Query psy12049
Match_columns 102
No_of_seqs 13 out of 15
Neff 2.1
Searched_HMMs 46136
Date Fri Aug 16 17:18:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08789 PBCV_basic_adap: PBCV 9.0 1.8E+02 0.0038 18.0 0.9 17 20-36 7-23 (40)
2 PF06136 DUF966: Domain of unk 4.9 2.6E+02 0.0057 23.0 0.2 8 21-28 79-86 (337)
3 cd08973 BaFpgNei_N_1 Uncharact 4.5 2.8E+02 0.0061 18.8 0.1 20 19-38 44-63 (122)
4 KOG1273|consensus 4.0 3.9E+02 0.0085 23.6 0.6 17 18-34 162-178 (405)
5 COG4738 Predicted transcriptio 3.9 4.2E+02 0.009 20.0 0.6 8 2-9 79-86 (124)
6 CHL00141 rpl24 ribosomal prote 3.8 4E+02 0.0088 17.8 0.4 11 23-33 16-26 (83)
7 cd08773 FpgNei_N N-terminal do 3.6 3.7E+02 0.0081 17.7 0.1 19 19-37 44-62 (117)
8 COG0745 OmpR Response regulato 3.5 3.8E+02 0.0082 20.3 0.0 6 97-102 94-99 (229)
9 cd08974 BaFpgNei_N_2 Uncharact 3.3 4.2E+02 0.0091 17.6 0.1 19 19-37 36-54 (98)
10 PF04255 DUF433: Protein of un 3.2 4.8E+02 0.01 15.7 0.4 12 19-30 8-19 (56)
No 1
>PF08789 PBCV_basic_adap: PBCV-specific basic adaptor domain; InterPro: IPR014897 The small PBCV-specific basic adaptor protein is found fused to S/T protein kinases and the 2-Cysteine domain [].
Probab=9.00 E-value=1.8e+02 Score=17.96 Aligned_cols=17 Identities=35% Similarity=0.827 Sum_probs=8.7
Q ss_pred ccccccccccccccccc
Q psy12049 20 EGKYVMKGSDKGEYVMK 36 (102)
Q Consensus 20 ~gk~vlkgtrrGk~~lK 36 (102)
.|..|++|++=|++|+.
T Consensus 7 kgR~i~~g~rGg~yV~~ 23 (40)
T PF08789_consen 7 KGRKIFKGPRGGTYVIS 23 (40)
T ss_pred cCCEEEECCCCCEEEeC
Confidence 34455555555555543
No 2
>PF06136 DUF966: Domain of unknown function (DUF966); InterPro: IPR010369 This is a family of plant proteins confined to monocotyledons and mosses, with unknown function
Probab=4.92 E-value=2.6e+02 Score=23.03 Aligned_cols=8 Identities=63% Similarity=1.149 Sum_probs=4.1
Q ss_pred cccccccc
Q psy12049 21 GKYVMKGS 28 (102)
Q Consensus 21 gk~vlkgt 28 (102)
+-|||||+
T Consensus 79 ~EYVLKGS 86 (337)
T PF06136_consen 79 NEYVLKGS 86 (337)
T ss_pred CceEeecc
Confidence 44555554
No 3
>cd08973 BaFpgNei_N_1 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=4.47 E-value=2.8e+02 Score=18.84 Aligned_cols=20 Identities=20% Similarity=0.076 Sum_probs=14.4
Q ss_pred cccccccccccccccccccc
Q psy12049 19 DEGKYVMKGSDKGEYVMKSS 38 (102)
Q Consensus 19 ~~gk~vlkgtrrGk~~lKgt 38 (102)
-.|+.|..=.|+||+++=-.
T Consensus 44 L~G~~i~~v~RrGK~l~~~~ 63 (122)
T cd08973 44 LEGRTVTGVRRHGKRLDFEF 63 (122)
T ss_pred CCCCEEeEEEEEeeEEEEEc
Confidence 45777778888888876543
No 4
>KOG1273|consensus
Probab=3.99 E-value=3.9e+02 Score=23.56 Aligned_cols=17 Identities=35% Similarity=0.888 Sum_probs=13.4
Q ss_pred ccccccccccccccccc
Q psy12049 18 SDEGKYVMKGSDKGEYV 34 (102)
Q Consensus 18 ~~~gk~vlkgtrrGk~~ 34 (102)
+++|||++-||-+||-.
T Consensus 162 dr~g~yIitGtsKGkll 178 (405)
T KOG1273|consen 162 DRRGKYIITGTSKGKLL 178 (405)
T ss_pred cCCCCEEEEecCcceEE
Confidence 57888888888888753
No 5
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=3.90 E-value=4.2e+02 Score=20.00 Aligned_cols=8 Identities=63% Similarity=1.182 Sum_probs=6.3
Q ss_pred CCCccccc
Q psy12049 2 KGKGRSVH 9 (102)
Q Consensus 2 ~~~~~~~~ 9 (102)
+||||.+|
T Consensus 79 kGKGRPik 86 (124)
T COG4738 79 KGKGRPIK 86 (124)
T ss_pred cCCCCCce
Confidence 58888876
No 6
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=3.76 E-value=4e+02 Score=17.80 Aligned_cols=11 Identities=45% Similarity=0.830 Sum_probs=6.7
Q ss_pred ccccccccccc
Q psy12049 23 YVMKGSDKGEY 33 (102)
Q Consensus 23 ~vlkgtrrGk~ 33 (102)
+||.|.++||+
T Consensus 16 ~Vi~G~dKGK~ 26 (83)
T CHL00141 16 KIISGSDKGKI 26 (83)
T ss_pred EEeEcCCCCcE
Confidence 45666666654
No 7
>cd08773 FpgNei_N N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One e
Probab=3.63 E-value=3.7e+02 Score=17.68 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=13.6
Q ss_pred ccccccccccccccccccc
Q psy12049 19 DEGKYVMKGSDKGEYVMKS 37 (102)
Q Consensus 19 ~~gk~vlkgtrrGk~~lKg 37 (102)
-.|+.|..=.++||+++=-
T Consensus 44 l~G~~i~~v~r~GK~l~~~ 62 (117)
T cd08773 44 LIGRRVRGAERRGKYLLLE 62 (117)
T ss_pred cCCCEEeeEEEeeeEEEEE
Confidence 3577777778888887643
No 8
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=3.46 E-value=3.8e+02 Score=20.27 Aligned_cols=6 Identities=67% Similarity=1.481 Sum_probs=2.8
Q ss_pred CCCCCC
Q psy12049 97 GSDDYV 102 (102)
Q Consensus 97 ~~~~~~ 102 (102)
|+||||
T Consensus 94 GADDYl 99 (229)
T COG0745 94 GADDYL 99 (229)
T ss_pred cCCeee
Confidence 445553
No 9
>cd08974 BaFpgNei_N_2 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=3.27 E-value=4.2e+02 Score=17.65 Aligned_cols=19 Identities=16% Similarity=0.120 Sum_probs=13.6
Q ss_pred ccccccccccccccccccc
Q psy12049 19 DEGKYVMKGSDKGEYVMKS 37 (102)
Q Consensus 19 ~~gk~vlkgtrrGk~~lKg 37 (102)
-.|..+..=.|+||+.+=-
T Consensus 36 l~G~~i~~v~RrGK~L~~~ 54 (98)
T cd08974 36 LAGQKVLAIRSWGKHFLLE 54 (98)
T ss_pred cCCCEEEEEEEEccEEEEE
Confidence 4577777778888887643
No 10
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=3.25 E-value=4.8e+02 Score=15.67 Aligned_cols=12 Identities=25% Similarity=0.404 Sum_probs=6.2
Q ss_pred cccccccccccc
Q psy12049 19 DEGKYVMKGSDK 30 (102)
Q Consensus 19 ~~gk~vlkgtrr 30 (102)
-.|+-|++|||-
T Consensus 8 ~~G~P~i~GTRI 19 (56)
T PF04255_consen 8 LGGQPVIRGTRI 19 (56)
T ss_dssp GGG--EETTSS-
T ss_pred cCCcceEcCcee
Confidence 356777777763
Done!