Query 029175
Match_columns 197
No_of_seqs 117 out of 181
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 08:42:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029175hhsearch_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, 99.9 9.3E-26 2E-30 166.2 7.4 72 88-160 2-75 (77)
2 smart00391 MBD Methyl-CpG bind 99.9 2.7E-24 5.9E-29 158.3 7.2 69 86-156 2-73 (77)
3 cd01397 HAT_MBD Methyl-CpG bin 99.9 3.1E-23 6.8E-28 152.7 5.9 63 93-156 6-70 (73)
4 cd00122 MBD MeCP2, MBD1, MBD2, 99.9 2.4E-22 5.3E-27 141.2 6.2 59 88-148 2-62 (62)
5 PF01429 MBD: Methyl-CpG bindi 99.8 2.7E-21 5.9E-26 141.0 5.8 64 91-154 9-75 (77)
6 KOG4161 Methyl-CpG binding tra 99.8 4.3E-19 9.4E-24 156.3 5.9 144 20-163 104-249 (272)
7 cd01395 HMT_MBD Methyl-CpG bin 99.5 1.1E-14 2.3E-19 104.0 4.7 53 94-148 7-60 (60)
8 KOG4161 Methyl-CpG binding tra 99.3 4.8E-12 1E-16 111.8 4.6 71 79-159 10-83 (272)
9 PF07496 zf-CW: CW-type Zinc F 99.2 4.5E-12 9.8E-17 86.4 0.3 46 28-76 2-50 (50)
10 COG1218 CysQ 3'-Phosphoadenosi 62.0 11 0.00023 34.3 3.9 38 46-87 54-91 (276)
11 PF00397 WW: WW domain; Inter 43.5 30 0.00065 21.0 2.6 21 93-117 1-21 (31)
12 KOG1141 Predicted histone meth 43.3 15 0.00032 38.9 1.9 109 41-156 554-664 (1262)
13 PF05180 zf-DNL: DNL zinc fing 40.4 18 0.00038 26.6 1.4 18 25-42 25-42 (66)
14 KOG1141 Predicted histone meth 40.1 29 0.00062 36.9 3.4 102 43-153 759-863 (1262)
15 PF07624 PSD2: Protein of unkn 37.7 28 0.00061 25.2 2.2 37 117-153 1-39 (76)
16 PF09851 SHOCT: Short C-termin 36.6 29 0.00063 21.4 1.8 13 43-55 18-30 (31)
17 PF12528 DUF3728: Prepilin pep 34.3 70 0.0015 24.0 3.9 35 88-122 37-74 (84)
18 COG4479 Uncharacterized protei 32.1 34 0.00074 25.9 1.9 28 119-147 35-62 (74)
19 KOG3794 CBF1-interacting corep 32.0 20 0.00044 34.7 0.8 22 24-45 119-140 (453)
20 PHA00616 hypothetical protein 31.1 26 0.00057 23.9 1.0 29 118-146 7-35 (44)
21 PRK13672 hypothetical protein; 31.0 26 0.00057 26.1 1.1 27 120-147 36-62 (71)
22 KOG1891 Proline binding protei 30.1 52 0.0011 30.0 3.0 50 66-120 83-151 (271)
23 PLN02553 inositol-phosphate ph 29.7 71 0.0015 27.5 3.7 57 46-107 55-116 (270)
24 cd01636 FIG FIG, FBPase/IMPase 27.5 93 0.002 24.9 3.8 39 46-88 48-86 (184)
25 cd01639 IMPase IMPase, inosito 26.9 79 0.0017 26.5 3.5 54 46-107 48-106 (244)
26 PF13465 zf-H2C2_2: Zinc-finge 25.6 61 0.0013 18.9 1.8 13 50-62 6-18 (26)
27 smart00252 SH2 Src homology 2 24.5 93 0.002 21.6 3.0 26 111-137 58-83 (84)
28 PF14542 Acetyltransf_CG: GCN5 24.5 34 0.00073 24.7 0.7 16 126-141 63-78 (78)
29 TIGR02067 his_9_proposed histi 24.0 91 0.002 26.5 3.3 54 46-107 47-105 (251)
30 smart00592 BRK domain in trans 23.7 94 0.002 21.0 2.7 20 121-141 21-40 (45)
31 cd01641 Bacterial_IMPase_like_ 23.6 99 0.0021 26.2 3.5 53 46-107 46-103 (248)
32 cd01643 Bacterial_IMPase_like_ 22.9 1.1E+02 0.0023 26.1 3.6 52 47-107 46-102 (242)
33 cd04896 ACT_ACR-like_3 ACT dom 22.6 1.1E+02 0.0023 22.6 3.1 25 110-134 43-70 (75)
34 PF12874 zf-met: Zinc-finger o 21.9 1.1E+02 0.0024 16.9 2.4 22 113-134 1-22 (25)
35 smart00497 IENR1 Intron encode 21.4 90 0.0019 19.9 2.2 26 111-136 3-31 (53)
36 PRK10757 inositol monophosphat 20.8 1.1E+02 0.0024 26.3 3.3 54 46-107 51-109 (267)
37 PHA00691 hypothetical protein 20.5 56 0.0012 24.1 1.2 18 73-90 6-23 (68)
38 smart00456 WW Domain with 2 co 20.2 1.5E+02 0.0032 17.3 2.8 20 93-117 1-20 (32)
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=99.92 E-value=9.3e-26 Score=166.20 Aligned_cols=72 Identities=47% Similarity=0.758 Sum_probs=66.8
Q ss_pred CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCCCCCC
Q 029175 88 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPE 160 (197)
Q Consensus 88 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~~~p~ 160 (197)
+++|.+|+||+|++++|++| +++||||++|+|++|||++||++||+.||.. +|++++|||++++++.++++.
T Consensus 2 ~~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~~-~~~~~~FdF~~~k~~~~~~~~ 75 (77)
T cd01396 2 PEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPT-SLDLSDFDFTVPKKLGLGSPR 75 (77)
T ss_pred CCCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCCC-CCcHhHcccCCCcccccccCC
Confidence 57888999999999999997 5899999999999999999999999999854 899999999999999988765
No 2
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=99.90 E-value=2.7e-24 Score=158.27 Aligned_cols=69 Identities=36% Similarity=0.618 Sum_probs=63.4
Q ss_pred cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175 86 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 156 (197)
Q Consensus 86 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~ 156 (197)
++.++| +|+||+|++++|++| +++||||+||+||+|||++||++||.+|+++ .+++++|||.+..++..
T Consensus 2 ~~~~~P-lp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~-~~~~~~F~F~~~~~~~~ 73 (77)
T smart00391 2 DPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDL-SLDLECFDFNATVPVGP 73 (77)
T ss_pred CcccCC-CCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCc-ccccccccCcCCccccc
Confidence 456788 899999999999998 4899999999999999999999999999997 78999999999988765
No 3
>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=99.88 E-value=3.1e-23 Score=152.72 Aligned_cols=63 Identities=30% Similarity=0.392 Sum_probs=58.7
Q ss_pred CCCCceEEEEEcccCC--cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175 93 TPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 156 (197)
Q Consensus 93 ~P~GWkRevv~R~~gs--K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~ 156 (197)
+|+||+|++|+|+.++ ++|||||+||||||||++||++||..|+.. +|+++||+|+++.++.+
T Consensus 6 l~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~~-~Lt~dnFsF~~~~~vg~ 70 (73)
T cd01397 6 LELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGIS-LLSRENFSFSARAPVGD 70 (73)
T ss_pred CCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCcc-CccHhHccccCCccccc
Confidence 4899999999999884 699999999999999999999999999975 89999999999988776
No 4
>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=99.87 E-value=2.4e-22 Score=141.21 Aligned_cols=59 Identities=44% Similarity=0.695 Sum_probs=54.1
Q ss_pred CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCcee
Q 029175 88 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 148 (197)
Q Consensus 88 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF 148 (197)
..+|. |+||+|++++|++| +++||||++|+|++|||+.||++||.+|+.. +|++++|||
T Consensus 2 l~~P~-p~GW~R~~~~r~~g~~~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~~~~-~l~~~~F~F 62 (62)
T cd00122 2 LRDPL-PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPS-SLDLENFSF 62 (62)
T ss_pred CCCCC-CCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCCC-CCcHHHCCC
Confidence 35666 99999999999997 5899999999999999999999999999853 899999998
No 5
>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=99.84 E-value=2.7e-21 Score=140.97 Aligned_cols=64 Identities=41% Similarity=0.742 Sum_probs=53.4
Q ss_pred CCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCccc
Q 029175 91 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM 154 (197)
Q Consensus 91 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~ 154 (197)
+.+|+||+|++++|++| ++.||||+||+|++|||+.||.+||..++....|++++|+|.....+
T Consensus 9 ~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~F~~~~~~ 75 (77)
T PF01429_consen 9 PPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSEHDLKPENFSFSKRLIM 75 (77)
T ss_dssp TTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS---SS-CTTBBTTTTB--
T ss_pred CCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCcccCCHhHCCCCCCccc
Confidence 45699999999999998 47999999999999999999999999999544899999999988764
No 6
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.76 E-value=4.3e-19 Score=156.30 Aligned_cols=144 Identities=31% Similarity=0.296 Sum_probs=132.6
Q ss_pred CCccccceeeeecccccceeeeccHHHHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCCCCCCCCCceE
Q 029175 20 EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKR 99 (197)
Q Consensus 20 ~~~~~i~~ya~QC~~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~iP~~P~GWkR 99 (197)
.....|.+|++||..|++|+.|.++.+|+++|+.+.+++|+|..+..+.|++++|+++++.+.|.||.++++.+|.||.|
T Consensus 104 ~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql~~~~~~~~l~~~s~~~e~~d~~~l~~~~~g~~~ 183 (272)
T KOG4161|consen 104 DLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQLFWLERLQDLEADSSRGESIDKLSLPKTPQGSGR 183 (272)
T ss_pred ccccCCchhhhhccccccceeeccccchhhhhccccccccccccceEEEeccccccccccccccccCccccCcCCCccCc
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcccCCcceEEEECCCCCcccchHHHHHhhhhCC--CCCCCCcCCceeeCCcccCCCCCCcce
Q 029175 100 SLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANP--EYSDVSLSDFTFSVPKVMDDTIPEDVV 163 (197)
Q Consensus 100 evv~R~~gsK~DVYY~SP~GKKlRSk~EV~ryL~~np--e~~~l~le~FsF~~pk~~~~~~p~~~~ 163 (197)
.+..+......++||.+|+++.+++.++++.++..|+ ++....+.+|.|+.+.++.+...-..+
T Consensus 184 ~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~ 249 (272)
T KOG4161|consen 184 SSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNV 249 (272)
T ss_pred cccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhh
Confidence 9999988889999999999999999999999999994 444578999999999888886654333
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=99.52 E-value=1.1e-14 Score=103.98 Aligned_cols=53 Identities=28% Similarity=0.456 Sum_probs=49.0
Q ss_pred CCCceEEEEEcccCC-cceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCcee
Q 029175 94 PGGFKRSLVLRKDFS-KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 148 (197)
Q Consensus 94 P~GWkRevv~R~~gs-K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF 148 (197)
-.||+|....|+.|+ |.||+|.+||||+||++.||++||.++ . ..|++++|+|
T Consensus 7 l~gw~R~~~~~~~~~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t-~-~~L~~d~FsF 60 (60)
T cd01395 7 LCGFQRMKYRARVGKVKKHVIYKAPCGRSLRNMSEVHRYLRET-C-SFLTVDNFSF 60 (60)
T ss_pred ccCeEEEEEeccCCCcccceEEECCcchhhhcHHHHHHHHHhc-c-ccceeecccC
Confidence 699999999998765 899999999999999999999999999 3 3799999998
No 8
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.25 E-value=4.8e-12 Score=111.85 Aligned_cols=71 Identities=35% Similarity=0.510 Sum_probs=58.0
Q ss_pred CcceeeecCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccC
Q 029175 79 ASRVWVIDRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMD 155 (197)
Q Consensus 79 ~sr~W~iDkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~ 155 (197)
.+.+| |++. +|+||.|++++|..| ++.||||+||.|++|||+.+++.||+.+ .+.+.|+|...+++.
T Consensus 10 ~~~~~--~c~~---lp~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~-----~~~s~~~~v~~k~~~ 79 (272)
T KOG4161|consen 10 AGKRS--DCPA---LPPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV-----GDLSLFDFVTGKMSP 79 (272)
T ss_pred ccCcc--cCCC---CCCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc-----cccccCccccccccc
Confidence 34444 5554 499999999999987 4899999999999999999999999994 467888888887766
Q ss_pred CCCC
Q 029175 156 DTIP 159 (197)
Q Consensus 156 ~~~p 159 (197)
....
T Consensus 80 ~~~~ 83 (272)
T KOG4161|consen 80 SERQ 83 (272)
T ss_pred cccc
Confidence 6333
No 9
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=99.17 E-value=4.5e-12 Score=86.36 Aligned_cols=46 Identities=41% Similarity=0.954 Sum_probs=32.1
Q ss_pred eeeecccccceeeeccHHHHHHHHhHhcCCCeeecc---CCCCCCCCCCCcc
Q 029175 28 YAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE 76 (197)
Q Consensus 28 ya~QC~~C~KwR~i~t~e~yEeiR~~~~~~pf~C~~---~~~~sC~dP~Di~ 76 (197)
|.|||..|.|||.|| .++..|++.+.+ +|+|.. .+..||+.|+|++
T Consensus 2 ~WVQCd~C~KWR~lp--~~~~~~~~~~~d-~W~C~~n~~~~~~sC~~pee~e 50 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP--EEVDPIREELPD-PWYCSMNPDPPFNSCDAPEEIE 50 (50)
T ss_dssp EEEE-TTT--EEEE---CCHHCTSCCSST-T--GGGSS-CCC-STTS--SS-
T ss_pred eEEECCCCCceeeCC--hhhCcccccCCC-eEEcCCCCCCCCCCCCCcccCC
Confidence 789999999999999 788888888877 999998 6689999999985
No 10
>COG1218 CysQ 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase [Inorganic ion transport and metabolism]
Probab=61.96 E-value=11 Score=34.34 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=28.2
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDR 87 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDk 87 (197)
=++.|+..+.+.|++++ .+|..+--......|.|+||+
T Consensus 54 I~~~L~a~~P~ipvv~E----E~~~~~~~~~~~~~rfWLiDP 91 (276)
T COG1218 54 ILEGLRALFPDIPVVSE----EEEAIDWEERLHWDRFWLVDP 91 (276)
T ss_pred HHHHHHHhCCCCCEEEe----ccccCCCCCcccCceEEEECC
Confidence 47899999999999999 334433333334679999997
No 11
>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=43.46 E-value=30 Score=20.98 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=13.3
Q ss_pred CCCCceEEEEEcccCCcceEEEECC
Q 029175 93 TPGGFKRSLVLRKDFSKMDAYYITP 117 (197)
Q Consensus 93 ~P~GWkRevv~R~~gsK~DVYY~SP 117 (197)
+|.||+...- . ..+.+||+..
T Consensus 1 LP~gW~~~~~--~--~~g~~YY~N~ 21 (31)
T PF00397_consen 1 LPPGWEEYFD--P--DSGRPYYYNH 21 (31)
T ss_dssp SSTTEEEEEE--T--TTSEEEEEET
T ss_pred CCcCCEEEEc--C--CCCCEEEEeC
Confidence 5899963221 1 2578899875
No 12
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=43.34 E-value=15 Score=38.94 Aligned_cols=109 Identities=18% Similarity=0.226 Sum_probs=67.9
Q ss_pred eccHHHHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCCCCCCCCCceEEEEEccc-CC-cceEEEECCC
Q 029175 41 INSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKD-FS-KMDAYYITPT 118 (197)
Q Consensus 41 i~t~e~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~iP~~P~GWkRevv~R~~-gs-K~DVYY~SP~ 118 (197)
.|..=-||.--|++.--|++|+ ..|-.-.-|.--.+.. .-.+.+||- -.-|+|.-.-|++ .. -+-|-|-+|+
T Consensus 554 ~p~ep~y~~~seklsy~sh~cs----~acl~~~~~~~~~~~~-g~npl~lp~-~~~F~r~~a~~rs~~~~~fhv~yktpc 627 (1262)
T KOG1141|consen 554 MPGEPGYEVASEKLSYFSHKCS----IACLNAAQIAIMVGQP-GGNPLNLPY-FLTFHRIRASHRSAYIRDFHVEYKTPC 627 (1262)
T ss_pred CCCCcccccccccccccchhhH----HHHHhccchhhhccCC-CCCccccce-EEEeeehhhhhhhhhhhcceeeccCCC
Confidence 3444456666666666777787 6666555553111100 001223322 2445554444433 22 3789999999
Q ss_pred CCcccchHHHHHhhhhCCCCCCCCcCCceeeCCcccCC
Q 029175 119 GKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 156 (197)
Q Consensus 119 GKKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~~~~ 156 (197)
|.=||.+.||-+||-+... +-|.++.|+|..-..+..
T Consensus 628 g~~lr~~~el~ryL~et~c-~flf~~~f~~~~yV~~~r 664 (1262)
T KOG1141|consen 628 GMPLRMRIELYRYLVETRC-KFLFVIGFDRAFYVVRHR 664 (1262)
T ss_pred ccchHHHHHHHHHHHHhcC-cEEEEeecccchheeecc
Confidence 9999999999999999654 258899999987666555
No 13
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=40.41 E-value=18 Score=26.61 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=12.1
Q ss_pred cceeeeecccccceeeec
Q 029175 25 IDTYAAQCEKCFKWRVIN 42 (197)
Q Consensus 25 i~~ya~QC~~C~KwR~i~ 42 (197)
-|+.-|||..|..|.+|-
T Consensus 25 ~GvViv~C~gC~~~HlIa 42 (66)
T PF05180_consen 25 KGVVIVQCPGCKNRHLIA 42 (66)
T ss_dssp TSEEEEE-TTS--EEES-
T ss_pred CCeEEEECCCCcceeeeh
Confidence 367789999999999985
No 14
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=40.12 E-value=29 Score=36.95 Aligned_cols=102 Identities=15% Similarity=0.225 Sum_probs=66.0
Q ss_pred cHHHHHHHHhHhcCCCeeeccCCCCCCCCCCC---cccCCcceeeecCCCCCCCCCCceEEEEEcccCCcceEEEECCCC
Q 029175 43 SSEEYEEIRCKIAEIPFVCDRKPGVSCEDPAD---IEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTG 119 (197)
Q Consensus 43 t~e~yEeiR~~~~~~pf~C~~~~~~sC~dP~D---i~~d~sr~W~iDkp~iP~~P~GWkRevv~R~~gsK~DVYY~SP~G 119 (197)
+--+|..+-|.+...|++|.++ |-|+-|-= +-+++-.+.+.---.+ -.||.|.-.-=. .++-.-||.|+|
T Consensus 759 ~gykyKRl~e~~ptg~yEc~k~--ckc~~~~C~nrmvqhg~qvRlq~fkt~---~kGWg~rclddi--~~g~fVciy~g~ 831 (1262)
T KOG1141|consen 759 NGYKYKRLIEIRPTGPYECLKA--CKCCGPDCLNRMVQHGYQVRLQRFKTI---HKGWGRRCLDDI--TGGNFVCIYPGG 831 (1262)
T ss_pred cchhhHHHHHhcCCCHHHHHHh--hccCcHHHHHHHhhcCceeEeeecccc---ccccceEeeeec--CCceEEEEecch
Confidence 3457888888889999999975 44543321 2333333322111112 569977554322 244677888999
Q ss_pred CcccchHHHHHhhhhCCCCCCCCcCCceeeCCcc
Q 029175 120 KKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKV 153 (197)
Q Consensus 120 KKlRSk~EV~ryL~~npe~~~l~le~FsF~~pk~ 153 (197)
--++...|+..|+.-.- | -++|++|+|..+.-
T Consensus 832 ~l~~~~sdks~~~~~~~-~-~~~id~~~f~~~~d 863 (1262)
T KOG1141|consen 832 ALLHQISDKSEYIHVTR-S-LLTIDCFSFDARID 863 (1262)
T ss_pred hhhhhhchhhhhcccch-h-hhcccccchhcccc
Confidence 99999999998876632 2 57899999986644
No 15
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=37.65 E-value=28 Score=25.15 Aligned_cols=37 Identities=16% Similarity=0.364 Sum_probs=25.7
Q ss_pred CCCCcccchHHHHHhhhhC-CCCC-CCCcCCceeeCCcc
Q 029175 117 PTGKKLRTLNEVAGFLAAN-PEYS-DVSLSDFTFSVPKV 153 (197)
Q Consensus 117 P~GKKlRSk~EV~ryL~~n-pe~~-~l~le~FsF~~pk~ 153 (197)
|+|..|....||..||..+ +++. .+.-.-+.|..+-.
T Consensus 1 pdG~~f~~~~eLk~~L~~~~~~~~~~~~~kl~~YAlGR~ 39 (76)
T PF07624_consen 1 PDGTSFEGAAELKQYLAERKDQFARCFAEKLLTYALGRP 39 (76)
T ss_pred CCCCccCCHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCC
Confidence 8999999999999999997 3332 23334445555433
No 16
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=36.56 E-value=29 Score=21.40 Aligned_cols=13 Identities=38% Similarity=0.721 Sum_probs=11.6
Q ss_pred cHHHHHHHHhHhc
Q 029175 43 SSEEYEEIRCKIA 55 (197)
Q Consensus 43 t~e~yEeiR~~~~ 55 (197)
|.|||+..+..++
T Consensus 18 seeEy~~~k~~ll 30 (31)
T PF09851_consen 18 SEEEYEQKKARLL 30 (31)
T ss_pred CHHHHHHHHHHHh
Confidence 8999999998875
No 17
>PF12528 DUF3728: Prepilin peptidase dependent protein C (DUF3728); InterPro: IPR022204 This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 121 amino acids in length. The family is found in association with PF07963 from PFAM. There are two completely conserved C residues that may be functionally important. This family is frequently annotated as prepilin peptidase dependent protein C however there is little accompanying literature to confirm this.
Probab=34.29 E-value=70 Score=23.97 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=27.1
Q ss_pred CCCCCCCCCceEEEEEcc-cCC--cceEEEECCCCCcc
Q 029175 88 PGIPKTPGGFKRSLVLRK-DFS--KMDAYYITPTGKKL 122 (197)
Q Consensus 88 p~iP~~P~GWkRevv~R~-~gs--K~DVYY~SP~GKKl 122 (197)
+.++.+|.||+....... .++ ..-|-..+|.|+..
T Consensus 37 ~~~~~~~~gWq~~~~~~~~~~~C~~itvtv~tP~~~~a 74 (84)
T PF12528_consen 37 PALSGPPPGWQYSRQQTSIQGGCRSITVTVTTPQNQQA 74 (84)
T ss_pred ccccCCCCCceeeeeeeccCCCeEEEEEEEecCCCccc
Confidence 445667999999999887 544 57888889988764
No 18
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.13 E-value=34 Score=25.87 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=22.4
Q ss_pred CCcccchHHHHHhhhhCCCCCCCCcCCce
Q 029175 119 GKKLRTLNEVAGFLAANPEYSDVSLSDFT 147 (197)
Q Consensus 119 GKKlRSk~EV~ryL~~npe~~~l~le~Fs 147 (197)
-|.-+...+|.+||+.|..| ..+++.||
T Consensus 35 PK~t~Df~~is~YLE~~a~f-~~~m~~FD 62 (74)
T COG4479 35 PKHTDDFHEISDYLETNADF-LFNMSVFD 62 (74)
T ss_pred CCCCccHHHHHHHHHhcCCc-ccchhhHH
Confidence 35567789999999999988 66777775
No 19
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=31.96 E-value=20 Score=34.73 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=18.1
Q ss_pred ccceeeeecccccceeeeccHH
Q 029175 24 SIDTYAAQCEKCFKWRVINSSE 45 (197)
Q Consensus 24 ~i~~ya~QC~~C~KwR~i~t~e 45 (197)
-|..-.|+|++|+||=-|-|-.
T Consensus 119 GiqVRNVrC~kChkwGH~n~Dr 140 (453)
T KOG3794|consen 119 GIQVRNVRCLKCHKWGHINTDR 140 (453)
T ss_pred ceEeeeeeEEeecccccccCCc
Confidence 4778889999999999886543
No 20
>PHA00616 hypothetical protein
Probab=31.06 E-value=26 Score=23.88 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=22.5
Q ss_pred CCCcccchHHHHHhhhhCCCCCCCCcCCc
Q 029175 118 TGKKLRTLNEVAGFLAANPEYSDVSLSDF 146 (197)
Q Consensus 118 ~GKKlRSk~EV~ryL~~npe~~~l~le~F 146 (197)
||+.|+.+.+|.+.|..+-.-+.++++-|
T Consensus 7 CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 7 CGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred hhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 99999999999999988543334566555
No 21
>PRK13672 hypothetical protein; Provisional
Probab=31.01 E-value=26 Score=26.07 Aligned_cols=27 Identities=30% Similarity=0.476 Sum_probs=20.9
Q ss_pred CcccchHHHHHhhhhCCCCCCCCcCCce
Q 029175 120 KKLRTLNEVAGFLAANPEYSDVSLSDFT 147 (197)
Q Consensus 120 KKlRSk~EV~ryL~~npe~~~l~le~Fs 147 (197)
|.-.+..||.+||+.|+.| ..+++.||
T Consensus 36 K~s~d~~eIs~Yle~~~~y-~~sm~iFD 62 (71)
T PRK13672 36 KQSDDFDELSRYLELNASY-LFSMSIFD 62 (71)
T ss_pred CCcccHHHHHHHHHHcCcc-cccHHHHH
Confidence 4456789999999999988 55666664
No 22
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=30.09 E-value=52 Score=30.01 Aligned_cols=50 Identities=26% Similarity=0.444 Sum_probs=31.7
Q ss_pred CCCCCCCCCcccC---------CcceeeecCCCC----------CCCCCCceEEEEEcccCCcceEEEECCCCC
Q 029175 66 GVSCEDPADIEYD---------ASRVWVIDRPGI----------PKTPGGFKRSLVLRKDFSKMDAYYITPTGK 120 (197)
Q Consensus 66 ~~sC~dP~Di~~d---------~sr~W~iDkp~i----------P~~P~GWkRevv~R~~gsK~DVYY~SP~GK 120 (197)
-.+|+.++|+..- .+|..-||-.+- -.+|+||+|-+- .-.-+||+.-.-|
T Consensus 83 ~s~~~~sedlPLPpgWav~~T~~grkYYIDHn~~tTHW~HPlerEgLppGW~rv~s-----~e~GtyY~~~~~k 151 (271)
T KOG1891|consen 83 RSSCDCSEDLPLPPGWAVEFTTEGRKYYIDHNNRTTHWVHPLEREGLPPGWKRVFS-----PEKGTYYYHEEMK 151 (271)
T ss_pred cccCCCcccCCCCCCcceeeEecCceeEeecCCCcccccChhhhccCCcchhhccc-----cccceeeeecccc
Confidence 3578888998432 356677775542 246999988642 2356788876444
No 23
>PLN02553 inositol-phosphate phosphatase
Probab=29.68 E-value=71 Score=27.48 Aligned_cols=57 Identities=11% Similarity=0.160 Sum_probs=31.4
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
=.+.|++.+.+..|..+-.. ...+....+..++|+||+-. +-. -+.|==.|.+-.+|
T Consensus 55 i~~~L~~~~P~~~ilgEE~~----~~~~~~~~~~~~~WiIDPIDGT~NF~~g-~p~~avsIal~~~g 116 (270)
T PLN02553 55 IFNHLKQAFPSHKFIGEETT----AASGGTELTDEPTWIVDPLDGTTNFVHG-FPFVCVSIGLTIGK 116 (270)
T ss_pred HHHHHHHHCCCCEEEecccc----ccCCcccCCCCcEEEEecccchhhHhhc-CCceEEEEEEEECC
Confidence 35677778888888888421 11112223456899999743 111 13465555554444
No 24
>cd01636 FIG FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+.
Probab=27.55 E-value=93 Score=24.90 Aligned_cols=39 Identities=13% Similarity=0.220 Sum_probs=23.2
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRP 88 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp 88 (197)
=.+.|++.+...++..+-.. +.......+....|+||+-
T Consensus 48 i~~~L~~~~P~~~i~~EE~~----~~~~~~~~~~~~~WiiDPi 86 (184)
T cd01636 48 IRNMLKSSFPDVKIVGEESG----VAEEVMGRRDEYTWVIDPI 86 (184)
T ss_pred HHHHHHHHCCCCeEEecCcC----CccccccCCCCeEEEEecc
Confidence 34667778888888888321 1111111245689999973
No 25
>cd01639 IMPase IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be recycled into inositol lipids; in eukaryotes IMPase plays a vital role in intracellular signaling. IMPase is one of the proposed targets of Li+ therapy in manic-depressive illness. This family contains some bacterial members of the inositol monophosphatase family classified as SuhB-like. E. coli SuhB has been suggested to participate in posstranscriptional control of gene expression, and its inositol monophosphatase activity doesn't appear to be sufficient for its cellular function. It has been proposed, that SuhB plays a role in the biosynthesis of phosphatidylinositol in mycobacteria.
Probab=26.90 E-value=79 Score=26.55 Aligned_cols=54 Identities=15% Similarity=0.162 Sum_probs=31.3
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
=.+.|++.+.+.+|..+-... +...+..++|+||+-- +-.. +.|-=.|.+-.+|
T Consensus 48 i~~~L~~~~p~~~i~~EE~~~-------~~~~~~~~~WvIDPIDGT~nf~~g~-p~~~vsial~~~g 106 (244)
T cd01639 48 IIEILKKAYPDHGFLGEESGA-------AGGLTDEPTWIIDPLDGTTNFVHGF-PHFAVSIALAVKG 106 (244)
T ss_pred HHHHHHHHCCCCEEEecccCC-------CCCCCCCcEEEEecccChhHHhcCC-CcEEEEEEEEECC
Confidence 356777788888888884211 0003446899999733 1111 3566666555555
No 26
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.59 E-value=61 Score=18.87 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=11.5
Q ss_pred HHhHhcCCCeeec
Q 029175 50 IRCKIAEIPFVCD 62 (197)
Q Consensus 50 iR~~~~~~pf~C~ 62 (197)
+|.+..|.||.|.
T Consensus 6 ~~~H~~~k~~~C~ 18 (26)
T PF13465_consen 6 MRTHTGEKPYKCP 18 (26)
T ss_dssp HHHHSSSSSEEES
T ss_pred hhhcCCCCCCCCC
Confidence 5778899999998
No 27
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=24.50 E-value=93 Score=21.60 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=21.7
Q ss_pred eEEEECCCCCcccchHHHHHhhhhCCC
Q 029175 111 DAYYITPTGKKLRTLNEVAGFLAANPE 137 (197)
Q Consensus 111 DVYY~SP~GKKlRSk~EV~ryL~~npe 137 (197)
..|++.. ++.|.|..||..|...++.
T Consensus 58 ~~~~l~~-~~~F~sl~eLI~~y~~~~~ 83 (84)
T smart00252 58 GKFYLDG-GRKFPSLVELVEHYQKNSL 83 (84)
T ss_pred CcEEECC-CCccCCHHHHHHHHhhCCC
Confidence 3677765 7999999999999998763
No 28
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=24.46 E-value=34 Score=24.75 Aligned_cols=16 Identities=38% Similarity=0.744 Sum_probs=11.5
Q ss_pred HHHHHhhhhCCCCCCC
Q 029175 126 NEVAGFLAANPEYSDV 141 (197)
Q Consensus 126 ~EV~ryL~~npe~~~l 141 (197)
+=++.||..||+|.+|
T Consensus 63 ~y~~~~~~~hpey~dl 78 (78)
T PF14542_consen 63 SYVAKYFRRHPEYQDL 78 (78)
T ss_dssp HHHHHHHHH-GGGTTT
T ss_pred HHHHHHHHhCcccccC
Confidence 5578899999988654
No 29
>TIGR02067 his_9_proposed histidinol-phosphate phosphatase HisN, inositol monophosphatase family. This subfamily belongs to the inositol monophosphatase family (pfam00459). The members of this family consist of no more than one per species and are found only in species in which histidine is synthesized de novo but no histidinol phosphatase can be found in either of the two described families (TIGR01261, TIGR01856). In at least one species, the member of this family is found near known histidine biosynthesis genes.
Probab=24.03 E-value=91 Score=26.49 Aligned_cols=54 Identities=22% Similarity=0.175 Sum_probs=31.1
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
=.+.|++.+.+.+|.-+-... +...+..++|+||+-. +-. -+.|-=.+.+-.+|
T Consensus 47 i~~~L~~~~P~~~il~EE~~~-------~~~~~~~~~WiiDPIDGT~nF~~g-~p~~~vsial~~~g 105 (251)
T TIGR02067 47 MRELIAAFFPDHGILGEEFGH-------NEEGDAERVWVLDPIDGTKSFIRG-VPVWGTLIALVEGG 105 (251)
T ss_pred HHHHHHHHCCCCEEEecccCC-------CCCCCCceEEEEecCcChhHHhcC-CCceEEEEEEEECC
Confidence 356777788888888884221 1223446899999743 111 13465555554444
No 30
>smart00592 BRK domain in transcription and CHROMO domain helicases.
Probab=23.68 E-value=94 Score=20.99 Aligned_cols=20 Identities=30% Similarity=0.635 Sum_probs=16.2
Q ss_pred cccchHHHHHhhhhCCCCCCC
Q 029175 121 KLRTLNEVAGFLAANPEYSDV 141 (197)
Q Consensus 121 KlRSk~EV~ryL~~npe~~~l 141 (197)
..=...+|.++|..||.| .+
T Consensus 21 ~aP~~~~l~~WL~~~p~y-ev 40 (45)
T smart00592 21 DAPKAKDLERWLEENPEY-EV 40 (45)
T ss_pred cCCcHHHHHHHHhcCCCc-cc
Confidence 345678999999999999 54
No 31
>cd01641 Bacterial_IMPase_like_1 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates.
Probab=23.61 E-value=99 Score=26.23 Aligned_cols=53 Identities=21% Similarity=0.148 Sum_probs=31.7
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
=.+.|++.+.+.+|.-+-... ...+..++|+||+-- +-. -+.|-=.|.+-.+|
T Consensus 46 i~~~L~~~~P~~~il~EE~~~--------~~~~~~~~WviDPIDGT~nf~~g-~p~~~vsial~~~g 103 (248)
T cd01641 46 MRELIAAAFPDHGILGEEFGN--------EGGDAGYVWVLDPIDGTKSFIRG-LPVWGTLIALLHDG 103 (248)
T ss_pred HHHHHHHHCCCCeEEEccccC--------CCCCCCcEEEEecCcCchhHhcC-CCceEEEEEEEECC
Confidence 356788888888998884321 112346899999743 111 13566556555554
No 32
>cd01643 Bacterial_IMPase_like_2 Bacterial family of Mg++ dependent phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate inositol monophosphate or similar substrates.
Probab=22.87 E-value=1.1e+02 Score=26.10 Aligned_cols=52 Identities=15% Similarity=0.105 Sum_probs=31.9
Q ss_pred HHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 47 YEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 47 yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
.+.|++.+.+..++-+-... ...++..+|+||+-. +-. -+.|-=.|.+-.+|
T Consensus 46 ~~~L~~~~P~~~i~gEE~~~--------~~~~~~~~WiIDPIDGT~nF~~g-~p~~~vsial~~~g 102 (242)
T cd01643 46 RARLAAQFPDDGVLGEEGGG--------IFPSSGWYWVIDPIDGTTNFARG-IPIWAISIALLYRG 102 (242)
T ss_pred HHHHHHHCCCCeEEecCCCC--------CCCCCCCEEEEeCccChHHHhcC-CCceEEEEEEEECC
Confidence 47788888888898884321 122345799999743 111 13566666665555
No 33
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.64 E-value=1.1e+02 Score=22.56 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=18.2
Q ss_pred ceEEEECCCCCcccch---HHHHHhhhh
Q 029175 110 MDAYYITPTGKKLRTL---NEVAGFLAA 134 (197)
Q Consensus 110 ~DVYY~SP~GKKlRSk---~EV~ryL~~ 134 (197)
.||||++..|.++..- .+|...|..
T Consensus 43 ~D~Fyv~~~g~kl~d~~~~~~L~~~L~~ 70 (75)
T cd04896 43 VDLFIVQSDGKKIMDPKKQAALCARLRE 70 (75)
T ss_pred EEEEEEeCCCCccCCHHHHHHHHHHHHH
Confidence 7999999899888663 455555544
No 34
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.91 E-value=1.1e+02 Score=16.86 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=19.2
Q ss_pred EEECCCCCcccchHHHHHhhhh
Q 029175 113 YYITPTGKKLRTLNEVAGFLAA 134 (197)
Q Consensus 113 YY~SP~GKKlRSk~EV~ryL~~ 134 (197)
||-..+++.|.|...+...|..
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 7888999999999999888764
No 35
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=21.39 E-value=90 Score=19.93 Aligned_cols=26 Identities=19% Similarity=0.408 Sum_probs=20.4
Q ss_pred eEEEECCCCC---cccchHHHHHhhhhCC
Q 029175 111 DAYYITPTGK---KLRTLNEVAGFLAANP 136 (197)
Q Consensus 111 DVYY~SP~GK---KlRSk~EV~ryL~~np 136 (197)
-||-++.+|. .|.|..|.+++|+-+.
T Consensus 3 ~V~~~d~~~~~i~~f~S~~eAa~~lg~~~ 31 (53)
T smart00497 3 PVYVYDLDGNLIGEFSSIREAAKYLGISH 31 (53)
T ss_pred cEEEEeCCCCEEEEecCHHHHHHHhCCCH
Confidence 3677787774 5899999999998754
No 36
>PRK10757 inositol monophosphatase; Provisional
Probab=20.80 E-value=1.1e+02 Score=26.34 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=30.4
Q ss_pred HHHHHHhHhcCCCeeeccCCCCCCCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029175 46 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 107 (197)
Q Consensus 46 ~yEeiR~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 107 (197)
=.|.|++.+.+..|.-+-... +...+...+|+||+-. +-. -+.|-=.|.+-.+|
T Consensus 51 i~~~L~~~~P~~~ilgEE~~~-------~~~~~~~~~WiIDPIDGT~nf~~g-~p~~~vsial~~~g 109 (267)
T PRK10757 51 IIDTIRKSYPQHTIITEESGE-------LEGEDQDVQWVIDPLDGTTNFIKR-LPHFAVSIAVRIKG 109 (267)
T ss_pred HHHHHHHHCCCCEEEecccCC-------ccCCCCCCEEEEeCccCchHHHhC-CCcEEEEEEEEECC
Confidence 357778888888888773211 1111345789999743 001 13465556555554
No 37
>PHA00691 hypothetical protein
Probab=20.49 E-value=56 Score=24.08 Aligned_cols=18 Identities=39% Similarity=0.913 Sum_probs=15.2
Q ss_pred CCcccCCcceeeecCCCC
Q 029175 73 ADIEYDASRVWVIDRPGI 90 (197)
Q Consensus 73 ~Di~~d~sr~W~iDkp~i 90 (197)
.||-+.++|.||+.+...
T Consensus 6 ~~I~~ENGr~WVL~K~~~ 23 (68)
T PHA00691 6 KDIAYENGRVWVLKKSDS 23 (68)
T ss_pred hhhhccCCeEEEEEeCCc
Confidence 589999999999987654
No 38
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=20.16 E-value=1.5e+02 Score=17.32 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=12.6
Q ss_pred CCCCceEEEEEcccCCcceEEEECC
Q 029175 93 TPGGFKRSLVLRKDFSKMDAYYITP 117 (197)
Q Consensus 93 ~P~GWkRevv~R~~gsK~DVYY~SP 117 (197)
+|.||.... . .+ +.+||+..
T Consensus 1 lp~gW~~~~---~-~~-g~~yy~n~ 20 (32)
T smart00456 1 LPPGWEERK---D-PD-GRPYYYNH 20 (32)
T ss_pred CCCCCEEEE---C-CC-CCEEEEEC
Confidence 488995433 2 22 68888865
Done!