Query psy6895
Match_columns 63
No_of_seqs 63 out of 65
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 21:12:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04516 CP2: CP2 transcriptio 99.1 2.6E-11 5.6E-16 87.5 1.2 43 21-63 85-127 (236)
2 KOG4091|consensus 99.0 1.1E-10 2.5E-15 90.7 3.1 43 21-63 117-159 (463)
3 PF04516 CP2: CP2 transcriptio 97.8 3.2E-06 7E-11 61.2 -0.2 39 1-39 94-133 (236)
4 KOG4091|consensus 97.7 9.8E-06 2.1E-10 63.5 0.9 33 1-33 126-158 (463)
5 PF12759 HTH_Tnp_IS1: InsA C-t 27.0 13 0.00028 21.2 -0.9 15 49-63 3-17 (46)
6 PF11491 DUF3213: Protein of u 24.5 53 0.0012 21.1 1.5 15 29-43 38-52 (88)
7 PF00511 PPV_E2_C: E2 (early) 19.3 31 0.00066 21.3 -0.4 10 39-48 8-17 (81)
8 PF12512 DUF3717: Protein of u 15.5 60 0.0013 19.9 0.3 17 39-55 5-22 (71)
9 PF08761 dUTPase_2: dUTPase; 13.9 40 0.00086 22.4 -0.9 7 44-50 54-60 (167)
10 PF09866 DUF2093: Uncharacteri 13.8 2.2E+02 0.0047 16.0 2.2 17 30-46 9-25 (42)
No 1
>PF04516 CP2: CP2 transcription factor; InterPro: IPR007604 This entry represents a conserved region in the CP2 transcription factor family.
Probab=99.09 E-value=2.6e-11 Score=87.46 Aligned_cols=43 Identities=28% Similarity=0.552 Sum_probs=40.2
Q ss_pred ccCccceeeEEeeecCCCcHHHHhhcccCCCCCCCccceeecC
Q psy6895 21 HSRQHSSIVMLMFREEKSPEDEIKAWQFWHSRQHSVKYFRIHF 63 (63)
Q Consensus 21 hsrqv~Sv~mvVf~e~K~~e~elk~wq~WhsrQ~~~kqr~~~~ 63 (63)
+...++|++||+|.|++.+.+|+++|++||++||++|||||||
T Consensus 85 ~~~~~kS~I~v~F~d~~~~~~~~~~w~~W~~~q~g~k~r~lei 127 (236)
T PF04516_consen 85 QPSKVKSVIRVVFHDEKLRYEEAKQWQLWKARQPGGKQRALEI 127 (236)
T ss_pred CCcceeEEEEEEEcCCccccCHHHHHHHHHHhCCCchhhhhhh
Confidence 4445899999999999999999999999999999999999986
No 2
>KOG4091|consensus
Probab=99.04 E-value=1.1e-10 Score=90.74 Aligned_cols=43 Identities=47% Similarity=0.740 Sum_probs=39.8
Q ss_pred ccCccceeeEEeeecCCCcHHHHhhcccCCCCCCCccceeecC
Q psy6895 21 HSRQHSSIVMLMFREEKSPEDEIKAWQFWHSRQHSVKYFRIHF 63 (63)
Q Consensus 21 hsrqv~Sv~mvVf~e~K~~e~elk~wq~WhsrQ~~~kqr~~~~ 63 (63)
++..++|++||||.|.|+.++|++.|++||++||+++||++||
T Consensus 117 ns~~~~Sii~vvf~e~k~~~~e~k~~q~w~~~~~~~~~r~ldv 159 (463)
T KOG4091|consen 117 NSKVVKSIIMVVFHEDKNQETEHKQWQGWHSRQHSAKQRILDI 159 (463)
T ss_pred cccccceEEEEEeeccccchhHhhhhhhhhhcCccccCceecc
Confidence 4455579999999999999999999999999999999999996
No 3
>PF04516 CP2: CP2 transcription factor; InterPro: IPR007604 This entry represents a conserved region in the CP2 transcription factor family.
Probab=97.84 E-value=3.2e-06 Score=61.20 Aligned_cols=39 Identities=28% Similarity=0.491 Sum_probs=35.7
Q ss_pred CccccCCCCchHHhhhhcccccCccceeeEEeee-cCCCc
Q psy6895 1 MLMFREEKSPEDEIKAWQFWHSRQHSSIVMLMFR-EEKSP 39 (63)
Q Consensus 1 m~vf~e~k~~e~~~k~w~~Whsrqv~Sv~mvVf~-e~K~~ 39 (63)
||||.|++.++.+++||++||++|+..++++|.. |-+..
T Consensus 94 ~v~F~d~~~~~~~~~~w~~W~~~q~g~k~r~leivD~~~s 133 (236)
T PF04516_consen 94 RVVFHDEKLRYEEAKQWQLWKARQPGGKQRALEIVDIKQS 133 (236)
T ss_pred EEEEcCCccccCHHHHHHHHHHhCCCchhhhhhhccCCCC
Confidence 6899999999999999999999999999999988 66553
No 4
>KOG4091|consensus
Probab=97.74 E-value=9.8e-06 Score=63.54 Aligned_cols=33 Identities=48% Similarity=0.809 Sum_probs=32.4
Q ss_pred CccccCCCCchHHhhhhcccccCccceeeEEee
Q psy6895 1 MLMFREEKSPEDEIKAWQFWHSRQHSSIVMLMF 33 (63)
Q Consensus 1 m~vf~e~k~~e~~~k~w~~Whsrqv~Sv~mvVf 33 (63)
||||+|+|+.++|+|.|++||+++|++..++.+
T Consensus 126 ~vvf~e~k~~~~e~k~~q~w~~~~~~~~~r~ld 158 (463)
T KOG4091|consen 126 MVVFHEDKNQETEHKQWQGWHSRQHSAKQRILD 158 (463)
T ss_pred EEEeeccccchhHhhhhhhhhhcCccccCceec
Confidence 799999999999999999999999999999998
No 5
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=26.96 E-value=13 Score=21.23 Aligned_cols=15 Identities=13% Similarity=0.330 Sum_probs=12.5
Q ss_pred CCCCCCCccceeecC
Q psy6895 49 WHSRQHSVKYFRIHF 63 (63)
Q Consensus 49 WhsrQ~~~kqr~~~~ 63 (63)
+.+++|..|+.|+|+
T Consensus 3 Y~A~kpgikeqIvem 17 (46)
T PF12759_consen 3 YEARKPGIKEQIVEM 17 (46)
T ss_pred ccccCccHHHHHHHH
Confidence 468899999999875
No 6
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=24.46 E-value=53 Score=21.12 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=8.7
Q ss_pred eEEeeecCCCcHHHH
Q psy6895 29 VMLMFREEKSPEDEI 43 (63)
Q Consensus 29 ~mvVf~e~K~~e~el 43 (63)
-+|||.++|.+.++|
T Consensus 38 g~VifDe~kl~~e~l 52 (88)
T PF11491_consen 38 GFVIFDESKLSKEEL 52 (88)
T ss_dssp -EEE--B-S-SHHHH
T ss_pred eEEEECcccCCHHHH
Confidence 378999999998887
No 7
>PF00511 PPV_E2_C: E2 (early) protein, C terminal; InterPro: IPR000427 E2 is an early regulatory protein found in the dsDNA papillomaviruses. The viral genome is a 7.9-kb circular DNA that codes for at least eight early and two late (capsid) proteins. The products of the early genes E6 and E7 are oncoproteins that destabilise the cellular tumour suppressors p53 and pRB. The product of the E1 gene is a helicase necessary for viral DNA replication. The products of the E2 gene play key roles in the regulation of viral gene transcription and DNA replication. During early stages of viral infection, the E2 protein represses the transcription of the oncogenes E6 and E7, reintroduction of E2 into cervical cancer cell-lines leads to repression of E6/E7 transcription, stabilisation of the tumour suppressor p53, and cell-cycle arrest at the G1 phase of the cell cycle. E2 can also induce apoptosis by a p53-independent mechanism. E2 proteins from all papillomavirus strains bind a consensus palindromic sequence ACCgNNNNcGGT present in multiple copies in the regulatory region. It can either activate or repress transcription, depending on E2RE's position with regard to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E2 protein is composed of a C-terminal DNA-binding domain and an N-terminal trans-activation domain. E2 exists in solution and binds to DNA as a dimer The E2-DNA binding domain forms a dimeric beta-barrel, with each subunit contributing an anti-parallel 4-stranded beta-sheet "half-barrel" [, ]. The topology of each subunit is beta1-1-beta2-beta3-2-beta4. Helix 1 is the recognition helix housing all of the amino acid residues involved in direct DNA sequence specification. Upon dimerisation, strands beta2 and beta4 at the edges of each subunit participate in a continuous hydrogen-bonding network, which results in an 8-stranded beta-barrel. The dimer interface is extensive, made up of hydrogen bonds between subunits and a substantial hydrophobic beta-barrel core. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006275 regulation of DNA replication, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1JJH_C 1DBD_B 2BOP_A 1DHM_B 1A7G_E 1JJ4_B 1F9F_D 2AYG_A 2AYE_E 2AYB_A ....
Probab=19.28 E-value=31 Score=21.26 Aligned_cols=10 Identities=30% Similarity=1.292 Sum_probs=6.6
Q ss_pred cHHHHhhccc
Q psy6895 39 PEDEIKAWQF 48 (63)
Q Consensus 39 ~e~elk~wq~ 48 (63)
+-.+||||+|
T Consensus 8 ~~N~LKC~Ry 17 (81)
T PF00511_consen 8 PANQLKCWRY 17 (81)
T ss_dssp EHHHHHHHHH
T ss_pred CCccccChhh
Confidence 4566777765
No 8
>PF12512 DUF3717: Protein of unknown function (DUF3717) ; InterPro: IPR022191 This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 117 amino acids in length. There is a conserved AIN sequence motif. There are two completely conserved residues (L and Y) that may be functionally important.
Probab=15.50 E-value=60 Score=19.89 Aligned_cols=17 Identities=29% Similarity=0.634 Sum_probs=13.3
Q ss_pred cHHHH-hhcccCCCCCCC
Q psy6895 39 PEDEI-KAWQFWHSRQHS 55 (63)
Q Consensus 39 ~e~el-k~wq~WhsrQ~~ 55 (63)
.+.|| .+++||-.|.|+
T Consensus 5 ~I~dIE~AIN~WR~r~Ps 22 (71)
T PF12512_consen 5 SITDIEAAINYWRARSPS 22 (71)
T ss_pred CHHHHHHHHHHHHhcCCC
Confidence 34566 789999888888
No 9
>PF08761 dUTPase_2: dUTPase; InterPro: IPR014871 2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate (3.6.1.23 from EC). Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms. This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4. ; PDB: 2YB0_E 2YAZ_B 2YAY_A 2CJE_A 1OGK_A 1OGL_A 1W2Y_B 2CIC_A.
Probab=13.87 E-value=40 Score=22.39 Aligned_cols=7 Identities=14% Similarity=1.341 Sum_probs=1.5
Q ss_pred hhcccCC
Q psy6895 44 KAWQFWH 50 (63)
Q Consensus 44 k~wq~Wh 50 (63)
++|+||-
T Consensus 54 ~~fK~Wk 60 (167)
T PF08761_consen 54 RCFKYWK 60 (167)
T ss_dssp ----SSS
T ss_pred cchHhhc
Confidence 4555553
No 10
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=13.78 E-value=2.2e+02 Score=16.02 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=10.3
Q ss_pred EEeeecCCCcHHHHhhc
Q psy6895 30 MLMFREEKSPEDEIKAW 46 (63)
Q Consensus 30 mvVf~e~K~~e~elk~w 46 (63)
.--.+..+.|.|+|+.|
T Consensus 9 ~CAVTg~~IpLd~LrYW 25 (42)
T PF09866_consen 9 RCAVTGQPIPLDELRYW 25 (42)
T ss_pred EEEeeCCcccHHHhccC
Confidence 33445667777777644
Done!