Query gi|254780324|ref|YP_003064737.1| hypothetical protein CLIBASIA_01045 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 61 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 29 14:28:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780324.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG3667 PcoB Uncharacterized p 60.1 3.3 8.4E-05 22.6 0.6 33 1-33 146-178 (321) 2 pfam08756 YfkB YfkB-like domai 55.8 1.2 3.2E-05 24.9 -2.1 19 20-38 27-45 (153) 3 KOG3894 consensus 39.0 21 0.00054 18.1 2.0 24 19-42 286-311 (316) 4 pfam10066 DUF2304 Uncharacteri 25.2 26 0.00066 17.6 0.6 32 18-51 27-58 (115) 5 cd00929 Cyt_c_Oxidase_VIIc Cyt 23.9 43 0.0011 16.3 1.5 35 12-46 4-38 (46) 6 TIGR02614 ftsW cell division p 23.1 73 0.0019 15.1 2.6 27 28-57 12-40 (370) 7 KOG3393 consensus 22.6 75 0.0019 15.0 2.6 36 19-54 86-123 (157) 8 pfam09499 RE_ApaLI ApaLI-like 22.1 38 0.00098 16.6 0.9 11 16-26 113-123 (191) 9 TIGR01545 YfhB_g-proteo HAD su 21.7 24 0.00061 17.7 -0.2 26 21-46 109-139 (210) 10 pfam05255 UPF0220 Uncharacteri 20.6 71 0.0018 15.1 2.1 51 1-51 73-126 (164) No 1 >COG3667 PcoB Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism] Probab=60.09 E-value=3.3 Score=22.56 Aligned_cols=33 Identities=36% Similarity=0.565 Sum_probs=28.9 Q ss_pred CCCCCCCEEEEECCCEEEEEECCCCHHHHHHHH Q ss_conf 985210013430474888884264016887999 Q gi|254780324|r 1 MGNSVNSTILKAEGSIVNIKWRDANVWLLFGVV 33 (61) Q Consensus 1 mgnsvnstilkaegsivnikwrdanvwllfgvv 33 (61) .|.+.+.-.||+||.++.=+|.+|.|-+|||-- T Consensus 146 iGtdi~kl~lkaeGe~~~Gr~e~a~ve~L~gh~ 178 (321) T COG3667 146 IGTDISKLVLKAEGERVDGRWEKAEVEGLKGHA 178 (321) T ss_pred ECCCHHHEEEECCCCEECCCHHHHHHHHHHCCC T ss_conf 245653503201572407621566655551575 No 2 >pfam08756 YfkB YfkB-like domain. This protein is adjacent to YfkA in B. subtilis. In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them. Probab=55.83 E-value=1.2 Score=24.93 Aligned_cols=19 Identities=47% Similarity=0.938 Sum_probs=14.9 Q ss_pred EECCCCHHHHHHHHHHHHH Q ss_conf 8426401688799999863 Q gi|254780324|r 20 KWRDANVWLLFGVVMVYFS 38 (61) Q Consensus 20 kwrdanvwllfgvvmvyfs 38 (61) .-||.|+|.|||..-.|-. T Consensus 27 d~Rd~~~WMLFGTLPfypC 45 (153) T pfam08756 27 DIRDENVWMLFGTLPFYPC 45 (153) T ss_pred HCCCCCEEEEECCCCCCCC T ss_conf 2669885788545553447 No 3 >KOG3894 consensus Probab=39.00 E-value=21 Score=18.07 Aligned_cols=24 Identities=33% Similarity=0.567 Sum_probs=17.9 Q ss_pred EEECCC--CHHHHHHHHHHHHHHHHH Q ss_conf 884264--016887999998632035 Q gi|254780324|r 19 IKWRDA--NVWLLFGVVMVYFSISFS 42 (61) Q Consensus 19 ikwrda--nvwllfgvvmvyfsisfs 42 (61) ++|+.+ .+|++|+.++.-|++-|. T Consensus 286 a~~~~~~~r~~~lf~llvlsf~lLFl 311 (316) T KOG3894 286 AKRNNGGLRVFLLFFLLVLSFSLLFL 311 (316) T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHH T ss_conf 99723553168999999999999988 No 4 >pfam10066 DUF2304 Uncharacterized conserved protein (DUF2304). Members of this family of hypothetical archaeal proteins have no known function. Probab=25.16 E-value=26 Score=17.56 Aligned_cols=32 Identities=22% Similarity=0.487 Sum_probs=22.4 Q ss_pred EEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8884264016887999998632035579998742 Q gi|254780324|r 18 NIKWRDANVWLLFGVVMVYFSISFSSRIVDYVDQ 51 (61) Q Consensus 18 nikwrdanvwllfgvvmvyfsisfssrivdyvdq 51 (61) .++++++-.|+.|+++++-+++-- .+.+++.. T Consensus 27 kl~~~~~l~Wl~~~~~~li~~ifP--~i~~~iA~ 58 (115) T pfam10066 27 RLSISDLLFWLFFWIVVLLFALFP--KISGRIAN 58 (115) T ss_pred HCCHHHHHHHHHHHHHHHHHHHCC--CHHHHHHH T ss_conf 077999999999999999999875--18899999 No 5 >cd00929 Cyt_c_Oxidase_VIIc Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits. Probab=23.90 E-value=43 Score=16.34 Aligned_cols=35 Identities=26% Similarity=0.535 Sum_probs=28.1 Q ss_pred ECCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 04748888842640168879999986320355799 Q gi|254780324|r 12 AEGSIVNIKWRDANVWLLFGVVMVYFSISFSSRIV 46 (61) Q Consensus 12 aegsivnikwrdanvwllfgvvmvyfsisfssriv 46 (61) .||.--|+-..-.|-|.+.....+||.+.|+.--+ T Consensus 4 ~~gPg~NLPF~v~Nk~~l~a~~~~ffg~Gf~~PF~ 38 (46) T cd00929 4 GEGPGSNLPFSVTNKWRLTALFHLFFGSGFSAPFI 38 (46) T ss_pred CCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCHH T ss_conf 88898877746545138799999999987424267 No 6 >TIGR02614 ftsW cell division protein FtsW; InterPro: IPR013437 FtsW is an integral membrane protein with ten transmembrane segments . In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. The FtsW designation is not used in endospore-forming bacteria (e.g. Bacillus subtilis), where these proteins are designated SpoVE, and three or more RodA/FtsW/SpoVE family paralogs are present. SpoVE acts in spore cortex formation and is dispensable for growth. Biological roles for FtsW in cell division include recruitment of penicillin-binding protein 3 to the division site.; GO: 0009252 peptidoglycan biosynthetic process, 0051301 cell division, 0016021 integral to membrane. Probab=23.08 E-value=73 Score=15.05 Aligned_cols=27 Identities=33% Similarity=0.481 Sum_probs=12.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH Q ss_conf 8879999986320355799987423--34667 Q gi|254780324|r 28 LLFGVVMVYFSISFSSRIVDYVDQK--HDLYH 57 (61) Q Consensus 28 llfgvvmvyfsisfssrivdyvdqk--hdlyh 57 (61) +.+|.|||| |-|+-+..+-... ||-+| T Consensus 12 ~~~GlvMV~---SaS~~~a~~~~~~d~~~~~~ 40 (370) T TIGR02614 12 LGIGLVMVY---SASAAVAERLGLSDEGDPFY 40 (370) T ss_pred HHHHHHHHH---HHHHHHHHHHCCCCCCCHHH T ss_conf 999999999---76699998606888763689 No 7 >KOG3393 consensus Probab=22.59 E-value=75 Score=15.00 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=26.7 Q ss_pred EEECCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH Q ss_conf 884264016887999998632035--579998742334 Q gi|254780324|r 19 IKWRDANVWLLFGVVMVYFSISFS--SRIVDYVDQKHD 54 (61) Q Consensus 19 ikwrdanvwllfgvvmvyfsisfs--srivdyvdqkhd 54 (61) .--|.|..||++|-.|..=|+.-| --|-+||-+.-| T Consensus 86 sga~~AR~wLfiGF~l~fgsLias~wVli~~yv~~~~~ 123 (157) T KOG3393 86 SGARGARIWLFIGFALLFGSLIASIWVLIGKYVVKEYD 123 (157) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 22310256889999999701556678874898852778 No 8 >pfam09499 RE_ApaLI ApaLI-like restriction endonuclease. This family includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognizes and cleaves the sequence GTGCAC. Probab=22.11 E-value=38 Score=16.62 Aligned_cols=11 Identities=55% Similarity=0.990 Sum_probs=8.1 Q ss_pred EEEEEECCCCH Q ss_conf 88888426401 Q gi|254780324|r 16 IVNIKWRDANV 26 (61) Q Consensus 16 ivnikwrdanv 26 (61) -..||||||.. T Consensus 113 AyEiKwRdAtT 123 (191) T pfam09499 113 AYEIKWRDATT 123 (191) T ss_pred EEEEEEECCCC T ss_conf 07988512677 No 9 >TIGR01545 YfhB_g-proteo HAD superfamily (subfamily IF) hydrolase, YfhB; InterPro: IPR006435 This group describes a clade of sequences limited to the gamma proteobacteria. This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present . Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive alpha helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF).. Probab=21.74 E-value=24 Score=17.74 Aligned_cols=26 Identities=46% Similarity=0.796 Sum_probs=20.2 Q ss_pred ECCCCHHHHHH-----HHHHHHHHHHHHHHH Q ss_conf 42640168879-----999986320355799 Q gi|254780324|r 21 WRDANVWLLFG-----VVMVYFSISFSSRIV 46 (61) Q Consensus 21 wrdanvwllfg-----vvmvyfsisfssriv 46 (61) -.||++||.-| |-.|||.-.|-.|+- T Consensus 109 ssda~~WlitGsPq~lve~vy~d~~~~~r~~ 139 (210) T TIGR01545 109 SSDAEVWLITGSPQRLVEAVYFDSNFLHRLR 139 (210) T ss_pred HCCCCEEEEECCCHHHHHHHHHCCHHHHHHH T ss_conf 0577368974686788887750421577888 No 10 >pfam05255 UPF0220 Uncharacterized protein family (UPF0220). This family of proteins is functionally uncharacterized. Probab=20.61 E-value=71 Score=15.11 Aligned_cols=51 Identities=25% Similarity=0.404 Sum_probs=30.4 Q ss_pred CCCCCCCEEEEECCCEE-EEEECCCCHHHHHHHHHHHHHHHHHHH--HHHHHHH Q ss_conf 98521001343047488-888426401688799999863203557--9998742 Q gi|254780324|r 1 MGNSVNSTILKAEGSIV-NIKWRDANVWLLFGVVMVYFSISFSSR--IVDYVDQ 51 (61) Q Consensus 1 mgnsvnstilkaegsiv-nikwrdanvwllfgvvmvyfsisfssr--ivdyvdq 51 (61) |=|+|+..-|..+..-- +.--+.|.+||..|-++..=++.-|-- +.+|+.. T Consensus 73 miN~V~k~~l~~d~~~~g~~~~~~ARvwLFiGF~l~fgglags~wvli~~yv~~ 126 (164) T pfam05255 73 MVNSIEKSRLRGDSLSEGSGGAWGARVWLFLGFALLFGSLAASIWVLILKYLVK 126 (164) T ss_pred HHCCCCHHHCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 523153865347877678765421102457999999988999999999998647 Done!