Query gi|254781134|ref|YP_003065547.1| hypothetical protein CLIBASIA_05180 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 320 No_of_seqs 163 out of 290 Neff 6.6 Searched_HMMs 39220 Date Mon May 30 05:12:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781134.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam11134 Phage_stabilize Phag 85.7 2.2 5.7E-05 21.1 5.3 100 57-159 228-330 (468) 2 TIGR00264 TIGR00264 alpha-NAC 39.5 4.7 0.00012 19.2 -1.3 13 24-36 34-46 (125) 3 cd01557 BCAT_beta_family BCAT_ 36.3 26 0.00068 14.9 2.2 35 168-204 163-197 (279) 4 TIGR02262 benz_CoA_lig benzoat 23.9 48 0.0012 13.4 2.7 34 167-202 399-432 (520) 5 pfam05694 SBP56 56kDa selenium 19.9 58 0.0015 13.0 5.9 43 32-74 98-145 (461) 6 TIGR01734 D-ala-DACP-lig D-ala 19.9 58 0.0015 13.0 2.2 23 116-138 139-161 (513) 7 COG1935 Uncharacterized conser 19.7 33 0.00083 14.4 0.2 17 69-85 41-57 (122) 8 TIGR02275 DHB_AMP_lig 2,3-dihy 19.1 61 0.0015 12.9 2.1 23 40-62 262-289 (534) 9 pfam07591 DUF1557 Protein of u 15.3 66 0.0017 12.7 0.9 21 73-94 1-21 (130) 10 KOG3580 consensus 15.0 77 0.002 12.3 2.9 75 62-136 207-291 (1027) No 1 >pfam11134 Phage_stabilize Phage stabilisation protein. Phage stabilisation protein, also referred to as gp10 has a structure rich in beta sheets which spontaneously assembles into hexamers. Gp10 forms part of the baseplate of bacteriophage T4 and functions as a molecular lever that rotates and extends the hinged short tail fibers to facilitate cell attachment. Probab=85.69 E-value=2.2 Score=21.07 Aligned_cols=100 Identities=11% Similarity=0.138 Sum_probs=57.0 Q ss_pred CCCCCCHHEEEECCCEEEEECCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHCCC--CCEEEEEEECCCCEEEEEECCC Q ss_conf 46137011342078099992688065210122155421100234046555431046--7425999907982899982688 Q gi|254781134|r 57 GRPLGKRAIVFVKNDVWIATNNGLISMKNILLQEEKTNLPLSWPIQEQWEQAIMVA--PTGWSMILWEKRNMLLISCPKN 134 (320) Q Consensus 57 ~~~i~~~~i~~~GgDl~fls~dGlr~ls~t~~~g~~~l~~iS~~Iq~~~~~~~~~~--~~~~s~v~~~k~~~~lf~~~~~ 134 (320) -||.++.|.+++|.--+|++..-=-+.|-=+..+--.+.--+..|..+++.....+ ..+-..+-+...-++++..|.. T Consensus 228 kGIAg~~~k~~~~DtyafIs~~atgaPsVyii~~g~a~~IstasIdkiLr~yta~ELa~~vmea~rfd~helllihL~rh 307 (468) T pfam11134 228 KGIAGTSCKCRVGDTYAFISHQATGAPSVYIINGGQALRISTATIDKILRSYTADELAESVMETRRFDSHELLLIHLPRH 307 (468) T ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCC T ss_conf 45357641110276779954788899659997688423201778999998632588999888886528716899983682 Q ss_pred CCCCEEEEEEECCCCCEEEEEE-CCC Q ss_conf 7631014676212353037863-551 Q gi|254781134|r 135 SLLSDKTFVMNVAHNNRWSSFH-NWF 159 (320) Q Consensus 135 ~~~~~~~~v~~~~~~gaws~~~-g~~ 159 (320) ...++. .... .+-+||-++ |+. T Consensus 308 tL~yd~--~ss~-~g~Qw~lLktG~y 330 (468) T pfam11134 308 TLCYDA--SASQ-NGEQWSLLKSGFY 330 (468) T ss_pred EEEEEC--CCCC-CCCEEEEEECCCC T ss_conf 589973--4566-6741588631567 No 2 >TIGR00264 TIGR00264 alpha-NAC homolog; InterPro: IPR005231 Eukaryotic NAC, an abundant heterodimer composed of two homologous subunits, reversibly binds eukaryotic ribosomes and is located in direct proximity to nascent polypeptides as they emerge from the ribosome . Despite being implicated in diverse cellular functions, its role in vivo is still not completely understood. It is thought that NAC may function as a shield protecting the nascent chain from inappropriate interactions with cytosolic factors, and could regulate further translation of the polypeptide through its interaction with the ribosome. Archaeal NAC is a homodimer which appears to be functionally analogous to the eukaryotic form, associating with ribosomes and contacting the nascent polypeptide chain emerging on the ribosome . It has two domains; the NAC domain, which it shares with eukaryotic NAC, and a C-terminal UBA domain also found on the alpha, but not beta, subunit of eukaryotic NAC. The NAC domain forms a six-stranded beta-barrel structure which shows some similarities to the OB fold. This domain appears to be responsible for dimerisation, nucleic acid binding, and nascent polypeptide binding. The UBA domain is typical of ubiquitin or polyubquitin-binding proteins; its physiological role is unclear but it was suggested that it may compete with the proteosome for ubiquitin, thus inhibiting ubiquitin-mediated protein degradation. . Probab=39.48 E-value=4.7 Score=19.24 Aligned_cols=13 Identities=8% Similarity=-0.072 Sum_probs=6.1 Q ss_pred EEEEEECCCCEEE Q ss_conf 7999963881899 Q gi|254781134|r 24 LCVFLSTLGEVAV 36 (320) Q Consensus 24 ~~v~i~~~g~v~v 36 (320) -++|.+++.|+++ T Consensus 34 eVii~~~deE~if 46 (125) T TIGR00264 34 EVIIKLKDEELIF 46 (125) T ss_pred EEEEEECCCEEEE T ss_conf 6778735725785 No 3 >cd01557 BCAT_beta_family BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and alpha-ketoisovalerate. The enzyme requires pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze the reaction. It has been found that mammals have two foms of the enzyme - mitochondrial and cytosolic forms while bacteria contain only one form of the enzyme. The mitochondrial form plays a significant role in skeletal muscle glutamine and alanine synthesis and in interorgan nitrogen metabolism.Members of this subgroup are widely distributed in all three forms of life. Probab=36.34 E-value=26 Score=14.93 Aligned_cols=35 Identities=11% Similarity=-0.032 Sum_probs=16.9 Q ss_pred CEEEEECCCCEEEECCCCCCCCCCEEEEEEEECCCCC Q ss_conf 4299940583899744256757750799998257677 Q gi|254781134|r 168 ENLFFGDYEGTFWQGDISGSDNARPFIGIYLSPFHAI 204 (320) Q Consensus 168 ~~lyfG~~dG~Vy~~e~G~sddG~~i~a~y~sp~~~f 204 (320) |-++.=..||+|-+.-.+|-|-= ......||.+.- T Consensus 163 eal~ld~~~G~V~Egs~sNiF~v--k~~~l~TP~l~~ 197 (279) T cd01557 163 QALWLDGAHGYVAEVGTMNIFFV--KDGELITPPLDG 197 (279) T ss_pred EEEEECCCCCEEEEECCEEEEEE--ECCEEEECCCCC T ss_conf 59999189877998267038999--477688468646 No 4 >TIGR02262 benz_CoA_lig benzoate-CoA ligase family; InterPro: IPR011957 Characterised members of this protein family include benzoate-CoA ligase, 4-hydroxybenzoate-CoA ligase, 2-aminobenzoate-CoA ligase, etc. Members are related to fatty acid and acetate CoA ligases.. Probab=23.85 E-value=48 Score=13.44 Aligned_cols=34 Identities=24% Similarity=0.513 Sum_probs=29.0 Q ss_pred CCEEEEECCCCEEEECCCCCCCCCCEEEEEEEECCC Q ss_conf 442999405838997442567577507999982576 Q gi|254781134|r 167 NENLFFGDYEGTFWQGDISGSDNARPFIGIYLSPFH 202 (320) Q Consensus 167 ~~~lyfG~~dG~Vy~~e~G~sddG~~i~a~y~sp~~ 202 (320) .+.-|+-++||+--+ -|=+||=-..-++|.|||- T Consensus 399 sGDKY~r~~dG~YtY--aGR~DDmlKVSGIyVSPfE 432 (520) T TIGR02262 399 SGDKYVRNDDGVYTY--AGRTDDMLKVSGIYVSPFE 432 (520) T ss_pred CCCCEEECCCCEEEE--ECCCCCCEEECCEEECCHH T ss_conf 487103637850687--0244352355241678179 No 5 >pfam05694 SBP56 56kDa selenium binding protein (SBP56). This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homologue of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport. Probab=19.87 E-value=58 Score=12.96 Aligned_cols=43 Identities=5% Similarity=0.097 Sum_probs=16.3 Q ss_pred CCEEEEE-ECCCCCCCCEEEEE---EEEECCCCCCHHEEEEC-CCEEE Q ss_conf 8189996-05888756248965---88704613701134207-80999 Q gi|254781134|r 32 GEVAVYG-GDNPDDSSSFSLKA---IYHIGRPLGKRAIVFVK-NDVWI 74 (320) Q Consensus 32 g~v~v~~-g~~p~~~~~~~l~~---~~~~~~~i~~~~i~~~G-gDl~f 74 (320) +.|.|+- ++||-.+.-...+. +.+..+...+.++--.+ |++++ T Consensus 98 srIyIiDv~tdPr~P~l~KvIe~eev~~k~g~s~PHT~HClp~G~ImI 145 (461) T pfam05694 98 SRIYIVDTKPDPRKPRLVKVIEPEEVAEKTGYSRPHTVHCGPDGEIYI 145 (461) T ss_pred CCEEEEECCCCCCCCEEEEECCHHHHHHHCCCCCCCCCCCCCCCCEEE T ss_conf 878999788998997279970789988634987785111579865899 No 6 >TIGR01734 D-ala-DACP-lig D-alanine-activating enzyme; InterPro: IPR010072 This entry represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP to D-ala-AMP + PPi, and further catalyses the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in Gram-positive bacteria, both polysacchatides .; GO: 0016208 AMP binding, 0047473 D-alanine-poly(phosphoribitol) ligase activity, 0019350 teichoic acid biosynthetic process. Probab=19.86 E-value=58 Score=12.96 Aligned_cols=23 Identities=9% Similarity=0.044 Sum_probs=11.8 Q ss_pred EEEEEECCCCEEEEEECCCCCCC Q ss_conf 59999079828999826887631 Q gi|254781134|r 116 WSMILWEKRNMLLISCPKNSLLS 138 (320) Q Consensus 116 ~s~v~~~k~~~~lf~~~~~~~~~ 138 (320) .+..+....+||+++.--+++.. T Consensus 139 ~~~~V~~dD~yYIIyTSGtTG~P 161 (513) T TIGR01734 139 FDHAVKGDDNYYIIYTSGTTGKP 161 (513) T ss_pred CCCCCCCCCCEEEEEEECCCCCC T ss_conf 10000579966899853664888 No 7 >COG1935 Uncharacterized conserved protein [Function unknown] Probab=19.68 E-value=33 Score=14.40 Aligned_cols=17 Identities=18% Similarity=0.298 Sum_probs=12.2 Q ss_pred CCCEEEEECCCEEEEEE Q ss_conf 78099992688065210 Q gi|254781134|r 69 KNDVWIATNNGLISMKN 85 (320) Q Consensus 69 GgDl~fls~dGlr~ls~ 85 (320) .||++||++.+++-|.+ T Consensus 41 ~GDlVFlT~~~~~Dl~~ 57 (122) T COG1935 41 EGDLVFLTSTSLEDLTK 57 (122) T ss_pred CCCEEEEEHHHHHHHHC T ss_conf 88889996457667626 No 8 >TIGR02275 DHB_AMP_lig 2,3-dihydroxybenzoate-AMP ligase; InterPro: IPR011963 Siderophores are low molecular weight iron-chelating compounds synthesised by many bacteria to aid in the aquisition of this vital trace element . Proteins in this entry are adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores. These proteins belong to the AMP-binding family and are mostly thought to activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. One of these proteins, however, is believed to differ in function, activating salicylate rather than DHB. The crystal structure of 2,3-dihydroxybenzoate-AMP ligase (P40871 from SWISSPROT) from Bacillus subtilis has been examined . This protein is composed of a large N-terminal domain (~420 aa) and a more compact C-terminal domain (~110 aa), with an overall "hammer-and-anvil" fold similar to that of firefly luciferase . The active site is located in a deep compartment located at the interface of the domains, with a p-loop thought to be involved in catalysis located at the entrance to the cavity. Relatively little conformational change was observed during catalysis.; GO: 0008668 (23-dihydroxybenzoyl)adenylate synthase activity, 0019290 siderophore biosynthetic process. Probab=19.10 E-value=61 Score=12.86 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=10.8 Q ss_pred CCCCCCCCEEEEE-----EEEECCCCCC Q ss_conf 5888756248965-----8870461370 Q gi|254781134|r 40 DNPDDSSSFSLKA-----IYHIGRPLGK 62 (320) Q Consensus 40 ~~p~~~~~~~l~~-----~~~~~~~i~~ 62 (320) +||+...-|.|+. ++..++|+.- T Consensus 262 ~dPsP~~cFpLIE~HkVt~TALVPPav~ 289 (534) T TIGR02275 262 ADPSPTDCFPLIERHKVTVTALVPPAVA 289 (534) T ss_pred CCCCHHHHCHHHHHCCCEEEECCHHHHH T ss_conf 8888212110445547307873356899 No 9 >pfam07591 DUF1557 Protein of unknown function (DUF1557). A cluster of homologous proteins identified in Leptospira interrogans. One member has been predicted to be a phenazine biosynthesis family protein. Probab=15.25 E-value=66 Score=12.65 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=15.0 Q ss_pred EEEECCCEEEEEEEEECCCCCC Q ss_conf 9992688065210122155421 Q gi|254781134|r 73 WIATNNGLISMKNILLQEEKTN 94 (320) Q Consensus 73 ~fls~dGlr~ls~t~~~g~~~l 94 (320) |++++||++|+.. ++.||.-+ T Consensus 1 lV~t~dG~k~IE~-I~vGD~V~ 21 (130) T pfam07591 1 LVLTADGYKAIAH-IKAGDKVL 21 (130) T ss_pred CEECCCCCEEHHH-CCCCCEEE T ss_conf 9798988478113-37999999 No 10 >KOG3580 consensus Probab=14.97 E-value=77 Score=12.27 Aligned_cols=75 Identities=13% Similarity=0.055 Sum_probs=38.4 Q ss_pred CHHEEEECCCE---EE---EECCCEEEEEEEEECCCCCC---CCCCCCHH-HHHHHHHCCCCCEEEEEEECCCCEEEEEE Q ss_conf 01134207809---99---92688065210122155421---10023404-65554310467425999907982899982 Q gi|254781134|r 62 KRAIVFVKNDV---WI---ATNNGLISMKNILLQEEKTN---LPLSWPIQ-EQWEQAIMVAPTGWSMILWEKRNMLLISC 131 (320) Q Consensus 62 ~~~i~~~GgDl---~f---ls~dGlr~ls~t~~~g~~~l---~~iS~~Iq-~~~~~~~~~~~~~~s~v~~~k~~~~lf~~ 131 (320) +|.-.|+|--| +| ++.+||-.-.+-+|+||+-| ++++.|.- .+.+.++......-++++-..++.-|++. T Consensus 207 sR~nEEyGlrLgSqIFvKeit~~gLAardgnlqEGDiiLkINGtvteNmSLtDar~LIEkS~GKL~lvVlRD~~qtLiNi 286 (1027) T KOG3580 207 SRANEEYGLRLGSQIFVKEITRTGLAARDGNLQEGDIILKINGTVTENMSLTDARKLIEKSRGKLQLVVLRDSQQTLINI 286 (1027) T ss_pred ECCCHHHCCCCCCHHHHHHHCCCCHHHCCCCCCCCCEEEEECCEEECCCCCHHHHHHHHHCCCCEEEEEEECCCCEEEEC T ss_conf 02555544010021234333023111124886556379997767403444056788987436736899993278515506 Q ss_pred CCCCC Q ss_conf 68876 Q gi|254781134|r 132 PKNSL 136 (320) Q Consensus 132 ~~~~~ 136 (320) |+..- T Consensus 287 P~l~d 291 (1027) T KOG3580 287 PSLND 291 (1027) T ss_pred CCCCC T ss_conf 88766 Done!