Query psy9658
Match_columns 79
No_of_seqs 73 out of 75
Neff 4.6
Searched_HMMs 46136
Date Sat Aug 17 01:17:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9658hhsearch_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 1.1E-41 2.4E-46 235.5 4.1 74 2-75 18-93 (140)
2 KOG2350|consensus 100.0 5.3E-37 1.1E-41 224.2 3.9 75 2-76 96-171 (221)
3 PRK13710 plasmid maintenance p 57.8 11 0.00023 23.6 2.3 24 51-74 49-72 (72)
4 PF05299 Peptidase_M61: M61 gl 55.2 5.3 0.00011 27.1 0.6 29 4-32 11-42 (122)
5 PF08246 Inhibitor_I29: Cathep 37.7 17 0.00037 20.5 0.9 12 39-50 46-57 (58)
6 COG5109 Uncharacterized conser 33.4 32 0.0007 27.8 2.0 23 41-63 56-78 (396)
7 PF06286 Coleoptericin: Coleop 32.6 27 0.00059 24.6 1.3 37 6-42 34-75 (143)
8 PF13902 R3H-assoc: R3H-associ 31.8 38 0.00082 22.5 1.9 12 51-62 69-80 (131)
9 PF14881 Tubulin_3: Tubulin do 28.9 47 0.001 23.5 2.1 16 2-17 16-31 (180)
10 PF07362 CcdA: Post-segregatio 27.9 5.9 0.00013 24.5 -2.4 20 52-71 50-69 (72)
11 TIGR02894 DNA_bind_RsfA transc 24.2 38 0.00083 24.4 0.9 10 55-64 49-58 (161)
12 smart00848 Inhibitor_I29 Cathe 22.0 30 0.00065 18.9 0.0 12 39-50 46-57 (57)
13 PF08616 SPA: Stabilization of 20.9 77 0.0017 20.8 1.8 25 51-75 13-37 (113)
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=1.1e-41 Score=235.47 Aligned_cols=74 Identities=46% Similarity=0.745 Sum_probs=73.3
Q ss_pred CccceecccCcccCCCCC--CCCCCCCCCHHHHHHHHHHHhcccCCCChhHHHHHHHHHHHHhhhcccccccCccc
Q psy9658 2 YRLYHHTITCLPVLPKEM--DQDSDDQKDPKWLQTKTKMMIDEFTDVNEGEKELMKLWNLHVMKYGWGRHLSSASQ 75 (79)
Q Consensus 2 ~R~y~Hs~t~~pl~~~e~--d~DSEdE~D~~Wl~~k~r~~l~dF~Dv~~~EKe~M~~WN~fv~r~~~~AD~~vp~~ 75 (79)
||+||||+||+||+|+|+ |+|||||+|++||++++|++|+||+|||++||+||++||+||+|||++||+|||++
T Consensus 18 ~R~y~Hs~t~~p~~~~e~~sd~DSedE~D~~wl~~~~r~~l~dF~Dv~~~EKefM~lWN~fv~k~r~~aD~~ip~a 93 (140)
T PF09733_consen 18 NRQYFHSRTCQPMRPEEVLSDRDSEDEVDDEWLDQKHRRMLDDFSDVNEEEKEFMKLWNSFVMKQRVIADGHIPWA 93 (140)
T ss_pred CcceeccccceeccHHHhcCCCCCCCcCCHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHccCcchHHHHHH
Confidence 899999999999999999 99999999999999999999999999999999999999999999999999999987
No 2
>KOG2350|consensus
Probab=100.00 E-value=5.3e-37 Score=224.22 Aligned_cols=75 Identities=37% Similarity=0.571 Sum_probs=69.0
Q ss_pred CccceecccCcccCCCCCCCCCCCCCC-HHHHHHHHHHHhcccCCCChhHHHHHHHHHHHHhhhcccccccCcccc
Q psy9658 2 YRLYHHTITCLPVLPKEMDQDSDDQKD-PKWLQTKTKMMIDEFTDVNEGEKELMKLWNLHVMKYGWGRHLSSASQS 76 (79)
Q Consensus 2 ~R~y~Hs~t~~pl~~~e~d~DSEdE~D-~~Wl~~k~r~~l~dF~Dv~~~EKe~M~~WN~fv~r~~~~AD~~vp~~~ 76 (79)
|||||||+|||||+++++..|+|+|.| ++||+.++++||++|+|||++||+||++||+||+|||||||+|||||-
T Consensus 96 kRqffHS~t~qPl~leqvmsdrdsE~d~dd~a~~e~~~mLe~fvdvne~ekr~mkLWNsfVrkqrviAD~hipwAC 171 (221)
T KOG2350|consen 96 KRQFFHSDTCQPLRLEQVMSDRDSEKDEDDWARLETSTMLEEFVDVNEGEKRVMKLWNSFVRKQRVIADGHIPWAC 171 (221)
T ss_pred cceeeeccccCCCCHHHHhccccccccchhhhhhHHHHHHHHhccccHHHHHHHHHHHHHHHHhheeccCCCcHHH
Confidence 899999999999999999544444444 999999999999999999999999999999999999999999999984
No 3
>PRK13710 plasmid maintenance protein CcdA; Provisional
Probab=57.77 E-value=11 Score=23.58 Aligned_cols=24 Identities=13% Similarity=-0.160 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhhcccccccCcc
Q psy9658 51 KELMKLWNLHVMKYGWGRHLSSAS 74 (79)
Q Consensus 51 Ke~M~~WN~fv~r~~~~AD~~vp~ 74 (79)
++.|..+|.||-++|..+|.+=+|
T Consensus 49 ~eai~~~n~~ve~~G~~~de~R~~ 72 (72)
T PRK13710 49 REGMAEVARFIEMNGSFADENRNW 72 (72)
T ss_pred HHHHHHHHHHHHHhCCcHHhcCCC
Confidence 678999999999999999876543
No 4
>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=55.22 E-value=5.3 Score=27.11 Aligned_cols=29 Identities=17% Similarity=0.460 Sum_probs=23.0
Q ss_pred cceecccCcccCCCCC---CCCCCCCCCHHHH
Q psy9658 4 LYHHTITCLPVLPKEM---DQDSDDQKDPKWL 32 (79)
Q Consensus 4 ~y~Hs~t~~pl~~~e~---d~DSEdE~D~~Wl 32 (79)
.|||+.+..-++|.++ |.+.+.-...-|+
T Consensus 11 EffH~WnvkrirP~~l~p~dy~~~~~t~~LWv 42 (122)
T PF05299_consen 11 EFFHSWNVKRIRPAELGPFDYEKPNYTELLWV 42 (122)
T ss_pred hccccccceEeccccccCCCCCCCCCCCCEee
Confidence 5999999999999998 6666666655665
No 5
>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=37.69 E-value=17 Score=20.50 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=9.6
Q ss_pred HhcccCCCChhH
Q psy9658 39 MIDEFTDVNEGE 50 (79)
Q Consensus 39 ~l~dF~Dv~~~E 50 (79)
-|+.|+|++.+|
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 478899999887
No 6
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.45 E-value=32 Score=27.81 Aligned_cols=23 Identities=22% Similarity=0.523 Sum_probs=20.9
Q ss_pred cccCCCChhHHHHHHHHHHHHhh
Q psy9658 41 DEFTDVNEGEKELMKLWNLHVMK 63 (79)
Q Consensus 41 ~dF~Dv~~~EKe~M~~WN~fv~r 63 (79)
+.|.++++.|+.+-..||+|+.-
T Consensus 56 q~fd~Ls~~e~~~~~s~k~~~k~ 78 (396)
T COG5109 56 QEFDTLSHAEADLVGSWKSLLKE 78 (396)
T ss_pred CCcchhhHHHHHHHHHHHHHHHH
Confidence 57889999999999999999864
No 7
>PF06286 Coleoptericin: Coleoptericin; InterPro: IPR009382 This family consists of several insect coleoptericin, acaloleptin, holotricin and rhinocerosin proteins which are all known to be antibacterial proteins []. These all appear to be short, glycine-rich molecules, inducible by infection.; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=32.61 E-value=27 Score=24.65 Aligned_cols=37 Identities=11% Similarity=0.170 Sum_probs=27.3
Q ss_pred eecccCcc-cCCCCC----CCCCCCCCCHHHHHHHHHHHhcc
Q psy9658 6 HHTITCLP-VLPKEM----DQDSDDQKDPKWLQTKTKMMIDE 42 (79)
Q Consensus 6 ~Hs~t~~p-l~~~e~----d~DSEdE~D~~Wl~~k~r~~l~d 42 (79)
||+....| +.|-|+ +.-.|+|++....-+..|+.|+.
T Consensus 34 ~~~~r~~~~~~PaE~~~~~~~~de~~~em~~~~ir~rRSLQp 75 (143)
T PF06286_consen 34 YRLRRSEPQDSPAELNEYVDITDEPEAEMPYEYIRERRSLQP 75 (143)
T ss_pred hhhhcccccCChHHhhhccccccCcchhhhHHHHHHHhccCC
Confidence 66666666 778776 44558888888877888888874
No 8
>PF13902 R3H-assoc: R3H-associated N-terminal domain
Probab=31.81 E-value=38 Score=22.45 Aligned_cols=12 Identities=17% Similarity=0.266 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHh
Q psy9658 51 KELMKLWNLHVM 62 (79)
Q Consensus 51 Ke~M~~WN~fv~ 62 (79)
.++|..||.|+-
T Consensus 69 ~~~~~~Wd~f~~ 80 (131)
T PF13902_consen 69 YQNAQLWDDFRN 80 (131)
T ss_pred HHHHHHHHHHhh
Confidence 677888888874
No 9
>PF14881 Tubulin_3: Tubulin domain
Probab=28.87 E-value=47 Score=23.51 Aligned_cols=16 Identities=13% Similarity=-0.056 Sum_probs=14.0
Q ss_pred CccceecccCcccCCC
Q psy9658 2 YRLYHHTITCLPVLPK 17 (79)
Q Consensus 2 ~R~y~Hs~t~~pl~~~ 17 (79)
+|.+||.+|.++|..-
T Consensus 16 ~r~~yhPrSl~~l~~~ 31 (180)
T PF14881_consen 16 NRVHYHPRSLNQLNDY 31 (180)
T ss_pred CcceeCCCceEEcCcc
Confidence 6999999999999754
No 10
>PF07362 CcdA: Post-segregation antitoxin CcdA; InterPro: IPR009956 This entry consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein [].; PDB: 3HPW_C 2H3C_A 2H3A_B 2ADN_B 2ADL_B.
Probab=27.85 E-value=5.9 Score=24.51 Aligned_cols=20 Identities=20% Similarity=0.120 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhhhccccccc
Q psy9658 52 ELMKLWNLHVMKYGWGRHLS 71 (79)
Q Consensus 52 e~M~~WN~fv~r~~~~AD~~ 71 (79)
+.|..||.||-++|..+|.+
T Consensus 50 ~ai~~~N~~ve~~G~~~de~ 69 (72)
T PF07362_consen 50 EAIEAYNRFVEEHGLFSDEY 69 (72)
T ss_dssp CSCCSSSHSSSCSSSCSSSC
T ss_pred HHHHHHHHHHHHcCCcHHHc
Confidence 45778999999999999876
No 11
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=24.23 E-value=38 Score=24.36 Aligned_cols=10 Identities=40% Similarity=0.411 Sum_probs=8.4
Q ss_pred HHHHHHHhhh
Q psy9658 55 KLWNLHVMKY 64 (79)
Q Consensus 55 ~~WN~fv~r~ 64 (79)
..||+.|+|+
T Consensus 49 FRWNs~VRkq 58 (161)
T TIGR02894 49 FRWNAYVRKQ 58 (161)
T ss_pred chHHHHHHHH
Confidence 4799999975
No 12
>smart00848 Inhibitor_I29 Cathepsin propeptide inhibitor domain (I29). This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS. 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 s
Probab=22.00 E-value=30 Score=18.94 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=8.8
Q ss_pred HhcccCCCChhH
Q psy9658 39 MIDEFTDVNEGE 50 (79)
Q Consensus 39 ~l~dF~Dv~~~E 50 (79)
-++.|+|++++|
T Consensus 46 ~~N~fsDlt~eE 57 (57)
T smart00848 46 GLNQFADLTNEE 57 (57)
T ss_pred cCcccccCCCCC
Confidence 357888888765
No 13
>PF08616 SPA: Stabilization of polarity axis
Probab=20.94 E-value=77 Score=20.78 Aligned_cols=25 Identities=20% Similarity=0.217 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhhhcccccccCccc
Q psy9658 51 KELMKLWNLHVMKYGWGRHLSSASQ 75 (79)
Q Consensus 51 Ke~M~~WN~fv~r~~~~AD~~vp~~ 75 (79)
-+.|.+||+-+.++|++-=++-|++
T Consensus 13 ~~i~~L~~alL~~krivv~s~~~~~ 37 (113)
T PF08616_consen 13 PEIILLWEALLLGKRIVVYSPSPSA 37 (113)
T ss_pred hHHHHHHHHHHhCCCEEEECCCCCH
Confidence 4689999999999998877776665
Done!