Query psy9320
Match_columns 183
No_of_seqs 29 out of 31
Neff 2.3
Searched_HMMs 46136
Date Sat Aug 17 00:22:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9320hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14084 DUF4264: Protein of u 26.5 34 0.00073 24.2 1.0 29 144-172 2-30 (52)
2 PF14293 YWFCY: YWFCY protein 19.5 28 0.0006 25.4 -0.6 24 153-181 1-24 (61)
3 PF01552 Pico_P2B: Picornaviru 15.3 1E+02 0.0022 24.0 1.6 19 161-179 34-52 (99)
4 PF14265 DUF4355: Domain of un 10.8 89 0.0019 23.3 0.1 28 147-174 92-119 (125)
5 COG3092 Uncharacterized protei 8.0 2.3E+02 0.0049 23.9 1.4 22 154-175 123-144 (149)
6 smart00526 H15 Domain in histo 7.4 2.9E+02 0.0064 18.5 1.6 22 157-178 40-61 (66)
7 PF00538 Linker_histone: linke 6.0 5.5E+02 0.012 17.8 2.3 21 159-179 42-62 (77)
8 PF07140 IFNGR1: Interferon ga 5.5 2.9E+02 0.0063 22.4 0.8 22 153-174 88-109 (134)
9 PF07120 DUF1376: Protein of u 5.2 1.7E+02 0.0037 21.1 -0.6 29 155-183 40-68 (88)
10 KOG2825|consensus 4.7 4.9E+02 0.011 24.4 1.8 33 144-176 143-177 (323)
No 1
>PF14084 DUF4264: Protein of unknown function (DUF4264)
Probab=26.48 E-value=34 Score=24.21 Aligned_cols=29 Identities=28% Similarity=0.470 Sum_probs=21.9
Q ss_pred cceeeccccccccccccchHHHHHHHHHH
Q psy9320 144 SEVLAEKDENKGENVKNLPNFVNKSLKKM 172 (183)
Q Consensus 144 ~E~IAeade~t~~dVq~~a~~~~~~~~~~ 172 (183)
.+.||-..=+...|.-.+-||+||+||.-
T Consensus 2 leliat~~~~~~~dlYKvVDfLNktLK~~ 30 (52)
T PF14084_consen 2 LELIATKEFEYNDDLYKVVDFLNKTLKDK 30 (52)
T ss_pred eEEEEEEEecCCccHHHHHHHHhhhhhhc
Confidence 45666666666677778889999999864
No 2
>PF14293 YWFCY: YWFCY protein
Probab=19.52 E-value=28 Score=25.37 Aligned_cols=24 Identities=21% Similarity=0.569 Sum_probs=16.8
Q ss_pred ccccccccchHHHHHHHHHHHhhheeeec
Q psy9320 153 NKGENVKNLPNFVNKSLKKMVKIISIVLL 181 (183)
Q Consensus 153 ~t~~dVq~~a~~~~~~~~~~~~~~~~~~~ 181 (183)
|++.|.|-++.+++ |.+.|||.+|
T Consensus 1 Q~eddlr~L~KImd-----f~R~iSI~~l 24 (61)
T PF14293_consen 1 QTEDDLRALRKIMD-----FMRAISILFL 24 (61)
T ss_pred CCcHHHHHHHHHHH-----HHHHHHHHHH
Confidence 67788888877664 5666777654
No 3
>PF01552 Pico_P2B: Picornavirus 2B protein; InterPro: IPR002527 Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability [, ].; GO: 0000166 nucleotide binding, 0003968 RNA-directed RNA polymerase activity, 0005198 structural molecule activity, 0008233 peptidase activity, 0008234 cysteine-type peptidase activity, 0016740 transferase activity, 0016779 nucleotidyltransferase activity, 0016787 hydrolase activity, 0018144 RNA-protein covalent cross-linking, 0019012 virion
Probab=15.35 E-value=1e+02 Score=24.04 Aligned_cols=19 Identities=42% Similarity=0.459 Sum_probs=15.2
Q ss_pred chHHHHHHHHHHHhhheee
Q psy9320 161 LPNFVNKSLKKMVKIISIV 179 (183)
Q Consensus 161 ~a~~~~~~~~~~~~~~~~~ 179 (183)
...++.|.||.++||||-+
T Consensus 34 ~~~~~~kilK~LvKiIsAl 52 (99)
T PF01552_consen 34 QDKITEKILKWLVKIISAL 52 (99)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3457789999999999854
No 4
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=10.82 E-value=89 Score=23.28 Aligned_cols=28 Identities=32% Similarity=0.547 Sum_probs=23.1
Q ss_pred eeccccccccccccchHHHHHHHHHHHh
Q psy9320 147 LAEKDENKGENVKNLPNFVNKSLKKMVK 174 (183)
Q Consensus 147 IAeade~t~~dVq~~a~~~~~~~~~~~~ 174 (183)
+....+.+..+|+.|.+++|+.+..-|+
T Consensus 92 ~g~d~e~~~~~v~~l~~~~~~~v~~~v~ 119 (125)
T PF14265_consen 92 VGDDEEETKANVKALKKLFNKAVQEKVK 119 (125)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566778999999999999998877664
No 5
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=8.01 E-value=2.3e+02 Score=23.89 Aligned_cols=22 Identities=14% Similarity=0.341 Sum_probs=18.8
Q ss_pred cccccccchHHHHHHHHHHHhh
Q psy9320 154 KGENVKNLPNFVNKSLKKMVKI 175 (183)
Q Consensus 154 t~~dVq~~a~~~~~~~~~~~~~ 175 (183)
.|-+.|++|+++||..|++-|-
T Consensus 123 ~kP~Yq~LAdvLkrAf~qLdkt 144 (149)
T COG3092 123 EKPTYQALADVLKRAFKQLDKT 144 (149)
T ss_pred CCCcHHHHHHHHHHHHHHHHHH
Confidence 3478999999999999998764
No 6
>smart00526 H15 Domain in histone families 1 and 5.
Probab=7.45 E-value=2.9e+02 Score=18.48 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=16.4
Q ss_pred ccccchHHHHHHHHHHHhhhee
Q psy9320 157 NVKNLPNFVNKSLKKMVKIISI 178 (183)
Q Consensus 157 dVq~~a~~~~~~~~~~~~~~~~ 178 (183)
+..+|...++..|+++|.--.+
T Consensus 40 ~~~~~~~~l~~~Lk~~v~~G~l 61 (66)
T smart00526 40 LPNNFRSLLKLALKKLVASGKL 61 (66)
T ss_pred ChHHHHHHHHHHHHHHHhcCce
Confidence 4467888999999999864433
No 7
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=5.97 E-value=5.5e+02 Score=17.78 Aligned_cols=21 Identities=24% Similarity=0.312 Sum_probs=16.7
Q ss_pred ccchHHHHHHHHHHHhhheee
Q psy9320 159 KNLPNFVNKSLKKMVKIISIV 179 (183)
Q Consensus 159 q~~a~~~~~~~~~~~~~~~~~ 179 (183)
.+|..++++.||+++.-=.++
T Consensus 42 ~~~~~~l~~aLk~~v~~G~l~ 62 (77)
T PF00538_consen 42 ANFKSRLKRALKRGVEKGKLV 62 (77)
T ss_dssp TTHHHHHHHHHHHHHHCTSEE
T ss_pred HHHHHHHHHHHHHHHHCCcEE
Confidence 469999999999998754444
No 8
>PF07140 IFNGR1: Interferon gamma receptor (IFNGR1); InterPro: IPR021126 Interferon (INF)-gamma is a dimeric glycoprotein produced by activated T cells and natural killer cells. Although originally isolated based on its antiviral activity, INF-gamma also displays powerful anti-proliferative and immuno-modulatory activities, which are essential for developing appropriate cellular defences against a variety of infectious agents. The first step in eliciting these responses is the specific high affinity interaction of INF- gamma with its cell-surface receptor (INF-gammaRalpha); the complex then interacts with at least one of a family of additional species-specific accessory factors (AF-1 or INF-gammabeta), which convey different cellular responses. One such response is the association and phosphorylation of two protein tyrosine kinases (Jak-1 and Jak-2), which in turn stimulate nuclear transcription activators []. The human INF-gammaR, is a member of the hematopoietic cytokine receptor superfamily. It is expressed in a membrane-bound form in many cell types, and is over-expressed in tumour cells. It comprises an extracellular portion of 229 residues, a single transmembrane region, and a cytoplasmic domain of 221 residues. As with other members of its superfamily, the cytokine-binding sites are formed by a small set of closely-spaced surface loops that extend from a beta-sheet core, much like antigen-binding sites on antibodies. The extracellular INF-gammaR monomer comprises two domains (domain D1 from residue 14-102, and domain D2 from residue 114-221), each resembling an Ig fold with fibronectin type III topology []. The vaccinia virus interferon (IFN)-gamma receptor (IFN-gammaR) is a 43 kDa soluble glycoprotein that is secreted from infected cells early during infection. IFN-gammaR from vaccinia virus, cowpox virus and camelpox virus exist naturally as homodimers, whereas the cellular IFN-gammaR dimerizes only upon binding the homodimeric IFN-gamma. The existence of the virus protein as a dimer in the absence of ligand may provide an advantage to the virus in efficient binding and inhibition of IFN-gamma in solution []. ; GO: 0019955 cytokine binding, 0016020 membrane; PDB: 3BES_R 1FYH_E 1FG9_D.
Probab=5.53 E-value=2.9e+02 Score=22.44 Aligned_cols=22 Identities=32% Similarity=0.264 Sum_probs=16.8
Q ss_pred ccccccccchHHHHHHHHHHHh
Q psy9320 153 NKGENVKNLPNFVNKSLKKMVK 174 (183)
Q Consensus 153 ~t~~dVq~~a~~~~~~~~~~~~ 174 (183)
.+.+|+|++-+.+.|||...+|
T Consensus 88 Kk~n~~~~~~~~lpksl~svv~ 109 (134)
T PF07140_consen 88 KKKNDFKRKKIKLPKSLLSVVK 109 (134)
T ss_dssp -SGGGHHHHHHHHHHHHHHHS-
T ss_pred ecCcccchhchhccHHHHHHHh
Confidence 4568999999999999876654
No 9
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=5.20 E-value=1.7e+02 Score=21.06 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=23.0
Q ss_pred ccccccchHHHHHHHHHHHhhheeeeccC
Q psy9320 155 GENVKNLPNFVNKSLKKMVKIISIVLLKF 183 (183)
Q Consensus 155 ~~dVq~~a~~~~~~~~~~~~~~~~~~~~~ 183 (183)
..|-+.+|.+.+-|.++..++...+|-.|
T Consensus 40 p~d~~~Lar~~~~s~~~~~~a~~~ll~~f 68 (88)
T PF07120_consen 40 PDDDKRLARICGCSTKEWRKALDFLLREF 68 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHhC
Confidence 35677889999999999888888777554
No 10
>KOG2825|consensus
Probab=4.74 E-value=4.9e+02 Score=24.35 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=21.2
Q ss_pred cceeeccccccccc--cccchHHHHHHHHHHHhhh
Q psy9320 144 SEVLAEKDENKGEN--VKNLPNFVNKSLKKMVKII 176 (183)
Q Consensus 144 ~E~IAeade~t~~d--Vq~~a~~~~~~~~~~~~~~ 176 (183)
|-.|-=--+-||-- .-+||+++.|+|.|+.++-
T Consensus 143 F~~vVFDTAPTGHTLRlL~fP~~lek~lgKl~~l~ 177 (323)
T KOG2825|consen 143 FDVVVFDTAPTGHTLRLLQFPTTLEKGLGKLLSLK 177 (323)
T ss_pred cceEEeccCCCcceehhhccchHHHHHHHHHHHHH
Confidence 33333333344443 4589999999999988764
Done!