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!