Query 537021.9.peg.15_1 Match_columns 47 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 22 15:58:10 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_15.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK11424 DNA-binding transcrip 21.1 76 0.0019 14.6 2.3 33 14-46 65-105 (114) 2 TIGR01934 MenG_MenH_UbiE ubiqu 19.8 59 0.0015 15.1 1.5 27 17-43 198-224 (242) 3 pfam12070 DUF3550 Protein of u 18.5 87 0.0022 14.3 2.6 29 6-34 63-91 (512) 4 cd03186 GST_C_SspA GST_N famil 17.5 76 0.0019 14.5 1.6 19 28-46 43-62 (107) 5 TIGR00588 ogg 8-oxoguanine DNA 14.5 77 0.002 14.5 1.0 17 12-28 230-246 (379) 6 TIGR02235 menA_cyano-plnt 1,4- 11.2 1.4E+02 0.0036 13.2 1.5 15 28-42 179-193 (293) 7 pfam05568 ASFV_J13L African sw 9.5 1.3E+02 0.0033 13.4 0.9 11 29-39 45-55 (189) 8 PRK10494 hypothetical protein; 9.0 1.7E+02 0.0044 12.7 3.8 27 20-46 36-62 (259) 9 PRK00753 psbL photosystem II r 8.2 1.7E+02 0.0044 12.7 1.1 12 30-41 27-38 (39) 10 KOG1589 consensus 7.8 1.2E+02 0.0031 13.5 0.2 10 34-43 77-86 (118) No 1 >PRK11424 DNA-binding transcriptional activator TdcR; Provisional Probab=21.10 E-value=76 Score=14.56 Aligned_cols=33 Identities=39% Similarity=0.684 Sum_probs=22.7 Q ss_pred HHHHHHHHHHHHHHH--------HHHHHHHHHCCHHHHHCC Q ss_conf 999999887789999--------999999982461242104 Q 537021.9.peg.1 14 YFAKYLRESTRAFFS--------LATLLYLFSSNFFLSDRF 46 (47) Q Consensus 14 yfakylrestraffs--------latllylfssnfflsdrf 46 (47) .|..||-|...-|+. ...|--|...|||-|||- T Consensus 65 ifsryllenkhlfyqyfkisntgidhleqlinvnffssdrt 105 (114) T PRK11424 65 IFSRYLLENKHLFYQYFKISNTGIDHLEQLINVNFFSSDRT 105 (114) T ss_pred HHHHHHHHCCHHHHHEEEECCCCHHHHHHHHCCCEECCCCC T ss_conf 99999973223444012313666578998751120116764 No 2 >TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities . Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity. Probab=19.80 E-value=59 Score=15.11 Aligned_cols=27 Identities=37% Similarity=0.405 Sum_probs=21.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHH Q ss_conf 999887789999999999982461242 Q 537021.9.peg.1 17 KYLRESTRAFFSLATLLYLFSSNFFLS 43 (47) Q Consensus 17 kylrestraffslatllylfssnffls 43 (47) .||-||+++|-+-.++--.+.+-=|-+ T Consensus 198 ~YL~eSi~~FP~~~~l~~~~~~aGF~~ 224 (242) T TIGR01934 198 EYLPESIRAFPSQEELAAMLKEAGFEE 224 (242) T ss_pred HHHHHHHHHCCCHHHHHHHHHHCCCCC T ss_conf 778899875389889999999738632 No 3 >pfam12070 DUF3550 Protein of unknown function (DUF3550/UPF0682). This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length. Probab=18.54 E-value=87 Score=14.25 Aligned_cols=29 Identities=31% Similarity=0.519 Sum_probs=22.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999887789999999999 Q 537021.9.peg.1 6 IHDFLIFLYFAKYLRESTRAFFSLATLLY 34 (47) Q Consensus 6 ihdfliflyfakylrestraffslatlly 34 (47) |---.--||+.-|||.|...|.+-|...| T Consensus 63 IASkIgQLYY~yYLRTSet~yL~Eay~FY 91 (512) T pfam12070 63 IASKIGQLYYHYYLRTSETNYLNEAFVFY 91 (512) T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHH T ss_conf 99999999999888614322567999999 No 4 >cd03186 GST_C_SspA GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival during nutrient starvation. SspA adopts the GST fold with an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, but it does not bind glutathione (GSH) and lacks GST activity. SspA is highly conserved among gram-negative bacteria. Related proteins found in Neisseria (called RegF), Francisella and Vibrio regulate the expression of virulence factors necessary for pathogenesis. Probab=17.54 E-value=76 Score=14.55 Aligned_cols=19 Identities=37% Similarity=0.754 Sum_probs=14.0 Q ss_pred HHHHHHHHHHCC-HHHHHCC Q ss_conf 999999998246-1242104 Q 537021.9.peg.1 28 SLATLLYLFSSN-FFLSDRF 46 (47) Q Consensus 28 slatllylfssn-fflsdrf 46 (47) +|.++.-+|+.+ ||+||.| T Consensus 43 ~L~~l~p~F~~~pyFmsdEF 62 (107) T cd03186 43 SLLALAPVFAHKPYFMSEEF 62 (107) T ss_pred HHHHHHHHHCCCCCCCCCCC T ss_conf 99999999804844022652 No 5 >TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus. Probab=14.50 E-value=77 Score=14.53 Aligned_cols=17 Identities=41% Similarity=0.776 Sum_probs=12.8 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999887789999 Q 537021.9.peg.1 12 FLYFAKYLRESTRAFFS 28 (47) Q Consensus 12 flyfakylrestraffs 28 (47) +=|=|+|.+||.|+... T Consensus 230 ~GYRA~Yi~~tar~l~e 246 (379) T TIGR00588 230 LGYRARYIRETARALLE 246 (379) T ss_pred CCCCCHHHHHHHHHHHH T ss_conf 87540689999999884 No 6 >TIGR02235 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase; InterPro: IPR011937 This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I . The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility.. Probab=11.16 E-value=1.4e+02 Score=13.20 Aligned_cols=15 Identities=53% Similarity=0.707 Sum_probs=12.6 Q ss_pred HHHHHHHHHHCCHHH Q ss_conf 999999998246124 Q 537021.9.peg.1 28 SLATLLYLFSSNFFL 42 (47) Q Consensus 28 slatllylfssnffl 42 (47) |++|-+-||.|||+- T Consensus 179 ~~~TtliLFCsHFHQ 193 (293) T TIGR02235 179 ALATTLILFCSHFHQ 193 (293) T ss_pred HHHHHHHHHHHCCCC T ss_conf 899999998423464 No 7 >pfam05568 ASFV_J13L African swine fever virus J13L protein. This family consists of several African swine fever virus J13L proteins. Probab=9.45 E-value=1.3e+02 Score=13.36 Aligned_cols=11 Identities=55% Similarity=0.978 Sum_probs=8.0 Q ss_pred HHHHHHHHHCC Q ss_conf 99999998246 Q 537021.9.peg.1 29 LATLLYLFSSN 39 (47) Q Consensus 29 latllylfssn 39 (47) .-.|.|||||. T Consensus 45 iivliylfssr 55 (189) T pfam05568 45 IIVLIYLFSSR 55 (189) T ss_pred HHHHHHHHHCC T ss_conf 99999997220 No 8 >PRK10494 hypothetical protein; Provisional Probab=8.97 E-value=1.7e+02 Score=12.72 Aligned_cols=27 Identities=26% Similarity=0.357 Sum_probs=15.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHCC Q ss_conf 887789999999999982461242104 Q 537021.9.peg.1 20 RESTRAFFSLATLLYLFSSNFFLSDRF 46 (47) Q Consensus 20 restraffslatllylfssnfflsdrf 46 (47) +...|.+..++.+++++.|+-..+|.. T Consensus 36 ~k~~~~~~~~~~l~l~~~s~~pv~~~L 62 (259) T PRK10494 36 QKTGKIFISIGWLALLLLSLQPVADRL 62 (259) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999989999999 No 9 >PRK00753 psbL photosystem II reaction center L; Provisional Probab=8.23 E-value=1.7e+02 Score=12.72 Aligned_cols=12 Identities=58% Similarity=0.683 Sum_probs=8.2 Q ss_pred HHHHHHHHCCHH Q ss_conf 999999824612 Q 537021.9.peg.1 30 ATLLYLFSSNFF 41 (47) Q Consensus 30 atllylfssnff 41 (47) ..+--||||-|| T Consensus 27 fvl~iLfsSYfF 38 (39) T PRK00753 27 FVLGILFSSYFF 38 (39) T ss_pred HHHHHHHHHHHC T ss_conf 999999998823 No 10 >KOG1589 consensus Probab=7.77 E-value=1.2e+02 Score=13.50 Aligned_cols=10 Identities=60% Similarity=1.032 Sum_probs=0.0 Q ss_pred HHHHCCHHHH Q ss_conf 9982461242 Q 537021.9.peg.1 34 YLFSSNFFLS 43 (47) Q Consensus 34 ylfssnffls 43 (47) +|||-|||+. T Consensus 77 ~LfsVN~f~~ 86 (118) T KOG1589 77 SLFSVNFFVA 86 (118) T ss_pred HHHHHHHHHH T ss_conf 2467899999 Done!