Query psy5312
Match_columns 124
No_of_seqs 112 out of 123
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 23:22:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01147 Crust_neurohorm: Crus 100.0 4.3E-40 9.3E-45 226.9 6.0 73 46-119 1-73 (73)
2 KOG4122|consensus 83.7 0.26 5.7E-06 30.7 -0.5 26 62-87 5-30 (38)
3 PF14432 DYW_deaminase: DYW fa 58.4 2.6 5.6E-05 30.5 -0.5 12 65-76 83-94 (116)
4 PF01322 Cytochrom_C_2: Cytoch 46.0 20 0.00043 25.3 2.4 18 59-76 105-122 (122)
5 PF09256 BaffR-Tall_bind: BAFF 37.3 2.2 4.8E-05 25.6 -3.0 19 61-80 10-28 (31)
6 PF14862 Defensin_big: Big def 35.8 9.8 0.00021 27.0 -0.5 17 80-96 46-62 (76)
7 PF05191 ADK_lid: Adenylate ki 34.1 5.7 0.00012 23.9 -1.6 10 66-75 2-11 (36)
8 PF11844 DUF3364: Domain of un 30.9 16 0.00036 24.3 0.0 14 69-82 9-22 (56)
9 COG1552 RPL40A Ribosomal prote 30.4 34 0.00073 22.6 1.4 23 66-91 15-37 (50)
10 PF05142 DUF702: Domain of unk 29.2 20 0.00044 28.2 0.3 26 66-91 5-30 (154)
11 PF00444 Ribosomal_L36: Riboso 28.3 3.9 8.5E-05 25.3 -3.1 23 65-87 8-30 (38)
12 PF12562 DUF3746: Protein of u 27.5 16 0.00035 22.7 -0.4 12 83-94 18-29 (37)
13 PF03488 Ins_beta: Nematode in 26.7 40 0.00087 20.7 1.3 30 58-88 6-37 (48)
14 PRK00831 rpmJ 50S ribosomal pr 26.5 11 0.00023 23.9 -1.4 29 59-87 5-33 (41)
15 PF07503 zf-HYPF: HypF finger; 26.0 36 0.00078 20.4 0.9 13 67-79 1-13 (35)
16 PF10717 ODV-E18: Occlusion-de 25.7 1.4E+02 0.003 21.6 4.0 14 6-19 31-44 (85)
17 COG0257 RpmJ Ribosomal protein 21.4 11 0.00024 23.6 -2.0 24 64-87 7-30 (38)
No 1
>PF01147 Crust_neurohorm: Crustacean CHH/MIH/GIH neurohormone family; InterPro: IPR001166 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. ; GO: 0005184 neuropeptide hormone activity, 0005576 extracellular region; PDB: 1J0T_A.
Probab=100.00 E-value=4.3e-40 Score=226.92 Aligned_cols=73 Identities=48% Similarity=1.114 Sum_probs=63.2
Q ss_pred cccCCCCcccccHHHHHHHHhHHHHHhhhhcccchhhhhhhccCCchHHHHHHHHhcccCchHHHHHHHHHHhc
Q psy5312 46 SFFDIQCKGVYDKSIFARLDRICEDCYDLFRAPQIHTLCRKDCFTSDYFKGCLEVLRLTDESDSIQADIMQLHG 119 (124)
Q Consensus 46 s~fD~sCkGvydR~lf~kLdRVCeDCyNLfR~p~v~~~CR~nCF~n~~F~~Cl~~L~l~de~e~~~~~v~~i~g 119 (124)
|+||++|||+|||+||+||||||||||||||+|+|+++||+|||+|++|++|+++|+++||+++|++|| +|+|
T Consensus 1 ~~fd~~CkGv~dr~l~~kldrVC~DCyNl~R~p~v~~~CR~nCF~n~~F~~Cl~~l~~~~e~~~~~~~v-~~l~ 73 (73)
T PF01147_consen 1 QFFDRSCKGVYDRALFKKLDRVCDDCYNLFREPNVASECRSNCFTNEVFRQCLDALLLPDEIEEYRRWV-QILG 73 (73)
T ss_dssp --SSS--SSTT-SSHHHHHHHHHHHHHHHHT-TTTHHHHTSSTT-SSHHHHHHHTTS--STHHHHHHHH-HHTT
T ss_pred CccCCcCccccCHHHHHHHHHHHHHHHHHHcCccHHHHHHHcccCChHHHHHHHHhcchhHHHHHHHHH-HHhC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 8887
No 2
>KOG4122|consensus
Probab=83.70 E-value=0.26 Score=30.75 Aligned_cols=26 Identities=27% Similarity=0.750 Sum_probs=22.7
Q ss_pred HHHHhHHHHHhhhhcccchhhhhhhc
Q psy5312 62 ARLDRICEDCYDLFRAPQIHTLCRKD 87 (124)
Q Consensus 62 ~kLdRVCeDCyNLfR~p~v~~~CR~n 87 (124)
..+-..|+|||-+=|...++..|.+|
T Consensus 5 ~svkk~C~~Cy~VrRrgR~yViC~~~ 30 (38)
T KOG4122|consen 5 ASVKKRCKDCYLVRRRGRVYVICKTH 30 (38)
T ss_pred HHHHHhhhhceEEEEcccEEEEcCCC
Confidence 45778999999999999999999865
No 3
>PF14432 DYW_deaminase: DYW family of nucleic acid deaminases
Probab=58.42 E-value=2.6 Score=30.54 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=10.1
Q ss_pred HhHHHHHhhhhc
Q psy5312 65 DRICEDCYDLFR 76 (124)
Q Consensus 65 dRVCeDCyNLfR 76 (124)
-|||.||++..+
T Consensus 83 ~RvC~DCH~~~K 94 (116)
T PF14432_consen 83 KRVCGDCHSFIK 94 (116)
T ss_pred CccchHHHHHHH
Confidence 399999999764
No 4
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=46.04 E-value=20 Score=25.31 Aligned_cols=18 Identities=33% Similarity=0.886 Sum_probs=15.6
Q ss_pred HHHHHHHhHHHHHhhhhc
Q psy5312 59 SIFARLDRICEDCYDLFR 76 (124)
Q Consensus 59 ~lf~kLdRVCeDCyNLfR 76 (124)
..|.+|..-|..||.-||
T Consensus 105 ~a~~~v~~~C~aCH~~fR 122 (122)
T PF01322_consen 105 AAFGEVGKSCKACHDAFR 122 (122)
T ss_dssp HHHHHHHHHHHHHHHHHB
T ss_pred HHHHHHHHHHHHHHHhhC
Confidence 467888899999999998
No 5
>PF09256 BaffR-Tall_bind: BAFF-R, TALL-1 binding; InterPro: IPR015336 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The domain represented by this entry is predominantly found in the tumour necrosis factor receptor superfamily member 13c, BAFF-R and is required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 1P0T_c 2HFG_R 1OSX_A 1OQE_N.
Probab=37.28 E-value=2.2 Score=25.64 Aligned_cols=19 Identities=42% Similarity=0.892 Sum_probs=13.7
Q ss_pred HHHHHhHHHHHhhhhcccch
Q psy5312 61 FARLDRICEDCYDLFRAPQI 80 (124)
Q Consensus 61 f~kLdRVCeDCyNLfR~p~v 80 (124)
|.-|-|.|-+| +|||.|+-
T Consensus 10 FDpLvR~CV~C-~Ll~tp~p 28 (31)
T PF09256_consen 10 FDPLVRHCVAC-ELLRTPEP 28 (31)
T ss_dssp EETTTTEEEEG-GGSSS--S
T ss_pred cCHhhhcceee-eeecCCCC
Confidence 45678999999 89998763
No 6
>PF14862 Defensin_big: Big defensin; PDB: 2RQ2_A 2RNG_A.
Probab=35.79 E-value=9.8 Score=26.97 Aligned_cols=17 Identities=29% Similarity=0.780 Sum_probs=9.6
Q ss_pred hhhhhhhccCCchHHHH
Q psy5312 80 IHTLCRKDCFTSDYFKG 96 (124)
Q Consensus 80 v~~~CR~nCF~n~~F~~ 96 (124)
-..-||+.||.+|+-.+
T Consensus 46 nRGwCRs~Cf~~Ey~d~ 62 (76)
T PF14862_consen 46 NRGWCRSRCFSHEYIDW 62 (76)
T ss_dssp TTEEEESS--TT-EE-T
T ss_pred CCCccccchhhhhhhhh
Confidence 35689999999886443
No 7
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=34.12 E-value=5.7 Score=23.87 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=4.6
Q ss_pred hHHHHHhhhh
Q psy5312 66 RICEDCYDLF 75 (124)
Q Consensus 66 RVCeDCyNLf 75 (124)
|+|..|..+|
T Consensus 2 r~C~~Cg~~Y 11 (36)
T PF05191_consen 2 RICPKCGRIY 11 (36)
T ss_dssp EEETTTTEEE
T ss_pred cCcCCCCCcc
Confidence 3455554443
No 8
>PF11844 DUF3364: Domain of unknown function (DUF3364); InterPro: IPR024564 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene [, ]. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE operon and of some other nif genes []. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I []. This entry represents the uncharacterised N-terminal domain of the molybdenum-iron protein beta chain, which is part of the nitrogenase complex that catalyses the key enzymatic reactions in nitrogen fixation. ; PDB: 3U7Q_B 3MIN_D 1M34_D 2AFI_D 2MIN_B 1G21_B 2AFK_D 1FP4_B 1M1Y_L 1G20_D ....
Probab=30.93 E-value=16 Score=24.34 Aligned_cols=14 Identities=36% Similarity=0.724 Sum_probs=10.5
Q ss_pred HHHhhhhcccchhh
Q psy5312 69 EDCYDLFRAPQIHT 82 (124)
Q Consensus 69 eDCyNLfR~p~v~~ 82 (124)
.||+.|||+|.--.
T Consensus 9 ~dh~~LF~~peYqe 22 (56)
T PF11844_consen 9 LDHFPLFREPEYQE 22 (56)
T ss_dssp -BHHHHTTSHHHHH
T ss_pred ccHHHHcCCHHHHH
Confidence 48999999987543
No 9
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=30.40 E-value=34 Score=22.57 Aligned_cols=23 Identities=43% Similarity=0.977 Sum_probs=19.1
Q ss_pred hHHHHHhhhhcccchhhhhhhccCCc
Q psy5312 66 RICEDCYDLFRAPQIHTLCRKDCFTS 91 (124)
Q Consensus 66 RVCeDCyNLfR~p~v~~~CR~nCF~n 91 (124)
-||-.||- |+|--++.|| .|+++
T Consensus 15 kIC~rC~A--rnp~~A~kCR-kC~~k 37 (50)
T COG1552 15 KICRRCYA--RNPPRATKCR-KCGYK 37 (50)
T ss_pred HHHHHhcC--CCCcchhHHh-hccCC
Confidence 48888885 8999999999 67765
No 10
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=29.25 E-value=20 Score=28.24 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=22.4
Q ss_pred hHHHHHhhhhcccchhhhhhhccCCc
Q psy5312 66 RICEDCYDLFRAPQIHTLCRKDCFTS 91 (124)
Q Consensus 66 RVCeDCyNLfR~p~v~~~CR~nCF~n 91 (124)
..|.||.|-=++.=.+..||.=|=..
T Consensus 5 ~~CqdCGNqAkk~C~~~rCRtCCk~r 30 (154)
T PF05142_consen 5 ISCQDCGNQAKKDCSHRRCRTCCKSR 30 (154)
T ss_pred cchhhhcchhhcCCCcchhhhhhccC
Confidence 57999999999999999999877544
No 11
>PF00444 Ribosomal_L36: Ribosomal protein L36; InterPro: IPR000473 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L36 is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [] can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36. L36 is a small basic and cysteine-rich protein of 37 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_6 2HGU_8 2HGJ_8 1DGZ_A 1DFE_A 2HGQ_8 1VSP_b 1VSA_b 3PIP_4 1VOU_6 ....
Probab=28.28 E-value=3.9 Score=25.28 Aligned_cols=23 Identities=30% Similarity=0.875 Sum_probs=18.9
Q ss_pred HhHHHHHhhhhcccchhhhhhhc
Q psy5312 65 DRICEDCYDLFRAPQIHTLCRKD 87 (124)
Q Consensus 65 dRVCeDCyNLfR~p~v~~~CR~n 87 (124)
-..|+||+=+=|...++..|++|
T Consensus 8 k~~c~~C~~vrR~gr~~Vick~n 30 (38)
T PF00444_consen 8 KKRCKDCYVVRRKGRLYVICKKN 30 (38)
T ss_dssp S-SSSTSEEEEETTEEEEEESSS
T ss_pred hhcCCCCceEEECCEEEEECCCC
Confidence 45799999999999999988765
No 12
>PF12562 DUF3746: Protein of unknown function (DUF3746); InterPro: IPR022219 This C-terminal domain characterises the poxvirus I6 proteins, it is approximately 40 amino acids in length. The family is found in association with PF04595 from PFAM.
Probab=27.54 E-value=16 Score=22.66 Aligned_cols=12 Identities=33% Similarity=1.099 Sum_probs=10.5
Q ss_pred hhhhccCCchHH
Q psy5312 83 LCRKDCFTSDYF 94 (124)
Q Consensus 83 ~CR~nCF~n~~F 94 (124)
-|+++||.|.-|
T Consensus 18 ~CkK~~f~nsty 29 (37)
T PF12562_consen 18 TCKKHCFDNSTY 29 (37)
T ss_pred hhhheeecCcee
Confidence 799999999876
No 13
>PF03488 Ins_beta: Nematode insulin-related peptide beta type; InterPro: IPR003235 The insulin family of proteins groups together several evolutionarily related active peptides []: these include insulin [, ], relaxin [, ], insect prothoracicotropic hormone (bombyxin) [], insulin-like growth factors (IGF1 and IGF2) [, ], mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP) (gene INSL4), locust insulin-related peptide (LIRP), molluscan insulin-related peptides (MIP), and Caenorhabditis elegans insulin-like peptides. The 3D structures of a number of family members have been determined [, , ]. The fold comprises two polypeptide chains (A and B) linked by two disulphide bonds: all share a conserved arrangement of 4 cysteines in their A chain, the first of which is linked by a disulphide bond to the third, while the second and fourth are linked by interchain disulphide bonds to cysteines in the B chain. Insulin is found in many animals, and is involved in the regulation of normal glucose homeostasis. It also has other specific physiological effects, such as increasing the permeability of cells to monosaccharides, amino acids and fatty acids, and accelerating glycolysis and glycogen synthesis in the liver []. Insulin exerts its effects by interaction with a cell-surface receptor, which may also result in the promotion of cell growth []. Insulin is synthesised as a prepropeptide from which an endoplasmic reticulum-targeting sequence is cleaved to yield proinsulin. The sequence of prosinsulin contains 2 well-conserved regions (designated A and B), separated by an intervening connecting region (C), which is variable between species []. The connecting region is cleaved, liberating the active protein, which contains the A and B chains, held together by 2 disulphide bonds []. This entry represents Caenorhabditis elegans insulin-like peptides [], beta type.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 2KJI_A.
Probab=26.74 E-value=40 Score=20.65 Aligned_cols=30 Identities=27% Similarity=0.662 Sum_probs=18.1
Q ss_pred HHHHHHHHhHHHH-Hhhhhcccchhhh-hhhcc
Q psy5312 58 KSIFARLDRICED-CYDLFRAPQIHTL-CRKDC 88 (124)
Q Consensus 58 R~lf~kLdRVCeD-CyNLfR~p~v~~~-CR~nC 88 (124)
|.|+.++..||.+ |..-. +-.+++. |...|
T Consensus 6 ~~l~~~v~~vCg~~C~~~~-~~dia~~cC~~~c 37 (48)
T PF03488_consen 6 RKLVKRVMSVCGGPCTPNT-DVDIATICCSKGC 37 (48)
T ss_dssp HHHHHHHHHHTSSSS---S--TTHHHHHTTT--
T ss_pred HHHHHHHHHHcCCCCCCCC-chHHHHHHHcCCC
Confidence 7899999999988 86532 3345655 66664
No 14
>PRK00831 rpmJ 50S ribosomal protein L36; Validated
Probab=26.54 E-value=11 Score=23.90 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=23.2
Q ss_pred HHHHHHHhHHHHHhhhhcccchhhhhhhc
Q psy5312 59 SIFARLDRICEDCYDLFRAPQIHTLCRKD 87 (124)
Q Consensus 59 ~lf~kLdRVCeDCyNLfR~p~v~~~CR~n 87 (124)
+-.+++-+.|++|+-+=|.-.++..|.+|
T Consensus 5 ~SvKk~~~~~~~c~vvrR~grv~Vick~n 33 (41)
T PRK00831 5 NSLKSLKNRHRDCQVVRRKGRVYVINKKN 33 (41)
T ss_pred hhhhhhhccCCCCEEEEeCCEEEEEcCCC
Confidence 34556667889999999999999988754
No 15
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=25.99 E-value=36 Score=20.39 Aligned_cols=13 Identities=31% Similarity=1.032 Sum_probs=9.6
Q ss_pred HHHHHhhhhcccc
Q psy5312 67 ICEDCYDLFRAPQ 79 (124)
Q Consensus 67 VCeDCyNLfR~p~ 79 (124)
+|++|-.-|.+|.
T Consensus 1 lC~~C~~Ey~~p~ 13 (35)
T PF07503_consen 1 LCDDCLKEYFDPS 13 (35)
T ss_dssp --HHHHHHHCSTT
T ss_pred CCHHHHHHHcCCC
Confidence 5999999998875
No 16
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=25.74 E-value=1.4e+02 Score=21.61 Aligned_cols=14 Identities=36% Similarity=0.766 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHH
Q psy5312 6 LTLLVLIIMTVTML 19 (124)
Q Consensus 6 ~~~~~~~~~~~~~~ 19 (124)
|.++|++++++...
T Consensus 31 LivLVIIiLlImlf 44 (85)
T PF10717_consen 31 LIVLVIIILLIMLF 44 (85)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555555554443
No 17
>COG0257 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=21.41 E-value=11 Score=23.60 Aligned_cols=24 Identities=25% Similarity=0.707 Sum_probs=19.8
Q ss_pred HHhHHHHHhhhhcccchhhhhhhc
Q psy5312 64 LDRICEDCYDLFRAPQIHTLCRKD 87 (124)
Q Consensus 64 LdRVCeDCyNLfR~p~v~~~CR~n 87 (124)
+--.|+||.-+=|.-.|+..|.+|
T Consensus 7 vK~~c~~CkivrRkGrv~VIck~~ 30 (38)
T COG0257 7 VKKRCRDCKIVRRKGRVYVICKKN 30 (38)
T ss_pred cccccCCceEEEecCEEEEEeCCC
Confidence 345799999999999999988754
Done!