Query gi|254781140|ref|YP_003065553.1| hypothetical protein CLIBASIA_05210 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 44 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 05:12:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781140.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam10500 SR-25 Nuclear RNA-sp 50.3 6.1 0.00016 22.0 0.7 15 12-26 24-38 (74) 2 pfam10535 PQQ_C Pyrrolo-quinol 41.7 11 0.00027 20.7 0.8 15 8-22 1-15 (26) 3 pfam03088 Str_synth Strictosid 38.5 20 0.00052 19.1 1.9 20 5-24 34-53 (89) 4 pfam08223 PaaX_C PaaX-like pro 37.1 20 0.00052 19.1 1.7 17 4-20 4-20 (170) 5 pfam04096 Nucleoporin2 Nucleop 34.2 29 0.00075 18.2 2.1 15 8-22 118-132 (137) 6 TIGR01107 Na_K_ATPase_bet Na+/ 34.1 22 0.00056 18.9 1.5 15 4-18 13-27 (317) 7 pfam06206 CpeT CpeT/CpcT famil 26.7 31 0.0008 18.1 1.2 13 12-24 159-171 (180) 8 TIGR01778 TonB-copper TonB-dep 24.4 34 0.00087 17.9 1.0 14 15-28 654-667 (668) 9 pfam11171 DUF2958 Protein of u 23.8 81 0.0021 15.8 3.0 24 5-28 37-60 (112) 10 TIGR00005 rluA_subfam pseudour 22.0 41 0.001 17.4 1.1 16 5-20 225-240 (337) No 1 >pfam10500 SR-25 Nuclear RNA-splicing-associated protein. SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway. Probab=50.33 E-value=6.1 Score=22.04 Aligned_cols=15 Identities=53% Similarity=0.570 Sum_probs=11.0 Q ss_pred EECCCCCCEEEEEEC Q ss_conf 765888858999970 Q gi|254781140|r 12 SYDPETGRTVWYMLD 26 (44) Q Consensus 12 sydpetgrtvwymld 26 (44) -|||||||+-..--| T Consensus 24 v~DpeTGR~RLIkGd 38 (74) T pfam10500 24 VVDPETGRTRLIKGD 38 (74) T ss_pred HCCCCCCCEEEECCC T ss_conf 507665754244176 No 2 >pfam10535 PQQ_C Pyrrolo-quinoline quinone coenzyme C-terminus. This domain is a highly conserved signature at the C-terminus for coenzyme pyrrolo-quinoline quinone. Probab=41.70 E-value=11 Score=20.68 Aligned_cols=15 Identities=47% Similarity=0.875 Sum_probs=11.5 Q ss_pred EEEEEECCCCCCEEE Q ss_conf 778876588885899 Q gi|254781140|r 8 WKLISYDPETGRTVW 22 (44) Q Consensus 8 wklisydpetgrtvw 22 (44) |--+|||||+|-..+ T Consensus 1 W~~~syDp~~~lvY~ 15 (26) T pfam10535 1 WGPMSYDPELGLVYI 15 (26) T ss_pred CCCCCCCCCCCEEEE T ss_conf 975220887793884 No 3 >pfam03088 Str_synth Strictosidine synthase. Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyses the condensation of tryptamine with secologanin to form strictosidine. Probab=38.52 E-value=20 Score=19.13 Aligned_cols=20 Identities=35% Similarity=0.519 Sum_probs=15.2 Q ss_pred CCCEEEEEECCCCCCEEEEE Q ss_conf 57277887658888589999 Q gi|254781140|r 5 DGSWKLISYDPETGRTVWYM 24 (44) Q Consensus 5 dgswklisydpetgrtvwym 24 (44) +++=.|+.|||.|+++---| T Consensus 34 ~~tGRLl~ydp~t~~~~vL~ 53 (89) T pfam03088 34 DKTGRLMKYDPSTKVTKVLL 53 (89) T ss_pred CCCCEEEEEECCCCEEEEEE T ss_conf 99753999959999489942 No 4 >pfam08223 PaaX_C PaaX-like protein C-terminal domain. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. Probab=37.14 E-value=20 Score=19.14 Aligned_cols=17 Identities=47% Similarity=1.118 Sum_probs=14.7 Q ss_pred ECCCEEEEEECCCCCCE Q ss_conf 15727788765888858 Q gi|254781140|r 4 YDGSWKLISYDPETGRT 20 (44) Q Consensus 4 ydgswklisydpetgrt 20 (44) .||+|.++.+.||+.|. T Consensus 4 WdG~W~lv~~spe~~r~ 20 (170) T pfam08223 4 WDGSWHLVVLSPESDRA 20 (170) T ss_pred CCCEEEEEEECCCCCHH T ss_conf 99626898858865899 No 5 >pfam04096 Nucleoporin2 Nucleoporin autopeptidase. Probab=34.23 E-value=29 Score=18.22 Aligned_cols=15 Identities=60% Similarity=0.931 Sum_probs=11.1 Q ss_pred EEEEEECCCCCCEEE Q ss_conf 778876588885899 Q gi|254781140|r 8 WKLISYDPETGRTVW 22 (44) Q Consensus 8 wklisydpetgrtvw 22 (44) -+.|||||+||-=+. T Consensus 118 ~~FvsYd~~tG~W~F 132 (137) T pfam04096 118 AEFISYDPETGTWVF 132 (137) T ss_pred CEEEEEECCCCEEEE T ss_conf 999978479988999 No 6 >TIGR01107 Na_K_ATPase_bet Na+/K+ ATPase, beta subunit; InterPro: IPR000402 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H^+, Na^+, K^+, Mg^2+, Ca^2+, Ag^+ and Ag^2+, Zn^2+, Co^2+, Pb^2+, Ni^2+, Cd^2+, Cu^+ and Cu^2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the beta subunit found in the P-type cation exchange ATPases located in the plasma membranes of animal cells. These P-ATPases include both H^+/K^+-ATPases (3.6.3.10 from EC) and Na^+/K^+-ATPases (3.6.3.9 from EC), which belong to the IIC subfamily of ATPases , . These ATPases catalyse the hydrolysis of ATP coupled with the exchange of cations, pumping one cation out of the cell (H^+ or Na^+) in exchange for K^+. These ATPases contain an alpha subunit (IPR005775 from INTERPRO) that is the catalytic component, and a glycosylated beta subunit that regulates the number of sodium pumps transported to the plasma membrane through the assembly of alpha/beta heterodimers. The beta subunit has three highly conserved disulphide bonds within the extracellular domain that stabilize the alpha subunit, the alpha/beta interaction, and the catalytic activity of the alpha subunit . Different beta isoforms exist, permitting greater regulatory control. An example of a H^+/K^+-ATPase is the gastric pump responsible for acid secretion in the stomach, transporting protons from the cytoplasm of parietal cells to create a large pH gradient in exchange for the internalization of potassium ions, using ATP hydrolysis to drive the pump . More information about this protein can be found at Protein of the Month: ATP Synthases . ; GO: 0005391 sodium:potassium-exchanging ATPase activity, 0006813 potassium ion transport, 0006814 sodium ion transport, 0016020 membrane. Probab=34.06 E-value=22 Score=18.92 Aligned_cols=15 Identities=33% Similarity=0.709 Sum_probs=13.2 Q ss_pred ECCCEEEEEECCCCC Q ss_conf 157277887658888 Q gi|254781140|r 4 YDGSWKLISYDPETG 18 (44) Q Consensus 4 ydgswklisydpetg 18 (44) -+|+||.--|+|||+ T Consensus 13 ~~~~WK~F~WNp~~~ 27 (317) T TIGR01107 13 SLGEWKKFIWNPEKK 27 (317) T ss_pred CCCCCEEEEECCCCC T ss_conf 201010354668985 No 7 >pfam06206 CpeT CpeT/CpcT family (DUF1001). This family consists of proteins of proteins belonging to the CpeT/CpcT family. These proteins are around 200 amino acids in length. The proteins contain a conserved motif PYR in the amino terminal half of the protein that may be functionally important. The species distribution of the family is interesting. So far it is restricted to cyanobacteria, cryptomonads and plants. It has been shown that CpcT encodes a bilin lyase responsible for attachment of phycocyanobilin to the beta subunit of phycocyanin. Probab=26.73 E-value=31 Score=18.08 Aligned_cols=13 Identities=54% Similarity=1.104 Sum_probs=9.6 Q ss_pred EECCCCCCEEEEE Q ss_conf 7658888589999 Q gi|254781140|r 12 SYDPETGRTVWYM 24 (44) Q Consensus 12 sydpetgrtvwym 24 (44) .||||||.-||=- T Consensus 159 G~D~etg~~vWGs 171 (180) T pfam06206 159 GFDPETGEQVWGS 171 (180) T ss_pred EECCCCCCEEECC T ss_conf 1239889562178 No 8 >TIGR01778 TonB-copper TonB-dependent copper receptor; InterPro: IPR010100 This entry represents a family of proteobacterial TonB-dependent outer membrane receptor/transporters which bind and translocate copper ions. Two characterised members of this family exist, outer membrane protein C (OprC) from Pseudomonas aeruginosa and NosA from Pseudomonas stutzeri, which is responsible for providing copper for the copper-containing N2O reductase .. Probab=24.44 E-value=34 Score=17.87 Aligned_cols=14 Identities=50% Similarity=0.864 Sum_probs=11.1 Q ss_pred CCCCCEEEEEECCC Q ss_conf 88885899997084 Q gi|254781140|r 15 PETGRTVWYMLDNQ 28 (44) Q Consensus 15 petgrtvwymldnq 28 (44) +|-|||.|.-||-+ T Consensus 654 ~EPGRtlW~kl~~~ 667 (668) T TIGR01778 654 NEPGRTLWAKLDFE 667 (668) T ss_pred CCCCCCCCEEECCC T ss_conf 68886432241135 No 9 >pfam11171 DUF2958 Protein of unknown function (DUF2958). Some members are annotated as lipoproteins however this cannot be confirmed. This family of proteins has no known function. Probab=23.77 E-value=81 Score=15.76 Aligned_cols=24 Identities=29% Similarity=0.583 Sum_probs=20.3 Q ss_pred CCCEEEEEECCCCCCEEEEEECCC Q ss_conf 572778876588885899997084 Q gi|254781140|r 5 DGSWKLISYDPETGRTVWYMLDNQ 28 (44) Q Consensus 5 dgswklisydpetgrtvwymldnq 28 (44) .+.|-+..+||+.|.+.|-..|-- T Consensus 37 ~atWllteldp~dgd~~fGL~DlG 60 (112) T pfam11171 37 AATWLLTELDPADGDTLFGLCDLG 60 (112) T ss_pred CCEEEEEEECCCCCCEEEEEECCC T ss_conf 714577740678887499886179 No 10 >TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis. Probab=21.99 E-value=41 Score=17.41 Aligned_cols=16 Identities=50% Similarity=0.746 Sum_probs=13.5 Q ss_pred CCCEEEEEECCCCCCE Q ss_conf 5727788765888858 Q gi|254781140|r 5 DGSWKLISYDPETGRT 20 (44) Q Consensus 5 dgswklisydpetgrt 20 (44) ++.--||...|||||| T Consensus 225 ~~~~sl~~~~L~TGRT 240 (337) T TIGR00005 225 DGNASLVECELETGRT 240 (337) T ss_pred CCCCCEEEEEECCCCC T ss_conf 4452189998534897 Done!