Query psy15933
Match_columns 59
No_of_seqs 33 out of 35
Neff 2.3
Searched_HMMs 46136
Date Fri Aug 16 16:49:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15933hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07466 DUF1517: Protein of u 57.7 4.8 0.0001 29.5 0.8 23 26-51 264-286 (289)
2 cd01797 NIRF_N amino-terminal 42.6 5.9 0.00013 23.3 -0.6 16 35-50 48-63 (78)
3 PF05182 Fip1: Fip1 motif; In 35.4 12 0.00027 21.4 -0.0 10 17-26 19-28 (45)
4 PF00062 Lys: C-type lysozyme/ 32.8 11 0.00025 24.9 -0.5 13 19-31 48-60 (125)
5 cd01798 parkin_N amino-termina 29.9 14 0.00031 20.4 -0.4 16 35-50 44-59 (70)
6 PF10790 DUF2604: Protein of U 25.7 56 0.0012 20.8 1.8 49 4-54 12-64 (76)
7 cd01792 ISG15_repeat1 ISG15 ub 25.6 20 0.00044 20.6 -0.2 17 35-51 50-66 (80)
8 cd01803 Ubiquitin Ubiquitin. U 24.2 28 0.0006 18.9 0.2 17 35-51 46-62 (76)
9 cd01806 Nedd8 Nebb8-like ubiq 23.3 29 0.00063 18.8 0.1 17 35-51 46-62 (76)
10 cd01809 Scythe_N Ubiquitin-lik 22.6 30 0.00065 18.5 0.1 17 35-51 46-62 (72)
11 PTZ00044 ubiquitin; Provisiona 20.5 39 0.00085 18.6 0.3 17 35-51 46-62 (76)
12 cd01802 AN1_N ubiquitin-like d 20.4 36 0.00078 21.1 0.1 17 35-51 73-89 (103)
No 1
>PF07466 DUF1517: Protein of unknown function (DUF1517); InterPro: IPR010903 This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown.
Probab=57.73 E-value=4.8 Score=29.53 Aligned_cols=23 Identities=43% Similarity=0.687 Sum_probs=18.9
Q ss_pred eecCCCCCCCCCccchhcccCCCCCC
Q psy15933 26 LFYPPANGKAGKFLDEERRLGDYPFN 51 (59)
Q Consensus 26 Lf~Pp~~Gr~GKFLdEERlLreYP~~ 51 (59)
|+.|... |-.|.||.+|.+||.=
T Consensus 264 lWtP~~~---gd~Ls~~ell~~yP~L 286 (289)
T PF07466_consen 264 LWTPQAE---GDTLSEDELLADYPDL 286 (289)
T ss_pred EECCCCC---CCccCHHHHHHhCccc
Confidence 6777764 5699999999999963
No 2
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=42.58 E-value=5.9 Score=23.27 Aligned_cols=16 Identities=31% Similarity=0.520 Sum_probs=14.5
Q ss_pred CCCccchhcccCCCCC
Q psy15933 35 AGKFLDEERRLGDYPF 50 (59)
Q Consensus 35 ~GKFLdEERlLreYP~ 50 (59)
.||.|+++++|.+|-.
T Consensus 48 ~Gk~L~D~~tL~~y~i 63 (78)
T cd01797 48 RGKQMEDGHTLFDYNV 63 (78)
T ss_pred CCEECCCCCCHHHcCC
Confidence 5899999999999975
No 3
>PF05182 Fip1: Fip1 motif; InterPro: IPR007854 This short motif is about 40 amino acids in length and is found in the Fip1 protein that is a component of a Saccharomyces cerevisiae pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase []. This region of Fip1 is needed for the interaction with the Yth1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor [].
Probab=35.39 E-value=12 Score=21.36 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=8.2
Q ss_pred hcccccccee
Q psy15933 17 EFKEGFNYGL 26 (59)
Q Consensus 17 ~L~d~lNYGL 26 (59)
.+.|.+|||+
T Consensus 19 DisDyFNYGf 28 (45)
T PF05182_consen 19 DISDYFNYGF 28 (45)
T ss_pred ChhhhcCCCC
Confidence 4678999997
No 4
>PF00062 Lys: C-type lysozyme/alpha-lactalbumin family; InterPro: IPR001916 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 22 GH22 from CAZY comprises enzymes with two known activities; lysozyme type C (3.2.1.17 from EC) and alpha-lactalbumins. Asp and/or the carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base. Alpha-lactalbumin [, ] is a milk protein that acts as the regulatory subunit of lactose synthetase, acting to promote the conversion of galactosyltransferase to lactose synthase, which is essential for milk production. In the mammary gland, alpha-lactalbumin changes the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. Lysozymes (3.2.1.17 from EC) act as bacteriolytic enzymes by hydrolyzing the beta(1->4) bonds between N-acetylglucosamine and N-acetylmuramic acid in the peptidoglycan of prokaryotic cell walls. It has also been recruited for a digestive role in certain ruminants and colobine monkeys []. There are at least five different classes of lysozymes []: C (chicken type), G (goose type), phage-type (T4), fungi (Chalaropsis), and bacterial (Bacillus subtilis). There are few similarities in the sequences of the different types of lysozymes. Lysozyme type C and alpha-lactalbumin are similar both in terms of primary sequence and structure, and probably evolved from a common ancestral protein []. Around 35 to 40% of the residues are conserved in both proteins as well as the positions of the four disulphide bonds. There is, however, no similarity in function. Another significant difference between the two enzymes is that all lactalbumins have the ability to bind calcium [], while this property is restricted to only a few lysozymes []. The binding site was deduced using high resolution X-ray structure analysis and was shown to consist of three aspartic acid residues. It was first suggested that calcium bound to lactalbumin stabilised the structure, but recently it has been claimed that calcium controls the release of lactalbumin from the golgi membrane and that the pattern of ion binding may also affect the catalytic properties of the lactose synthetase complex.; PDB: 1HFX_A 1HMK_A 1HFY_B 1FKQ_A 1FKV_A 3B0K_B 1HML_A 1B9O_A 1A4V_A 3B0O_A ....
Probab=32.84 E-value=11 Score=24.86 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=10.1
Q ss_pred cccccceeecCCC
Q psy15933 19 KEGFNYGLFYPPA 31 (59)
Q Consensus 19 ~d~lNYGLf~Pp~ 31 (59)
..+-+|||||=.+
T Consensus 48 ~gS~dyGIFQIns 60 (125)
T PF00062_consen 48 DGSTDYGIFQINS 60 (125)
T ss_dssp TSEEEETTTTEET
T ss_pred CCccccceeecCc
Confidence 6688999999543
No 5
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=29.87 E-value=14 Score=20.43 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=14.1
Q ss_pred CCCccchhcccCCCCC
Q psy15933 35 AGKFLDEERRLGDYPF 50 (59)
Q Consensus 35 ~GKFLdEERlLreYP~ 50 (59)
+||.|+.++.|.+|-.
T Consensus 44 ~G~~L~d~~~l~~~~i 59 (70)
T cd01798 44 AGKELRNTTTIQECDL 59 (70)
T ss_pred CCeECCCCCcHHHcCC
Confidence 5888999999999975
No 6
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=25.74 E-value=56 Score=20.84 Aligned_cols=49 Identities=29% Similarity=0.531 Sum_probs=40.3
Q ss_pred ccccchhhhhhhhhccccccceeecCCCC----CCCCCccchhcccCCCCCCCCc
Q psy15933 4 TNFNATFKTYWFTEFKEGFNYGLFYPPAN----GKAGKFLDEERRLGDYPFNGPV 54 (59)
Q Consensus 4 ~~~~~~~~~~~~~~L~d~lNYGLf~Pp~~----Gr~GKFLdEERlLreYP~~~~v 54 (59)
.|-||...+.....|....|-| ||+.| -.+|.-||-.|-+.||-+..+|
T Consensus 12 ANvnaPLh~v~akALe~sgNvg--QP~ENWElkDe~G~vlD~~kKveD~Gftngv 64 (76)
T PF10790_consen 12 ANVNAPLHPVRAKALEQSGNVG--QPPENWELKDESGQVLDVNKKVEDFGFTNGV 64 (76)
T ss_pred cCCCCcchHHHHHHHhhccccC--CCcccceeeccCCcEeeccchhhhccccccc
Confidence 4678888888889999999987 88876 3578899999999999886554
No 7
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=25.61 E-value=20 Score=20.56 Aligned_cols=17 Identities=12% Similarity=0.112 Sum_probs=14.5
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.||.|+.++.|.||-..
T Consensus 50 ~G~~L~D~~tL~~~gi~ 66 (80)
T cd01792 50 SREVLQDGVPLVSQGLG 66 (80)
T ss_pred CCCCCCCCCCHHHcCCC
Confidence 57899999999999763
No 8
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=24.15 E-value=28 Score=18.87 Aligned_cols=17 Identities=47% Similarity=0.792 Sum_probs=14.3
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.|+-|++++.|.+|...
T Consensus 46 ~g~~L~d~~~L~~~~i~ 62 (76)
T cd01803 46 AGKQLEDGRTLSDYNIQ 62 (76)
T ss_pred CCEECCCCCcHHHcCCC
Confidence 37789999999999874
No 9
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=23.34 E-value=29 Score=18.79 Aligned_cols=17 Identities=24% Similarity=0.692 Sum_probs=14.4
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.|+.|++++.|.+|-..
T Consensus 46 ~g~~L~d~~tl~~~~i~ 62 (76)
T cd01806 46 SGKQMNDDKTAADYKLE 62 (76)
T ss_pred CCeEccCCCCHHHcCCC
Confidence 47899999999999863
No 10
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=22.55 E-value=30 Score=18.55 Aligned_cols=17 Identities=24% Similarity=0.704 Sum_probs=14.3
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.|+-|++++.|.+|...
T Consensus 46 ~g~~L~d~~~L~~~~i~ 62 (72)
T cd01809 46 SGRVLKDDETLSEYKVE 62 (72)
T ss_pred CCEECCCcCcHHHCCCC
Confidence 37899999999999863
No 11
>PTZ00044 ubiquitin; Provisional
Probab=20.46 E-value=39 Score=18.62 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=14.2
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.|+-|+.+++|.+|...
T Consensus 46 ~g~~L~d~~~l~~~~i~ 62 (76)
T PTZ00044 46 SGKQMSDDLKLSDYKVV 62 (76)
T ss_pred CCEEccCCCcHHHcCCC
Confidence 57789999999999863
No 12
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=20.35 E-value=36 Score=21.11 Aligned_cols=17 Identities=29% Similarity=0.426 Sum_probs=14.9
Q ss_pred CCCccchhcccCCCCCC
Q psy15933 35 AGKFLDEERRLGDYPFN 51 (59)
Q Consensus 35 ~GKFLdEERlLreYP~~ 51 (59)
.||.|+.+++|.+|...
T Consensus 73 ~Gk~L~D~~tL~dy~I~ 89 (103)
T cd01802 73 NNMELEDEYCLNDYNIS 89 (103)
T ss_pred CCEECCCCCcHHHcCCC
Confidence 58999999999999863
Done!