCLKILQIFKEQHIETTTSGKRKQTHRLPCNPEQLEI 311 (461)
Q Consensus 232 ~FsP~kFV~HsH~~~e~r~cHwGfDSanWr~yl~l~~~~~~~~~~~~~l~~~k~~~~~lN~ggKRKq~~rv~ctp~QLe~ 311 (461)
.|.|+-.|+.|. ....+..=.|=|..+..-.++-.+|-..++..++++.-+...+.... ..|+....+..
T Consensus 3 ~f~~~v~v~~s~-~~pk~i~~~gsdG~~y~fl~K~~dDlR~D~r~~ql~~~~n~il~~~~--~~~~~~l~~~t------- 72 (280)
T cd05169 3 SFDPVLKVIPSK-QRPRRLTIVGSDGKEYKFLLKGHEDLRLDERVMQLFGLINTLLKNDS--ETSKRNLSIQT------- 72 (280)
T ss_pred cccCeEEEEeCC-CCCeEEEEECCCCCEEEEeecCCCcchHHHHHHHHHHHHHHHHHhCh--hhhhcCcceee-------
Confidence 488888999965 45556554466654443333323333333444444444433332211 22333344333
Q ss_pred HHhcCCCCCCCCccCCCCC
Q psy1165 312 LKLSGILPLTAASCGLMTK 330 (461)
Q Consensus 312 LK~~giLP~sa~sCGLITK 330 (461)
+.|+|.+ +.||||.=
T Consensus 73 ---y~Vipls-~~~GlIE~ 87 (280)
T cd05169 73 ---YSVIPLS-PNVGLIGW 87 (280)
T ss_pred ---ccEEecC-CCcceEEe
Confidence 8889985 89999654
No 18
>cd03742 SOCS_Rab40 SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=24.31 E-value=18 Score=27.64 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.2
Q ss_pred EEECCeeecchHHHHHHHhhcCChH
Q psy1165 101 FVVGGEKRLCLPQILNSVLRDFSLP 125 (461)
Q Consensus 101 F~VgGe~rLCLpQi~~~vLk~fsl~ 125 (461)
..++|-.+|.||..+...||+|++.
T Consensus 18 t~~~~I~~LPLP~~Lk~yLkey~~~ 42 (43)
T cd03742 18 TPVYLIDKLPLPVSIKSHLKSFAMA 42 (43)
T ss_pred CCcchhhhCCCCHHHHHHHHhcccc
Confidence 3467889999999999999999753
No 19
>PF14001 YdfZ: YdfZ protein
Probab=23.10 E-value=41 Score=27.86 Aligned_cols=21 Identities=24% Similarity=0.797 Sum_probs=18.5
Q ss_pred CCCCceeccccccccCCCcee
Q psy1165 219 GESRCIQCLECHGFFSPQKFV 239 (461)
Q Consensus 219 ~~a~CI~C~~C~~~FsP~kFV 239 (461)
.+++|+++..|+.+|.|..-|
T Consensus 41 rR~kcVel~g~~g~f~P~eLi 61 (64)
T PF14001_consen 41 RRAKCVELEGCEGRFAPVELI 61 (64)
T ss_pred hhccEEEEeCCCceEcchheE
Confidence 478999999999999998765
No 20
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=22.51 E-value=34 Score=25.07 Aligned_cols=25 Identities=20% Similarity=0.822 Sum_probs=14.0
Q ss_pred cccccccccccCCceeeeccCCCCCccccCCCCCccccc
Q psy1165 387 IQCLECHGFFSPQKFVCHVHLSSENRTCHWGFESVKWRS 425 (461)
Q Consensus 387 I~C~~C~~~fSP~kFV~HsHr~~e~rtcHwGFds~nWr~ 425 (461)
++|..|+.|+.|- ++|-++...|.+
T Consensus 3 ~rC~~C~aylNp~--------------~~~~~~~~~w~C 27 (40)
T PF04810_consen 3 VRCRRCRAYLNPF--------------CQFDDGGKTWIC 27 (40)
T ss_dssp -B-TTT--BS-TT--------------SEEETTTTEEEE
T ss_pred cccCCCCCEECCc--------------ceEcCCCCEEEC
Confidence 5788899999885 555666666765
No 21
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.83 E-value=64 Score=26.34 Aligned_cols=26 Identities=23% Similarity=0.540 Sum_probs=22.0
Q ss_pred CCCCceeccccccccCCCceeE-eecc
Q psy1165 219 GESRCIQCLECHGFFSPQKFVC-HVHL 244 (461)
Q Consensus 219 ~~a~CI~C~~C~~~FsP~kFV~-HsH~ 244 (461)
.+...|+|..|+..+-=+.||+ +.|+
T Consensus 36 ~~~s~I~C~~Ckk~~Cf~Hfiv~~~H~ 62 (63)
T PF04236_consen 36 NNTSFIRCAYCKKSLCFNHFIVSEYHL 62 (63)
T ss_pred CCcCEEEccccCCcccccceeeeeeEc
Confidence 4557899999999999999996 6774
No 22
>PRK00766 hypothetical protein; Provisional
Probab=20.84 E-value=4.9e+02 Score=25.56 Aligned_cols=82 Identities=22% Similarity=0.323 Sum_probs=54.5
Q ss_pred CceeeeeEcCeeEEEEEEC---------Ceeecch----H--HHHHHHh-hcCChHHHHhhhcccceeeccCCHHHHHHH
Q psy1165 86 SELSETLLEGETISCFVVG---------GEKRLCL----P--QILNSVL-RDFSLPQINQVCDDLQIFCSRCNPEQLEIL 149 (461)
Q Consensus 86 ~e~~~t~l~G~~I~~F~Vg---------Ge~rLCL----p--Qi~~~vL-k~fsl~~I~~~~~~L~I~c~~Ctp~QL~~L 149 (461)
.+..-+.|+|..++.|||= |-+-+|+ | +-+...| ++|+=.+ +-++++
T Consensus 70 ~~i~~V~L~Git~agFNvvD~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~-----------------~R~~~~ 132 (194)
T PRK00766 70 GQLRVIMLDGITYGGFNVVDIEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWE-----------------ERIKLI 132 (194)
T ss_pred cceEEEEECCEeeeeeEEecHHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHH-----------------HHHHHH
Confidence 4677899999999999996 4555555 3 2333333 5564221 235677
Q ss_pred HHcCCC-CCCC-----ccccccchhHHHHHHHHhcCCCCCC
Q psy1165 150 KLSGIL-PLTA-----ASCGLMTKTDAERLCSTLLHQRPGP 184 (461)
Q Consensus 150 k~~gil-P~~a-----~sCgLITktDAERLc~~ll~~~~~p 184 (461)
+.+|-+ |... -|.--|+..+|.+|+..+...+.-|
T Consensus 133 ~~~g~~~~~~~~~~vyvs~~gi~l~~A~~lv~~~~~~~riP 173 (194)
T PRK00766 133 KKAGKIVELITRGPLYIQAAGIDPETAAEIVRLTSTRSLIP 173 (194)
T ss_pred HhCCCceEeccCCCEEEEEcCCCHHHHHHHHHHhccCCCCc
Confidence 777733 2221 1346899999999999999876665
Done!