Query psy6841
Match_columns 113
No_of_seqs 70 out of 72
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 19:47:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09733 VEFS-Box: VEFS-Box of 100.0 6.1E-39 1.3E-43 238.2 5.0 80 34-113 2-83 (140)
2 KOG2350|consensus 100.0 1.2E-37 2.5E-42 245.9 2.8 99 8-113 61-160 (221)
3 PF05299 Peptidase_M61: M61 gl 40.5 12 0.00027 27.4 0.7 33 48-80 7-42 (122)
4 PF13902 R3H-assoc: R3H-associ 25.4 46 0.001 23.8 1.5 12 99-110 69-80 (131)
5 PHA02687 ORF061 late transcrip 21.1 55 0.0012 26.8 1.3 33 68-100 148-180 (231)
6 PF10987 DUF2806: Protein of u 19.8 1.7E+02 0.0037 23.0 3.8 36 68-109 32-67 (219)
7 PF08671 SinI: Anti-repressor 19.4 1.8E+02 0.0038 16.7 2.9 24 75-103 1-27 (30)
8 COG5109 Uncharacterized conser 18.8 74 0.0016 28.0 1.7 22 89-110 56-77 (396)
9 PF11161 DUF2944: Protein of u 17.4 75 0.0016 25.4 1.3 14 54-67 99-113 (187)
10 PF08246 Inhibitor_I29: Cathep 17.3 62 0.0013 19.6 0.7 12 87-98 46-57 (58)
No 1
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=100.00 E-value=6.1e-39 Score=238.18 Aligned_cols=80 Identities=49% Similarity=0.873 Sum_probs=77.4
Q ss_pred ccCCCcCCCCCcccCCCcceeeccCccccCCCCC--CCCCCCCCCHHHHHHHHHHHhhccCCCChhhHHHHHHHHHHhhh
Q psy6841 34 ADDADTDGHRPVVSGHNRLYHHTITCLPVLPKEM--DQDSDDQKDPKWLQTKTKMMIDEFTDVNEGEKELMKLWNLHVMK 111 (113)
Q Consensus 34 ~~~~~~~~~r~~~~~~~R~yfHs~T~~Pl~p~E~--D~DSEdE~D~~WL~~k~r~~LddF~DVn~~EKe~M~lWN~FV~k 111 (113)
.++++++++|+|++||||+||||+||+||+++|+ |+|||||+|++||+++++++|+||+|||++||+||++||+||+|
T Consensus 2 ~~~~~~~~~r~~~~~~~R~y~Hs~t~~p~~~~e~~sd~DSedE~D~~wl~~~~r~~l~dF~Dv~~~EKefM~lWN~fv~k 81 (140)
T PF09733_consen 2 KEPAERSDQRPYILLHNRQYFHSRTCQPMRPEEVLSDRDSEDEVDDEWLDQKHRRMLDDFSDVNEEEKEFMKLWNSFVMK 81 (140)
T ss_pred CCchhhhcchhHhhccCcceeccccceeccHHHhcCCCCCCCcCCHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHH
Confidence 4678889999999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred cC
Q psy6841 112 YG 113 (113)
Q Consensus 112 q~ 113 (113)
|+
T Consensus 82 ~r 83 (140)
T PF09733_consen 82 QR 83 (140)
T ss_pred cc
Confidence 86
No 2
>KOG2350|consensus
Probab=100.00 E-value=1.2e-37 Score=245.86 Aligned_cols=99 Identities=37% Similarity=0.651 Sum_probs=90.3
Q ss_pred CCCccceEeccCCCCCCChHHHHhhcccCCCcCCCCCcccCCCcceeeccCccccCCCCCCCCCCCCCC-HHHHHHHHHH
Q psy6841 8 SDGSELLVYYPRRHRKHSMSEFLNDMADDADTDGHRPVVSGHNRLYHHTITCLPVLPKEMDQDSDDQKD-PKWLQTKTKM 86 (113)
Q Consensus 8 ~~~t~~lv~rp~r~~~~slsefle~~~~~~~~~~~r~~~~~~~R~yfHs~T~~Pl~p~E~D~DSEdE~D-~~WL~~k~r~ 86 (113)
.|+|+|++|+|+|.+ .++++|+| .+|++..++ .|||||||||+|||||+++|+.+|+|+|.| ++||+.++++
T Consensus 61 ~p~t~i~~~~p~~~a-tt~k~~ae--rsd~~v~~l----~lhkRqffHS~t~qPl~leqvmsdrdsE~d~dd~a~~e~~~ 133 (221)
T KOG2350|consen 61 TPITHILVCRPKRTA-TTMKEFAE--RSDGEVEQL----RLHKRQFFHSDTCQPLRLEQVMSDRDSEKDEDDWARLETST 133 (221)
T ss_pred CcchhhhccchHhhh-hccccccc--ccccceeee----ccccceeeeccccCCCCHHHHhccccccccchhhhhhHHHH
Confidence 489999999999999 99999999 999987644 499999999999999999999555555555 8999999999
Q ss_pred HhhccCCCChhhHHHHHHHHHHhhhcC
Q psy6841 87 MIDEFTDVNEGEKELMKLWNLHVMKYG 113 (113)
Q Consensus 87 ~LddF~DVn~~EKe~M~lWN~FV~kq~ 113 (113)
||++|+|||++||+||+|||+||+||+
T Consensus 134 mLe~fvdvne~ekr~mkLWNsfVrkqr 160 (221)
T KOG2350|consen 134 MLEEFVDVNEGEKRVMKLWNSFVRKQR 160 (221)
T ss_pred HHHHhccccHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999996
No 3
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M61 (glycyl aminopeptidase family, clan MA(E)).The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=40.47 E-value=12 Score=27.39 Aligned_cols=33 Identities=15% Similarity=0.356 Sum_probs=25.9
Q ss_pred CCCcceeeccCccccCCCCC---CCCCCCCCCHHHH
Q psy6841 48 GHNRLYHHTITCLPVLPKEM---DQDSDDQKDPKWL 80 (113)
Q Consensus 48 ~~~R~yfHs~T~~Pl~p~E~---D~DSEdE~D~~WL 80 (113)
+-.=.|||+.+..-++|.++ |.+.+.-...-|+
T Consensus 7 l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv 42 (122)
T PF05299_consen 7 LLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWV 42 (122)
T ss_pred hhhhhccccccceEeccccccCCCCCCCCCCCCEee
Confidence 33447999999999999997 6677776776775
No 4
>PF13902 R3H-assoc: R3H-associated N-terminal domain
Probab=25.45 E-value=46 Score=23.79 Aligned_cols=12 Identities=17% Similarity=0.266 Sum_probs=8.2
Q ss_pred HHHHHHHHHHhh
Q psy6841 99 KELMKLWNLHVM 110 (113)
Q Consensus 99 Ke~M~lWN~FV~ 110 (113)
..+|.+||.|+-
T Consensus 69 ~~~~~~Wd~f~~ 80 (131)
T PF13902_consen 69 YQNAQLWDDFRN 80 (131)
T ss_pred HHHHHHHHHHhh
Confidence 567777777764
No 5
>PHA02687 ORF061 late transcription factor VLTF-4; Provisional
Probab=21.07 E-value=55 Score=26.83 Aligned_cols=33 Identities=24% Similarity=0.314 Sum_probs=29.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhccCCCChhhHH
Q psy6841 68 DQDSDDQKDPKWLQTKTKMMIDEFTDVNEGEKE 100 (113)
Q Consensus 68 D~DSEdE~D~~WL~~k~r~~LddF~DVn~~EKe 100 (113)
|.|.+|+.|..-|..-+..+|.||-++|.--+.
T Consensus 148 d~dn~D~md~SDLklAt~~IikDlK~Ln~RVsA 180 (231)
T PHA02687 148 DDDNLDEMDDSDLMLAFSAILADFKDLTGRVKA 180 (231)
T ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999888766554
No 6
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=19.84 E-value=1.7e+02 Score=22.98 Aligned_cols=36 Identities=25% Similarity=0.540 Sum_probs=20.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhccCCCChhhHHHHHHHHHHh
Q psy6841 68 DQDSDDQKDPKWLQTKTKMMIDEFTDVNEGEKELMKLWNLHV 109 (113)
Q Consensus 68 D~DSEdE~D~~WL~~k~r~~LddF~DVn~~EKe~M~lWN~FV 109 (113)
+..+.+++|++|+..- ..+-+ +|+..+ +=++|-.-+
T Consensus 32 ~~~~~~~vD~DWl~~f-~~~A~---~isn~~--mQ~LWakIL 67 (219)
T PF10987_consen 32 SEVTGEPVDPDWLYRF-FDMAE---DISNEE--MQELWAKIL 67 (219)
T ss_pred cccCCCCCChHHHHHH-HHHHH---hcCcHH--HHHHHHHHH
Confidence 3456667799999654 22323 344443 336776543
No 7
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=19.42 E-value=1.8e+02 Score=16.74 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=10.4
Q ss_pred CCHHHHH--HHHHHHhhccCCCChhh-HHHHH
Q psy6841 75 KDPKWLQ--TKTKMMIDEFTDVNEGE-KELMK 103 (113)
Q Consensus 75 ~D~~WL~--~k~r~~LddF~DVn~~E-Ke~M~ 103 (113)
.|++|.. .+-+. ..++.+| ++|.+
T Consensus 1 LD~EW~~Li~eA~~-----~Gls~eeir~FL~ 27 (30)
T PF08671_consen 1 LDEEWVELIKEAKE-----SGLSKEEIREFLE 27 (30)
T ss_dssp --HHHHHHHHHHHH-----TT--HHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHH
Confidence 3788943 33333 3566666 55543
No 8
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=18.81 E-value=74 Score=27.98 Aligned_cols=22 Identities=23% Similarity=0.528 Sum_probs=20.2
Q ss_pred hccCCCChhhHHHHHHHHHHhh
Q psy6841 89 DEFTDVNEGEKELMKLWNLHVM 110 (113)
Q Consensus 89 ddF~DVn~~EKe~M~lWN~FV~ 110 (113)
+.|.++++.|+.+-+.||+|+.
T Consensus 56 q~fd~Ls~~e~~~~~s~k~~~k 77 (396)
T COG5109 56 QEFDTLSHAEADLVGSWKSLLK 77 (396)
T ss_pred CCcchhhHHHHHHHHHHHHHHH
Confidence 5688999999999999999985
No 9
>PF11161 DUF2944: Protein of unknown function (DUF2946); InterPro: IPR021332 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=17.36 E-value=75 Score=25.39 Aligned_cols=14 Identities=29% Similarity=0.240 Sum_probs=9.1
Q ss_pred eeccCccccC-CCCC
Q psy6841 54 HHTITCLPVL-PKEM 67 (113)
Q Consensus 54 fHs~T~~Pl~-p~E~ 67 (113)
+.++|.+|+. +...
T Consensus 99 l~thTg~~~~~~~~~ 113 (187)
T PF11161_consen 99 LVTHTGAPFEAPRAC 113 (187)
T ss_pred eeecCCCcccchhhe
Confidence 4577888777 5443
No 10
>PF08246 Inhibitor_I29: Cathepsin propeptide inhibitor domain (I29); InterPro: IPR013201 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This entry represents a peptidase inhibitor domain, which belongs to MEROPS peptidase inhibitor family I29. The domain is also found at the N terminus of a variety of peptidase precursors that belong to MEROPS peptidase subfamily C1A; these include cathepsin L, papain, and procaricain (P10056 from SWISSPROT) []. It forms an alpha-helical domain that runs through the substrate-binding site, preventing access. Removal of this region by proteolytic cleavage results in activation of the enzyme. This domain is also found, in one or more copies, in a variety of cysteine peptidase inhibitors such as salarin [].; PDB: 3QT4_A 3QJ3_A 2C0Y_A 2L95_A 1CJL_A 1CS8_A 7PCK_A 1BY8_A 1PCI_A 2O6X_A ....
Probab=17.31 E-value=62 Score=19.60 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=8.3
Q ss_pred HhhccCCCChhh
Q psy6841 87 MIDEFTDVNEGE 98 (113)
Q Consensus 87 ~LddF~DVn~~E 98 (113)
-|+.|+|.+.+|
T Consensus 46 ~~N~fsD~t~eE 57 (58)
T PF08246_consen 46 GLNQFSDMTPEE 57 (58)
T ss_dssp -SSTTTTSSHHH
T ss_pred eCccccCcChhh
Confidence 457788888776
Done!