Query 008894
Match_columns 549
No_of_seqs 84 out of 86
Neff 2.7
Searched_HMMs 46136
Date Thu Mar 28 17:54:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008894hhsearch_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 1.1E-12 2.3E-17 109.1 4.9 48 37-85 4-51 (77)
2 PF01429 MBD: Methyl-CpG bindi 99.3 2.8E-12 6.1E-17 105.4 4.5 50 36-86 7-57 (77)
3 cd00122 MBD MeCP2, MBD1, MBD2, 99.2 2E-11 4.4E-16 96.7 4.5 47 38-85 4-50 (62)
4 smart00391 MBD Methyl-CpG bind 98.9 2E-09 4.4E-14 89.6 4.5 46 40-86 8-55 (77)
5 cd01397 HAT_MBD Methyl-CpG bin 98.7 1.4E-08 3.1E-13 84.8 4.4 58 38-96 4-64 (73)
6 KOG4161 Methyl-CpG binding tra 98.0 4.1E-06 8.9E-11 83.9 3.2 62 36-98 15-78 (272)
7 cd01395 HMT_MBD Methyl-CpG bin 96.6 0.0021 4.5E-08 52.5 3.3 40 42-83 8-47 (60)
8 KOG4161 Methyl-CpG binding tra 93.6 0.021 4.6E-07 57.8 0.2 62 38-101 106-170 (272)
9 PF01429 MBD: Methyl-CpG bindi 93.2 0.059 1.3E-06 44.8 2.2 23 5-27 5-27 (77)
10 cd01396 MeCP2_MBD MeCP2, MBD1, 89.8 0.26 5.7E-06 41.6 2.6 16 10-25 6-21 (77)
11 KOG1891 Proline binding protei 89.6 0.3 6.4E-06 49.7 3.2 41 6-48 89-137 (271)
12 cd00122 MBD MeCP2, MBD1, MBD2, 86.7 0.69 1.5E-05 37.0 3.0 19 7-25 2-20 (62)
13 PF00397 WW: WW domain; Inter 76.7 1.2 2.5E-05 31.4 0.8 25 40-70 1-25 (31)
14 smart00456 WW Domain with 2 co 67.7 4.6 0.0001 27.7 2.1 24 40-70 1-24 (32)
15 KOG1891 Proline binding protei 62.1 3.9 8.5E-05 41.9 1.3 23 39-68 93-115 (271)
16 PRK10984 DNA-binding transcrip 60.6 5.6 0.00012 37.3 1.9 41 2-48 46-86 (127)
17 PF07417 Crl: Transcriptional 58.2 7.1 0.00015 36.6 2.1 43 2-50 44-86 (125)
18 smart00391 MBD Methyl-CpG bind 49.3 17 0.00037 30.8 2.8 18 6-25 5-22 (77)
19 KOG3259 Peptidyl-prolyl cis-tr 44.0 12 0.00027 36.3 1.4 29 37-71 4-32 (163)
20 PHA03165 hypothetical protein; 36.2 11 0.00023 30.8 -0.3 12 360-371 44-55 (57)
21 PF00408 PGM_PMM_IV: Phosphogl 35.6 35 0.00076 27.5 2.6 26 10-35 31-56 (73)
22 cd00201 WW Two conserved trypt 30.1 44 0.00095 22.4 2.0 23 41-70 1-23 (31)
23 PF14657 Integrase_AP2: AP2-li 22.1 62 0.0013 24.4 1.7 21 64-84 9-36 (46)
24 PF08265 YL1_C: YL1 nuclear pr 21.8 52 0.0011 24.0 1.2 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=1.1e-12 Score=109.10 Aligned_cols=48 Identities=42% Similarity=0.800 Sum_probs=43.5
Q ss_pred CCCCCCCceEEEEEecCCCcccccccccCCCCCccccchHHHHHHHhhc
Q 008894 37 PDGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVETG 85 (549)
Q Consensus 37 ~~~LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGykFRSkkdV~RYLeTG 85 (549)
.-.||.||.+|+++|++|...++|.||++| +|++|||+++|.+||+..
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 345999999999999999767999999999 589999999999999974
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=99.28 E-value=2.8e-12 Score=105.37 Aligned_cols=50 Identities=40% Similarity=0.780 Sum_probs=44.0
Q ss_pred CCCCCCCCceEEEEEecCCCc-ccccccccCCCCCccccchHHHHHHHhhcc
Q 008894 36 TPDGLPPGWTKEIKVTKTGRK-VRRDPYYIDPASGYIFRSMKDAVRYVETGE 86 (549)
Q Consensus 36 ~~~~LP~GWvkE~~~Rk~G~~-ir~DkYY~DPvsGykFRSkkdV~RYLeTG~ 86 (549)
.+.+||+||.+|+++|++|.. .+.|.||++| +|++|||+++|.+||+.+.
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 456899999999999998864 5899999999 9999999999999998766
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=99.18 E-value=2e-11 Score=96.71 Aligned_cols=47 Identities=40% Similarity=0.834 Sum_probs=43.1
Q ss_pred CCCCCCceEEEEEecCCCcccccccccCCCCCccccchHHHHHHHhhc
Q 008894 38 DGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVETG 85 (549)
Q Consensus 38 ~~LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGykFRSkkdV~RYLeTG 85 (549)
.+||.||.+|+++|+.|..++.|.||+.| +|++|||+.+|.+||...
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 599999999999999864
No 4
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=98.87 E-value=2e-09 Score=89.60 Aligned_cols=46 Identities=43% Similarity=0.829 Sum_probs=41.7
Q ss_pred CCCCceEEEEEecCCC-cccccccccCCCCCccccchHHHHHHHhh-cc
Q 008894 40 LPPGWTKEIKVTKTGR-KVRRDPYYIDPASGYIFRSMKDAVRYVET-GE 86 (549)
Q Consensus 40 LP~GWvkE~~~Rk~G~-~ir~DkYY~DPvsGykFRSkkdV~RYLeT-G~ 86 (549)
||.||.+++++|+.|. ..+.|.||+.| +|++|||+.||.+||.. |+
T Consensus 8 lp~GW~R~~~~r~~g~~~~~~dV~Y~sP-~GkklRs~~ev~~YL~~~~~ 55 (77)
T smart00391 8 LPCGWRRETKQRKSGRSAGKFDVYYISP-CGKKLRSKSELARYLHKNGD 55 (77)
T ss_pred CCCCcEEEEEEecCCCCCCcccEEEECC-CCCeeeCHHHHHHHHHhCCC
Confidence 9999999999999984 56899999999 79999999999999974 44
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=98.70 E-value=1.4e-08 Score=84.84 Aligned_cols=58 Identities=19% Similarity=0.472 Sum_probs=48.4
Q ss_pred CCCCCCceEEEEEecCCCcccccccccCCCCCccccchHHHHHHHhh---ccccceeeccCC
Q 008894 38 DGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVET---GEIGRLAYKPKD 96 (549)
Q Consensus 38 ~~LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGykFRSkkdV~RYLeT---G~Isr~a~kPk~ 96 (549)
-.||-||..|+++|+.|.+++.|.||+.| +|++|||+.||.+||.. ..+++-.|....
T Consensus 4 ~Pl~~GW~Re~vir~~~~~~~~dV~Y~aP-cGKklRs~~ev~~yL~~~~~~~Lt~dnFsF~~ 64 (73)
T cd01397 4 VPLELGWRRETRIRGLGGRIQGEVAYYAP-CGKKLRQYPEVIKYLSKNGISLLSRENFSFSA 64 (73)
T ss_pred CCCCCCceeEEEeccCCCCccceEEEECC-CCcccccHHHHHHHHHhCCccCccHhHccccC
Confidence 35899999999999998778999999999 69999999999999985 445554444443
No 6
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=97.98 E-value=4.1e-06 Score=83.89 Aligned_cols=62 Identities=34% Similarity=0.629 Sum_probs=51.0
Q ss_pred CCCCCCCCceEEEEEecCCC-cccccccccCCCCCccccchHHHHHHHh-hccccceeeccCCCC
Q 008894 36 TPDGLPPGWTKEIKVTKTGR-KVRRDPYYIDPASGYIFRSMKDAVRYVE-TGEIGRLAYKPKDDG 98 (549)
Q Consensus 36 ~~~~LP~GWvkE~~~Rk~G~-~ir~DkYY~DPvsGykFRSkkdV~RYLe-TG~Isr~a~kPk~r~ 98 (549)
.|..||+||.++++.|++|. .++.|.||+.| .|.+|||+.+..+||+ .|+.+.-.++..+..
T Consensus 15 ~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp-~g~~frsk~~l~~~~~~~~~~s~~~~v~~k~~ 78 (272)
T KOG4161|consen 15 DCPALPPGWTREEVQRSSGLSAGKSDVYYISP-SGKKFRSKPQLARYLGKVGDLSLFDFVTGKMS 78 (272)
T ss_pred cCCCCCCCcchhhhcccCCCcccccceEEeCC-cccccccccHHHHHhccccccccCcccccccc
Confidence 67789999999999999987 55999999999 7999999999999998 455555444444433
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=96.58 E-value=0.0021 Score=52.51 Aligned_cols=40 Identities=28% Similarity=0.542 Sum_probs=35.8
Q ss_pred CCceEEEEEecCCCcccccccccCCCCCccccchHHHHHHHh
Q 008894 42 PGWTKEIKVTKTGRKVRRDPYYIDPASGYIFRSMKDAVRYVE 83 (549)
Q Consensus 42 ~GWvkE~~~Rk~G~~ir~DkYY~DPvsGykFRSkkdV~RYLe 83 (549)
=||......|+.| +++.+.+|.-| .|++.|++.||++||-
T Consensus 8 ~gw~R~~~~~~~~-~~k~~V~Y~aP-CGr~Lr~~~EV~~YL~ 47 (60)
T cd01395 8 CGFQRMKYRARVG-KVKKHVIYKAP-CGRSLRNMSEVHRYLR 47 (60)
T ss_pred cCeEEEEEeccCC-CcccceEEECC-cchhhhcHHHHHHHHH
Confidence 5999999888777 56889999999 6999999999999995
No 8
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=93.61 E-value=0.021 Score=57.77 Aligned_cols=62 Identities=18% Similarity=0.184 Sum_probs=48.2
Q ss_pred CCCCCCceEEEEEecCCCcc-cccccc--cCCCCCccccchHHHHHHHhhccccceeeccCCCCCCC
Q 008894 38 DGLPPGWTKEIKVTKTGRKV-RRDPYY--IDPASGYIFRSMKDAVRYVETGEIGRLAYKPKDDGNQD 101 (549)
Q Consensus 38 ~~LP~GWvkE~~~Rk~G~~i-r~DkYY--~DPvsGykFRSkkdV~RYLeTG~Isr~a~kPk~r~~~d 101 (549)
.++++.|+.+..+|+.+..| -.|.|| .++..+..||.++..+-|++-+..-. +..++....|
T Consensus 106 ~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~--~~s~~~e~~d 170 (272)
T KOG4161|consen 106 NLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLE--ADSSRGESID 170 (272)
T ss_pred ccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccc--cccccccccC
Confidence 56999999999999999988 667888 88988899999999998887666433 3444444444
No 9
>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=93.24 E-value=0.059 Score=44.75 Aligned_cols=23 Identities=48% Similarity=0.663 Sum_probs=18.7
Q ss_pred CCCCCCCCCCeeEEEEEccCCcc
Q 008894 5 ENSDELLPDGCRVEVRVRKNGKK 27 (549)
Q Consensus 5 e~s~~WLPdGW~vEvr~~knG~K 27 (549)
...+.|||+||.+|++++++|+.
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 45678999999999999998743
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=89.76 E-value=0.26 Score=41.59 Aligned_cols=16 Identities=44% Similarity=0.667 Sum_probs=14.9
Q ss_pred CCCCCeeEEEEEccCC
Q 008894 10 LLPDGCRVEVRVRKNG 25 (549)
Q Consensus 10 WLPdGW~vEvr~~knG 25 (549)
+||.||..|++++++|
T Consensus 6 ~lp~GW~r~~~~R~~g 21 (77)
T cd01396 6 RLPPGWKRELVPRKSG 21 (77)
T ss_pred CCCCCCEEEEEEecCC
Confidence 3999999999999997
No 11
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=89.64 E-value=0.3 Score=49.70 Aligned_cols=41 Identities=37% Similarity=0.661 Sum_probs=28.4
Q ss_pred CCCCCCCCCeeEEEEEccCCcceeeE--------eeccCCCCCCCCceEEE
Q 008894 6 NSDELLPDGCRVEVRVRKNGKKDKII--------IEKDTPDGLPPGWTKEI 48 (549)
Q Consensus 6 ~s~~WLPdGW~vEvr~~knG~K~K~v--------iEr~~~~~LP~GWvkE~ 48 (549)
..|-=||+||-||--. -|+||-|- +-.+..++||+||.+=.
T Consensus 89 sedlPLPpgWav~~T~--~grkYYIDHn~~tTHW~HPlerEgLppGW~rv~ 137 (271)
T KOG1891|consen 89 SEDLPLPPGWAVEFTT--EGRKYYIDHNNRTTHWVHPLEREGLPPGWKRVF 137 (271)
T ss_pred cccCCCCCCcceeeEe--cCceeEeecCCCcccccChhhhccCCcchhhcc
Confidence 3455599999999765 47776651 22235689999997644
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=86.66 E-value=0.69 Score=37.02 Aligned_cols=19 Identities=37% Similarity=0.651 Sum_probs=17.2
Q ss_pred CCCCCCCCeeEEEEEccCC
Q 008894 7 SDELLPDGCRVEVRVRKNG 25 (549)
Q Consensus 7 s~~WLPdGW~vEvr~~knG 25 (549)
..+|||.||..|++.+++|
T Consensus 2 l~~P~p~GW~R~~~~r~~g 20 (62)
T cd00122 2 LRDPLPPGWKRELVIRKSG 20 (62)
T ss_pred CCCCCCCCeEEEEEEcCCC
Confidence 4578999999999999997
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=76.70 E-value=1.2 Score=31.41 Aligned_cols=25 Identities=36% Similarity=0.884 Sum_probs=16.4
Q ss_pred CCCCceEEEEEecCCCcccccccccCCCCCc
Q 008894 40 LPPGWTKEIKVTKTGRKVRRDPYYIDPASGY 70 (549)
Q Consensus 40 LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGy 70 (549)
||+||..-. ... ....||++..||.
T Consensus 1 LP~gW~~~~--~~~----~g~~YY~N~~t~~ 25 (31)
T PF00397_consen 1 LPPGWEEYF--DPD----SGRPYYYNHETGE 25 (31)
T ss_dssp SSTTEEEEE--ETT----TSEEEEEETTTTE
T ss_pred CCcCCEEEE--cCC----CCCEEEEeCCCCC
Confidence 899997333 222 1357999998775
No 14
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=67.75 E-value=4.6 Score=27.69 Aligned_cols=24 Identities=33% Similarity=0.816 Sum_probs=17.1
Q ss_pred CCCCceEEEEEecCCCcccccccccCCCCCc
Q 008894 40 LPPGWTKEIKVTKTGRKVRRDPYYIDPASGY 70 (549)
Q Consensus 40 LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGy 70 (549)
||.||.+.. -.+ ...||++..|+.
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 799998887 222 357898887664
No 15
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=62.14 E-value=3.9 Score=41.91 Aligned_cols=23 Identities=43% Similarity=0.931 Sum_probs=18.3
Q ss_pred CCCCCceEEEEEecCCCcccccccccCCCC
Q 008894 39 GLPPGWTKEIKVTKTGRKVRRDPYYIDPAS 68 (549)
Q Consensus 39 ~LP~GWvkE~~~Rk~G~~ir~DkYY~DPvs 68 (549)
-||+||.+|. .++.-|||||=.+
T Consensus 93 PLPpgWav~~-------T~~grkYYIDHn~ 115 (271)
T KOG1891|consen 93 PLPPGWAVEF-------TTEGRKYYIDHNN 115 (271)
T ss_pred CCCCCcceee-------EecCceeEeecCC
Confidence 4999999999 5556789999543
No 16
>PRK10984 DNA-binding transcriptional regulator Crl; Provisional
Probab=60.61 E-value=5.6 Score=37.34 Aligned_cols=41 Identities=15% Similarity=0.182 Sum_probs=33.7
Q ss_pred CCCCCCCCCCCCCeeEEEEEccCCcceeeEeeccCCCCCCCCceEEE
Q 008894 2 GDRENSDELLPDGCRVEVRVRKNGKKDKIIIEKDTPDGLPPGWTKEI 48 (549)
Q Consensus 2 ~~~e~s~~WLPdGW~vEvr~~knG~K~K~viEr~~~~~LP~GWvkE~ 48 (549)
..||++..| |||||.....+|=.|.|.+=+|+..| .|+.+.
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=58.18 E-value=7.1 Score=36.60 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCCCeeEEEEEccCCcceeeEeeccCCCCCCCCceEEEEE
Q 008894 2 GDRENSDELLPDGCRVEVRVRKNGKKDKIIIEKDTPDGLPPGWTKEIKV 50 (549)
Q Consensus 2 ~~~e~s~~WLPdGW~vEvr~~knG~K~K~viEr~~~~~LP~GWvkE~~~ 50 (549)
..||++..| |||||.....+|=.|+|.+=+|+..| .|+.+..+
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 46655533
No 18
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=49.26 E-value=17 Score=30.83 Aligned_cols=18 Identities=44% Similarity=0.637 Sum_probs=15.8
Q ss_pred CCCCCCCCCeeEEEEEccCC
Q 008894 6 NSDELLPDGCRVEVRVRKNG 25 (549)
Q Consensus 6 ~s~~WLPdGW~vEvr~~knG 25 (549)
+-| ||.||.-|+.+++.|
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=44.04 E-value=12 Score=36.26 Aligned_cols=29 Identities=31% Similarity=0.802 Sum_probs=19.3
Q ss_pred CCCCCCCceEEEEEecCCCcccccccccCCCCCcc
Q 008894 37 PDGLPPGWTKEIKVTKTGRKVRRDPYYIDPASGYI 71 (549)
Q Consensus 37 ~~~LP~GWvkE~~~Rk~G~~ir~DkYY~DPvsGyk 71 (549)
.+.||+||.|-+ +-. +.-.||+.+.|+..
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 23478988776544
No 20
>PHA03165 hypothetical protein; Provisional
Probab=36.18 E-value=11 Score=30.78 Aligned_cols=12 Identities=67% Similarity=1.508 Sum_probs=11.2
Q ss_pred cccCcccCChhH
Q 008894 360 LPFGDLLSDPCI 371 (549)
Q Consensus 360 ~~~~~~wsDPci 371 (549)
+|||+++|.|||
T Consensus 44 spfgeilsspci 55 (57)
T PHA03165 44 SPFGEILSSPCI 55 (57)
T ss_pred CchhhhhcCccc
Confidence 699999999998
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=35.59 E-value=35 Score=27.55 Aligned_cols=26 Identities=31% Similarity=0.433 Sum_probs=20.9
Q ss_pred CCCCCeeEEEEEccCCcceeeEeecc
Q 008894 10 LLPDGCRVEVRVRKNGKKDKIIIEKD 35 (549)
Q Consensus 10 WLPdGW~vEvr~~knG~K~K~viEr~ 35 (549)
.+.|||++.+|...+.-+-|+.+|..
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 35689999988888888888888864
No 22
>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=30.15 E-value=44 Score=22.37 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=15.0
Q ss_pred CCCceEEEEEecCCCcccccccccCCCCCc
Q 008894 41 PPGWTKEIKVTKTGRKVRRDPYYIDPASGY 70 (549)
Q Consensus 41 P~GWvkE~~~Rk~G~~ir~DkYY~DPvsGy 70 (549)
|.||.+-. -+. ...||++..++.
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 357888887654
No 23
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=22.12 E-value=62 Score=24.44 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=16.1
Q ss_pred cCCCCCc-------cccchHHHHHHHhh
Q 008894 64 IDPASGY-------IFRSMKDAVRYVET 84 (549)
Q Consensus 64 ~DPvsGy-------kFRSkkdV~RYLeT 84 (549)
++|.+|. -|.+++++..++..
T Consensus 9 ~~~~~Gkrk~~~k~GF~TkkeA~~~~~~ 36 (46)
T PF14657_consen 9 YDDETGKRKQKTKRGFKTKKEAEKALAK 36 (46)
T ss_pred EECCCCCEEEEEcCCCCcHHHHHHHHHH
Confidence 6676774 39999999998853
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=21.84 E-value=52 Score=24.04 Aligned_cols=17 Identities=24% Similarity=0.514 Sum_probs=14.1
Q ss_pred ccccCCCCCccccchHH
Q 008894 61 PYYIDPASGYIFRSMKD 77 (549)
Q Consensus 61 kYY~DPvsGykFRSkkd 77 (549)
--|+||.||..|.+...
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!