Query 008463
Match_columns 564
No_of_seqs 79 out of 81
Neff 2.6
Searched_HMMs 46136
Date Thu Mar 28 12:28:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008463hhsearch_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, 99.3 1.9E-12 4.1E-17 107.7 5.8 48 37-85 4-51 (77)
2 PF01429 MBD: Methyl-CpG bindi 99.3 2.8E-12 6.1E-17 105.3 4.9 50 36-86 7-57 (77)
3 cd00122 MBD MeCP2, MBD1, MBD2, 99.2 1.6E-11 3.5E-16 97.3 4.8 47 38-85 4-50 (62)
4 smart00391 MBD Methyl-CpG bind 98.9 1.7E-09 3.7E-14 90.0 4.9 44 40-84 8-52 (77)
5 cd01397 HAT_MBD Methyl-CpG bin 98.7 1.9E-08 4.1E-13 84.3 4.6 45 39-84 5-49 (73)
6 KOG4161 Methyl-CpG binding tra 97.9 4.5E-06 9.8E-11 83.5 2.5 49 35-84 14-63 (272)
7 cd01395 HMT_MBD Methyl-CpG bin 96.6 0.0019 4.1E-08 52.8 3.4 41 42-84 8-48 (60)
8 PF01429 MBD: Methyl-CpG bindi 93.2 0.061 1.3E-06 44.7 2.2 23 5-27 5-27 (77)
9 KOG4161 Methyl-CpG binding tra 91.2 0.044 9.5E-07 55.5 -1.0 53 36-88 104-159 (272)
10 cd01396 MeCP2_MBD MeCP2, MBD1, 88.6 0.55 1.2E-05 39.7 3.7 17 9-25 4-21 (77)
11 KOG1891 Proline binding protei 88.1 0.45 9.8E-06 48.5 3.3 55 6-69 89-151 (271)
12 cd00122 MBD MeCP2, MBD1, MBD2, 86.3 1.2 2.5E-05 35.8 4.1 19 7-25 2-20 (62)
13 PF00397 WW: WW domain; Inter 76.7 1.5 3.3E-05 30.9 1.4 26 40-71 1-26 (31)
14 smart00456 WW Domain with 2 co 69.5 4.6 0.0001 27.7 2.4 24 40-70 1-24 (32)
15 KOG1891 Proline binding protei 64.0 3.7 7.9E-05 42.2 1.5 24 39-69 93-116 (271)
16 PRK10984 DNA-binding transcrip 59.0 6.1 0.00013 37.1 1.9 41 2-48 46-86 (127)
17 PF07417 Crl: Transcriptional 58.9 7.4 0.00016 36.5 2.4 43 2-50 44-86 (125)
18 smart00391 MBD Methyl-CpG bind 48.9 17 0.00037 30.8 2.8 18 6-25 5-22 (77)
19 KOG3259 Peptidyl-prolyl cis-tr 47.2 11 0.00024 36.7 1.6 29 37-71 4-32 (163)
20 cd00201 WW Two conserved trypt 32.7 43 0.00093 22.4 2.3 23 41-70 1-23 (31)
21 PF00408 PGM_PMM_IV: Phosphogl 30.9 58 0.0012 26.3 3.1 26 10-35 31-56 (73)
22 PHA03165 hypothetical protein; 29.0 17 0.00036 29.8 -0.2 12 375-386 44-55 (57)
23 PF14657 Integrase_AP2: AP2-li 26.2 54 0.0012 24.8 2.1 22 62-83 6-35 (46)
24 PF08265 YL1_C: YL1 nuclear pr 23.7 44 0.00096 24.5 1.1 17 61-77 10-26 (30)
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=99.33 E-value=1.9e-12 Score=107.67 Aligned_cols=48 Identities=42% Similarity=0.800 Sum_probs=43.7
Q ss_pred CCCCCCCceEEEEEecCCCccccccceeCCCCCceecchHHHHHHHhhC
Q 008463 37 PDGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVETG 85 (564)
Q Consensus 37 ~egLP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~FRSkkdV~RYLeTG 85 (564)
+..||.||.+|+++|++|...++|.||++| +|++|||+++|.+||+..
T Consensus 4 ~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP-~Gkk~RS~~ev~~yL~~~ 51 (77)
T cd01396 4 DPRLPPGWKRELVPRKSGSAGKFDVYYISP-TGKKFRSKVELARYLEKN 51 (77)
T ss_pred CCCCCCCCEEEEEEecCCCCCcceEEEECC-CCCEEECHHHHHHHHHhC
Confidence 445999999999999999777999999999 589999999999999874
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=99.29 E-value=2.8e-12 Score=105.32 Aligned_cols=50 Identities=40% Similarity=0.777 Sum_probs=43.7
Q ss_pred CCCCCCCCceEEEEEecCCC-ccccccceeCCCCCceecchHHHHHHHhhCC
Q 008463 36 TPDGLPPGWTKEIKVTKTGR-KVRRDPYYIDPASGYIFRSMKDAVRYVETGE 86 (564)
Q Consensus 36 ~~egLP~GWvkE~r~RKsG~-~ir~DkYYiDPvsGy~FRSkkdV~RYLeTG~ 86 (564)
.+.+||+||.+|+++|++|. ..+.|.||++| +|++|||+++|.+||+.+.
T Consensus 7 ~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP-~Gk~~RS~~eV~~yL~~~~ 57 (77)
T PF01429_consen 7 LDPPLPDGWKREVVVRKSGSSAGKKDVYYYSP-CGKRFRSKKEVVRYLKENP 57 (77)
T ss_dssp EBTTSTTT-EEEEEESSSSTTTTSEEEEEEET-TSEEESSHHHHHHHHTTSS
T ss_pred ccCCCCCCCEEEEEEecCCCcCCceEEEEECC-CCCEEeCHHHHHHHHHhCC
Confidence 45689999999999999886 46899999999 9999999999999998776
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=99.20 E-value=1.6e-11 Score=97.26 Aligned_cols=47 Identities=40% Similarity=0.834 Sum_probs=43.1
Q ss_pred CCCCCCceEEEEEecCCCccccccceeCCCCCceecchHHHHHHHhhC
Q 008463 38 DGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVETG 85 (564)
Q Consensus 38 egLP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~FRSkkdV~RYLeTG 85 (564)
.+||.||.+|+++|+.|..+++|.||+.| +|++|||+.+|.+||...
T Consensus 4 ~P~p~GW~R~~~~r~~g~~~k~dv~Y~sP-~Gk~~Rs~~ev~~yL~~~ 50 (62)
T cd00122 4 DPLPPGWKRELVIRKSGSAGKGDVYYYSP-CGKKLRSKPEVARYLEKT 50 (62)
T ss_pred CCCCCCeEEEEEEcCCCCCCcceEEEECC-CCceecCHHHHHHHHHhC
Confidence 47899999999999999777999999999 599999999999999765
No 4
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=98.89 E-value=1.7e-09 Score=90.04 Aligned_cols=44 Identities=43% Similarity=0.797 Sum_probs=40.9
Q ss_pred CCCCceEEEEEecCCC-ccccccceeCCCCCceecchHHHHHHHhh
Q 008463 40 LPPGWTKEIKVTKTGR-KVRRDPYYIDPASGYIFRSMKDAVRYVET 84 (564)
Q Consensus 40 LP~GWvkE~r~RKsG~-~ir~DkYYiDPvsGy~FRSkkdV~RYLeT 84 (564)
||.||.+++++|+.|. ..+.|.||+.| +|++|||+.||.+||..
T Consensus 8 lp~GW~R~~~~r~~g~~~~~~dV~Y~sP-~GkklRs~~ev~~YL~~ 52 (77)
T smart00391 8 LPCGWRRETKQRKSGRSAGKFDVYYISP-CGKKLRSKSELARYLHK 52 (77)
T ss_pred CCCCcEEEEEEecCCCCCCcccEEEECC-CCCeeeCHHHHHHHHHh
Confidence 9999999999999984 66899999999 89999999999999964
No 5
>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=98.69 E-value=1.9e-08 Score=84.25 Aligned_cols=45 Identities=22% Similarity=0.602 Sum_probs=42.4
Q ss_pred CCCCCceEEEEEecCCCccccccceeCCCCCceecchHHHHHHHhh
Q 008463 39 GLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVET 84 (564)
Q Consensus 39 gLP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~FRSkkdV~RYLeT 84 (564)
-||-||..|+++|+.|.+++.|.||+.| +|++|||+.||.+||..
T Consensus 5 Pl~~GW~Re~vir~~~~~~~~dV~Y~aP-cGKklRs~~ev~~yL~~ 49 (73)
T cd01397 5 PLELGWRRETRIRGLGGRIQGEVAYYAP-CGKKLRQYPEVIKYLSK 49 (73)
T ss_pred CCCCCceeEEEeccCCCCccceEEEECC-CCcccccHHHHHHHHHh
Confidence 5899999999999999888999999999 79999999999999974
No 6
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=97.93 E-value=4.5e-06 Score=83.52 Aligned_cols=49 Identities=41% Similarity=0.716 Sum_probs=44.7
Q ss_pred cCCCCCCCCceEEEEEecCCC-ccccccceeCCCCCceecchHHHHHHHhh
Q 008463 35 DTPDGLPPGWTKEIKVTKTGR-KVRRDPYYIDPASGYIFRSMKDAVRYVET 84 (564)
Q Consensus 35 ~~~egLP~GWvkE~r~RKsG~-~ir~DkYYiDPvsGy~FRSkkdV~RYLeT 84 (564)
..|..||+||.++++.|++|. .++.|.||+.| .|.+|||+.+..+||+.
T Consensus 14 ~~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp-~g~~frsk~~l~~~~~~ 63 (272)
T KOG4161|consen 14 SDCPALPPGWTREEVQRSSGLSAGKSDVYYISP-SGKKFRSKPQLARYLGK 63 (272)
T ss_pred ccCCCCCCCcchhhhcccCCCcccccceEEeCC-cccccccccHHHHHhcc
Confidence 478899999999999999987 55999999999 89999999999999953
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=96.63 E-value=0.0019 Score=52.84 Aligned_cols=41 Identities=27% Similarity=0.528 Sum_probs=36.3
Q ss_pred CCceEEEEEecCCCccccccceeCCCCCceecchHHHHHHHhh
Q 008463 42 PGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVET 84 (564)
Q Consensus 42 ~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~FRSkkdV~RYLeT 84 (564)
=||......|+.| +++.+.+|.-| .|++.|++.+|++||..
T Consensus 8 ~gw~R~~~~~~~~-~~k~~V~Y~aP-CGr~Lr~~~EV~~YL~~ 48 (60)
T cd01395 8 CGFQRMKYRARVG-KVKKHVIYKAP-CGRSLRNMSEVHRYLRE 48 (60)
T ss_pred cCeEEEEEeccCC-CcccceEEECC-cchhhhcHHHHHHHHHh
Confidence 5999999888777 56889999999 79999999999999953
No 8
>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=93.18 E-value=0.061 Score=44.66 Aligned_cols=23 Identities=48% Similarity=0.663 Sum_probs=18.7
Q ss_pred CCCCCCCCCCeEEEEEEccCCcc
Q 008463 5 ENSDELLPDGCRVEVRVRKNGKK 27 (564)
Q Consensus 5 e~s~dWLPDGW~vEvr~~knG~k 27 (564)
...+-|||+||.+|+.++++|+.
T Consensus 5 ~~~~~~Lp~GW~re~~~R~~g~~ 27 (77)
T PF01429_consen 5 SPLDPPLPDGWKREVVVRKSGSS 27 (77)
T ss_dssp ECEBTTSTTT-EEEEEESSSSTT
T ss_pred ccccCCCCCCCEEEEEEecCCCc
Confidence 45678999999999999999743
No 9
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=91.22 E-value=0.044 Score=55.50 Aligned_cols=53 Identities=19% Similarity=0.189 Sum_probs=43.8
Q ss_pred CCCCCCCCceEEEEEecCCCcc-ccccce--eCCCCCceecchHHHHHHHhhCCcc
Q 008463 36 TPDGLPPGWTKEIKVTKTGRKV-RRDPYY--IDPASGYIFRSMKDAVRYVETGEIG 88 (564)
Q Consensus 36 ~~egLP~GWvkE~r~RKsG~~i-r~DkYY--iDPvsGy~FRSkkdV~RYLeTG~I~ 88 (564)
+-.++++.|+.+..+|+.+..| -.|.|| .++..+..||.++..+-|++-|..-
T Consensus 104 ~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l 159 (272)
T KOG4161|consen 104 DLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDL 159 (272)
T ss_pred ccccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEecccccc
Confidence 3356999999999999999988 567888 7888889999999988777776643
No 10
>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=88.61 E-value=0.55 Score=39.73 Aligned_cols=17 Identities=41% Similarity=0.679 Sum_probs=15.4
Q ss_pred CC-CCCCeEEEEEEccCC
Q 008463 9 EL-LPDGCRVEVRVRKNG 25 (564)
Q Consensus 9 dW-LPDGW~vEvr~~knG 25 (564)
+| ||.||..|+..+++|
T Consensus 4 ~~~lp~GW~r~~~~R~~g 21 (77)
T cd01396 4 DPRLPPGWKRELVPRKSG 21 (77)
T ss_pred CCCCCCCCEEEEEEecCC
Confidence 44 999999999999997
No 11
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=88.08 E-value=0.45 Score=48.50 Aligned_cols=55 Identities=31% Similarity=0.587 Sum_probs=35.2
Q ss_pred CCCCCCCCCeEEEEEEccCCcceee--------EeeecCCCCCCCCceEEEEEecCCCccccccceeCCCCC
Q 008463 6 NSDELLPDGCRVEVRVRKNGKKDKI--------IIEKDTPDGLPPGWTKEIKVTKTGRKVRRDPYYIDPASG 69 (564)
Q Consensus 6 ~s~dWLPDGW~vEvr~~knG~k~K~--------viEk~~~egLP~GWvkE~r~RKsG~~ir~DkYYiDPvsG 69 (564)
..|-=||+||-||--. -|+||-| -+-....++||+||.+=.-+- .-.||+|-.++
T Consensus 89 sedlPLPpgWav~~T~--~grkYYIDHn~~tTHW~HPlerEgLppGW~rv~s~e-------~GtyY~~~~~k 151 (271)
T KOG1891|consen 89 SEDLPLPPGWAVEFTT--EGRKYYIDHNNRTTHWVHPLEREGLPPGWKRVFSPE-------KGTYYYHEEMK 151 (271)
T ss_pred cccCCCCCCcceeeEe--cCceeEeecCCCcccccChhhhccCCcchhhccccc-------cceeeeecccc
Confidence 3444599999999765 4788765 122346789999997654211 23567665433
No 12
>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=86.27 E-value=1.2 Score=35.79 Aligned_cols=19 Identities=37% Similarity=0.651 Sum_probs=17.2
Q ss_pred CCCCCCCCeEEEEEEccCC
Q 008463 7 SDELLPDGCRVEVRVRKNG 25 (564)
Q Consensus 7 s~dWLPDGW~vEvr~~knG 25 (564)
..+|||.||..|+..+++|
T Consensus 2 l~~P~p~GW~R~~~~r~~g 20 (62)
T cd00122 2 LRDPLPPGWKRELVIRKSG 20 (62)
T ss_pred CCCCCCCCeEEEEEEcCCC
Confidence 4679999999999999997
No 13
>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=76.73 E-value=1.5 Score=30.89 Aligned_cols=26 Identities=35% Similarity=0.827 Sum_probs=16.9
Q ss_pred CCCCceEEEEEecCCCccccccceeCCCCCce
Q 008463 40 LPPGWTKEIKVTKTGRKVRRDPYYIDPASGYI 71 (564)
Q Consensus 40 LP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~ 71 (564)
||+||..-. ... ....||++..||..
T Consensus 1 LP~gW~~~~--~~~----~g~~YY~N~~t~~s 26 (31)
T PF00397_consen 1 LPPGWEEYF--DPD----SGRPYYYNHETGES 26 (31)
T ss_dssp SSTTEEEEE--ETT----TSEEEEEETTTTEE
T ss_pred CCcCCEEEE--cCC----CCCEEEEeCCCCCE
Confidence 899997333 222 13579999988753
No 14
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=69.51 E-value=4.6 Score=27.72 Aligned_cols=24 Identities=33% Similarity=0.816 Sum_probs=17.3
Q ss_pred CCCCceEEEEEecCCCccccccceeCCCCCc
Q 008463 40 LPPGWTKEIKVTKTGRKVRRDPYYIDPASGY 70 (564)
Q Consensus 40 LP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy 70 (564)
||.||.+.. -.+ ...||++..|+.
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 799998877 222 357999887764
No 15
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=64.05 E-value=3.7 Score=42.19 Aligned_cols=24 Identities=42% Similarity=0.879 Sum_probs=19.5
Q ss_pred CCCCCceEEEEEecCCCccccccceeCCCCC
Q 008463 39 GLPPGWTKEIKVTKTGRKVRRDPYYIDPASG 69 (564)
Q Consensus 39 gLP~GWvkE~r~RKsG~~ir~DkYYiDPvsG 69 (564)
-||+||.+|. .++.-|||||=.+.
T Consensus 93 PLPpgWav~~-------T~~grkYYIDHn~~ 116 (271)
T KOG1891|consen 93 PLPPGWAVEF-------TTEGRKYYIDHNNR 116 (271)
T ss_pred CCCCCcceee-------EecCceeEeecCCC
Confidence 4999999999 56677999997554
No 16
>PRK10984 DNA-binding transcriptional regulator Crl; Provisional
Probab=58.98 E-value=6.1 Score=37.14 Aligned_cols=41 Identities=15% Similarity=0.182 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCCeEEEEEEccCCcceeeEeeecCCCCCCCCceEEE
Q 008463 2 GDRENSDELLPDGCRVEVRVRKNGKKDKIIIEKDTPDGLPPGWTKEI 48 (564)
Q Consensus 2 ~~~e~s~dWLPDGW~vEvr~~knG~k~K~viEk~~~egLP~GWvkE~ 48 (564)
..||++..| |||||.....+|=.|.|.+=.++..| .|+.+.
T Consensus 46 ~aPEkREFW---GWWmeL~~~e~~F~y~Y~~Glydk~G---~W~~~~ 86 (127)
T PRK10984 46 PAPEKREFW---GWWMELEAQEGRFTYSYQFGLFDKEG---NWVAEP 86 (127)
T ss_pred CChhhhhhh---hhheeeeecCCcEEEEEecccccCCC---Ceeecc
Confidence 368999999 99999999999999999888876554 455444
No 17
>PF07417 Crl: Transcriptional regulator Crl; InterPro: IPR009986 This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [].These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. They also stimulate RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.; GO: 0016987 sigma factor activity, 0045893 positive regulation of transcription, DNA-dependent, 0005737 cytoplasm; PDB: 3RPJ_A.
Probab=58.89 E-value=7.4 Score=36.53 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCCCeEEEEEEccCCcceeeEeeecCCCCCCCCceEEEEE
Q 008463 2 GDRENSDELLPDGCRVEVRVRKNGKKDKIIIEKDTPDGLPPGWTKEIKV 50 (564)
Q Consensus 2 ~~~e~s~dWLPDGW~vEvr~~knG~k~K~viEk~~~egLP~GWvkE~r~ 50 (564)
..||++..| |||||.....+|=.|+|.+=.++..| .|+.+..+
T Consensus 44 ~aPEkREFW---GWWleL~~~e~~F~y~Y~~Glydk~G---~W~~~~i~ 86 (125)
T PF07417_consen 44 KAPEKREFW---GWWLELEAQEDGFEYRYQFGLYDKEG---NWQAEKIK 86 (125)
T ss_dssp S-CCC--EE---EEEEEEEEETTEEEEEEEEEEE-TTS----EES----
T ss_pred CChhhhhhh---hhheeeEecCCcEEEEEeeccccCCC---CeeecCCC
Confidence 368999999 99999999999999999888876654 46555433
No 18
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=48.93 E-value=17 Score=30.80 Aligned_cols=18 Identities=44% Similarity=0.637 Sum_probs=15.9
Q ss_pred CCCCCCCCCeEEEEEEccCC
Q 008463 6 NSDELLPDGCRVEVRVRKNG 25 (564)
Q Consensus 6 ~s~dWLPDGW~vEvr~~knG 25 (564)
+-| ||.||.-++..+++|
T Consensus 5 ~~P--lp~GW~R~~~~r~~g 22 (77)
T smart00391 5 RLP--LPCGWRRETKQRKSG 22 (77)
T ss_pred cCC--CCCCcEEEEEEecCC
Confidence 445 999999999999987
No 19
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=47.22 E-value=11 Score=36.68 Aligned_cols=29 Identities=31% Similarity=0.802 Sum_probs=19.5
Q ss_pred CCCCCCCceEEEEEecCCCccccccceeCCCCCce
Q 008463 37 PDGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYI 71 (564)
Q Consensus 37 ~egLP~GWvkE~r~RKsG~~ir~DkYYiDPvsGy~ 71 (564)
.+.||+||.|-+ +-. +.-.||+.+.|+..
T Consensus 4 ~~~LP~~Wekr~----Srs--~gr~YyfN~~T~~S 32 (163)
T KOG3259|consen 4 EEKLPPGWEKRM----SRS--SGRPYYFNTETNES 32 (163)
T ss_pred cccCCchhheec----ccc--CCCcceeccccchh
Confidence 468999998855 222 23479988776543
No 20
>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=32.66 E-value=43 Score=22.44 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=15.4
Q ss_pred CCCceEEEEEecCCCccccccceeCCCCCc
Q 008463 41 PPGWTKEIKVTKTGRKVRRDPYYIDPASGY 70 (564)
Q Consensus 41 P~GWvkE~r~RKsG~~ir~DkYYiDPvsGy 70 (564)
|.||.+-. -+. ...||++..|+.
T Consensus 1 p~~W~~~~--~~~-----g~~yy~n~~t~~ 23 (31)
T cd00201 1 PPGWEERW--DPD-----GRVYYYNHNTKE 23 (31)
T ss_pred CCCCEEEE--CCC-----CCEEEEECCCCC
Confidence 78888666 111 367999887664
No 21
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=30.92 E-value=58 Score=26.32 Aligned_cols=26 Identities=31% Similarity=0.433 Sum_probs=19.3
Q ss_pred CCCCCeEEEEEEccCCcceeeEeeec
Q 008463 10 LLPDGCRVEVRVRKNGKKDKIIIEKD 35 (564)
Q Consensus 10 WLPDGW~vEvr~~knG~k~K~viEk~ 35 (564)
.+.||||+.+|...+.-+-|+.+|..
T Consensus 31 ~~~dG~~l~vR~SgTEP~iRv~~Ea~ 56 (73)
T PF00408_consen 31 LFEDGWRLLVRPSGTEPKIRVYVEAP 56 (73)
T ss_dssp EETTEEEEEEEEESSSSEEEEEEEES
T ss_pred ECCCceEEEEECCCCCceEEEEEEeC
Confidence 35688888877777777777777765
No 22
>PHA03165 hypothetical protein; Provisional
Probab=28.96 E-value=17 Score=29.77 Aligned_cols=12 Identities=67% Similarity=1.508 Sum_probs=11.1
Q ss_pred CccCcccCChhH
Q 008463 375 LPFGDLLSDPCI 386 (564)
Q Consensus 375 ~p~~~~~~DP~i 386 (564)
.|||++++.|||
T Consensus 44 spfgeilsspci 55 (57)
T PHA03165 44 SPFGEILSSPCI 55 (57)
T ss_pred CchhhhhcCccc
Confidence 599999999998
No 23
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=26.19 E-value=54 Score=24.80 Aligned_cols=22 Identities=27% Similarity=0.487 Sum_probs=17.1
Q ss_pred ce-eCCCCCce-------ecchHHHHHHHh
Q 008463 62 YY-IDPASGYI-------FRSMKDAVRYVE 83 (564)
Q Consensus 62 YY-iDPvsGy~-------FRSkkdV~RYLe 83 (564)
+| ++|.+|.+ |.+++++..++.
T Consensus 6 v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~ 35 (46)
T PF14657_consen 6 VYGYDDETGKRKQKTKRGFKTKKEAEKALA 35 (46)
T ss_pred EEEEECCCCCEEEEEcCCCCcHHHHHHHHH
Confidence 45 67777743 999999999884
No 24
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=23.69 E-value=44 Score=24.46 Aligned_cols=17 Identities=24% Similarity=0.514 Sum_probs=14.1
Q ss_pred cceeCCCCCceecchHH
Q 008463 61 PYYIDPASGYIFRSMKD 77 (564)
Q Consensus 61 kYYiDPvsGy~FRSkkd 77 (564)
--|+||.||..|.+...
T Consensus 10 A~Y~DP~T~l~Y~n~~a 26 (30)
T PF08265_consen 10 ARYRDPKTGLPYANSEA 26 (30)
T ss_pred ccccCCCCCCcccCHHH
Confidence 45999999999988754
Done!