Query gi|254780651|ref|YP_003065064.1| hypothetical protein CLIBASIA_02690 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 30 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 29 20:41:58 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780651.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK04115 hypothetical protein; 38.6 15 0.00038 19.5 1.2 24 7-30 17-40 (130) 2 pfam01886 DUF61 Protein of unk 35.9 17 0.00045 19.2 1.2 24 7-30 21-44 (132) 3 pfam06488 L_lac_phage_MSP Lact 27.5 44 0.0011 17.3 2.1 20 4-23 190-209 (301) 4 pfam07765 KIP1 KIP1-like prote 19.4 62 0.0016 16.6 1.5 13 2-14 38-50 (74) 5 pfam08140 Cuticle_1 Crustacean 14.2 80 0.002 16.1 1.0 16 15-30 25-40 (40) 6 TIGR02562 cas3_yersinia CRISPR 14.1 73 0.0019 16.3 0.8 20 5-24 594-613 (1153) 7 pfam10830 DUF2553 Protein of u 10.5 1E+02 0.0025 15.6 0.6 16 15-30 40-55 (76) 8 COG1849 Uncharacterized protei 10.4 1.7E+02 0.0044 14.5 1.8 20 1-20 2-21 (90) 9 TIGR01933 hflK HflK protein; I 8.8 1.1E+02 0.0028 15.4 0.3 14 16-29 7-20 (285) 10 COG2952 Uncharacterized protei 8.1 2.4E+02 0.0061 13.8 1.8 12 7-18 131-142 (183) No 1 >PRK04115 hypothetical protein; Provisional Probab=38.63 E-value=15 Score=19.50 Aligned_cols=24 Identities=29% Similarity=0.275 Sum_probs=16.4 Q ss_pred HHHHHHHHHHHHCCEEECCCEECC Q ss_conf 899999999850413346822049 Q gi|254780651|r 7 KRIKGYLKIMESGLVLRNGSFYRF 30 (30) Q Consensus 7 krikgylkimesglvlrngsfyrf 30 (30) |...--|+--...+++||||+|+| T Consensus 17 ktL~ELL~ed~P~v~~rdGs~h~~ 40 (130) T PRK04115 17 KTLCELLKEDKPYVILRDGSRHYI 40 (130) T ss_pred HHHHHHHHCCCCEEEECCCCEEEE T ss_conf 469999727698599318956866 No 2 >pfam01886 DUF61 Protein of unknown function DUF61. Protein found in Archaebacteria. These proteins have no known function. Probab=35.89 E-value=17 Score=19.20 Aligned_cols=24 Identities=38% Similarity=0.455 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHCCEEECCCEECC Q ss_conf 899999999850413346822049 Q gi|254780651|r 7 KRIKGYLKIMESGLVLRNGSFYRF 30 (30) Q Consensus 7 krikgylkimesglvlrngsfyrf 30 (30) |..+--|+--....++||||.|+| T Consensus 21 ktL~eLL~e~~P~i~lrdGs~h~~ 44 (132) T pfam01886 21 KTLKELLKEDKPYIILRDGSRHYF 44 (132) T ss_pred HHHHHHHHCCCCEEEECCCCEEEE T ss_conf 679999828798599318954755 No 3 >pfam06488 L_lac_phage_MSP Lactococcus lactis bacteriophage major structural protein. This family consists of several Lactococcus lactis bacteriophage major structural proteins. Probab=27.55 E-value=44 Score=17.30 Aligned_cols=20 Identities=40% Similarity=0.664 Sum_probs=16.9 Q ss_pred HHHHHHHHHHHHHHHCCEEE Q ss_conf 47889999999985041334 Q gi|254780651|r 4 SFGKRIKGYLKIMESGLVLR 23 (30) Q Consensus 4 sfgkrikgylkimesglvlr 23 (30) -+|...|.+.|-|||||.+- T Consensus 190 iwgeqakdfakkmesglfi~ 209 (301) T pfam06488 190 IWGEQAKDFAKKMESGLFII 209 (301) T ss_pred HHHHHHHHHHHHHHCCEEEE T ss_conf 24577789998754562796 No 4 >pfam07765 KIP1 KIP1-like protein. This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions. It has also been suggested that the protein's coiled- coils allow it to dimerize in vivo. Probab=19.39 E-value=62 Score=16.60 Aligned_cols=13 Identities=62% Similarity=0.835 Sum_probs=10.1 Q ss_pred CHHHHHHHHHHHH Q ss_conf 5047889999999 Q gi|254780651|r 2 ADSFGKRIKGYLK 14 (30) Q Consensus 2 adsfgkrikgylk 14 (30) +|||.||-..|.+ T Consensus 38 gdSfakrAemyy~ 50 (74) T pfam07765 38 ADSFAKRAEMYYK 50 (74) T ss_pred CCCHHHHHHHHHH T ss_conf 5418999999983 No 5 >pfam08140 Cuticle_1 Crustacean cuticle protein repeat. This family consists of the cuticle proteins from the Cancer pagurus and the Homarus americanus. These proteins are isolated from the calcified regions of the crustacean and they contain two copies of an 18 residue sequence motif, which thus far has been found only in crustacean calcified exoskeletons. Probab=14.17 E-value=80 Score=16.06 Aligned_cols=16 Identities=44% Similarity=0.584 Sum_probs=12.1 Q ss_pred HHHHCCEEECCCEECC Q ss_conf 9850413346822049 Q gi|254780651|r 15 IMESGLVLRNGSFYRF 30 (30) Q Consensus 15 imesglvlrngsfyrf 30 (30) +-+||.|+.||..-.| T Consensus 25 ~GpSG~V~sdG~nvQf 40 (40) T pfam08140 25 IGPSGAVLSDGKNVQF 40 (40) T ss_pred ECCCEEEEECCCEECC T ss_conf 7684259768838029 No 6 >TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3, Yersinia-type; InterPro: IPR013395 The helicase encoded in many CRISPR-associated (cas) gene clusters is designated Cas3. The Yersinia-type helicase Cas3 proteins differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.. Probab=14.07 E-value=73 Score=16.26 Aligned_cols=20 Identities=30% Similarity=0.516 Sum_probs=17.5 Q ss_pred HHHHHHHHHHHHHHCCEEEC Q ss_conf 78899999999850413346 Q gi|254780651|r 5 FGKRIKGYLKIMESGLVLRN 24 (30) Q Consensus 5 fgkrikgylkimesglvlrn 24 (30) =|+.|+--|.||-|-|||-. T Consensus 594 gG~~i~p~LRllsSDLiLDE 613 (1153) T TIGR02562 594 GGHHIAPMLRLLSSDLILDE 613 (1153) T ss_pred CCEEHHHHHHHHHHHHEECC T ss_conf 56107889987532320048 No 7 >pfam10830 DUF2553 Protein of unknown function (DUF2553). This family of bacterial proteins has no known function. Probab=10.46 E-value=1e+02 Score=15.61 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=13.3 Q ss_pred HHHHCCEEECCCEECC Q ss_conf 9850413346822049 Q gi|254780651|r 15 IMESGLVLRNGSFYRF 30 (30) Q Consensus 15 imesglvlrngsfyrf 30 (30) .|++|.+..++.|||. T Consensus 40 ~L~~GY~~e~~K~yr~ 55 (76) T pfam10830 40 ELKSGYSFEDGKFYKT 55 (76) T ss_pred EECCCCEEECCEEEEE T ss_conf 8638855508889998 No 8 >COG1849 Uncharacterized protein conserved in archaea [Function unknown] Probab=10.44 E-value=1.7e+02 Score=14.48 Aligned_cols=20 Identities=30% Similarity=0.763 Sum_probs=16.1 Q ss_pred CCHHHHHHHHHHHHHHHHCC Q ss_conf 95047889999999985041 Q gi|254780651|r 1 MADSFGKRIKGYLKIMESGL 20 (30) Q Consensus 1 madsfgkrikgylkimesgl 20 (30) |++-...||.-|++++|..| T Consensus 2 ~~~~l~ekiekYi~~leeaL 21 (90) T COG1849 2 MAEELAEKIEKYIELLEEAL 21 (90) T ss_pred CHHHHHHHHHHHHHHHHHHH T ss_conf 27899999999999899999 No 9 >TIGR01933 hflK HflK protein; InterPro: IPR010201 The accumulation of abnormal membrane proteins is something which must be avoided in order to maintain cell viability. In Escherichia coli, the membrane-bound, ATP-dependent protease FtsH plays a central role in the degradation of these abnormal proteins . Known substrates of this protease include several lambda bacteriophage proteins, the heat-shock transcription factor sigma-32, and the unassembled form of the membrane protein SecY. While FtsH is active as a protease on its own, in vivo it forms a complex with a membrane-bound HflKC heterodimer. HflKC has a generally inhibitory effect on the protease activity of FtsH, though the mechanism of this inhibition is not known. The HflK and HflC polypeptides are paralogous, and often encoded by tandem genes within bacterial genomes. This entry represents the HflK subunit of the HflKC heterodimer.; GO: 0005515 protein binding, 0016021 integral to membrane. Probab=8.78 E-value=1.1e+02 Score=15.41 Aligned_cols=14 Identities=50% Similarity=0.819 Sum_probs=9.3 Q ss_pred HHHCCEEECCCEEC Q ss_conf 85041334682204 Q gi|254780651|r 16 MESGLVLRNGSFYR 29 (30) Q Consensus 16 mesglvlrngsfyr 29 (30) -|.|.|||=|.|.| T Consensus 7 ~e~gVVlRfGk~~~ 20 (285) T TIGR01933 7 AERGVVLRFGKYHR 20 (285) T ss_pred CCCCEEECCCCHHH T ss_conf 33604510331022 No 10 >COG2952 Uncharacterized protein conserved in bacteria [Function unknown] Probab=8.13 E-value=2.4e+02 Score=13.82 Aligned_cols=12 Identities=67% Similarity=0.861 Sum_probs=9.2 Q ss_pred HHHHHHHHHHHH Q ss_conf 899999999850 Q gi|254780651|r 7 KRIKGYLKIMES 18 (30) Q Consensus 7 krikgylkimes 18 (30) +-|-|||||-|+ T Consensus 131 ~si~~yLKIyE~ 142 (183) T COG2952 131 KSIDTYLKIYES 142 (183) T ss_pred HHHHHHHHHHHH T ss_conf 999999999999 Done!