Query gi|254780969|ref|YP_003065382.1| hypothetical protein CLIBASIA_04350 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 79 No_of_seqs 106 out of 1637 Neff 6.0 Searched_HMMs 39220 Date Mon May 30 02:10:31 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780969.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK11628 transcriptional regul 99.9 2E-26 5.1E-31 166.5 8.3 77 1-78 1-84 (105) 2 COG0271 BolA Stress-induced mo 99.9 1.6E-25 4.2E-30 161.4 10.1 78 1-78 1-86 (90) 3 pfam01722 BolA BolA-like prote 99.9 7.4E-24 1.9E-28 152.3 9.0 69 11-79 2-72 (72) 4 COG5007 Predicted transcriptio 99.9 6.7E-23 1.7E-27 147.0 8.7 73 3-78 1-74 (80) 5 KOG3348 consensus 99.9 3.7E-23 9.4E-28 148.5 6.7 77 1-78 1-78 (85) 6 KOG2313 consensus 99.8 2.6E-20 6.7E-25 132.8 9.6 74 5-78 12-99 (100) 7 pfam04298 Zn_peptidase_2 Putat 35.3 42 0.0011 16.1 4.8 49 1-49 35-89 (222) 8 COG3325 ChiA Chitinase [Carboh 28.9 54 0.0014 15.5 3.0 48 8-61 199-246 (441) 9 pfam06183 DinI DinI-like famil 27.7 56 0.0014 15.3 3.4 48 5-62 10-57 (65) 10 pfam10330 Stb3 Putative Sin3 b 25.6 51 0.0013 15.6 2.1 23 37-59 32-54 (93) 11 cd06256 M14_ASTE_ASPA_like_6 A 25.5 62 0.0016 15.1 3.8 71 5-75 109-185 (327) 12 TIGR00350 lytR_cpsA_psr cell e 25.3 62 0.0016 15.1 2.5 22 42-63 160-181 (182) No 1 >PRK11628 transcriptional regulator BolA; Provisional Probab=99.93 E-value=2e-26 Score=166.46 Aligned_cols=77 Identities=22% Similarity=0.533 Sum_probs=73.0 Q ss_pred CCCCHHHHHHHHHHCCCCCEEEEEECC-------CCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEE Q ss_conf 977889999999821996679999748-------9996699999704668999789999999999987279726889882 Q gi|254780969|r 1 MSMNPHEIEKMIKKGIPQSIVTIHDLA-------GDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMGNALHALSIKT 73 (79) Q Consensus 1 M~m~~~~I~~~i~~~l~~~~v~V~d~s-------g~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~~~IHAlsikt 73 (79) |++ .++|+++|...|++.+++|.|+| |+++||+|+|||+.|.|+++|+|||+||++|+++|+++||||+|+| T Consensus 1 M~i-~~~I~~kL~~~f~p~~L~V~deS~~H~~~~g~esHf~v~IvS~~F~g~s~i~RHR~Vy~~L~~el~~~IHALsi~~ 79 (105) T PRK11628 1 MMI-REQIEEKLRAAFQPVFLEVVDESYRHNVPAGSESHFKVVLVSDRFTGERFLNRHRMIYSTLAEELSTTVHALALHT 79 (105) T ss_pred CCH-HHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHEEEC T ss_conf 977-9999999984279858999879877789999977489999856759998999999999999999828975124541 Q ss_pred CCCCC Q ss_conf 06788 Q gi|254780969|r 74 SVPDS 78 (79) Q Consensus 74 ~tpee 78 (79) +||+| T Consensus 80 ~Tp~E 84 (105) T PRK11628 80 YTIKE 84 (105) T ss_pred CCHHH T ss_conf 89999 No 2 >COG0271 BolA Stress-induced morphogen (activity unknown) [Signal transduction mechanisms] Probab=99.93 E-value=1.6e-25 Score=161.43 Aligned_cols=78 Identities=35% Similarity=0.703 Sum_probs=74.8 Q ss_pred CCCCHHHHHHHHHHCCCCCEEEEEECC--------CCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 977889999999821996679999748--------999669999970466899978999999999998727972688988 Q gi|254780969|r 1 MSMNPHEIEKMIKKGIPQSIVTIHDLA--------GDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMGNALHALSIK 72 (79) Q Consensus 1 M~m~~~~I~~~i~~~l~~~~v~V~d~s--------g~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~~~IHAlsik 72 (79) |+|+.++|+++|+.+|+|..++|.|+| |||+||+|.|||+.|.|+|+|+|||+||++|+|+|.++||||+|+ T Consensus 1 m~i~~~~Ie~~l~~~f~p~~l~i~deS~~h~~~~~g~~~Hf~i~IVS~~F~G~s~v~rHr~V~~~L~del~~~iHALal~ 80 (90) T COG0271 1 MSIQRERIEKKLRAAFPPSFLEIIDESHRHHGHAGGGGSHFKVVIVSEAFQGKSLVARHRLVYSALKDELSGGIHALALH 80 (90) T ss_pred CCCCHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 96538999999981189756999863445355789988708999976554885299999999999999983532004767 Q ss_pred ECCCCC Q ss_conf 206788 Q gi|254780969|r 73 TSVPDS 78 (79) Q Consensus 73 t~tpee 78 (79) |+||+| T Consensus 81 t~t~~e 86 (90) T COG0271 81 TYTPEE 86 (90) T ss_pred EECCCH T ss_conf 316611 No 3 >pfam01722 BolA BolA-like protein. This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5. Probab=99.90 E-value=7.4e-24 Score=152.31 Aligned_cols=69 Identities=29% Similarity=0.659 Sum_probs=65.7 Q ss_pred HHHHCCCCCEEEEEECCC--CCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCC Q ss_conf 998219966799997489--996699999704668999789999999999987279726889882067889 Q gi|254780969|r 11 MIKKGIPQSIVTIHDLAG--DGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMGNALHALSIKTSVPDSQ 79 (79) Q Consensus 11 ~i~~~l~~~~v~V~d~sg--~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~~~IHAlsikt~tpee~ 79 (79) +|+++|+++.++|.|+|+ ||+||+|+|||+.|+|||+|+|||+||++|+++|+++||||+|+|+||+|. T Consensus 2 lL~~~~~~~~l~V~d~S~~~~gsHf~i~IvS~~F~g~s~i~rhr~V~~~L~~~~~~~iHAlsikt~t~~E~ 72 (72) T pfam01722 2 LLTAALPPAHLEVEDESHKGGGSHFKVVVVSDAFEGKSLVKRHRLVYAALKEELASGIHALSIKTYTPEEW 72 (72) T ss_pred HHHHHCCCCEEEEEECCCCCCCCCEEEEEEEHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC T ss_conf 45854998489999689999877189999826768996899999999999999748961579894770129 No 4 >COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription] Probab=99.89 E-value=6.7e-23 Score=147.04 Aligned_cols=73 Identities=40% Similarity=0.723 Sum_probs=70.1 Q ss_pred CCHHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHC-CCEEEEEEEECCCCC Q ss_conf 7889999999821996679999748999669999970466899978999999999998727-972688988206788 Q gi|254780969|r 3 MNPHEIEKMIKKGIPQSIVTIHDLAGDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMG-NALHALSIKTSVPDS 78 (79) Q Consensus 3 m~~~~I~~~i~~~l~~~~v~V~d~sg~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~-~~IHAlsikt~tpee 78 (79) |+.++|+.+|.++||.+.++|. |+|+||.+++||+.|+|+|+|+|||+||+.|.+.|. +.||||||||+||+| T Consensus 1 M~~e~Ik~ll~~~L~~e~v~V~---Gdg~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~~IHAlsikt~Tp~e 74 (80) T COG5007 1 MDNEEIKSLLENALPLEEVEVE---GDGSHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADNEIHALSIKTYTPAE 74 (80) T ss_pred CCHHHHHHHHHHCCCCCEEEEE---CCCCEEEEEEEHHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHH T ss_conf 9879999999822885278996---2772489988648666723778788889989988512852788865158889 No 5 >KOG3348 consensus Probab=99.88 E-value=3.7e-23 Score=148.47 Aligned_cols=77 Identities=27% Similarity=0.582 Sum_probs=73.6 Q ss_pred CCCCHHHHHHHHHHCCCCCEEEEEECC-CCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCC Q ss_conf 977889999999821996679999748-999669999970466899978999999999998727972688988206788 Q gi|254780969|r 1 MSMNPHEIEKMIKKGIPQSIVTIHDLA-GDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMGNALHALSIKTSVPDS 78 (79) Q Consensus 1 M~m~~~~I~~~i~~~l~~~~v~V~d~s-g~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~~~IHAlsikt~tpee 78 (79) |+.+++.++++|+++|.+.+++|.|.| |||+.|.|.|||+.|+|+|+++|||+|+++|.++|+ +||||+++|+||++ T Consensus 1 m~~~e~~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~IvS~~FeGKs~L~rHRlVN~~L~Eeik-~iHalt~kt~t~~~ 78 (85) T KOG3348 1 MTVTEERLEELLTEALEPEHVEVQDVSGGCGSMFDVVIVSAAFEGKSLLARHRLVNSILAEEIK-EIHALTIKTYTPEE 78 (85) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEEECCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHEEEECCHHH T ss_conf 9506899999998344846999997579866407899973100771799999999999999999-87653333237655 No 6 >KOG2313 consensus Probab=99.83 E-value=2.6e-20 Score=132.77 Aligned_cols=74 Identities=23% Similarity=0.500 Sum_probs=68.9 Q ss_pred HHHHHHHHHHCCCCCEEEEEECC----------C---CCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHCC-CEEEEE Q ss_conf 89999999821996679999748----------9---996699999704668999789999999999987279-726889 Q gi|254780969|r 5 PHEIEKMIKKGIPQSIVTIHDLA----------G---DGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKMGN-ALHALS 70 (79) Q Consensus 5 ~~~I~~~i~~~l~~~~v~V~d~s----------g---~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i~~-~IHAls 70 (79) ...|++++..+|.+..+++.++| | +++||+|.|||+.|+|+|+|+|||+||++|+|++++ ++|||+ T Consensus 12 ~~ri~~~l~~~lkp~~le~~n~S~~hagH~~~kg~~~~EtHFrv~vVS~~FeG~s~v~RHRlVy~~L~eEl~~~gvHAL~ 91 (100) T KOG2313 12 ESRIREKLFEALKPLNLELYNESHQHAGHAVPKGMDGAETHFRVEVVSSAFEGLSLVKRHRLVYKALKEELAGTGVHALS 91 (100) T ss_pred HHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 99999875764075148886146554445556578788667899983344477418899999999999986065425777 Q ss_pred EEECCCCC Q ss_conf 88206788 Q gi|254780969|r 71 IKTSVPDS 78 (79) Q Consensus 71 ikt~tpee 78 (79) |.++||.| T Consensus 92 i~aKTP~e 99 (100) T KOG2313 92 IMAKTPSE 99 (100) T ss_pred EECCCCCC T ss_conf 63258777 No 7 >pfam04298 Zn_peptidase_2 Putative neutral zinc metallopeptidase. Zinc metallopeptidase zinc binding regions have been predicted in some family members by a pattern match (Prosite:PS00142). Probab=35.30 E-value=42 Score=16.07 Aligned_cols=49 Identities=16% Similarity=0.320 Sum_probs=39.9 Q ss_pred CCCCHHHHHHHHHHCCCCCEEEEEECCCC-CCEE-----EEEEECHHHCCCCHHH Q ss_conf 97788999999982199667999974899-9669-----9999704668999789 Q gi|254780969|r 1 MSMNPHEIEKMIKKGIPQSIVTIHDLAGD-GNHY-----AAEIISEEFRGKNRIQ 49 (79) Q Consensus 1 M~m~~~~I~~~i~~~l~~~~v~V~d~sg~-~~Hf-----~i~VvS~~F~g~s~i~ 49 (79) +.++..|+...|.+......|.|+-..|. ++|| .|....+.|.|.|.-. T Consensus 35 ~~~TG~e~Ar~iL~~~gl~dV~Ve~~~G~LtDHYDP~~k~vrLS~~~y~~~SlaA 89 (222) T pfam04298 35 SGMTGAEVARRILDDNGLYDVRVESVPGQLTDHYDPRNKVVRLSEDVYNGRSVAA 89 (222) T ss_pred CCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCEEEECCCCCCCCCHHH T ss_conf 9989999999999987999827998589878887998785881501147988999 No 8 >COG3325 ChiA Chitinase [Carbohydrate transport and metabolism] Probab=28.88 E-value=54 Score=15.45 Aligned_cols=48 Identities=19% Similarity=0.249 Sum_probs=36.5 Q ss_pred HHHHHHHCCCCCEEEEEECCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHH Q ss_conf 999998219966799997489996699999704668999789999999999987 Q gi|254780969|r 8 IEKMIKKGIPQSIVTIHDLAGDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNK 61 (79) Q Consensus 8 I~~~i~~~l~~~~v~V~d~sg~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~ 61 (79) +-.-|+++|..+.++ +|.||.++|-++.+..+-.--.|..+-+.|.-. T Consensus 199 Ll~eLR~~LD~a~~e------dgr~Y~LTiA~~as~~~l~~~~~~~~~~~vDyi 246 (441) T COG3325 199 LLQELRKKLDKAGVE------DGRHYQLTIAAPASKDKLEGLNHAEIAQYVDYI 246 (441) T ss_pred HHHHHHHHHHHCCCC------CCCEEEEEEECCCCHHHHHCCCHHHHHHHHHHH T ss_conf 999999987650244------585589998447761143045278899887545 No 9 >pfam06183 DinI DinI-like family. This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known. Probab=27.75 E-value=56 Score=15.34 Aligned_cols=48 Identities=19% Similarity=0.344 Sum_probs=29.2 Q ss_pred HHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEEECHHHCCCCHHHHHHHHHHHHHHHH Q ss_conf 8999999982199667999974899966999997046689997899999999999872 Q gi|254780969|r 5 PHEIEKMIKKGIPQSIVTIHDLAGDGNHYAAEIISEEFRGKNRIQQHQMVYDSLGNKM 62 (79) Q Consensus 5 ~~~I~~~i~~~l~~~~v~V~d~sg~~~Hf~i~VvS~~F~g~s~i~rhr~Vy~~L~~~i 62 (79) ..|+..+|...||++.|.|.- +...++.|.=-++ ..+ ..|..+|.+-. T Consensus 10 ~~EL~kRl~~~fPd~~V~Vr~--~s~n~l~v~g~~k--~dK------~~i~eiLqE~w 57 (65) T pfam06183 10 QNELTKRIQSLYPDTVVSVRK--GSANGLSVTGAAK--DDK------ERIMEILQETW 57 (65) T ss_pred HHHHHHHHHHHCCCCEEEEEE--CCCCCEEECCCCH--HHH------HHHHHHHHHHH T ss_conf 999999865338995798710--5679705438774--039------99999999999 No 10 >pfam10330 Stb3 Putative Sin3 binding protein. This is a family of the conserved N-terminal end of a group of proteins conserved in fungi. It is likely to be a Sin3 binding protein. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein. Probab=25.56 E-value=51 Score=15.59 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=20.3 Q ss_pred EECHHHCCCCHHHHHHHHHHHHH Q ss_conf 97046689997899999999999 Q gi|254780969|r 37 IISEEFRGKNRIQQHQMVYDSLG 59 (79) Q Consensus 37 VvS~~F~g~s~i~rhr~Vy~~L~ 59 (79) ..-+.|.++|.-++-|+|.++|. T Consensus 32 ~~vPgF~~l~~sKqRRLi~~AlE 54 (93) T pfam10330 32 TSVPGFSDLSPSKQRRLIVAALE 54 (93) T ss_pred CCCCCCCCCCHHHHHHHHHHHHH T ss_conf 14788465898999999999986 No 11 >cd06256 M14_ASTE_ASPA_like_6 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=25.49 E-value=62 Score=15.10 Aligned_cols=71 Identities=15% Similarity=0.265 Sum_probs=44.6 Q ss_pred HHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEEE-CHHHCCCCHHHHHHHHHH-----HHHHHHCCCEEEEEEEECC Q ss_conf 8999999982199667999974899966999997-046689997899999999-----9998727972688988206 Q gi|254780969|r 5 PHEIEKMIKKGIPQSIVTIHDLAGDGNHYAAEII-SEEFRGKNRIQQHQMVYD-----SLGNKMGNALHALSIKTSV 75 (79) Q Consensus 5 ~~~I~~~i~~~l~~~~v~V~d~sg~~~Hf~i~Vv-S~~F~g~s~i~rhr~Vy~-----~L~~~i~~~IHAlsikt~t 75 (79) +.+|-+++...=|.+.|.+.|.||.+-||.+... ++.|..+..+=..++||. ++.+.+..--=|+++.|=- T Consensus 109 a~~vl~~l~~~~p~a~IDiHNntG~nPhygc~n~ld~~~l~LaslFsrtlV~f~~p~Gvls~a~~~~cPaVTlECG~ 185 (327) T cd06256 109 AEEVLELLADERPEASIDIHNNTGSNPHYGCVNRLDAPHLALASLFSRTLVYFTLPLGVLSEASARLCPAVTLECGG 185 (327) T ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCHHHHHHHHHHCCCEEEECCCCHHHHHHHHCCCCEEEEEECC T ss_conf 99999999744980699812689989982487447767889999856818998267078999766009758997079 No 12 >TIGR00350 lytR_cpsA_psr cell envelope-related function transcriptional attenuator common domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.. Probab=25.31 E-value=62 Score=15.11 Aligned_cols=22 Identities=27% Similarity=0.299 Sum_probs=18.5 Q ss_pred HCCCCHHHHHHHHHHHHHHHHC Q ss_conf 6899978999999999998727 Q gi|254780969|r 42 FRGKNRIQQHQMVYDSLGNKMG 63 (79) Q Consensus 42 F~g~s~i~rhr~Vy~~L~~~i~ 63 (79) =.+..|++|||.+..+|-+.++ T Consensus 160 ~gD~GRi~rQ~~~l~aL~~~~~ 181 (182) T TIGR00350 160 RGDYGRIDRQQQVLSALLERMK 181 (182) T ss_pred CCCHHHHHHHHHHHHHHHHHHH T ss_conf 8833267899999999999860 Done!