Query 029286
Match_columns 196
No_of_seqs 119 out of 183
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:28:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029286.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029286hhsearch_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 1.7E-25 3.7E-30 164.7 7.4 72 87-159 2-75 (77)
2 smart00391 MBD Methyl-CpG bind 99.9 3.1E-24 6.7E-29 157.8 7.2 69 85-155 2-73 (77)
3 cd01397 HAT_MBD Methyl-CpG bin 99.9 4.7E-23 1E-27 151.7 5.9 63 92-155 6-70 (73)
4 cd00122 MBD MeCP2, MBD1, MBD2, 99.9 2.3E-22 5E-27 141.2 6.2 59 87-147 2-62 (62)
5 PF01429 MBD: Methyl-CpG bindi 99.8 2.4E-21 5.3E-26 141.1 5.9 64 90-153 9-75 (77)
6 KOG4161 Methyl-CpG binding tra 99.8 1.2E-19 2.5E-24 159.7 5.9 145 19-163 104-250 (272)
7 cd01395 HMT_MBD Methyl-CpG bin 99.5 1E-14 2.2E-19 104.1 4.7 53 93-147 7-60 (60)
8 KOG4161 Methyl-CpG binding tra 99.3 2.3E-12 5E-17 113.8 4.6 63 85-155 15-80 (272)
9 PF07496 zf-CW: CW-type Zinc F 99.2 2.8E-12 6E-17 87.3 -0.5 46 27-75 2-50 (50)
10 COG1218 CysQ 3'-Phosphoadenosi 51.7 20 0.00043 32.6 3.9 38 45-86 54-91 (276)
11 KOG1141 Predicted histone meth 40.6 18 0.00038 38.4 2.0 61 94-155 602-664 (1262)
12 PF12528 DUF3728: Prepilin pep 39.4 51 0.0011 24.7 3.8 35 87-121 37-74 (84)
13 PF09851 SHOCT: Short C-termin 38.9 25 0.00054 21.7 1.8 13 42-54 18-30 (31)
14 PF00397 WW: WW domain; Inter 38.3 38 0.00082 20.5 2.5 21 92-116 1-21 (31)
15 PF07624 PSD2: Protein of unkn 37.6 28 0.00061 25.1 2.2 37 116-152 1-39 (76)
16 KOG1891 Proline binding protei 32.7 44 0.00096 30.5 3.0 50 65-119 83-151 (271)
17 PF05180 zf-DNL: DNL zinc fing 30.3 19 0.00042 26.4 0.3 18 25-42 26-43 (66)
18 COG4479 Uncharacterized protei 27.4 43 0.00094 25.3 1.7 27 119-146 36-62 (74)
19 PHA00616 hypothetical protein 27.3 36 0.00079 23.2 1.2 29 117-145 7-35 (44)
20 KOG1141 Predicted histone meth 26.1 70 0.0015 34.3 3.5 103 42-153 759-864 (1262)
21 PF13465 zf-H2C2_2: Zinc-finge 25.7 60 0.0013 18.9 1.8 13 49-61 6-18 (26)
22 cd01639 IMPase IMPase, inosito 24.9 91 0.002 26.2 3.5 53 46-106 49-106 (244)
23 PRK13672 hypothetical protein; 23.9 39 0.00085 25.1 0.9 27 119-146 36-62 (71)
24 PF14542 Acetyltransf_CG: GCN5 23.6 38 0.00082 24.4 0.8 16 125-140 63-78 (78)
25 smart00252 SH2 Src homology 2 23.3 1E+02 0.0022 21.4 3.0 26 110-136 58-83 (84)
26 cd04896 ACT_ACR-like_3 ACT dom 23.1 1.1E+02 0.0023 22.6 3.1 25 109-133 43-70 (75)
27 smart00592 BRK domain in trans 22.7 99 0.0022 20.9 2.6 19 121-140 22-40 (45)
28 cd01641 Bacterial_IMPase_like_ 22.3 1.1E+02 0.0024 25.9 3.5 52 46-106 47-103 (248)
29 smart00497 IENR1 Intron encode 22.2 94 0.002 19.8 2.4 26 110-135 3-31 (53)
30 TIGR02067 his_9_proposed histi 21.9 1.1E+02 0.0023 26.0 3.3 53 46-106 48-105 (251)
31 PF07603 DUF1566: Protein of u 21.6 70 0.0015 23.8 1.9 16 36-52 50-65 (124)
32 cd01643 Bacterial_IMPase_like_ 21.5 1.2E+02 0.0026 25.8 3.5 52 46-106 46-102 (242)
33 PF12874 zf-met: Zinc-finger o 21.3 1.2E+02 0.0027 16.6 2.5 22 112-133 1-22 (25)
34 KOG3794 CBF1-interacting corep 21.0 32 0.00068 33.5 -0.1 22 23-44 119-140 (453)
35 smart00456 WW Domain with 2 co 20.4 1.4E+02 0.003 17.4 2.7 20 92-116 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=1.7e-25 Score=164.65 Aligned_cols=72 Identities=47% Similarity=0.758 Sum_probs=66.6
Q ss_pred CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCCCCCC
Q 029286 87 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDDTIPE 159 (196)
Q Consensus 87 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~~ip~ 159 (196)
+++|.+|+||+|++++|++| +++||||++|+|++|||++||++||+.||.. +|++++|||++++++.++++.
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 899999999999999987765
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=3.1e-24 Score=157.82 Aligned_cols=69 Identities=36% Similarity=0.618 Sum_probs=63.3
Q ss_pred cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286 85 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 155 (196)
Q Consensus 85 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~ 155 (196)
++..+| +|+||+|++++|++| +++||||+||+||+|||++||++||.+|+++ .+++++|||.+..++..
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 5899999999999999999999999999997 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=4.7e-23 Score=151.72 Aligned_cols=63 Identities=30% Similarity=0.392 Sum_probs=58.6
Q ss_pred CCCCceEEEEEcccCC--cceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286 92 TPGGFKRSLVLRKDFS--KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 155 (196)
Q Consensus 92 ~P~GWkRevv~R~~gs--K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~ 155 (196)
+|.||+|++|+|+.++ ++||||++||||||||++||++||..|+.. +|+++||+|+++.++.+
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 799999999999999999999999999975 89999999999988765
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=2.3e-22 Score=141.20 Aligned_cols=59 Identities=44% Similarity=0.695 Sum_probs=54.1
Q ss_pred CCCCCCCCCceEEEEEcccC--CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeee
Q 029286 87 PGIPKTPGGFKRSLVLRKDF--SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 147 (196)
Q Consensus 87 p~iP~~P~GWkRevv~R~~g--sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F 147 (196)
..+|. |+||+|++++|++| +++||||++|+|++|||+.||++||..|+.. +|++++|||
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 5899999999999999999999999999843 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=2.4e-21 Score=141.06 Aligned_cols=64 Identities=41% Similarity=0.742 Sum_probs=53.5
Q ss_pred CCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCccc
Q 029286 90 PKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM 153 (196)
Q Consensus 90 P~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~ 153 (196)
+.+|+||+|++++|++| ++.||||+||+|++|||+.||.+||..++....|++++|+|.....+
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 47999999999999999999999999999644899999999988764
No 6
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.78 E-value=1.2e-19 Score=159.73 Aligned_cols=145 Identities=30% Similarity=0.300 Sum_probs=133.5
Q ss_pred CCccccchhhhccccccceeeeccHHHHHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCCCCCCCCCceE
Q 029286 19 EPIRSIDTYAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPGIPKTPGGFKR 98 (196)
Q Consensus 19 ~~~~~i~~yavQC~~C~KwR~ipt~e~yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~iP~~P~GWkR 98 (196)
....+|.+|++||..|++|+.|.++.+|+++|+.+.++||+|..+..+.|++++|+++++++.|.||.++++.+|.||.|
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 44569999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcccCCcceEEEECCCCCccccHHHHHHhhhhCC--CCCCCCcCCeeeeCCcccCCCCCCcccc
Q 029286 99 SLVLRKDFSKMDAYYITPTGKKLRTLNEVAGFLAANP--EYSDVSLSDFTFSVPKVMDDTIPEDVVK 163 (196)
Q Consensus 99 evv~R~~gsK~DVYY~SP~GKKlRSk~EV~ryL~~np--e~~~l~le~F~F~~pk~~~~~ip~~~~~ 163 (196)
.+..+......++||.+|+|+.+++..+++.++..|+ ++....+.+|.|+.+.++.+.+.-.-++
T Consensus 184 ~~~~~s~~~~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~r 250 (272)
T KOG4161|consen 184 SSAGESLLSSVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNVR 250 (272)
T ss_pred cccccccccccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhhh
Confidence 9999988889999999999999999999999999994 4446789999999998888866543333
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=99.53 E-value=1e-14 Score=104.08 Aligned_cols=53 Identities=28% Similarity=0.456 Sum_probs=48.9
Q ss_pred CCCceEEEEEcccCC-cceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeee
Q 029286 93 PGGFKRSLVLRKDFS-KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTF 147 (196)
Q Consensus 93 P~GWkRevv~R~~gs-K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F 147 (196)
-.||+|....|+.|+ |.||+|.+||||+||++.||++||..+ . ..|++++|+|
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=99.29 E-value=2.3e-12 Score=113.75 Aligned_cols=63 Identities=38% Similarity=0.609 Sum_probs=54.8
Q ss_pred cCCCCCCCCCCceEEEEEcccC---CcceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286 85 DRPGIPKTPGGFKRSLVLRKDF---SKMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 155 (196)
Q Consensus 85 Dkp~iP~~P~GWkRevv~R~~g---sK~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~ 155 (196)
|++.| |+||.|++++|++| ++.||||+||.|++|||+.+++.||+.+ .+.+.|+|-..+++..
T Consensus 15 ~c~~l---p~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~-----~~~s~~~~v~~k~~~~ 80 (272)
T KOG4161|consen 15 DCPAL---PPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV-----GDLSLFDFVTGKMSPS 80 (272)
T ss_pred cCCCC---CCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc-----cccccCcccccccccc
Confidence 55545 99999999999987 5899999999999999999999999994 4678888888877665
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=99.18 E-value=2.8e-12 Score=87.35 Aligned_cols=46 Identities=41% Similarity=0.954 Sum_probs=32.4
Q ss_pred hhhccccccceeeeccHHHHHHHHhhhcCCCeeecc---CCCCCcCCCCCcc
Q 029286 27 YAAQCEKCFKWRVINSSEEYEEIRCKIAEIPFVCDR---KPGVSCEDPADIE 75 (196)
Q Consensus 27 yavQC~~C~KwR~ipt~e~yEeir~~~~~~pf~C~~---~~~~sC~dP~Di~ 75 (196)
|.|||..|.|||.|| .++..|++.+.+ +|+|.. .+..||+.|+|++
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 689999999999999 888888888888 999998 6689999999985
No 10
>COG1218 CysQ 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase [Inorganic ion transport and metabolism]
Probab=51.71 E-value=20 Score=32.58 Aligned_cols=38 Identities=21% Similarity=0.385 Sum_probs=26.8
Q ss_pred HHHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecC
Q 029286 45 EYEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDR 86 (196)
Q Consensus 45 ~yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDk 86 (196)
=++.|++.+.+.|++++-. |..+--......|.|+||+
T Consensus 54 I~~~L~a~~P~ipvv~EE~----~~~~~~~~~~~~rfWLiDP 91 (276)
T COG1218 54 ILEGLRALFPDIPVVSEEE----EAIDWEERLHWDRFWLVDP 91 (276)
T ss_pred HHHHHHHhCCCCCEEEecc----ccCCCCCcccCceEEEECC
Confidence 4789999999999999931 2222122233679999997
No 11
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=40.62 E-value=18 Score=38.40 Aligned_cols=61 Identities=20% Similarity=0.196 Sum_probs=45.2
Q ss_pred CCceEEEEEccc-CC-cceEEEECCCCCccccHHHHHHhhhhCCCCCCCCcCCeeeeCCcccCC
Q 029286 94 GGFKRSLVLRKD-FS-KMDAYYITPTGKKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVMDD 155 (196)
Q Consensus 94 ~GWkRevv~R~~-gs-K~DVYY~SP~GKKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~~~ 155 (196)
.-|+|.-.-|++ .. -+-|-|-+|+|.=||.+.||-+||-+... +-|.++.|+|..-..+..
T Consensus 602 ~~F~r~~a~~rs~~~~~fhv~yktpcg~~lr~~~el~ryL~et~c-~flf~~~f~~~~yV~~~r 664 (1262)
T KOG1141|consen 602 LTFHRIRASHRSAYIRDFHVEYKTPCGMPLRMRIELYRYLVETRC-KFLFVIGFDRAFYVVRHR 664 (1262)
T ss_pred EEeeehhhhhhhhhhhcceeeccCCCccchHHHHHHHHHHHHhcC-cEEEEeecccchheeecc
Confidence 445554444443 22 47899999999999999999999999653 248899999987665554
No 12
>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=39.35 E-value=51 Score=24.67 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=27.3
Q ss_pred CCCCCCCCCceEEEEEcc-cCC--cceEEEECCCCCcc
Q 029286 87 PGIPKTPGGFKRSLVLRK-DFS--KMDAYYITPTGKKL 121 (196)
Q Consensus 87 p~iP~~P~GWkRevv~R~-~gs--K~DVYY~SP~GKKl 121 (196)
+.++.+|.||+....... .++ ..-|-..+|.|+..
T Consensus 37 ~~~~~~~~gWq~~~~~~~~~~~C~~itvtv~tP~~~~a 74 (84)
T PF12528_consen 37 PALSGPPPGWQYSRQQTSIQGGCRSITVTVTTPQNQQA 74 (84)
T ss_pred ccccCCCCCceeeeeeeccCCCeEEEEEEEecCCCccc
Confidence 445667999999999987 544 57888899988764
No 13
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=38.92 E-value=25 Score=21.70 Aligned_cols=13 Identities=38% Similarity=0.721 Sum_probs=11.7
Q ss_pred cHHHHHHHHhhhc
Q 029286 42 SSEEYEEIRCKIA 54 (196)
Q Consensus 42 t~e~yEeir~~~~ 54 (196)
|.|||+..+..++
T Consensus 18 seeEy~~~k~~ll 30 (31)
T PF09851_consen 18 SEEEYEQKKARLL 30 (31)
T ss_pred CHHHHHHHHHHHh
Confidence 8999999999876
No 14
>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=38.35 E-value=38 Score=20.51 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=13.2
Q ss_pred CCCCceEEEEEcccCCcceEEEECC
Q 029286 92 TPGGFKRSLVLRKDFSKMDAYYITP 116 (196)
Q Consensus 92 ~P~GWkRevv~R~~gsK~DVYY~SP 116 (196)
+|.||+...- . ....+||+..
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 2577888875
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=37.64 E-value=28 Score=25.13 Aligned_cols=37 Identities=16% Similarity=0.364 Sum_probs=25.8
Q ss_pred CCCCccccHHHHHHhhhhC-CCCC-CCCcCCeeeeCCcc
Q 029286 116 PTGKKLRTLNEVAGFLAAN-PEYS-DVSLSDFTFSVPKV 152 (196)
Q Consensus 116 P~GKKlRSk~EV~ryL~~n-pe~~-~l~le~F~F~~pk~ 152 (196)
|+|..|....||..||..+ +++. .+.-.-+.|..+-.
T Consensus 1 pdG~~f~~~~eLk~~L~~~~~~~~~~~~~kl~~YAlGR~ 39 (76)
T PF07624_consen 1 PDGTSFEGAAELKQYLAERKDQFARCFAEKLLTYALGRP 39 (76)
T ss_pred CCCCccCCHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCC
Confidence 8999999999999999998 3332 23333445555443
No 16
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=32.71 E-value=44 Score=30.47 Aligned_cols=50 Identities=26% Similarity=0.444 Sum_probs=31.7
Q ss_pred CCCcCCCCCcccC---------CcceeeecCCCC----------CCCCCCceEEEEEcccCCcceEEEECCCCC
Q 029286 65 GVSCEDPADIEYD---------ASRVWVIDRPGI----------PKTPGGFKRSLVLRKDFSKMDAYYITPTGK 119 (196)
Q Consensus 65 ~~sC~dP~Di~~d---------~sr~W~iDkp~i----------P~~P~GWkRevv~R~~gsK~DVYY~SP~GK 119 (196)
-.+|+.++|+..- .+|..-||-.+- -.+|+||+|.+- .-.-+||+.-.-|
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 256777775542 246999988652 2356788876444
No 17
>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=30.32 E-value=19 Score=26.40 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=10.9
Q ss_pred chhhhccccccceeeecc
Q 029286 25 DTYAAQCEKCFKWRVINS 42 (196)
Q Consensus 25 ~~yavQC~~C~KwR~ipt 42 (196)
|+.-|||..|..|.+|-.
T Consensus 26 GvViv~C~gC~~~HlIaD 43 (66)
T PF05180_consen 26 GVVIVQCPGCKNRHLIAD 43 (66)
T ss_dssp SEEEEE-TTS--EEES--
T ss_pred CeEEEECCCCcceeeehh
Confidence 456699999999999853
No 18
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.41 E-value=43 Score=25.34 Aligned_cols=27 Identities=22% Similarity=0.507 Sum_probs=21.6
Q ss_pred CccccHHHHHHhhhhCCCCCCCCcCCee
Q 029286 119 KKLRTLNEVAGFLAANPEYSDVSLSDFT 146 (196)
Q Consensus 119 KKlRSk~EV~ryL~~npe~~~l~le~F~ 146 (196)
|.-+...+|.+||+.|..| ..+++.||
T Consensus 36 K~t~Df~~is~YLE~~a~f-~~~m~~FD 62 (74)
T COG4479 36 KHTDDFHEISDYLETNADF-LFNMSVFD 62 (74)
T ss_pred CCCccHHHHHHHHHhcCCc-ccchhhHH
Confidence 4556789999999999887 66777775
No 19
>PHA00616 hypothetical protein
Probab=27.32 E-value=36 Score=23.18 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=22.2
Q ss_pred CCCccccHHHHHHhhhhCCCCCCCCcCCe
Q 029286 117 TGKKLRTLNEVAGFLAANPEYSDVSLSDF 145 (196)
Q Consensus 117 ~GKKlRSk~EV~ryL~~npe~~~l~le~F 145 (196)
+|+.|+.+.+|.+.|..+-.-+.++++-|
T Consensus 7 CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 7 CGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred hhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 89999999999999988533234566554
No 20
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=26.12 E-value=70 Score=34.26 Aligned_cols=103 Identities=15% Similarity=0.235 Sum_probs=66.0
Q ss_pred cHHHHHHHHhhhcCCCeeeccCCCCCcCCCC---CcccCCcceeeecCCCCCCCCCCceEEEEEcccCCcceEEEECCCC
Q 029286 42 SSEEYEEIRCKIAEIPFVCDRKPGVSCEDPA---DIEYDASRVWVIDRPGIPKTPGGFKRSLVLRKDFSKMDAYYITPTG 118 (196)
Q Consensus 42 t~e~yEeir~~~~~~pf~C~~~~~~sC~dP~---Di~~d~sr~W~iDkp~iP~~P~GWkRevv~R~~gsK~DVYY~SP~G 118 (196)
+--+|..+-|.+...|+.|.++ |-|+-|- -+-+++-.+.+.--..+ -.||.|.-.-=. .++-.-||.|.|
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 3457888888999999999975 2343321 12333332222111112 579977654333 244667888999
Q ss_pred CccccHHHHHHhhhhCCCCCCCCcCCeeeeCCccc
Q 029286 119 KKLRTLNEVAGFLAANPEYSDVSLSDFTFSVPKVM 153 (196)
Q Consensus 119 KKlRSk~EV~ryL~~npe~~~l~le~F~F~~pk~~ 153 (196)
--++...|...|+.-. +| -++|+.|+|..+.-.
T Consensus 832 ~l~~~~sdks~~~~~~-~~-~~~id~~~f~~~~dt 864 (1262)
T KOG1141|consen 832 ALLHQISDKSEYIHVT-RS-LLTIDCFSFDARIDT 864 (1262)
T ss_pred hhhhhhchhhhhcccc-hh-hhcccccchhccccc
Confidence 9999999999887663 22 578999999866543
No 21
>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=25.65 E-value=60 Score=18.88 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=11.6
Q ss_pred HHhhhcCCCeeec
Q 029286 49 IRCKIAEIPFVCD 61 (196)
Q Consensus 49 ir~~~~~~pf~C~ 61 (196)
+|.+..|+||.|.
T Consensus 6 ~~~H~~~k~~~C~ 18 (26)
T PF13465_consen 6 MRTHTGEKPYKCP 18 (26)
T ss_dssp HHHHSSSSSEEES
T ss_pred hhhcCCCCCCCCC
Confidence 6778999999998
No 22
>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=24.93 E-value=91 Score=26.16 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=31.2
Q ss_pred HHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029286 46 YEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 106 (196)
Q Consensus 46 yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 106 (196)
.+.|++.+.+.+|..+-... +...+..++|+||+-- +-.. +.|-=.+.+-.+|
T Consensus 49 ~~~L~~~~p~~~i~~EE~~~-------~~~~~~~~~WvIDPIDGT~nf~~g~-p~~~vsial~~~g 106 (244)
T cd01639 49 IEILKKAYPDHGFLGEESGA-------AGGLTDEPTWIIDPLDGTTNFVHGF-PHFAVSIALAVKG 106 (244)
T ss_pred HHHHHHHCCCCEEEecccCC-------CCCCCCCcEEEEecccChhHHhcCC-CcEEEEEEEEECC
Confidence 56777788888898884321 0002346899999733 1111 3576666655555
No 23
>PRK13672 hypothetical protein; Provisional
Probab=23.91 E-value=39 Score=25.14 Aligned_cols=27 Identities=30% Similarity=0.476 Sum_probs=20.2
Q ss_pred CccccHHHHHHhhhhCCCCCCCCcCCee
Q 029286 119 KKLRTLNEVAGFLAANPEYSDVSLSDFT 146 (196)
Q Consensus 119 KKlRSk~EV~ryL~~npe~~~l~le~F~ 146 (196)
|.-.+..||-+||+.|+.| ..+++-||
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 3446788999999999988 54565554
No 24
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=23.62 E-value=38 Score=24.45 Aligned_cols=16 Identities=38% Similarity=0.744 Sum_probs=11.4
Q ss_pred HHHHHhhhhCCCCCCC
Q 029286 125 NEVAGFLAANPEYSDV 140 (196)
Q Consensus 125 ~EV~ryL~~npe~~~l 140 (196)
+=++.||..||+|.+|
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 4578899999988654
No 25
>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=23.33 E-value=1e+02 Score=21.37 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=21.6
Q ss_pred eEEEECCCCCccccHHHHHHhhhhCCC
Q 029286 110 DAYYITPTGKKLRTLNEVAGFLAANPE 136 (196)
Q Consensus 110 DVYY~SP~GKKlRSk~EV~ryL~~npe 136 (196)
..|++.. ++.|.|..||..|...++.
T Consensus 58 ~~~~l~~-~~~F~sl~eLI~~y~~~~~ 83 (84)
T smart00252 58 GKFYLDG-GRKFPSLVELVEHYQKNSL 83 (84)
T ss_pred CcEEECC-CCccCCHHHHHHHHhhCCC
Confidence 3577765 7999999999999988763
No 26
>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=23.09 E-value=1.1e+02 Score=22.60 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=18.1
Q ss_pred ceEEEECCCCCccccH---HHHHHhhhh
Q 029286 109 MDAYYITPTGKKLRTL---NEVAGFLAA 133 (196)
Q Consensus 109 ~DVYY~SP~GKKlRSk---~EV~ryL~~ 133 (196)
.||||++..|.++..- .+|...|..
T Consensus 43 ~D~Fyv~~~g~kl~d~~~~~~L~~~L~~ 70 (75)
T cd04896 43 VDLFIVQSDGKKIMDPKKQAALCARLRE 70 (75)
T ss_pred EEEEEEeCCCCccCCHHHHHHHHHHHHH
Confidence 7999999899888763 445555543
No 27
>smart00592 BRK domain in transcription and CHROMO domain helicases.
Probab=22.69 E-value=99 Score=20.87 Aligned_cols=19 Identities=32% Similarity=0.660 Sum_probs=15.8
Q ss_pred cccHHHHHHhhhhCCCCCCC
Q 029286 121 LRTLNEVAGFLAANPEYSDV 140 (196)
Q Consensus 121 lRSk~EV~ryL~~npe~~~l 140 (196)
.=...+|.++|..||.| .+
T Consensus 22 aP~~~~l~~WL~~~p~y-ev 40 (45)
T smart00592 22 APKAKDLERWLEENPEY-EV 40 (45)
T ss_pred CCcHHHHHHHHhcCCCc-cc
Confidence 35678999999999998 54
No 28
>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=22.29 E-value=1.1e+02 Score=25.95 Aligned_cols=52 Identities=21% Similarity=0.175 Sum_probs=31.6
Q ss_pred HHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029286 46 YEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 106 (196)
Q Consensus 46 yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 106 (196)
.+.|++.+.+.+|.-+-.... ..+..++|+||+-- +-.. +.|-=.+.+-.+|
T Consensus 47 ~~~L~~~~P~~~il~EE~~~~--------~~~~~~~WviDPIDGT~nf~~g~-p~~~vsial~~~g 103 (248)
T cd01641 47 RELIAAAFPDHGILGEEFGNE--------GGDAGYVWVLDPIDGTKSFIRGL-PVWGTLIALLHDG 103 (248)
T ss_pred HHHHHHHCCCCeEEEccccCC--------CCCCCcEEEEecCcCchhHhcCC-CceEEEEEEEECC
Confidence 467888888889988853321 12345899999743 1111 3566666655555
No 29
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.15 E-value=94 Score=19.82 Aligned_cols=26 Identities=19% Similarity=0.408 Sum_probs=20.4
Q ss_pred eEEEECCCCC---ccccHHHHHHhhhhCC
Q 029286 110 DAYYITPTGK---KLRTLNEVAGFLAANP 135 (196)
Q Consensus 110 DVYY~SP~GK---KlRSk~EV~ryL~~np 135 (196)
-||-++.+|. .|.|..|.+++|+-+.
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 30
>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=21.88 E-value=1.1e+02 Score=26.04 Aligned_cols=53 Identities=23% Similarity=0.191 Sum_probs=30.7
Q ss_pred HHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029286 46 YEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 106 (196)
Q Consensus 46 yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 106 (196)
.+.|++.+.+.+|.-+-... +...+..++|+||+-. +-. -+.|-=.+.+-.+|
T Consensus 48 ~~~L~~~~P~~~il~EE~~~-------~~~~~~~~~WiiDPIDGT~nF~~g-~p~~~vsial~~~g 105 (251)
T TIGR02067 48 RELIAAFFPDHGILGEEFGH-------NEEGDAERVWVLDPIDGTKSFIRG-VPVWGTLIALVEGG 105 (251)
T ss_pred HHHHHHHCCCCEEEecccCC-------CCCCCCceEEEEecCcChhHHhcC-CCceEEEEEEEECC
Confidence 46677778888888884321 1222345899999743 112 13465555554444
No 31
>PF07603 DUF1566: Protein of unknown function (DUF1566); InterPro: IPR011460 These proteins of unknown function are found in Leptospira interrogans and in several gamma proteobacteria.
Probab=21.64 E-value=70 Score=23.76 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=13.0
Q ss_pred ceeeeccHHHHHHHHhh
Q 029286 36 KWRVINSSEEYEEIRCK 52 (196)
Q Consensus 36 KwR~ipt~e~yEeir~~ 52 (196)
-|| +||.+|.+.|-..
T Consensus 50 dWR-LPt~~EL~~L~~~ 65 (124)
T PF07603_consen 50 DWR-LPTIEELQSLYDF 65 (124)
T ss_pred Ccc-CCCHHHHHHHHHh
Confidence 498 6999999999643
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=21.54 E-value=1.2e+02 Score=25.81 Aligned_cols=52 Identities=15% Similarity=0.118 Sum_probs=32.0
Q ss_pred HHHHHhhhcCCCeeeccCCCCCcCCCCCcccCCcceeeecCCC-----CCCCCCCceEEEEEcccC
Q 029286 46 YEEIRCKIAEIPFVCDRKPGVSCEDPADIEYDASRVWVIDRPG-----IPKTPGGFKRSLVLRKDF 106 (196)
Q Consensus 46 yEeir~~~~~~pf~C~~~~~~sC~dP~Di~~d~sr~W~iDkp~-----iP~~P~GWkRevv~R~~g 106 (196)
.+.|++.+.+..|+-+-... ...++..+|+||+-. +-.. +.|-=.+.+-.+|
T Consensus 46 ~~~L~~~~P~~~i~gEE~~~--------~~~~~~~~WiIDPIDGT~nF~~g~-p~~~vsial~~~g 102 (242)
T cd01643 46 RARLAAQFPDDGVLGEEGGG--------IFPSSGWYWVIDPIDGTTNFARGI-PIWAISIALLYRG 102 (242)
T ss_pred HHHHHHHCCCCeEEecCCCC--------CCCCCCCEEEEeCccChHHHhcCC-CceEEEEEEEECC
Confidence 46788888888898885322 112345799999743 1111 3566666666555
No 33
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.33 E-value=1.2e+02 Score=16.63 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=19.2
Q ss_pred EEECCCCCccccHHHHHHhhhh
Q 029286 112 YYITPTGKKLRTLNEVAGFLAA 133 (196)
Q Consensus 112 YY~SP~GKKlRSk~EV~ryL~~ 133 (196)
||-..+++.|.|...+...|..
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 34
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=21.01 E-value=32 Score=33.46 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=17.7
Q ss_pred ccchhhhccccccceeeeccHH
Q 029286 23 SIDTYAAQCEKCFKWRVINSSE 44 (196)
Q Consensus 23 ~i~~yavQC~~C~KwR~ipt~e 44 (196)
-|..=.|+|++|+||--|-|-.
T Consensus 119 GiqVRNVrC~kChkwGH~n~Dr 140 (453)
T KOG3794|consen 119 GIQVRNVRCLKCHKWGHINTDR 140 (453)
T ss_pred ceEeeeeeEEeecccccccCCc
Confidence 4677779999999999886543
No 35
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=20.37 E-value=1.4e+02 Score=17.40 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=12.5
Q ss_pred CCCCceEEEEEcccCCcceEEEECC
Q 029286 92 TPGGFKRSLVLRKDFSKMDAYYITP 116 (196)
Q Consensus 92 ~P~GWkRevv~R~~gsK~DVYY~SP 116 (196)
+|.||.... . .+ +.+||+..
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 488995443 2 22 67888865
Done!