Query 043591
Match_columns 95
No_of_seqs 108 out of 184
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 06:28:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043591hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 3.8E-42 8.2E-47 223.3 3.1 58 25-82 2-60 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 2.3E-41 5E-46 215.7 2.4 52 28-79 1-53 (53)
3 PHA02893 hypothetical protein; 72.7 1.4 3.1E-05 31.0 0.4 21 50-70 57-77 (88)
4 cd00029 C1 Protein kinase C co 61.6 3.7 8E-05 22.9 0.6 30 43-77 12-41 (50)
5 PF13698 DUF4156: Domain of un 56.8 4.1 8.9E-05 27.4 0.3 16 31-46 52-67 (93)
6 smart00109 C1 Protein kinase C 55.2 7.5 0.00016 21.3 1.1 29 43-77 12-40 (49)
7 PF01485 IBR: IBR domain; Int 45.6 18 0.00039 20.8 1.8 30 47-76 25-60 (64)
8 PF05077 DUF678: Protein of un 42.9 10 0.00022 26.0 0.5 11 60-70 55-65 (74)
9 PF00130 C1_1: Phorbol esters/ 41.8 18 0.00039 20.8 1.4 29 44-77 13-41 (53)
10 smart00661 RPOL9 RNA polymeras 41.6 19 0.00041 20.6 1.5 25 47-71 5-29 (52)
11 PHA02887 EGF-like protein; Pro 36.5 25 0.00054 26.1 1.7 59 5-75 50-117 (126)
12 KOG0705 GTPase-activating prot 32.6 17 0.00036 33.5 0.3 35 42-77 514-549 (749)
13 PF01873 eIF-5_eIF-2B: Domain 27.5 24 0.00051 25.2 0.3 15 58-72 110-124 (125)
14 KOG2767 Translation initiation 25.1 22 0.00047 30.7 -0.2 17 61-77 117-133 (400)
15 PF00628 PHD: PHD-finger; Int 22.1 55 0.0012 18.5 1.1 17 59-77 11-27 (51)
16 PRK03988 translation initiatio 22.0 43 0.00093 24.4 0.8 16 59-74 120-135 (138)
17 KOG4239 Ras GTPase effector RA 21.5 13 0.00028 31.5 -2.2 54 34-93 50-107 (348)
18 PRK00432 30S ribosomal protein 21.0 52 0.0011 20.1 0.9 19 48-70 26-45 (50)
No 1
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=100.00 E-value=3.8e-42 Score=223.28 Aligned_cols=58 Identities=74% Similarity=1.318 Sum_probs=55.5
Q ss_pred cceehHHhhhhhccccCCccccCccccccC-CCCCCcccccccCccccccCccccccCc
Q 043591 25 RSVRYAECQKNHAAGVGGYAVDGCREFMAS-GEEGTAAALTCAACGCHRSFHRREVDTE 82 (95)
Q Consensus 25 ~~v~Y~EC~kNHAa~~GghavDGCgEFmps-g~egt~~aL~CaACGCHRNFHRre~~~~ 82 (95)
..|+|+|||||||++||||+||||+||||+ |++|++++|+||||||||||||||+++|
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~e 60 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEGE 60 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCCC
Confidence 469999999999999999999999999999 8999999999999999999999999875
No 2
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=2.3e-41 Score=215.67 Aligned_cols=52 Identities=69% Similarity=1.296 Sum_probs=50.1
Q ss_pred ehHHhhhhhccccCCccccCcccccc-CCCCCCcccccccCccccccCccccc
Q 043591 28 RYAECQKNHAAGVGGYAVDGCREFMA-SGEEGTAAALTCAACGCHRSFHRREV 79 (95)
Q Consensus 28 ~Y~EC~kNHAa~~GghavDGCgEFmp-sg~egt~~aL~CaACGCHRNFHRre~ 79 (95)
+|+||||||||+|||||||||+|||| +|++|++++|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 68899999999999999999999985
No 3
>PHA02893 hypothetical protein; Provisional
Probab=72.67 E-value=1.4 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.751 Sum_probs=14.6
Q ss_pred ccccCCCCCCcccccccCccc
Q 043591 50 EFMASGEEGTAAALTCAACGC 70 (95)
Q Consensus 50 EFmpsg~egt~~aL~CaACGC 70 (95)
||.+.|.-+....|.|+|||-
T Consensus 57 ~~~~~Gk~~~~~tL~CaACGS 77 (88)
T PHA02893 57 DYLNIGKAFSNSNIKCIACGS 77 (88)
T ss_pred HHHhccccCCCCceeehhhch
Confidence 455555544557999999983
No 4
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=61.62 E-value=3.7 Score=22.93 Aligned_cols=30 Identities=23% Similarity=0.423 Sum_probs=21.3
Q ss_pred ccccCccccccCCCCCCcccccccCccccccCccc
Q 043591 43 YAVDGCREFMASGEEGTAAALTCAACGCHRSFHRR 77 (95)
Q Consensus 43 havDGCgEFmpsg~egt~~aL~CaACGCHRNFHRr 77 (95)
..=+-|+++|... ...+++|..| ..+.|.+
T Consensus 12 ~~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~ 41 (50)
T cd00029 12 TFCDVCRKSIWGL---FKQGLRCSWC--KVKCHKK 41 (50)
T ss_pred CChhhcchhhhcc---ccceeEcCCC--CCchhhh
Confidence 3457799999864 3579999987 4566654
No 5
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=56.82 E-value=4.1 Score=27.41 Aligned_cols=16 Identities=38% Similarity=0.447 Sum_probs=13.6
Q ss_pred HhhhhhccccCCcccc
Q 043591 31 ECQKNHAAGVGGYAVD 46 (95)
Q Consensus 31 EC~kNHAa~~GghavD 46 (95)
.=+||.||.+||.+|=
T Consensus 52 NdlrNeAa~lGgntV~ 67 (93)
T PF13698_consen 52 NDLRNEAAKLGGNTVV 67 (93)
T ss_pred HHHHHHHHHhCCCEEE
Confidence 4589999999998873
No 6
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=55.22 E-value=7.5 Score=21.32 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=19.8
Q ss_pred ccccCccccccCCCCCCcccccccCccccccCccc
Q 043591 43 YAVDGCREFMASGEEGTAAALTCAACGCHRSFHRR 77 (95)
Q Consensus 43 havDGCgEFmpsg~egt~~aL~CaACGCHRNFHRr 77 (95)
..=+-|+++|.... .+++|..|+ ...|.+
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~--~~~H~~ 40 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCK--VKCHKK 40 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCC--chHHHH
Confidence 34578999998633 489999874 444443
No 7
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=45.57 E-value=18 Score=20.81 Aligned_cols=30 Identities=23% Similarity=0.780 Sum_probs=15.8
Q ss_pred CccccccCCCCCCcccccccCcc------ccccCcc
Q 043591 47 GCREFMASGEEGTAAALTCAACG------CHRSFHR 76 (95)
Q Consensus 47 GCgEFmpsg~egt~~aL~CaACG------CHRNFHR 76 (95)
+|..++..........++|.+|+ |...+|.
T Consensus 25 ~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 25 DCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 58888876443222248899986 6666665
No 8
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=42.91 E-value=10 Score=25.95 Aligned_cols=11 Identities=45% Similarity=1.195 Sum_probs=9.1
Q ss_pred cccccccCccc
Q 043591 60 AAALTCAACGC 70 (95)
Q Consensus 60 ~~aL~CaACGC 70 (95)
...|.|+|||-
T Consensus 55 ~~tLsCsACGS 65 (74)
T PF05077_consen 55 GNTLSCSACGS 65 (74)
T ss_pred CCeEeehhccc
Confidence 46899999983
No 9
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=41.83 E-value=18 Score=20.80 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=19.0
Q ss_pred cccCccccccCCCCCCcccccccCccccccCccc
Q 043591 44 AVDGCREFMASGEEGTAAALTCAACGCHRSFHRR 77 (95)
Q Consensus 44 avDGCgEFmpsg~egt~~aL~CaACGCHRNFHRr 77 (95)
-=|-|+++|.+ ....+++|..|+ ...|.+
T Consensus 13 ~C~~C~~~i~g---~~~~g~~C~~C~--~~~H~~ 41 (53)
T PF00130_consen 13 YCDVCGKFIWG---LGKQGYRCSWCG--LVCHKK 41 (53)
T ss_dssp B-TTSSSBECS---SSSCEEEETTTT---EEETT
T ss_pred CCcccCcccCC---CCCCeEEECCCC--ChHhhh
Confidence 34779999954 235799999775 455554
No 10
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=41.55 E-value=19 Score=20.64 Aligned_cols=25 Identities=20% Similarity=0.583 Sum_probs=15.4
Q ss_pred CccccccCCCCCCcccccccCcccc
Q 043591 47 GCREFMASGEEGTAAALTCAACGCH 71 (95)
Q Consensus 47 GCgEFmpsg~egt~~aL~CaACGCH 71 (95)
-||..|...+.....-+.|..||-|
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCe
Confidence 3777775433222236789999954
No 11
>PHA02887 EGF-like protein; Provisional
Probab=36.46 E-value=25 Score=26.14 Aligned_cols=59 Identities=14% Similarity=0.328 Sum_probs=40.0
Q ss_pred EEEEeecCCCCCC---------CCCceeecceehHHhhhhhccccCCccccCccccccCCCCCCcccccccCccccccCc
Q 043591 5 QVVLRREEPSRNS---------TASSVTVRSVRYAECQKNHAAGVGGYAVDGCREFMASGEEGTAAALTCAACGCHRSFH 75 (95)
Q Consensus 5 ~vv~rr~~~~~~s---------~~~~~~~~~v~Y~EC~kNHAa~~GghavDGCgEFmpsg~egt~~aL~CaACGCHRNFH 75 (95)
..|+||+-++-.| ....+....+.|.+|...|. ++.+-|=.+|++.-. =+.|-|+.+|.
T Consensus 50 l~~i~rn~e~h~s~~~y~en~~~~~~~rk~~~hf~pC~~eyk----~YCiHG~C~yI~dL~--------epsCrC~~GYt 117 (126)
T PHA02887 50 LAIIKRNFESHISKFNYKENANAQNFKRKNSMFFEKCKNDFN----DFCINGECMNIIDLD--------EKFCICNKGYT 117 (126)
T ss_pred eeeeecccccceeeeehhccccccchhhccccCccccChHhh----CEeeCCEEEccccCC--------CceeECCCCcc
Confidence 4578887654221 11123345577999999886 788889888988633 25799999885
No 12
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=32.58 E-value=17 Score=33.47 Aligned_cols=35 Identities=26% Similarity=0.449 Sum_probs=24.4
Q ss_pred CccccCccccccCCCCCCcccccccCc-cccccCccc
Q 043591 42 GYAVDGCREFMASGEEGTAAALTCAAC-GCHRSFHRR 77 (95)
Q Consensus 42 ghavDGCgEFmpsg~egt~~aL~CaAC-GCHRNFHRr 77 (95)
++.+| |+---|.-..-.+.+|.|.-| |+|||++..
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~ 549 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTH 549 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhh
Confidence 46777 665444322335689999999 899999865
No 13
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=27.51 E-value=24 Score=25.18 Aligned_cols=15 Identities=47% Similarity=0.950 Sum_probs=11.7
Q ss_pred CCcccccccCccccc
Q 043591 58 GTAAALTCAACGCHR 72 (95)
Q Consensus 58 gt~~aL~CaACGCHR 72 (95)
+-.-.|+|.|||..|
T Consensus 110 ~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 110 GRLIFLKCKACGASR 124 (125)
T ss_dssp TTCCEEEETTTSCEE
T ss_pred CCEEEEEecccCCcC
Confidence 345689999999875
No 14
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=25.06 E-value=22 Score=30.71 Aligned_cols=17 Identities=35% Similarity=0.796 Sum_probs=13.0
Q ss_pred ccccccCccccccCccc
Q 043591 61 AALTCAACGCHRSFHRR 77 (95)
Q Consensus 61 ~aL~CaACGCHRNFHRr 77 (95)
-.++|.|||++-+---|
T Consensus 117 i~~~CkACG~r~~~d~r 133 (400)
T KOG2767|consen 117 ISLKCKACGFRSDMDLR 133 (400)
T ss_pred hhhHHHHcCCcccccch
Confidence 47899999998765443
No 15
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=22.14 E-value=55 Score=18.51 Aligned_cols=17 Identities=24% Similarity=0.817 Sum_probs=13.0
Q ss_pred CcccccccCccccccCccc
Q 043591 59 TAAALTCAACGCHRSFHRR 77 (95)
Q Consensus 59 t~~aL~CaACGCHRNFHRr 77 (95)
..+.+.|.. |.+.||..
T Consensus 11 ~~~~i~C~~--C~~~~H~~ 27 (51)
T PF00628_consen 11 DGDMIQCDS--CNRWYHQE 27 (51)
T ss_dssp TSSEEEBST--TSCEEETT
T ss_pred CCCeEEcCC--CChhhCcc
Confidence 346889995 56999986
No 16
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.02 E-value=43 Score=24.35 Aligned_cols=16 Identities=31% Similarity=0.684 Sum_probs=12.8
Q ss_pred CcccccccCccccccC
Q 043591 59 TAAALTCAACGCHRSF 74 (95)
Q Consensus 59 t~~aL~CaACGCHRNF 74 (95)
-.-.|+|.|||=+|..
T Consensus 120 r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 120 RIWVLKCEACGAETPV 135 (138)
T ss_pred CeEEEEcccCCCCCcC
Confidence 3468999999988765
No 17
>KOG4239 consensus Ras GTPase effector RASSF2 [Signal transduction mechanisms]
Probab=21.49 E-value=13 Score=31.54 Aligned_cols=54 Identities=26% Similarity=0.468 Sum_probs=31.9
Q ss_pred hhhccccCCccc----cCccccccCCCCCCcccccccCccccccCccccccCcccccCCCCCCC
Q 043591 34 KNHAAGVGGYAV----DGCREFMASGEEGTAAALTCAACGCHRSFHRREVDTEVVCECSSPSST 93 (95)
Q Consensus 34 kNHAa~~Gghav----DGCgEFmpsg~egt~~aL~CaACGCHRNFHRre~~~~~~~~~~s~~s~ 93 (95)
|+|..-.-|-++ |=|+||.-. --.++|+|++|+=-+-.--| ....-||.+|+++
T Consensus 50 r~~~~~~~g~~~~~~~~~c~~~~~~---vl~egL~c~~c~~tch~rcr---~lv~ldc~~p~~s 107 (348)
T KOG4239|consen 50 RGHNFYTAGLLLPTWCDKCGDFIWG---VLREGLLCIHCKFTCHIRCR---MLVDLDCRSPPSS 107 (348)
T ss_pred cccccccccccccccchhhhHHHHH---HHHHHHhhhhcCCccCHHHH---hhhhhhhcCCCCC
Confidence 666666666554 448998653 23479999999833222112 2233478777744
No 18
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.02 E-value=52 Score=20.12 Aligned_cols=19 Identities=37% Similarity=0.837 Sum_probs=13.6
Q ss_pred ccc-cccCCCCCCcccccccCccc
Q 043591 48 CRE-FMASGEEGTAAALTCAACGC 70 (95)
Q Consensus 48 CgE-Fmpsg~egt~~aL~CaACGC 70 (95)
||. ||.... +.+.|..||=
T Consensus 26 Cg~~~m~~~~----~r~~C~~Cgy 45 (50)
T PRK00432 26 CGSGFMAEHL----DRWHCGKCGY 45 (50)
T ss_pred CCcchheccC----CcEECCCcCC
Confidence 666 887643 5888998874
Done!