Query 041376
Match_columns 79
No_of_seqs 25 out of 27
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:28:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02068 Metallothio_PEC: Plan 100.0 6E-37 1.3E-41 201.3 0.7 69 11-79 1-73 (76)
2 PF01439 Metallothio_2: Metall 96.3 0.0033 7.2E-08 41.1 2.2 20 37-56 55-74 (74)
3 PF02067 Metallothio_5: Metall 77.3 2.1 4.5E-05 25.7 1.9 13 21-33 2-15 (41)
4 KOG4738 Predicted metallothion 67.7 6.9 0.00015 24.2 2.7 40 17-56 6-49 (51)
5 PF12749 Metallothio_Euk: Euka 65.2 4.9 0.00011 26.7 1.8 10 47-56 40-49 (74)
6 PF05522 Metallothio_6: Metall 41.8 12 0.00025 24.5 0.6 14 65-78 40-53 (65)
7 PF05033 Pre-SET: Pre-SET moti 26.8 77 0.0017 19.7 2.6 42 15-57 48-101 (103)
8 PF13008 zf-Paramyx-P: Zinc-bi 15.5 54 0.0012 19.8 0.1 21 51-73 15-35 (47)
9 PF02069 Metallothio_Pro: Prok 13.5 97 0.0021 19.1 0.8 22 49-70 8-32 (52)
10 smart00570 AWS associated with 12.4 94 0.002 18.8 0.5 10 41-50 33-42 (51)
No 1
>PF02068 Metallothio_PEC: Plant PEC family metallothionein; InterPro: IPR000316 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , , ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as MTs from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units []. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs. Family 15 consists of planta MTs. Its members are recognised by the sequence pattern [YFH]-x(5,25)-C-[SKD]-C-[GA]-[SDPAT]-x(0,1)-C-x-[CYF] which yields all plant sequences, but also MTCU_HELPO and the non-MT ITB3_HUMAN. The taxonomic range of the members extends to planta. Planta MTs are 45-84 residue proteins, containing 17 conserved cysteines that bind 5 zinc ions. Generally, there are two Cys-rich regions (domain 1 and domain 3) separated by a Cys-poor region (domain 2) and only the domain 2 contains unusual residues. It is believed that the proteins may have a role in Zn2+ homeostasis during embryogenesis. Family 15 includes the following subfamilies: p1, p2, p2v, p3, pec, p21. ; GO: 0008270 zinc ion binding; PDB: 2L62_A 2KAK_A 2L61_A.
Probab=100.00 E-value=6e-37 Score=201.27 Aligned_cols=69 Identities=57% Similarity=1.405 Sum_probs=34.0
Q ss_pred EeCCCCCCCcCCCCCCcceeeec-c-cCcccceeecCCCCccccCCccCCc--eeccCCccccccCCCcccCC
Q 041376 11 HCNDTCGCPVPCPGGAACSCSTV-A-YSEYYHKCCSCGGHCSCNPCTCSKI--QANKIGKAHCSCGTACKCPT 79 (79)
Q Consensus 11 ~C~d~CGC~vPCpgG~~CrC~~~-~-~~~~~H~~C~CGEHCgCNPCtC~k~--~~~g~gka~C~CG~~C~C~s 79 (79)
+|||+||||||||||++|||++. + +++++|+||+|||||+||||+|||+ +++|+||||||||++|+|++
T Consensus 1 ~Cdd~CGC~vPCpgG~~CrC~~~~a~~~~~~H~~C~CGEhCgCnPCtC~k~e~~~sg~gka~C~CG~~C~C~s 73 (76)
T PF02068_consen 1 GCDDRCGCPVPCPGGTACRCTSSSAGGGGGDHTTCSCGEHCGCNPCTCPKTETTASGSGKAFCKCGSGCTCAS 73 (76)
T ss_dssp ---GGGSS-SS-SSSTTSCCCS----------S-BTTTB--TTS--TT---------SS-S-----SS---HH
T ss_pred CCcCCcCCCccCCCCCccccccccCCCCCCCcccccCCCcccccCccCCCcccccccccccccccCCCccccc
Confidence 69999999999999999999887 3 8899999999999999999999998 68999999999999999974
No 2
>PF01439 Metallothio_2: Metallothionein; InterPro: IPR000347 Members of this family are metallothioneins. These proteins are cysteine rich proteins that bind to heavy metals. Members of this family appear to be closest to Class II metallothioneins.; GO: 0046872 metal ion binding
Probab=96.25 E-value=0.0033 Score=41.14 Aligned_cols=20 Identities=40% Similarity=1.323 Sum_probs=17.4
Q ss_pred cccceeecCCCCccccCCcc
Q 041376 37 EYYHKCCSCGGHCSCNPCTC 56 (79)
Q Consensus 37 ~~~H~~C~CGEHCgCNPCtC 56 (79)
+.++.-|.||..|.||||+|
T Consensus 55 ~~~~~GCKCGsnC~CdPCnC 74 (74)
T PF01439_consen 55 GAGGNGCKCGSNCTCDPCNC 74 (74)
T ss_pred cccCCCCCCCCCCccCCCcC
Confidence 33678899999999999997
No 3
>PF02067 Metallothio_5: Metallothionein family 5; InterPro: IPR000966 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ] species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class I MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. Diptera (Drosophila, family 5) MTs are 40-43 residue proteins that contain 10 conserved cysteines arranged in five Cys-X-Cys groups. In particular, the consensus pattern C-G-x(2)-C-x-C-x(2)-Q-x(5)-C-x-C-x(2)-D-C-x-C has been found to be diagnostic of family 5 MTs. The protein is found primarily in the alimentary canal, and its induction is stimulated by ingestion of cadmium or copper []. Mercury, silver and zinc induce the protein to a lesser extent. Family 5 includes subfamilies: d1, d2. Only one d2 is known until now. Subfamilies hit the same entry.; GO: 0046872 metal ion binding
Probab=77.27 E-value=2.1 Score=25.73 Aligned_cols=13 Identities=46% Similarity=1.247 Sum_probs=11.3
Q ss_pred CCC-CCCcceeeec
Q 041376 21 PCP-GGAACSCSTV 33 (79)
Q Consensus 21 PCp-gG~~CrC~~~ 33 (79)
||+ .|+.|+|++.
T Consensus 2 ~Ck~Cg~~CkC~~~ 15 (41)
T PF02067_consen 2 PCKGCGTNCKCSSQ 15 (41)
T ss_pred CCCccCCCCEecCC
Confidence 788 8999999885
No 4
>KOG4738 consensus Predicted metallothionein [Inorganic ion transport and metabolism]
Probab=67.75 E-value=6.9 Score=24.22 Aligned_cols=40 Identities=33% Similarity=0.917 Sum_probs=20.7
Q ss_pred CCCcCCCCCCcceeeecccCcccce---eecCCCCccccC-Ccc
Q 041376 17 GCPVPCPGGAACSCSTVAYSEYYHK---CCSCGGHCSCNP-CTC 56 (79)
Q Consensus 17 GC~vPCpgG~~CrC~~~~~~~~~H~---~C~CGEHCgCNP-CtC 56 (79)
...-+|+.+++|+|....=..=.+. +|.|++.+.|.+ |.|
T Consensus 6 ~~g~~C~Cgs~CkC~~~kC~sC~k~~~~~C~c~~~~kC~~~c~C 49 (51)
T KOG4738|consen 6 CKGGSCTCGSSCKCSDCKCTSCKKSCCSKCCCGGCCKCAKGCIC 49 (51)
T ss_pred cCCCccccCCccccCCCccCCcCCcccccccCCCCcccCCCCcc
Confidence 3345666677777755420011111 456666666666 555
No 5
>PF12749 Metallothio_Euk: Eukaryotic metallothionein; InterPro: IPR024306 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units []. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs [see http://www.bioc.unizh.ch/mtpage/protali.html]. This entry represents a subgroup of eukaryotic metallothioneins which includes copper-induced metallothioneins from the protist Tetrahymena [].
Probab=65.21 E-value=4.9 Score=26.74 Aligned_cols=10 Identities=50% Similarity=1.806 Sum_probs=6.9
Q ss_pred CCccccCCcc
Q 041376 47 GHCSCNPCTC 56 (79)
Q Consensus 47 EHCgCNPCtC 56 (79)
.-|+||||.|
T Consensus 40 s~CgC~~Ckc 49 (74)
T PF12749_consen 40 SPCGCSPCKC 49 (74)
T ss_pred CCCCCcCCee
Confidence 4577777766
No 6
>PF05522 Metallothio_6: Metallothionein; InterPro: IPR017980 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units []. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs [see http://www.bioc.unizh.ch/mtpage/protali.html]. Echinoidea (sea urchin, family 4) MTs are 64-67 residue proteins. Members of this family are recognised by the sequence pattern P-D-x-K-C-[V,F]-C-C-x(5)-C-x-C-x(4)-C-C-x(4)-C-C-x(4,6)-C-C located near the N terminus. The taxonomic range of the members extends to sea urchins (echinodea). The protein sequence is divided into two structural domains, each containing 9 and 11 Cys residues binding 3 and 4 bivalent metal ions, respectively. Family 4 includes subfamilies: e1, e2, they are separate phylogenetic groups. This entry includes the sea urchin proteins, and related sequences from worms.; PDB: 1QJK_A 1QJL_A.
Probab=41.82 E-value=12 Score=24.45 Aligned_cols=14 Identities=57% Similarity=1.531 Sum_probs=4.7
Q ss_pred CccccccCCCcccC
Q 041376 65 GKAHCSCGTACKCP 78 (79)
Q Consensus 65 gka~C~CG~~C~C~ 78 (79)
+.|.||||++|.|.
T Consensus 40 gNA~CKCga~CKC~ 53 (65)
T PF05522_consen 40 GNAACKCGAGCKCG 53 (65)
T ss_dssp --TT----TT--TT
T ss_pred CcccccccCCceeC
Confidence 45778999888886
No 7
>PF05033 Pre-SET: Pre-SET motif; InterPro: IPR007728 This region is found in a number of histone lysine methyltransferases (HMTase), N-terminal to the SET domain; it is generally described as the pre-SET domain. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils and stabilising the SET domain. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site [] when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity []. ; GO: 0008270 zinc ion binding, 0018024 histone-lysine N-methyltransferase activity, 0034968 histone lysine methylation, 0005634 nucleus; PDB: 3K5K_A 2O8J_D 3RJW_B 1ML9_A 1PEG_B 1MVH_A 1MVX_A 3BO5_A 2RFI_B 3MO5_B ....
Probab=26.79 E-value=77 Score=19.65 Aligned_cols=42 Identities=24% Similarity=0.748 Sum_probs=21.0
Q ss_pred CCCCCcCCCCCCcceeeecccC------------cccceeecCCCCccccCCccC
Q 041376 15 TCGCPVPCPGGAACSCSTVAYS------------EYYHKCCSCGGHCSCNPCTCS 57 (79)
Q Consensus 15 ~CGC~vPCpgG~~CrC~~~~~~------------~~~H~~C~CGEHCgCNPCtC~ 57 (79)
.|.|...|.....|.|....+. ......=.|++.|+|.+ +|+
T Consensus 48 ~C~C~~~C~~~~~C~C~~~~~~~~~Y~~~g~l~~~~~~~i~EC~~~C~C~~-~C~ 101 (103)
T PF05033_consen 48 GCDCSGDCSNPSNCECLQRNGGIFAYDSNGRLRIPDKPPIFECNDNCGCSP-SCR 101 (103)
T ss_dssp ----SSSSTCTTTSHHHCCTSSS-SB-TTSSBSSSSTSEEE---TTSSS-T-TST
T ss_pred cCccCCCCCCCCCCcCccccCccccccCCCcCccCCCCeEEeCCCCCCCCC-CCC
Confidence 5677777888888888553211 23334446777777777 665
No 8
>PF13008 zf-Paramyx-P: Zinc-binding domain of Paramyxoviridae V protein; InterPro: IPR024279 The paramyxoviruses, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT []. The P mRNA encodes a variety of proteins beyond P. Protein V consists of PNT fused to a C-terminal zinc-binding region. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction []. In the Henipavirus family, which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation [].; GO: 0046872 metal ion binding; PDB: 2HYE_B 2B5L_D.
Probab=15.45 E-value=54 Score=19.81 Aligned_cols=21 Identities=48% Similarity=1.157 Sum_probs=6.6
Q ss_pred ccCCccCCceeccCCccccccCC
Q 041376 51 CNPCTCSKIQANKIGKAHCSCGT 73 (79)
Q Consensus 51 CNPCtC~k~~~~g~gka~C~CG~ 73 (79)
||| .|+++.+. .-+..|+||.
T Consensus 15 CNP-~CspIt~~-p~r~~C~CG~ 35 (47)
T PF13008_consen 15 CNP-ICSPITAT-PRREKCTCGE 35 (47)
T ss_dssp EEE-TTS---SS--EEE--SSTT
T ss_pred eCC-cCcccccc-cEEeeEECCC
Confidence 455 45554321 1134466663
No 9
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=13.48 E-value=97 Score=19.05 Aligned_cols=22 Identities=41% Similarity=0.964 Sum_probs=9.7
Q ss_pred ccccCCccCCce---eccCCccccc
Q 041376 49 CSCNPCTCSKIQ---ANKIGKAHCS 70 (79)
Q Consensus 49 CgCNPCtC~k~~---~~g~gka~C~ 70 (79)
|.|..|.|--.. ..-.||.||+
T Consensus 8 CaC~~C~C~V~~~~Ai~~dGk~YCS 32 (52)
T PF02069_consen 8 CACPSCSCVVSEEEAIQKDGKYYCS 32 (52)
T ss_dssp -SSTT----B-TTTSEESSS-EESS
T ss_pred ecCCCCEeEECchHhHHhCCEeeec
Confidence 677788886552 4455688886
No 10
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=12.37 E-value=94 Score=18.81 Aligned_cols=10 Identities=50% Similarity=1.291 Sum_probs=7.8
Q ss_pred eeecCCCCcc
Q 041376 41 KCCSCGGHCS 50 (79)
Q Consensus 41 ~~C~CGEHCg 50 (79)
.+|+||++|.
T Consensus 33 ~~C~~G~~C~ 42 (51)
T smart00570 33 SDCPCGSYCS 42 (51)
T ss_pred CCCCCCcCcc
Confidence 4788888874
Done!