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!