Query 045019
Match_columns 248
No_of_seqs 109 out of 166
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:02:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045019.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045019hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01396 MeCP2_MBD MeCP2, MBD1, 99.7 3E-18 6.5E-23 130.0 6.9 60 103-164 3-62 (77)
2 PF01429 MBD: Methyl-CpG bindi 99.7 4.7E-18 1E-22 127.4 7.2 63 101-164 5-68 (77)
3 cd00122 MBD MeCP2, MBD1, MBD2, 99.7 4.7E-17 1E-21 117.7 6.3 58 105-164 4-61 (62)
4 smart00391 MBD Methyl-CpG bind 99.7 7.2E-17 1.6E-21 122.4 7.0 57 107-164 8-64 (77)
5 KOG4161 Methyl-CpG binding tra 99.5 1.2E-14 2.6E-19 131.9 7.1 148 96-245 9-264 (272)
6 cd01397 HAT_MBD Methyl-CpG bin 99.5 5.1E-14 1.1E-18 107.2 5.6 58 105-164 4-61 (73)
7 cd01395 HMT_MBD Methyl-CpG bin 98.5 1.8E-07 3.9E-12 69.1 4.8 55 106-164 5-59 (60)
8 PF00397 WW: WW domain; Inter 90.5 0.28 6E-06 31.2 2.5 26 107-139 1-26 (31)
9 smart00456 WW Domain with 2 co 78.7 4.1 8.9E-05 25.1 3.7 24 107-138 1-24 (32)
10 KOG3259 Peptidyl-prolyl cis-tr 52.5 9.1 0.0002 33.8 1.8 28 104-138 4-31 (163)
11 KOG4161 Methyl-CpG binding tra 51.5 13 0.00027 34.6 2.7 205 33-239 30-270 (272)
12 KOG1891 Proline binding protei 44.7 21 0.00045 33.6 2.9 26 102-135 89-114 (271)
13 PF13894 zf-C2H2_4: C2H2-type 41.6 41 0.00089 18.3 2.8 22 131-152 1-22 (24)
14 PF00096 zf-C2H2: Zinc finger, 39.3 45 0.00098 18.8 2.8 21 131-151 1-21 (23)
15 cd00201 WW Two conserved trypt 38.9 47 0.001 19.8 3.0 23 108-138 1-23 (31)
16 PF14657 Integrase_AP2: AP2-li 24.9 1.3E+02 0.0029 20.2 3.6 21 132-152 9-36 (46)
17 KOG1891 Proline binding protei 22.6 46 0.00099 31.4 1.3 28 103-138 125-152 (271)
18 KOG4718 Non-SMC (structural ma 20.1 64 0.0014 30.1 1.7 34 104-154 144-177 (235)
No 1
>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=99.74 E-value=3e-18 Score=130.02 Aligned_cols=60 Identities=37% Similarity=0.654 Sum_probs=55.0
Q ss_pred CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019 103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN 164 (248)
Q Consensus 103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~ 164 (248)
.++.||+||+||+++|++| +++++|+|||+| +|++|||+.||++||+.......+.+||+
T Consensus 3 ~~~~lp~GW~r~~~~R~~g-s~~k~DvyY~sP-~Gkk~RS~~ev~~yL~~~~~~~~~~~~Fd 62 (77)
T cd01396 3 EDPRLPPGWKRELVPRKSG-SAGKFDVYYISP-TGKKFRSKVELARYLEKNGPTSLDLSDFD 62 (77)
T ss_pred CCCCCCCCCEEEEEEecCC-CCCcceEEEECC-CCCEEECHHHHHHHHHhCCCCCCcHhHcc
Confidence 4667999999999999999 889999999999 89999999999999999876667778888
No 2
>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=99.74 E-value=4.7e-18 Score=127.43 Aligned_cols=63 Identities=41% Similarity=0.721 Sum_probs=54.7
Q ss_pred ccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCC-cccccccCCc
Q 045019 101 TATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGT-KRKRRKENSN 164 (248)
Q Consensus 101 ~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~-~~~~~~en~~ 164 (248)
.+.+.+||+||++|+++|++|.++|+.|+||++| +|++|||+.||.+||..+. ....+.++|+
T Consensus 5 ~~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP-~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~ 68 (77)
T PF01429_consen 5 SPLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSP-CGKRFRSKKEVVRYLKENPSEHDLKPENFS 68 (77)
T ss_dssp ECEBTTSTTT-EEEEEESSSSTTTTSEEEEEEET-TSEEESSHHHHHHHHTTSS---SS-CTTBB
T ss_pred ccccCCCCCCCEEEEEEecCCCcCCceEEEEECC-CCCEEeCHHHHHHHHHhCCCcccCCHhHCC
Confidence 4568899999999999999999999999999999 9999999999999999988 4666667776
No 3
>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=99.69 E-value=4.7e-17 Score=117.67 Aligned_cols=58 Identities=41% Similarity=0.662 Sum_probs=52.1
Q ss_pred CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019 105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN 164 (248)
Q Consensus 105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~ 164 (248)
.+||.||+||+++|++| +.+++|+||++| +|++|||+.||++||........+.+||+
T Consensus 4 ~P~p~GW~R~~~~r~~g-~~~k~dv~Y~sP-~Gk~~Rs~~ev~~yL~~~~~~~l~~~~F~ 61 (62)
T cd00122 4 DPLPPGWKRELVIRKSG-SAGKGDVYYYSP-CGKKLRSKPEVARYLEKTGPSSLDLENFS 61 (62)
T ss_pred CCCCCCeEEEEEEcCCC-CCCcceEEEECC-CCceecCHHHHHHHHHhCCCCCCcHHHCC
Confidence 46799999999999999 789999999999 89999999999999999875556667775
No 4
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=99.68 E-value=7.2e-17 Score=122.36 Aligned_cols=57 Identities=35% Similarity=0.609 Sum_probs=55.0
Q ss_pred CCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN 164 (248)
Q Consensus 107 LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~ 164 (248)
||.||.|++++|++|.++|+.|+||++| +|++|||+.||.+||.+.....++.++|+
T Consensus 8 lp~GW~R~~~~r~~g~~~~~~dV~Y~sP-~GkklRs~~ev~~YL~~~~~~~~~~~~F~ 64 (77)
T smart00391 8 LPCGWRRETKQRKSGRSAGKFDVYYISP-CGKKLRSKSELARYLHKNGDLSLDLECFD 64 (77)
T ss_pred CCCCcEEEEEEecCCCCCCcccEEEECC-CCCeeeCHHHHHHHHHhCCCccccccccc
Confidence 9999999999999999999999999999 99999999999999999998888889888
No 5
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.53 E-value=1.2e-14 Score=131.91 Aligned_cols=148 Identities=24% Similarity=0.387 Sum_probs=104.1
Q ss_pred cccccccCCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccc---------------
Q 045019 96 STRRLTATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRK--------------- 160 (248)
Q Consensus 96 ~~~kl~~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~--------------- 160 (248)
..++ ..+|..||+||.+++++|++|.++|+.|+||++| +|++||||.++.+||+..+......
T Consensus 9 ~~~~-~~~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp-~g~~frsk~~l~~~~~~~~~~s~~~~v~~k~~~~~~~~~~ 86 (272)
T KOG4161|consen 9 IAGK-RSDCPALPPGWTREEVQRSSGLSAGKSDVYYISP-SGKKFRSKPQLARYLGKVGDLSLFDFVTGKMSPSERQKNK 86 (272)
T ss_pred cccC-cccCCCCCCCcchhhhcccCCCcccccceEEeCC-cccccccccHHHHHhccccccccCcccccccccccccccC
Confidence 3344 6789999999999999999999999999999999 8999999999999999544322211
Q ss_pred --cCCcc----------CCC-----------------CCCcCC-------------------------------------
Q 045019 161 --ENSNA----------DMD-----------------SSGSAA------------------------------------- 174 (248)
Q Consensus 161 --en~~~----------~~n-----------------~~~~s~------------------------------------- 174 (248)
+..+. +.+ .+..|.
T Consensus 87 q~~~~~~~~~~k~~~r~~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~~~s~~~ 166 (272)
T KOG4161|consen 87 QRKPEDPSKSNKRKGRGDLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLEADSSRG 166 (272)
T ss_pred CCCCCchhhhhccCCCcccccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccccccccc
Confidence 11111 000 000000
Q ss_pred C----------CcCcCCCCcccc---------ccccccCCCCCCcceEEEEecCCCCCcccccCCcccC-hhhhhhHHH-
Q 045019 175 G----------STKQKKPNIKAK---------TSALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVP-ESVRQDWAA- 233 (248)
Q Consensus 175 ~----------~~Ks~K~~k~~k---------~~~~nfD~~npP~KV~WVLsgp~~~~WtPfidds~Vp-es~K~~Ws~- 233 (248)
+ ++...+.-.++. ..++.+++...|+.|.|....+..+.|.|++.+.+|+ +.++++|+.
T Consensus 167 e~~d~~~l~~~~~g~~~~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~ 246 (272)
T KOG4161|consen 167 ESIDKLSLPKTPQGSGRSSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRV 246 (272)
T ss_pred cccCccccCcCCCccCccccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccch
Confidence 0 000011001111 1156667788889999999998889999999999999 999999999
Q ss_pred ------HHHHhhhcCCCe
Q 045019 234 ------AFTDLTTSNNGS 245 (248)
Q Consensus 234 ------aF~~l~~~~~g~ 245 (248)
.|..|+.++-..
T Consensus 247 ~~~r~~~~~~l~sd~~~~ 264 (272)
T KOG4161|consen 247 KNVRRSLFSALTSDTLSK 264 (272)
T ss_pred hhhhhccccchhhcCcch
Confidence 777777765443
No 6
>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=99.48 E-value=5.1e-14 Score=107.16 Aligned_cols=58 Identities=26% Similarity=0.394 Sum_probs=53.2
Q ss_pred CCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019 105 AWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN 164 (248)
Q Consensus 105 ~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~ 164 (248)
-.||.||+||+++|+.| +.++.|+||++| +|+||||+.||.+||........+.|||.
T Consensus 4 ~Pl~~GW~Re~vir~~~-~~~~~dV~Y~aP-cGKklRs~~ev~~yL~~~~~~~Lt~dnFs 61 (73)
T cd01397 4 VPLELGWRRETRIRGLG-GRIQGEVAYYAP-CGKKLRQYPEVIKYLSKNGISLLSRENFS 61 (73)
T ss_pred CCCCCCceeEEEeccCC-CCccceEEEECC-CCcccccHHHHHHHHHhCCccCccHhHcc
Confidence 36899999999999998 779999999999 99999999999999998777777778887
No 7
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
Probab=98.50 E-value=1.8e-07 Score=69.12 Aligned_cols=55 Identities=20% Similarity=0.126 Sum_probs=46.9
Q ss_pred CCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCCcccccccCCc
Q 045019 106 WLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGTKRKRRKENSN 164 (248)
Q Consensus 106 ~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~~~~~~~en~~ 164 (248)
.|--||.|....|+.|. -+.|++|.+| +|+++|+..||++||... ......|||.
T Consensus 5 Pll~gw~R~~~~~~~~~--~k~~V~Y~aP-CGr~Lr~~~EV~~YL~~t-~~~L~~d~Fs 59 (60)
T cd01395 5 PLLCGFQRMKYRARVGK--VKKHVIYKAP-CGRSLRNMSEVHRYLRET-CSFLTVDNFS 59 (60)
T ss_pred ccccCeEEEEEeccCCC--cccceEEECC-cchhhhcHHHHHHHHHhc-cccceeeccc
Confidence 46789999998888773 5889999999 999999999999999988 5555557774
No 8
>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=90.51 E-value=0.28 Score=31.17 Aligned_cols=26 Identities=42% Similarity=0.864 Sum_probs=17.7
Q ss_pred CCCCceEEEEEccCCCCCCceeEEEeeCCCCCe
Q 045019 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGRR 139 (248)
Q Consensus 107 LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkK 139 (248)
||+||.+....+ +| ..||+...+|..
T Consensus 1 LP~gW~~~~~~~-~g------~~YY~N~~t~~s 26 (31)
T PF00397_consen 1 LPPGWEEYFDPD-SG------RPYYYNHETGES 26 (31)
T ss_dssp SSTTEEEEEETT-TS------EEEEEETTTTEE
T ss_pred CCcCCEEEEcCC-CC------CEEEEeCCCCCE
Confidence 899997443212 33 589999988753
No 9
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=78.73 E-value=4.1 Score=25.09 Aligned_cols=24 Identities=33% Similarity=0.814 Sum_probs=16.8
Q ss_pred CCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019 107 LPPGWEIEDRVRTSGATAGTVDKYYFHVASGR 138 (248)
Q Consensus 107 LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk 138 (248)
||.||.+.. -.+ ...||++..++.
T Consensus 1 lp~gW~~~~--~~~------g~~yy~n~~t~~ 24 (32)
T smart00456 1 LPPGWEERK--DPD------GRPYYYNHETKE 24 (32)
T ss_pred CCCCCEEEE--CCC------CCEEEEECCCCC
Confidence 799997763 222 358999887665
No 10
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=52.51 E-value=9.1 Score=33.78 Aligned_cols=28 Identities=46% Similarity=0.930 Sum_probs=18.8
Q ss_pred CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019 104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR 138 (248)
Q Consensus 104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk 138 (248)
...||+||++.. -|.+| -.||+.++|+.
T Consensus 4 ~~~LP~~Wekr~-Srs~g------r~YyfN~~T~~ 31 (163)
T KOG3259|consen 4 EEKLPPGWEKRM-SRSSG------RPYYFNTETNE 31 (163)
T ss_pred cccCCchhheec-cccCC------Ccceeccccch
Confidence 458999997653 34443 47999887553
No 11
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=51.53 E-value=13 Score=34.63 Aligned_cols=205 Identities=11% Similarity=0.007 Sum_probs=124.2
Q ss_pred CCCCCccccCCceecCCCCCCCCCCccccCCCCCCcccccccccccccccCCCCcCCCCc----c--cccccccccCCCC
Q 045019 33 NVPPDPLLDSGFFIDAAPPATSGSNTTTTNDQTSKKRGTIREHKSENLATTNGTESALTP----E--TASTRRLTATEAW 106 (248)
Q Consensus 33 ~~~~d~l~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p----~--~~~~~kl~~~~~~ 106 (248)
....+++...++|+-+...+...+.....+..+... .........-.|.+++.|...+ . ...++.....-.+
T Consensus 30 r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~~--~~s~~~~v~~k~~~~~~~~~~q~~~~~~~~~~k~~~r~~~~~ 107 (272)
T KOG4161|consen 30 RSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKVG--DLSLFDFVTGKMSPSERQKNKQRKPEDPSKSNKRKGRGDLNL 107 (272)
T ss_pred ccCCCcccccceEEeCCcccccccccHHHHHhcccc--ccccCcccccccccccccccCCCCCCchhhhhccCCCccccc
Confidence 345677888888888888787777776666655111 1111122333344444444211 1 1234444556678
Q ss_pred CCCCceEEEEEccCCCCCCceeEEE--eeCCCCCeeecHHHHHHHHHhCCccc-ccc--cCCccCC--------C--CCC
Q 045019 107 LPPGWEIEDRVRTSGATAGTVDKYY--FHVASGRRFRSKKEVLYFLETGTKRK-RRK--ENSNADM--------D--SSG 171 (248)
Q Consensus 107 LP~GW~rEv~~RksG~SaGk~DvYY--isP~sGkKFRSK~EV~rYL~sg~~~~-~~~--en~~~~~--------n--~~~ 171 (248)
+++.|..+...|+.+..+...|.|| +++..+..||.+...+-+++.+..-. |.. |.++--. + +..
T Consensus 108 ~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~~~s~~~e~~d~~~l~~~~~g~~~~~~~ 187 (272)
T KOG4161|consen 108 AIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLEADSSRGESIDKLSLPKTPQGSGRSSAG 187 (272)
T ss_pred CCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccccccccccccCccccCcCCCccCccccc
Confidence 9999999999999999999999999 88877799999999998887665433 333 3333110 0 000
Q ss_pred ----------cCCCCcCcCCCCc-c---cccc-ccccCCCCCCcceEEEEecCCCCCcccccCCcccChhhhhhHHHHHH
Q 045019 172 ----------SAAGSTKQKKPNI-K---AKTS-ALNFDYFNSPENVEWVLTDPSEGSWTPFIGKVEVPESVRQDWAAAFT 236 (248)
Q Consensus 172 ----------~s~~~~Ks~K~~k-~---~k~~-~~nfD~~npP~KV~WVLsgp~~~~WtPfidds~Vpes~K~~Ws~aF~ 236 (248)
.+.-..+-+.... . ..++ +.+.=..+..+.+.|+.+...++.-.=-..++......++.|+++++
T Consensus 188 ~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~r~~~~~~l~sd~~~~~~~ 267 (272)
T KOG4161|consen 188 ESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNVRRSLFSALTSDTLSKEAA 267 (272)
T ss_pred cccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhhhhccccchhhcCcchhhh
Confidence 0000111122222 1 1111 22222467778888888777765555567777778888999999887
Q ss_pred Hhh
Q 045019 237 DLT 239 (248)
Q Consensus 237 ~l~ 239 (248)
.+.
T Consensus 268 ~~~ 270 (272)
T KOG4161|consen 268 KLQ 270 (272)
T ss_pred ccc
Confidence 664
No 12
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=44.69 E-value=21 Score=33.61 Aligned_cols=26 Identities=35% Similarity=0.723 Sum_probs=19.4
Q ss_pred cCCCCCCCCceEEEEEccCCCCCCceeEEEeeCC
Q 045019 102 ATEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVA 135 (248)
Q Consensus 102 ~~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~ 135 (248)
..+-.||+||.++..+|. -+|||+-.
T Consensus 89 sedlPLPpgWav~~T~~g--------rkYYIDHn 114 (271)
T KOG1891|consen 89 SEDLPLPPGWAVEFTTEG--------RKYYIDHN 114 (271)
T ss_pred cccCCCCCCcceeeEecC--------ceeEeecC
Confidence 345689999999987653 37999864
No 13
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=41.58 E-value=41 Score=18.31 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=16.4
Q ss_pred EeeCCCCCeeecHHHHHHHHHh
Q 045019 131 YFHVASGRRFRSKKEVLYFLET 152 (248)
Q Consensus 131 YisP~sGkKFRSK~EV~rYL~s 152 (248)
|.-+..|+.|+++.++...+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 5567789999999999987753
No 14
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=39.26 E-value=45 Score=18.80 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.9
Q ss_pred EeeCCCCCeeecHHHHHHHHH
Q 045019 131 YFHVASGRRFRSKKEVLYFLE 151 (248)
Q Consensus 131 YisP~sGkKFRSK~EV~rYL~ 151 (248)
|.-+..|+.|.++.++.+.+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 566789999999999998765
No 15
>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=38.90 E-value=47 Score=19.83 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=15.2
Q ss_pred CCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019 108 PPGWEIEDRVRTSGATAGTVDKYYFHVASGR 138 (248)
Q Consensus 108 P~GW~rEv~~RksG~SaGk~DvYYisP~sGk 138 (248)
|+||.+.... + ...||++..++.
T Consensus 1 p~~W~~~~~~--~------g~~yy~n~~t~~ 23 (31)
T cd00201 1 PPGWEERWDP--D------GRVYYYNHNTKE 23 (31)
T ss_pred CCCCEEEECC--C------CCEEEEECCCCC
Confidence 7899765321 1 358999887665
No 16
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=24.85 E-value=1.3e+02 Score=20.23 Aligned_cols=21 Identities=33% Similarity=0.577 Sum_probs=16.4
Q ss_pred eeCCCCCe-------eecHHHHHHHHHh
Q 045019 132 FHVASGRR-------FRSKKEVLYFLET 152 (248)
Q Consensus 132 isP~sGkK-------FRSK~EV~rYL~s 152 (248)
+.|.+|++ |.++.|...+|..
T Consensus 9 ~~~~~Gkrk~~~k~GF~TkkeA~~~~~~ 36 (46)
T PF14657_consen 9 YDDETGKRKQKTKRGFKTKKEAEKALAK 36 (46)
T ss_pred EECCCCCEEEEEcCCCCcHHHHHHHHHH
Confidence 56667754 9999999998875
No 17
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=22.55 E-value=46 Score=31.43 Aligned_cols=28 Identities=32% Similarity=0.621 Sum_probs=18.6
Q ss_pred CCCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCC
Q 045019 103 TEAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGR 138 (248)
Q Consensus 103 ~~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGk 138 (248)
..+.||+||+|-+-. -.-+||++-.+++
T Consensus 125 erEgLppGW~rv~s~--------e~GtyY~~~~~k~ 152 (271)
T KOG1891|consen 125 EREGLPPGWKRVFSP--------EKGTYYYHEEMKR 152 (271)
T ss_pred hhccCCcchhhcccc--------ccceeeeecccch
Confidence 457899999776432 2336888875554
No 18
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=20.11 E-value=64 Score=30.07 Aligned_cols=34 Identities=18% Similarity=0.504 Sum_probs=28.3
Q ss_pred CCCCCCCceEEEEEccCCCCCCceeEEEeeCCCCCeeecHHHHHHHHHhCC
Q 045019 104 EAWLPPGWEIEDRVRTSGATAGTVDKYYFHVASGRRFRSKKEVLYFLETGT 154 (248)
Q Consensus 104 ~~~LP~GW~rEv~~RksG~SaGk~DvYYisP~sGkKFRSK~EV~rYL~sg~ 154 (248)
..+.-.||.+| +.++||+.| |+..|+..||-+.-
T Consensus 144 qkf~q~gwf~e-----------~eg~ftl~~------ralaELe~YL~s~y 177 (235)
T KOG4718|consen 144 QKFIQMGWFME-----------VEGRFTLGP------RALAELEFYLSSNY 177 (235)
T ss_pred HHHHHhchhhe-----------ecceEEEch------HHHHHHHHHHHhhh
Confidence 44678899887 456899999 99999999999765
Done!