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!