Query gi|254780838|ref|YP_003065251.1| hypothetical protein CLIBASIA_03665 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 103 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 00:06:10 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780838.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 KOG4528 consensus 26.7 51 0.0013 15.5 2.3 41 1-47 85-125 (168) 2 pfam06706 CTV_P6 Citrus triste 17.4 92 0.0024 14.1 2.9 23 1-26 1-23 (51) 3 pfam05108 DUF690 Protein of un 17.0 87 0.0022 14.2 1.8 39 2-40 42-88 (481) 4 PHA01757 hypothetical protein 16.6 97 0.0025 14.0 2.3 35 3-37 8-42 (98) 5 pfam09348 DUF1990 Domain of un 16.1 64 0.0016 14.9 1.0 24 20-43 104-128 (158) 6 TIGR01770 NDH_I_N proton-trans 15.2 1.1E+02 0.0027 13.8 3.2 34 4-38 174-209 (491) 7 PRK12705 hypothetical protein; 13.2 86 0.0022 14.3 1.0 15 64-80 293-307 (485) 8 COG1190 LysU Lysyl-tRNA synthe 13.2 67 0.0017 14.9 0.4 44 53-97 167-214 (502) 9 TIGR00048 TIGR00048 radical SA 13.1 62 0.0016 15.0 0.2 22 52-73 311-332 (378) 10 cd00034 ChSh Chromo Shadow Dom 12.8 1.2E+02 0.0032 13.4 1.9 35 28-69 7-42 (54) No 1 >KOG4528 consensus Probab=26.66 E-value=51 Score=15.50 Aligned_cols=41 Identities=39% Similarity=0.442 Sum_probs=29.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEE Q ss_conf 90579999999996336899999987620013661889999998760 Q gi|254780838|r 1 MNSLLFGFLAFLYAYGGSVVFSLFESFFVEKEDGELFIRIMVFEISW 47 (103) Q Consensus 1 mnsllfgflaflyayggsvvfslfesffvekedgelfirimvfeisw 47 (103) |.+|||-||.-+|- .|| -|.|||.|+---|-+...+|||+- T Consensus 85 l~gLLfhFlDe~l~-----~f~-aE~~~V~k~v~ilr~d~~~fei~~ 125 (168) T KOG4528 85 LQGLLFHFLDEWLY-----KFS-AEPFFVPKKVEILRFDQRNFEIAV 125 (168) T ss_pred HHHHHHHHHHHHHH-----HCC-CCCEEEEEEEEEEECCCEEEEEEE T ss_conf 88899999999974-----246-685454424555543441368999 No 2 >pfam06706 CTV_P6 Citrus tristeza virus 6-kDa protein. This family consists of several Citrus tristeza virus (CTV) 6-kDa, 51 residue long hydrophobic (P6) proteins. The function of this family is unknown. Probab=17.38 E-value=92 Score=14.08 Aligned_cols=23 Identities=43% Similarity=0.842 Sum_probs=17.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 90579999999996336899999987 Q gi|254780838|r 1 MNSLLFGFLAFLYAYGGSVVFSLFES 26 (103) Q Consensus 1 mnsllfgflaflyayggsvvfslfes 26 (103) |....-|||.||- |-.||+-|.. T Consensus 1 mdcviqgfltflv---giavf~afa~ 23 (51) T pfam06706 1 MDCVIQGFLTFLV---GIAVFCAFAE 23 (51) T ss_pred CCHHHHHHHHHHH---HHHHHHHHHH T ss_conf 9314788999999---9999998630 No 3 >pfam05108 DUF690 Protein of unknown function (DUF690). This family contains several uncharacterized bacterial membrane proteins. Probab=16.97 E-value=87 Score=14.22 Aligned_cols=39 Identities=21% Similarity=0.577 Sum_probs=30.3 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH--------HHHHCCCCCEEEEEE Q ss_conf 057999999999633689999998--------762001366188999 Q gi|254780838|r 2 NSLLFGFLAFLYAYGGSVVFSLFE--------SFFVEKEDGELFIRI 40 (103) Q Consensus 2 nsllfgflaflyayggsvvfslfe--------sffvekedgelfiri 40 (103) -++++|.+.-.-.-+|..++.+|. ...++||.|.+|+++ T Consensus 42 ra~~~G~vlavl~~aG~~v~gl~~P~~~~g~~~iVv~keTGa~YV~~ 88 (481) T pfam05108 42 RSVALGVVLAIVALIGAALLALIKPQGALGQSAILADRDTGALYVRV 88 (481) T ss_pred HHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCEEEECCCCCEEEEE T ss_conf 24899999999999998560366057988987679967887479998 No 4 >PHA01757 hypothetical protein Probab=16.60 E-value=97 Score=13.97 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=25.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE Q ss_conf 57999999999633689999998762001366188 Q gi|254780838|r 3 SLLFGFLAFLYAYGGSVVFSLFESFFVEKEDGELF 37 (103) Q Consensus 3 sllfgflaflyayggsvvfslfesffvekedgelf 37 (103) .-|+||+|..-+.-||.+..-.-..+-||...|-| T Consensus 8 ~al~gffavtg~l~~sfiigeivhlynekq~nenf 42 (98) T PHA01757 8 GALYGFFAVTGALSASFIIGEIVHLYNEKQRNENF 42 (98) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 88989999998888877799999998276411769 No 5 >pfam09348 DUF1990 Domain of unknown function (DUF1990). This family of proteins are functionally uncharacterized. Probab=16.09 E-value=64 Score=14.95 Aligned_cols=24 Identities=33% Similarity=0.527 Sum_probs=16.6 Q ss_pred HHHHHHHHHHCC-CCCEEEEEEEEE Q ss_conf 999998762001-366188999999 Q gi|254780838|r 20 VFSLFESFFVEK-EDGELFIRIMVF 43 (103) Q Consensus 20 vfslfesffvek-edgelfirimvf 43 (103) ..+-=|+|.||+ +||..+..|..| T Consensus 104 ~e~GEE~F~Ve~~~dg~V~~~v~af 128 (158) T pfam09348 104 PERGEERFLVERDDDGRVWYEITAF 128 (158) T ss_pred HHCCEEEEEEEECCCCEEEEEEEEE T ss_conf 1044799999997999099999997 No 6 >TIGR01770 NDH_I_N proton-translocating NADH-quinone oxidoreductase, chain N; InterPro: IPR010096 This entry describes the 14th (based on Escherichia coli) structural gene, N, of bacterial and chloroplast energy-transducing NADH (or NADPH) dehydrogenases. This entry does not describe any subunit of the mitochondrial complex I (for which the subunit composition is very different), nor NADH dehydrogenases that are not coupled to ion transport. The Enzyme Commission designation 1.6.5.3, for NADH dehydrogenase (ubiquinone), is applied broadly, perhaps unfortunately, even if the quinone is menaquinone (Thermus, Mycobacterium) or plastoquinone (chloroplast). For chloroplast members, the name NADH-plastoquinone oxidoreductase is used for the complex and this protein is designated as subunit 2 or B. This entry also includes a subunit of a related complex in the archaeal methanogen, Methanosarcina mazei, in which F420H2 replaces NADH and 2-hydroxyphenazine replaces the quinone.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport. Probab=15.18 E-value=1.1e+02 Score=13.76 Aligned_cols=34 Identities=35% Similarity=0.719 Sum_probs=22.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCEEEE Q ss_conf 79999999996336899999987620--013661889 Q gi|254780838|r 4 LLFGFLAFLYAYGGSVVFSLFESFFV--EKEDGELFI 38 (103) Q Consensus 4 llfgflaflyayggsvvfslfesffv--ekedgelfi 38 (103) +||| .|+.|+..||..|+---.++. ++++.++.+ T Consensus 174 lLfG-~sliYg~tG~~~~~~~~~~~~~~~~~~~~i~~ 209 (491) T TIGR01770 174 LLFG-ISLIYGFTGSLNFEDLLLFLSNLEKNISNILI 209 (491) T ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH T ss_conf 9999-99999867677799999985211023430310 No 7 >PRK12705 hypothetical protein; Provisional Probab=13.20 E-value=86 Score=14.25 Aligned_cols=15 Identities=60% Similarity=0.919 Sum_probs=5.7 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 12367776777446542 Q gi|254780838|r 64 RSSYQQRSNILSHRKEI 80 (103) Q Consensus 64 rssyqqrsnilshrkei 80 (103) |+||-| |+|.|-.|. T Consensus 293 RtSyGQ--NvL~HSiEv 307 (485) T PRK12705 293 RTSYGQ--NVLSHSLEV 307 (485) T ss_pred CCCCHH--HHHHHHHHH T ss_conf 023405--799999999 No 8 >COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] Probab=13.18 E-value=67 Score=14.86 Aligned_cols=44 Identities=34% Similarity=0.553 Sum_probs=29.8 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHCCCC Q ss_conf 998740240001236777677744654212201----371334102366 Q gi|254780838|r 53 YVDLLPFNFASRSSYQQRSNILSHRKEIAIDQR----RTPITQKLSMGN 97 (103) Q Consensus 53 yvdllpfnfasrssyqqrsnilshrkeiaidqr----rtpitqklsmgn 97 (103) ||||. .|-.+|....+||.|++.-.+-..++- -||+-|...-|. T Consensus 167 ylDLi-~N~e~r~~f~~Rs~ii~~iR~fl~~~gFlEVETP~lq~i~GGA 214 (502) T COG1190 167 YLDLI-VNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPGGA 214 (502) T ss_pred HHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCC T ss_conf 88986-5999999999999999999999987797584160003557873 No 9 >TIGR00048 TIGR00048 radical SAM enzyme, Cfr family; InterPro: IPR004383 This family of conserved hypothetical proteins groups bacterial proteins of unknown function.. Probab=13.12 E-value=62 Score=15.03 Aligned_cols=22 Identities=36% Similarity=0.570 Sum_probs=17.9 Q ss_pred EEEEEEECCCCHHHHHHHHHHH Q ss_conf 7998740240001236777677 Q gi|254780838|r 52 FYVDLLPFNFASRSSYQQRSNI 73 (103) Q Consensus 52 fyvdllpfnfasrssyqqrsni 73 (103) --|.|.|||..+-+.|+.-|+- T Consensus 311 ckvNLIP~NP~~e~~Y~R~s~~ 332 (378) T TIGR00048 311 CKVNLIPFNPFPEADYERPSNE 332 (378) T ss_pred CEEEEEECCCCCCCCCCCCCHH T ss_conf 5040121378798888888088 No 10 >cd00034 ChSh Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2) Probab=12.76 E-value=1.2e+02 Score=13.37 Aligned_cols=35 Identities=29% Similarity=0.407 Sum_probs=0.0 Q ss_pred HHCCCC-CEEEEEEEEEEEEECCCEEEEEEEECCCCHHHHHHH Q ss_conf 200136-618899999987603541799874024000123677 Q gi|254780838|r 28 FVEKED-GELFIRIMVFEISWSRGEFYVDLLPFNFASRSSYQQ 69 (103) Q Consensus 28 fveked-gelfirimvfeiswsrgefyvdllpfnfasrssyqq 69 (103) ++++.| ||| .|-+.|+.|+ .||.|-..|..-.-|. T Consensus 7 ~a~~~~~GeL-----~fl~kwk~~~--~~lv~ak~an~kcPq~ 42 (54) T cd00034 7 GASKSDDGEL-----TFLAKWKDGQ--ASLVPNKELNVKCPLL 42 (54) T ss_pred CEEECCCCEE-----EEEEEECCCC--CCCCCHHHHHHHCCHH T ss_conf 1153699669-----9999972995--0114488986348599 Done!