Query psy14585
Match_columns 66
No_of_seqs 27 out of 29
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 23:39:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09974 putative regulator Pr 34.9 26 0.00056 23.6 1.5 17 33-49 56-72 (111)
2 PF01640 Peptidase_C10: Peptid 32.9 28 0.0006 23.6 1.4 18 36-53 25-43 (192)
3 smart00685 DM14 Repeats in fly 30.2 26 0.00056 21.2 0.8 13 51-63 45-57 (59)
4 COG2085 Predicted dinucleotide 29.8 50 0.0011 24.2 2.4 25 27-52 149-173 (211)
5 PF03669 UPF0139: Uncharacteri 24.6 48 0.001 21.5 1.4 11 37-47 85-95 (103)
6 KOG3561|consensus 23.2 24 0.00052 30.5 -0.3 41 24-64 646-686 (803)
7 PF00681 Plectin: Plectin repe 22.6 52 0.0011 17.8 1.1 15 43-57 1-15 (45)
8 PRK10014 DNA-binding transcrip 21.6 93 0.002 21.0 2.3 28 27-54 244-271 (342)
9 PF10330 Stb3: Putative Sin3 b 21.2 1.2E+02 0.0025 20.3 2.7 37 25-63 33-69 (92)
10 PF09246 PHAT: PHAT; InterPro 20.7 88 0.0019 21.5 2.1 16 33-48 69-84 (108)
No 1
>PRK09974 putative regulator PrlF; Provisional
Probab=34.90 E-value=26 Score=23.59 Aligned_cols=17 Identities=18% Similarity=0.524 Sum_probs=14.4
Q ss_pred CChHHHHHHHHHHHHHh
Q psy14585 33 GNDEAAMAVIMSLLEAD 49 (66)
Q Consensus 33 ~NDeaaMA~~MslLEAD 49 (66)
..++-++++|.++||+|
T Consensus 56 ~~~Dp~ig~FL~fLa~D 72 (111)
T PRK09974 56 EEEDPVLGAFLDFLAAD 72 (111)
T ss_pred CCCCchHHHHHHHHHHH
Confidence 34567899999999999
No 2
>PF01640 Peptidase_C10: Peptidase C10 family classification.; InterPro: IPR000200 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C10 (streptopain family, clan CA). Streptopain is a cysteine protease found in Streptococcus pyogenes that shows some structural and functional similarity to papain (family C1) [, ]. The order of the catalytic cysteine/histidine dyad is the same and the surrounding sequences are similar. The two proteins also show similar specificities, both preferring a hydrophobic residue at the P2 site [, ]. Streptopain shows a high degree of sequence similarity to the S. pyogenes exotoxin B, and strong similarity to the prtT gene product of Porphyromonas gingivalis (Bacteroides gingivalis), both of which have been included in the family [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 4D8I_A 4D8E_A 4D8B_A 3BBA_B 3BB7_A 2JTC_A 1PVJ_A 1DKI_D 2UZJ_A.
Probab=32.91 E-value=28 Score=23.62 Aligned_cols=18 Identities=39% Similarity=0.517 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHH-HhcCCC
Q psy14585 36 EAAMAVIMSLLE-ADAGLG 53 (66)
Q Consensus 36 eaaMA~~MslLE-AD~gLG 53 (66)
-+|||-||+|++ -..+.|
T Consensus 25 atA~AQim~y~~~P~~~~g 43 (192)
T PF01640_consen 25 ATAMAQIMYYHKWPNKGTG 43 (192)
T ss_dssp HHHHHHHHHHHT--SB-SS
T ss_pred HHHHHHHHHHhcCCccCCC
Confidence 589999999998 333444
No 3
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=30.19 E-value=26 Score=21.23 Aligned_cols=13 Identities=54% Similarity=0.746 Sum_probs=10.4
Q ss_pred CCCCCccCCCCCC
Q psy14585 51 GLGGPVDFSGLPW 63 (66)
Q Consensus 51 gLG~p~Dfsdi~W 63 (66)
--|-|||+++||=
T Consensus 45 ~aG~pVd~~~lP~ 57 (59)
T smart00685 45 RAGRPVDLSELPP 57 (59)
T ss_pred HCCCCCChhcCCC
Confidence 3478999999974
No 4
>COG2085 Predicted dinucleotide-binding enzymes [General function prediction only]
Probab=29.78 E-value=50 Score=24.23 Aligned_cols=25 Identities=32% Similarity=0.419 Sum_probs=20.6
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhcCC
Q psy14585 27 GGAPTTGNDEAAMAVIMSLLEADAGL 52 (66)
Q Consensus 27 ~g~~~~~NDeaaMA~~MslLEAD~gL 52 (66)
.....|+||+.|+++.|.|.|.= |+
T Consensus 149 ~~v~vagDD~~Ak~~v~~L~~~i-G~ 173 (211)
T COG2085 149 RDVLVAGDDAEAKAVVAELAEDI-GF 173 (211)
T ss_pred eeEEEecCcHHHHHHHHHHHHhc-Cc
Confidence 35567999999999999999865 44
No 5
>PF03669 UPF0139: Uncharacterised protein family (UPF0139); InterPro: IPR005351 This is a small family of proteins of unknown function which appear to be related to the hypothetical protein CG10674 from Drosophila melanogaster (Fruit fly)(Q9VRJ8 from SWISSPROT).
Probab=24.62 E-value=48 Score=21.53 Aligned_cols=11 Identities=45% Similarity=0.757 Sum_probs=8.6
Q ss_pred HHHHHHHHHHH
Q psy14585 37 AAMAVIMSLLE 47 (66)
Q Consensus 37 aaMA~~MslLE 47 (66)
+.||++|+||-
T Consensus 85 sv~alvm~Yl~ 95 (103)
T PF03669_consen 85 SVMALVMSYLQ 95 (103)
T ss_pred HHHHHHHHHcC
Confidence 57888888874
No 6
>KOG3561|consensus
Probab=23.16 E-value=24 Score=30.54 Aligned_cols=41 Identities=15% Similarity=0.028 Sum_probs=36.9
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHHhcCCCCCccCCCCCCC
Q psy14585 24 PQSGGAPTTGNDEAAMAVIMSLLEADAGLGGPVDFSGLPWP 64 (66)
Q Consensus 24 ~~~~g~~~~~NDeaaMA~~MslLEAD~gLG~p~Dfsdi~W~ 64 (66)
.....+..+.+|..+++..++..++....+++.+|+.++|+
T Consensus 646 ~~~~q~~~~~~~~~~~~~~~s~g~~~~~~~~~~~l~~~~~~ 686 (803)
T KOG3561|consen 646 GDLQQLSSILDDSQARQLRFSQGQALTPQADPSCLALMSSP 686 (803)
T ss_pred cchhhcccccCcccccccccccCccccccCCccccccCCCc
Confidence 34567788889999999999999999999999999999997
No 7
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=22.58 E-value=52 Score=17.82 Aligned_cols=15 Identities=47% Similarity=0.753 Sum_probs=12.2
Q ss_pred HHHHHHhcCCCCCcc
Q psy14585 43 MSLLEADAGLGGPVD 57 (66)
Q Consensus 43 MslLEAD~gLG~p~D 57 (66)
|+|||+..-.|+=+|
T Consensus 1 ~rlLe~Q~~~gGiid 15 (45)
T PF00681_consen 1 LRLLEAQLATGGIID 15 (45)
T ss_dssp HHHHHHHHTTTSEEE
T ss_pred CceeeeeeeeeeEEe
Confidence 579999998887665
No 8
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=21.61 E-value=93 Score=21.00 Aligned_cols=28 Identities=29% Similarity=0.217 Sum_probs=18.8
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhcCCCC
Q psy14585 27 GGAPTTGNDEAAMAVIMSLLEADAGLGG 54 (66)
Q Consensus 27 ~g~~~~~NDeaaMA~~MslLEAD~gLG~ 54 (66)
+..-.|.||+.|++++-.+-|+---+++
T Consensus 244 ~~ai~~~nd~~A~g~~~~l~~~g~~vp~ 271 (342)
T PRK10014 244 ISAVVCYNETIAMGAWFGLLRAGRQSGE 271 (342)
T ss_pred CCEEEECCcHHHHHHHHHHHHcCCCCCC
Confidence 3455799999999877666555433444
No 9
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=21.18 E-value=1.2e+02 Score=20.27 Aligned_cols=37 Identities=24% Similarity=0.371 Sum_probs=28.1
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHhcCCCCCccCCCCCC
Q psy14585 25 QSGGAPTTGNDEAAMAVIMSLLEADAGLGGPVDFSGLPW 63 (66)
Q Consensus 25 ~~~g~~~~~NDeaaMA~~MslLEAD~gLG~p~Dfsdi~W 63 (66)
..|+.+.++. .-+-=++|+-|| .+|.-+.|-|+.+-|
T Consensus 33 ~vPgF~~ls~-sKqRRLi~~ALE-~gd~~~~VvFEKvGW 69 (92)
T PF10330_consen 33 SVPGFSDLSP-SKQRRLIMAALE-GGDKDGDVVFEKVGW 69 (92)
T ss_pred cCCCcccCCH-HHHHHHHHHHHh-cCCCCCCEEEEEecc
Confidence 3456666655 566778999999 677788899999987
No 10
>PF09246 PHAT: PHAT; InterPro: IPR015327 The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding []. ; PDB: 1OXJ_A.
Probab=20.73 E-value=88 Score=21.48 Aligned_cols=16 Identities=31% Similarity=0.505 Sum_probs=13.3
Q ss_pred CChHHHHHHHHHHHHH
Q psy14585 33 GNDEAAMAVIMSLLEA 48 (66)
Q Consensus 33 ~NDeaaMA~~MslLEA 48 (66)
.-||.++.+||++||.
T Consensus 69 ~qdde~L~v~~wIler 84 (108)
T PF09246_consen 69 PQDDEILCVFMWILER 84 (108)
T ss_dssp GG-HHHHHHHHHHHHH
T ss_pred ccchhHHHHHHHHHHH
Confidence 4589999999999995
Done!