Query 041672
Match_columns 127
No_of_seqs 117 out of 185
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 09:31:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041672.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041672hhsearch_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 1.7E-40 3.6E-45 224.4 3.8 58 11-68 2-60 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 8.5E-40 1.8E-44 216.7 3.1 52 14-65 1-53 (53)
3 PHA02893 hypothetical protein; 66.8 2.2 4.8E-05 31.3 0.4 21 36-56 57-77 (88)
4 PF13698 DUF4156: Domain of un 65.4 3.1 6.7E-05 29.4 0.9 15 18-32 53-67 (93)
5 cd00029 C1 Protein kinase C co 51.4 7 0.00015 22.9 0.7 30 29-63 12-41 (50)
6 smart00109 C1 Protein kinase C 45.1 14 0.0003 21.2 1.3 28 29-62 12-39 (49)
7 PF05077 DUF678: Protein of un 43.7 9.7 0.00021 27.2 0.5 11 46-56 55-65 (74)
8 PF01485 IBR: IBR domain; Int 35.9 31 0.00068 20.8 1.9 30 33-62 25-60 (64)
9 PF00130 C1_1: Phorbol esters/ 34.3 28 0.00061 21.0 1.5 23 30-55 13-35 (53)
10 KOG0705 GTPase-activating prot 33.5 18 0.00038 34.8 0.7 36 28-64 514-550 (749)
11 smart00661 RPOL9 RNA polymeras 29.7 40 0.00087 20.2 1.6 25 33-57 5-29 (52)
12 PF01873 eIF-5_eIF-2B: Domain 27.2 24 0.00051 26.4 0.3 14 45-58 111-124 (125)
13 KOG2767 Translation initiation 26.6 20 0.00043 32.3 -0.2 17 48-64 118-134 (400)
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=1.7e-40 Score=224.41 Aligned_cols=58 Identities=76% Similarity=1.422 Sum_probs=55.3
Q ss_pred ceeehHHHhhhhhhhcCCccccCccccccC-CCCCCccccccccccccccccccccCCC
Q 041672 11 KVVRYKECLKNHAAAIGGSATDGCGEFMPS-GEEGSIESLKCSACNCHRNFHRKEIGCD 68 (127)
Q Consensus 11 ~~v~Y~EC~kNHAa~~GghavDGCgEFmps-g~~gt~~aL~CaACgCHRnFHRre~~~~ 68 (127)
.+|+|+||||||||+||||+||||+||||+ +++|++++|+||||||||||||||++++
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 479999999999999999999999999999 8899999999999999999999998764
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=8.5e-40 Score=216.67 Aligned_cols=52 Identities=81% Similarity=1.421 Sum_probs=50.1
Q ss_pred ehHHHhhhhhhhcCCccccCcccccc-CCCCCCcccccccccccccccccccc
Q 041672 14 RYKECLKNHAAAIGGSATDGCGEFMP-SGEEGSIESLKCSACNCHRNFHRKEI 65 (127)
Q Consensus 14 ~Y~EC~kNHAa~~GghavDGCgEFmp-sg~~gt~~aL~CaACgCHRnFHRre~ 65 (127)
+|+||||||||+|||||||||+|||| +++++++++|+||||||||||||||+
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=66.79 E-value=2.2 Score=31.32 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=13.7
Q ss_pred ccccCCCCCCccccccccccc
Q 041672 36 EFMPSGEEGSIESLKCSACNC 56 (127)
Q Consensus 36 EFmpsg~~gt~~aL~CaACgC 56 (127)
+|.+.|.-+....|.|+|||-
T Consensus 57 ~~~~~Gk~~~~~tL~CaACGS 77 (88)
T PHA02893 57 DYLNIGKAFSNSNIKCIACGS 77 (88)
T ss_pred HHHhccccCCCCceeehhhch
Confidence 345554434446899999983
No 4
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=65.40 E-value=3.1 Score=29.40 Aligned_cols=15 Identities=40% Similarity=0.594 Sum_probs=13.1
Q ss_pred HhhhhhhhcCCcccc
Q 041672 18 CLKNHAAAIGGSATD 32 (127)
Q Consensus 18 C~kNHAa~~GghavD 32 (127)
=+||.||.+||.+|=
T Consensus 53 dlrNeAa~lGgntV~ 67 (93)
T PF13698_consen 53 DLRNEAAKLGGNTVV 67 (93)
T ss_pred HHHHHHHHhCCCEEE
Confidence 379999999998874
No 5
>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=51.35 E-value=7 Score=22.89 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=20.6
Q ss_pred ccccCccccccCCCCCCcccccccccccccccccc
Q 041672 29 SATDGCGEFMPSGEEGSIESLKCSACNCHRNFHRK 63 (127)
Q Consensus 29 havDGCgEFmpsg~~gt~~aL~CaACgCHRnFHRr 63 (127)
..=+-|+++|.+. ...+++|..| ..+.|.+
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 3456799999874 3468999888 4455544
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=45.08 E-value=14 Score=21.23 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=19.3
Q ss_pred ccccCccccccCCCCCCccccccccccccccccc
Q 041672 29 SATDGCGEFMPSGEEGSIESLKCSACNCHRNFHR 62 (127)
Q Consensus 29 havDGCgEFmpsg~~gt~~aL~CaACgCHRnFHR 62 (127)
..=+-|+++|.... .+++|+.|+ ...|.
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~--~~~H~ 39 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCK--VKCHK 39 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCC--chHHH
Confidence 34578999998643 479999874 44443
No 7
>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=43.70 E-value=9.7 Score=27.21 Aligned_cols=11 Identities=45% Similarity=0.911 Sum_probs=8.9
Q ss_pred ccccccccccc
Q 041672 46 IESLKCSACNC 56 (127)
Q Consensus 46 ~~aL~CaACgC 56 (127)
...|.|+|||-
T Consensus 55 ~~tLsCsACGS 65 (74)
T PF05077_consen 55 GNTLSCSACGS 65 (74)
T ss_pred CCeEeehhccc
Confidence 35799999983
No 8
>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=35.87 E-value=31 Score=20.84 Aligned_cols=30 Identities=17% Similarity=0.605 Sum_probs=16.1
Q ss_pred CccccccCCCCCCcccccccccc------ccccccc
Q 041672 33 GCGEFMPSGEEGSIESLKCSACN------CHRNFHR 62 (127)
Q Consensus 33 GCgEFmpsg~~gt~~aL~CaACg------CHRnFHR 62 (127)
+|..++...........+|.+|+ |.+.+|.
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 58888876543332248899886 6666665
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=34.30 E-value=28 Score=21.00 Aligned_cols=23 Identities=30% Similarity=0.632 Sum_probs=16.1
Q ss_pred cccCccccccCCCCCCcccccccccc
Q 041672 30 ATDGCGEFMPSGEEGSIESLKCSACN 55 (127)
Q Consensus 30 avDGCgEFmpsg~~gt~~aL~CaACg 55 (127)
-=|-|+++|.+ ....+++|..|+
T Consensus 13 ~C~~C~~~i~g---~~~~g~~C~~C~ 35 (53)
T PF00130_consen 13 YCDVCGKFIWG---LGKQGYRCSWCG 35 (53)
T ss_dssp B-TTSSSBECS---SSSCEEEETTTT
T ss_pred CCcccCcccCC---CCCCeEEECCCC
Confidence 34779999954 224689999775
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=33.51 E-value=18 Score=34.81 Aligned_cols=36 Identities=28% Similarity=0.506 Sum_probs=24.8
Q ss_pred CccccCccccccCCCCCCccccccccc-cccccccccc
Q 041672 28 GSATDGCGEFMPSGEEGSIESLKCSAC-NCHRNFHRKE 64 (127)
Q Consensus 28 ghavDGCgEFmpsg~~gt~~aL~CaAC-gCHRnFHRre 64 (127)
+++|| |+---|.-..-.+.+|.|.-| |||||++...
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~l 550 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTHL 550 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhhh
Confidence 46666 665544433334569999999 8999998653
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.71 E-value=40 Score=20.24 Aligned_cols=25 Identities=20% Similarity=0.561 Sum_probs=15.4
Q ss_pred CccccccCCCCCCcccccccccccc
Q 041672 33 GCGEFMPSGEEGSIESLKCSACNCH 57 (127)
Q Consensus 33 GCgEFmpsg~~gt~~aL~CaACgCH 57 (127)
-||..|...+.....-+.|..||=|
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCe
Confidence 4777775543222236889999943
No 12
>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=27.18 E-value=24 Score=26.44 Aligned_cols=14 Identities=43% Similarity=0.838 Sum_probs=11.1
Q ss_pred Cccccccccccccc
Q 041672 45 SIESLKCSACNCHR 58 (127)
Q Consensus 45 t~~aL~CaACgCHR 58 (127)
-.-.|+|.|||..|
T Consensus 111 r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 111 RLIFLKCKACGASR 124 (125)
T ss_dssp TCCEEEETTTSCEE
T ss_pred CEEEEEecccCCcC
Confidence 34589999999876
No 13
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=26.62 E-value=20 Score=32.33 Aligned_cols=17 Identities=35% Similarity=0.784 Sum_probs=12.9
Q ss_pred ccccccccccccccccc
Q 041672 48 SLKCSACNCHRNFHRKE 64 (127)
Q Consensus 48 aL~CaACgCHRnFHRre 64 (127)
.++|.||||+-+---|.
T Consensus 118 ~~~CkACG~r~~~d~rh 134 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDLRH 134 (400)
T ss_pred hhHHHHcCCcccccchh
Confidence 78999999987654433
Done!