Query         gi|254780699|ref|YP_003065112.1| hypothetical protein CLIBASIA_02930 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 97
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 19:56:29 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780699.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 cd03729 SOCS_ASB13 SOCS (suppr  60.4     5.8 0.00015   20.7   1.9   21   21-41      3-23  (42)
  2 pfam03618 DUF299 Domain of unk  34.3      12  0.0003   18.8   0.1   42   49-90    118-159 (255)
  3 cd03733 SOCS_WSB_SWIP SOCS (su  31.6      21 0.00054   17.4   1.0   33   21-53      3-38  (39)
  4 cd03724 SOCS_ASB5 SOCS (suppre  31.3      35 0.00089   16.1   2.1   17   22-38      4-20  (42)
  5 cd03746 SOCS_WSB1_SWIP1 SOCS (  30.8      23 0.00059   17.1   1.1   33   21-53      3-38  (40)
  6 PRK05339 hypothetical protein;  30.5      15 0.00038   18.2   0.1   38   49-90    129-170 (273)
  7 cd03745 SOCS_WSB2_SWIP2 SOCS (  24.7      34 0.00087   16.1   1.1   33   21-53      3-38  (39)
  8 pfam10448 chaperone_DMP 20S pr  24.5      60  0.0015   14.6   2.6   25   68-92     20-44  (134)
  9 COG1124 DppF ABC-type dipeptid  23.1      49  0.0013   15.2   1.7   22   22-43    142-163 (252)
 10 cd03246 ABCC_Protease_Secretio  20.8      67  0.0017   14.4   2.0   22   20-41     95-116 (173)
 11 cd03716 SOCS_ASB_like SOCS (su  20.7      57  0.0014   14.8   1.6   20   20-39      2-21  (42)
 12 TIGR00447 pth peptidyl-tRNA hy  20.4      33 0.00084   16.2   0.3   17   58-74     55-71  (193)

No 1  
>cd03729 SOCS_ASB13 SOCS (suppressors of cytokine signaling) box of ASB13-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=60.40  E-value=5.8  Score=20.73  Aligned_cols=21  Identities=43%  Similarity=0.476  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             688999988999987641110
Q gi|254780699|r   21 IKSLAQLQRIAIRTVLANRTK   41 (97)
Q Consensus        21 ikslaqlqriairtvlanrtk   41 (97)
                      -.||.||-|+++|+++..|.-
T Consensus         3 PlsLqQlcRv~lR~~lG~ra~   23 (42)
T cd03729           3 PLSLQQLCRINLRKALGTRAL   23 (42)
T ss_pred             CCCHHHHHHHHHHHHHHHHHH
T ss_conf             513999999999999808899


No 2  
>pfam03618 DUF299 Domain of unknown function (DUF299). Family of bacterial proteins with no known function.
Probab=34.34  E-value=12  Score=18.84  Aligned_cols=42  Identities=26%  Similarity=0.338  Sum_probs=28.2

Q ss_pred             HHHHHHHHHCCCHHCCCCCCEEEEEEEECCCCCCEEEEEEEC
Q ss_conf             999999863431000368823788887034652106899602
Q gi|254780699|r   49 EFMEYWIAHSSRAWRTSKPRTYLNLHIASQSKKIPVSIYIGN   90 (97)
Q Consensus        49 efmeywiahssrawrtskprtylnlhiasqskkipvsiyign   90 (97)
                      |-|||-++|..-.--..-...-+-|-=.|.+-|-|.|+|.+|
T Consensus       118 eAiefal~hDDG~~~~~l~~ADiiLvGVSRtsKTP~S~YLA~  159 (255)
T pfam03618       118 EAIEFALAHDDGQDPRGLDEADIILVGVSRTSKTPTSLYLAN  159 (255)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCEEEEECCCCCCCCHHHHHHH
T ss_conf             999989971799781146358899982255789837899985


No 3  
>cd03733 SOCS_WSB_SWIP SOCS (suppressors of cytokine signaling) box of WSB/SWiP-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2), and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh), as well as, their isoforms WSB-2 and SWiP-2. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=31.59  E-value=21  Score=17.35  Aligned_cols=33  Identities=36%  Similarity=0.587  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC---HHHHHHHHHHH
Q ss_conf             6889999889999876411100---79999999999
Q gi|254780699|r   21 IKSLAQLQRIAIRTVLANRTKN---IKSITKEFMEY   53 (97)
Q Consensus        21 ikslaqlqriairtvlanrtkn---iksitkefmey   53 (97)
                      +.||-.|-|.|+|.|+....-.   |-+--+||..|
T Consensus         3 v~SLqHLCRmalRrvm~T~qV~~LPiP~k~~efLtY   38 (39)
T cd03733           3 VSSLQHLCRMALRRVMTTQQVLALPIPKKMKEFLTY   38 (39)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHC
T ss_conf             404999999999972749884417898889978505


No 4  
>cd03724 SOCS_ASB5 SOCS (suppressors of cytokine signaling) box of ASB5-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB5 has been implicated in the initiation of arteriogenesis. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=31.27  E-value=35  Score=16.07  Aligned_cols=17  Identities=41%  Similarity=0.604  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             88999988999987641
Q gi|254780699|r   22 KSLAQLQRIAIRTVLAN   38 (97)
Q Consensus        22 kslaqlqriairtvlan   38 (97)
                      .||+||-|+.||..+..
T Consensus         4 ~SL~qLCRlcIR~~lGR   20 (42)
T cd03724           4 SSLCQLCRLCIRNYIGR   20 (42)
T ss_pred             HHHHHHHHHHHHHHHCH
T ss_conf             78999999999998056


No 5  
>cd03746 SOCS_WSB1_SWIP1 SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=30.78  E-value=23  Score=17.13  Aligned_cols=33  Identities=39%  Similarity=0.573  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHH
Q ss_conf             688999988999987641110---079999999999
Q gi|254780699|r   21 IKSLAQLQRIAIRTVLANRTK---NIKSITKEFMEY   53 (97)
Q Consensus        21 ikslaqlqriairtvlanrtk---niksitkefmey   53 (97)
                      +.||-.|-|.|+|.|+....-   -|-+--.||..|
T Consensus         3 v~SLqHLCRmalRrv~~T~qV~~LPiP~k~~efLtY   38 (40)
T cd03746           3 VASLQHLCRMAIRRVMPTQQVKELPIPSKLLEFLTY   38 (40)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHC
T ss_conf             305999999999982749874317898899978623


No 6  
>PRK05339 hypothetical protein; Provisional
Probab=30.54  E-value=15  Score=18.24  Aligned_cols=38  Identities=32%  Similarity=0.535  Sum_probs=27.2

Q ss_pred             HHHHHHHHHCCCHHCCCCCCEE----EEEEEECCCCCCEEEEEEEC
Q ss_conf             9999998634310003688237----88887034652106899602
Q gi|254780699|r   49 EFMEYWIAHSSRAWRTSKPRTY----LNLHIASQSKKIPVSIYIGN   90 (97)
Q Consensus        49 efmeywiahssrawrtskprty----lnlhiasqskkipvsiyign   90 (97)
                      |-|||-++|..-.    .|+.+    +-|-=.|.+-|-|.|+|.++
T Consensus       129 eAiefal~hDDG~----~~~~l~~ADiiLvGVSRtsKTPtS~YLA~  170 (273)
T PRK05339        129 EAINFALAHDDGQ----DPRGLDEADVILVGVSRTSKTPTSLYLAN  170 (273)
T ss_pred             HHHHHHHHCCCCC----CCCCHHHCCEEEEECCCCCCCCHHHHHHH
T ss_conf             9999899727997----81146358899982255789837899985


No 7  
>cd03745 SOCS_WSB2_SWIP2 SOCS (suppressors of cytokine signaling) box of WSB2/SWiP2-like proteins. This family consists of WSB-2 (SOCS-box-containing WD-40 protein) and SWiP-2 (SOCS box and WD-repeats in Protein). No functional information is available for WSB2 or SWiP-2, but limited information is available for the isoforms WSB-1 and SWiP-1.  The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=24.71  E-value=34  Score=16.13  Aligned_cols=33  Identities=36%  Similarity=0.493  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHH
Q ss_conf             688999988999987641110---079999999999
Q gi|254780699|r   21 IKSLAQLQRIAIRTVLANRTK---NIKSITKEFMEY   53 (97)
Q Consensus        21 ikslaqlqriairtvlanrtk---niksitkefmey   53 (97)
                      +.||-.|-|.|+|.|+..-.-   -|-+--+||..|
T Consensus         3 v~SLqHLCR~alR~~~~T~qV~~LPiP~k~~efLtY   38 (39)
T cd03745           3 LPSLRHLCRKALRHFLTTYQVLALPIPKKMKEFLTY   38 (39)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHC
T ss_conf             504999999999984529886607997889988605


No 8  
>pfam10448 chaperone_DMP 20S proteasome chaperone. This family contains chaperones of the 20S proteasome which function in early 20S proteasome assembly. The structures of two of the proteins in this family (DMP1 and DMP2) have been solved, and they closely resemble that of the mammalian proteasome assembling chaperone PAC3, although there is little sequence similarity between them.
Probab=24.48  E-value=60  Score=14.64  Aligned_cols=25  Identities=32%  Similarity=0.361  Sum_probs=18.7

Q ss_pred             CEEEEEEEECCCCCCEEEEEEECCC
Q ss_conf             2378888703465210689960200
Q gi|254780699|r   68 RTYLNLHIASQSKKIPVSIYIGNIQ   92 (97)
Q Consensus        68 rtylnlhiasqskkipvsiyigniq   92 (97)
                      ..-+-+|.-..+.|+|++|+|+...
T Consensus        20 d~e~~~~~~~~~~K~~l~I~ing~~   44 (134)
T pfam10448        20 DVEVVIHAIHYSNKIPLSIRINGEM   44 (134)
T ss_pred             EEEEEEEEEECCCCEEEEEEECCEE
T ss_conf             3899996450368148999987687


No 9  
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=23.15  E-value=49  Score=15.17  Aligned_cols=22  Identities=41%  Similarity=0.298  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCH
Q ss_conf             8899998899998764111007
Q gi|254780699|r   22 KSLAQLQRIAIRTVLANRTKNI   43 (97)
Q Consensus        22 kslaqlqriairtvlanrtkni   43 (97)
                      -|=.|+|||||--.|+-++|-+
T Consensus       142 LSGGQ~QRiaIARAL~~~PklL  163 (252)
T COG1124         142 LSGGQRQRIAIARALIPEPKLL  163 (252)
T ss_pred             CCHHHHHHHHHHHHHCCCCCEE
T ss_conf             2816899999999863688879


No 10 
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=20.85  E-value=67  Score=14.38  Aligned_cols=22  Identities=32%  Similarity=0.344  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             1688999988999987641110
Q gi|254780699|r   20 NIKSLAQLQRIAIRTVLANRTK   41 (97)
Q Consensus        20 nikslaqlqriairtvlanrtk   41 (97)
                      ||-|-.|-||+++-.+|+...+
T Consensus        95 NiLSGGQkQRvalARal~~~p~  116 (173)
T cd03246          95 NILSGGQRQRLGLARALYGNPR  116 (173)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCC
T ss_conf             7676999999999999827999


No 11 
>cd03716 SOCS_ASB_like SOCS (suppressors of cytokine signaling) box of ASB (ankyrin repeat and SOCS box) and SSB (SPRY domain-containing SOCS box proteins) protein families. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence of a variable number of repeats. SSB proteins contain a central SPRY domain and a C-terminal SOCS. Recently, it has been shown that all four SSB proteins interact with the MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF), and that SSB-1, SSB-2, and SSB-4 interact with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain.
Probab=20.72  E-value=57  Score=14.80  Aligned_cols=20  Identities=45%  Similarity=0.622  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHC
Q ss_conf             16889999889999876411
Q gi|254780699|r   20 NIKSLAQLQRIAIRTVLANR   39 (97)
Q Consensus        20 nikslaqlqriairtvlanr   39 (97)
                      +-.||.+|-|++||..+..+
T Consensus         2 ~P~sL~~LCR~~IR~~lg~~   21 (42)
T cd03716           2 TPRSLQHLCRLAIRRCLGRR   21 (42)
T ss_pred             CCCCHHHHHHHHHHHHHCHH
T ss_conf             88389999999999997841


No 12 
>TIGR00447 pth peptidyl-tRNA hydrolase; InterPro: IPR001328   Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis , . Bacterial PTH has been found to be evolutionary related to a yeast protein .; GO: 0004045 aminoacyl-tRNA hydrolase activity, 0006412 translation.
Probab=20.43  E-value=33  Score=16.22  Aligned_cols=17  Identities=41%  Similarity=0.507  Sum_probs=12.4

Q ss_pred             CCCHHCCCCCCEEEEEE
Q ss_conf             43100036882378888
Q gi|254780699|r   58 SSRAWRTSKPRTYLNLH   74 (97)
Q Consensus        58 ssrawrtskprtylnlh   74 (97)
                      +.+.-+--||.||.||-
T Consensus        55 ~~~~v~L~kP~TYMNlS   71 (193)
T TIGR00447        55 SGKKVILLKPLTYMNLS   71 (193)
T ss_pred             ECCEEEEECCCCCCCCH
T ss_conf             14258974697410011


Done!