Query psy6898
Match_columns 111
No_of_seqs 115 out of 1285
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 21:17:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3546|consensus 98.7 7.6E-08 1.6E-12 79.9 9.5 11 80-90 525-535 (1167)
2 PF08253 Leader_Erm: Erm Leade 16.8 97 0.0021 14.0 1.1 8 104-111 6-13 (19)
3 KOG4740|consensus 14.2 86 0.0019 26.5 1.0 8 104-111 539-546 (564)
4 PHA00003 B internal scaffoldin 8.8 1.3E+02 0.0027 20.1 0.2 6 106-111 105-110 (120)
5 KOG4207|consensus 8.5 1.8E+02 0.004 21.8 1.0 8 104-111 56-63 (256)
6 COG5134 Uncharacterized conser 7.8 1.9E+02 0.0041 21.7 0.8 10 102-111 70-79 (272)
7 PF02304 Phage_B: Scaffold pro 7.3 1.2E+02 0.0027 20.1 -0.3 5 107-111 103-107 (117)
8 PF11399 DUF3192: Protein of u 6.2 3E+02 0.0065 18.0 1.0 7 105-111 62-68 (102)
9 PF01834 XRCC1_N: XRCC1 N term 5.5 2E+02 0.0042 20.2 -0.1 15 97-111 138-152 (153)
10 KOG1924|consensus 5.3 2.2E+03 0.049 19.7 9.2 76 15-90 521-603 (1102)
No 1
>KOG3546|consensus
Probab=98.74 E-value=7.6e-08 Score=79.87 Aligned_cols=11 Identities=9% Similarity=-0.179 Sum_probs=4.1
Q ss_pred CCCCCCCCCCC
Q psy6898 80 YAMGADTKSFS 90 (111)
Q Consensus 80 G~~G~~g~~g~ 90 (111)
|.++.+++++.
T Consensus 525 gppgppgppgp 535 (1167)
T KOG3546|consen 525 GPPGPPGPPGP 535 (1167)
T ss_pred CCCCCCCCCCC
Confidence 33333333333
No 2
>PF08253 Leader_Erm: Erm Leader peptide ; InterPro: IPR013204 These short proteins are leader peptides (15-19 amino acids) of erm genes that code for resistance determinants in Staphylococcus aureus [].
Probab=16.83 E-value=97 Score=14.01 Aligned_cols=8 Identities=38% Similarity=0.393 Sum_probs=5.8
Q ss_pred ceeEEeeC
Q psy6898 104 GLVIYRFH 111 (111)
Q Consensus 104 g~~~~r~~ 111 (111)
-|+|.|||
T Consensus 6 iFVI~~vh 13 (19)
T PF08253_consen 6 IFVINTVH 13 (19)
T ss_pred EEEEEeec
Confidence 46777877
No 3
>KOG4740|consensus
Probab=14.18 E-value=86 Score=26.53 Aligned_cols=8 Identities=50% Similarity=1.123 Sum_probs=5.7
Q ss_pred ceeEEeeC
Q psy6898 104 GLVIYRFH 111 (111)
Q Consensus 104 g~~~~r~~ 111 (111)
=.+|||||
T Consensus 539 L~IFYRFH 546 (564)
T KOG4740|consen 539 LVIFYRFH 546 (564)
T ss_pred eEEEEecc
Confidence 35688888
No 4
>PHA00003 B internal scaffolding protein
Probab=8.75 E-value=1.3e+02 Score=20.09 Aligned_cols=6 Identities=50% Similarity=1.099 Sum_probs=3.8
Q ss_pred eEEeeC
Q psy6898 106 VIYRFH 111 (111)
Q Consensus 106 ~~~r~~ 111 (111)
.|||||
T Consensus 105 EFYRFn 110 (120)
T PHA00003 105 EFYRFN 110 (120)
T ss_pred Hheecc
Confidence 367776
No 5
>KOG4207|consensus
Probab=8.52 E-value=1.8e+02 Score=21.79 Aligned_cols=8 Identities=50% Similarity=1.094 Sum_probs=0.0
Q ss_pred ceeEEeeC
Q psy6898 104 GLVIYRFH 111 (111)
Q Consensus 104 g~~~~r~~ 111 (111)
||.|+|||
T Consensus 56 gFaFVrf~ 63 (256)
T KOG4207|consen 56 GFAFVRFH 63 (256)
T ss_pred ceeEEEee
No 6
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=7.85 E-value=1.9e+02 Score=21.74 Aligned_cols=10 Identities=40% Similarity=0.494 Sum_probs=0.0
Q ss_pred hcceeEEeeC
Q psy6898 102 AAGLVIYRFH 111 (111)
Q Consensus 102 ~~g~~~~r~~ 111 (111)
+.++.+||||
T Consensus 70 y~~~kiYRf~ 79 (272)
T COG5134 70 YYTTKIYRFS 79 (272)
T ss_pred cceeEEEEEE
No 7
>PF02304 Phage_B: Scaffold protein B; InterPro: IPR003513 This is a family of proteins from single-stranded DNA bacteriophages. Scaffold proteins B and D are required for procapsid formation. Sixty copies of the internal scaffold protein B are found in the procapsid.; GO: 0019069 viral capsid assembly, 0046729 viral procapsid; PDB: 1CD3_B 1AL0_B.
Probab=7.27 E-value=1.2e+02 Score=20.09 Aligned_cols=5 Identities=60% Similarity=1.444 Sum_probs=0.0
Q ss_pred EEeeC
Q psy6898 107 IYRFH 111 (111)
Q Consensus 107 ~~r~~ 111 (111)
|||||
T Consensus 103 FYRFn 107 (117)
T PF02304_consen 103 FYRFN 107 (117)
T ss_dssp S----
T ss_pred heeec
No 8
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=6.16 E-value=3e+02 Score=17.97 Aligned_cols=7 Identities=29% Similarity=0.766 Sum_probs=0.0
Q ss_pred eeEEeeC
Q psy6898 105 LVIYRFH 111 (111)
Q Consensus 105 ~~~~r~~ 111 (111)
++|||.|
T Consensus 62 VLfYrT~ 68 (102)
T PF11399_consen 62 VLFYRTQ 68 (102)
T ss_pred EEEEEEe
No 9
>PF01834 XRCC1_N: XRCC1 N terminal domain; InterPro: IPR002706 DNA-repair protein Xrcc1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP []. The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex [].; GO: 0003684 damaged DNA binding, 0000012 single strand break repair, 0005634 nucleus; PDB: 3K77_E 3K75_C 3LQC_A 1XNA_A 1XNT_A.
Probab=5.54 E-value=2e+02 Score=20.23 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=0.0
Q ss_pred HHHhhhcceeEEeeC
Q psy6898 97 VQRAIAAGLVIYRFH 111 (111)
Q Consensus 97 ~~~~~~~g~~~~r~~ 111 (111)
+......||.|+|||
T Consensus 138 fnk~~~yGLsFi~~~ 152 (153)
T PF01834_consen 138 FNKHVQYGLSFIKFH 152 (153)
T ss_dssp S-SSS--EEEEEEEE
T ss_pred CCCCCccceEEEEEe
No 10
>KOG1924|consensus
Probab=5.26 E-value=2.2e+03 Score=19.68 Aligned_cols=76 Identities=20% Similarity=0.062 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy6898 15 DRRDIGRAISTVIS--GRIGLDGRDGLPGEPGLDGIPGRNGMD-----GIPGKDGLPGKDGIPGTNGTKTDHYAMGADTK 87 (111)
Q Consensus 15 ~~g~~g~~g~~G~p--G~~G~~G~~G~~G~~G~~G~~G~~G~~-----G~~G~~G~~G~~G~~G~~G~~G~~G~~G~~g~ 87 (111)
...+.+.+.++..| |-.+.+-+++++=.+|-.|.|=++.+. +++-.+=++|..|.+=++-..|-+|-+-++=.
T Consensus 521 ~~~~~~iP~PP~~pp~gG~g~pppPppPPlpggag~PPPPpplPg~aG~PPpPppppg~~gppPPPpp~g~~Gg~ppPP~ 600 (1102)
T KOG1924|consen 521 LPIDGGIPPPPPLPPTGGTGPPPPPPPPPLPGGAGPPPPPPPLPGIAGGPPPPPPPPGGGGPPPPPPPGGFLGGPPPPPP 600 (1102)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCcccCCCCccCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q ss_pred CCC
Q psy6898 88 SFS 90 (111)
Q Consensus 88 ~g~ 90 (111)
++.
T Consensus 601 ~gm 603 (1102)
T KOG1924|consen 601 PGM 603 (1102)
T ss_pred CCc
Done!