Query         gi|254781081|ref|YP_003065494.1| hypothetical protein CLIBASIA_04915 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 93
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 05:02:13 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781081.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4634 Uncharacterized protei  37.0      17 0.00044   18.0   1.3   55    2-64     38-101 (113)
  2 KOG3680 consensus               31.9      39   0.001   16.0   2.4   76    3-78    726-817 (830)
  3 KOG1071 consensus               28.5      15 0.00039   18.2  -0.1   23   54-76    310-332 (340)
  4 pfam05021 NPL4 NPL4 family. Th  26.2      41  0.0011   15.9   1.8   20   52-71    235-259 (306)
  5 PRK09293 fructose-1,6-bisphosp  25.6      35  0.0009   16.3   1.3   14   62-75    238-251 (328)
  6 cd04418 NDPk5 Nucleoside dipho  25.4      31  0.0008   16.5   1.0   29   62-90     98-126 (132)
  7 pfam00316 FBPase Fructose-1-6-  23.6      42  0.0011   15.9   1.4   29   46-74    204-248 (325)
  8 cd04414 NDPk6 Nucleoside dipho  22.3      38 0.00098   16.0   1.0   29   62-90    101-129 (135)
  9 cd04416 NDPk_TX NDP kinase dom  19.4      41   0.001   15.9   0.6   29   62-90     99-127 (132)
 10 cd04413 NDPk_I Nucleoside diph  18.7      59  0.0015   15.0   1.3   30   61-90     96-125 (130)

No 1  
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.01  E-value=17  Score=17.95  Aligned_cols=55  Identities=24%  Similarity=0.183  Sum_probs=36.1

Q ss_pred             CHHHHHHHHHHHEEEEEEEECCCCCC---------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04678776410002467742046633---------2015778878864367786366889879999999998
Q gi|254781081|r    2 SEIMCEAYAEERYSVLLDLDFASDSD---------QITSDELSDLTQRYDYLLLNKHLLVDNLKSYLDKFGS   64 (93)
Q Consensus         2 seimceayaeerysvlldldfasdsd---------qitsdelsdltqrydylllnkhllvdnlksyldkfgs   64 (93)
                      -||+-.|++++|--|-.|.||+--+-         +++...+|...+        ..+++-+|+.+.++|-+
T Consensus        38 ~EI~a~A~~~~~iivTkDsDF~~la~~~G~Ppki~wLr~gNvs~~~i--------e~l~~~~l~~~~e~le~  101 (113)
T COG4634          38 IEIWAYARRNNRIIVTKDSDFADLALTLGSPPKIVWLRCGNVSTREI--------EILIRSVLRAIGEELES  101 (113)
T ss_pred             HHHHHHHHHCCCEEEECCCCHHHHHHHCCCCCEEEEEEECCCCHHHH--------HHHHHHHHHHHHHHHHC
T ss_conf             99999987569189971732899999708998589998368787999--------99999999999999838


No 2  
>KOG3680 consensus
Probab=31.89  E-value=39  Score=15.99  Aligned_cols=76  Identities=28%  Similarity=0.299  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHEEEEEEEECCCCCCCCCHH------HHHHHHHHHHHHHHHHH-----HH-----HHHHHHHHHHHHHHH
Q ss_conf             467877641000246774204663320157------78878864367786366-----88-----987999999999898
Q gi|254781081|r    3 EIMCEAYAEERYSVLLDLDFASDSDQITSD------ELSDLTQRYDYLLLNKH-----LL-----VDNLKSYLDKFGSLI   66 (93)
Q Consensus         3 eimceayaeerysvlldldfasdsdqitsd------elsdltqrydylllnkh-----ll-----vdnlksyldkfgsli   66 (93)
                      +||-.-|...|--.-=|.-|+.|-+.-..|      -|.-+-+||..-...+-     ..     ..+++|-+..+-+|-
T Consensus       726 ~~iSaIY~~vrhrL~DdWafg~Dis~r~~D~Q~eE~~LrA~Ie~fn~RrY~~~~~~~~~~~~~a~~~~~~svlG~~~~l~  805 (830)
T KOG3680         726 KIISAIYLKVRHRLTDDWAFGNDISARPWDAQAEECALRALIEFFNSRRYDRAMESLYQFVIDAEMNCLQSVLGQRLSLP  805 (830)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCHHHHHHHHHHHHCCCCCHH
T ss_conf             89999999876515543010467787800446788999999999877642400021002210788766776640233246


Q ss_pred             HHHHCCCCHHEE
Q ss_conf             786207701323
Q gi|254781081|r   67 SDFHRNSESELV   78 (93)
Q Consensus        67 sdfhrnseselv   78 (93)
                      -+||+|.++-|-
T Consensus       806 eyf~~ny~~wle  817 (830)
T KOG3680         806 EYFHRNYESWLE  817 (830)
T ss_pred             HHHHHHHHHHHH
T ss_conf             665543898888


No 3  
>KOG1071 consensus
Probab=28.51  E-value=15  Score=18.19  Aligned_cols=23  Identities=35%  Similarity=0.501  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHH
Q ss_conf             79999999998987862077013
Q gi|254781081|r   54 NLKSYLDKFGSLISDFHRNSESE   76 (93)
Q Consensus        54 nlksyldkfgslisdfhrnsese   76 (93)
                      ++|.|+|+++..|-||+|---.|
T Consensus       310 tv~~~l~~~~~~V~DfvR~E~Ge  332 (340)
T KOG1071         310 TVKEYLDPHNVSVVDFVRFEVGE  332 (340)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHCC
T ss_conf             48777366774068889988513


No 4  
>pfam05021 NPL4 NPL4 family. The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.
Probab=26.23  E-value=41  Score=15.87  Aligned_cols=20  Identities=40%  Similarity=0.640  Sum_probs=11.6

Q ss_pred             HHHHHHHHHH-----HHHHHHHHHC
Q ss_conf             9879999999-----9989878620
Q gi|254781081|r   52 VDNLKSYLDK-----FGSLISDFHR   71 (93)
Q Consensus        52 vdnlksyldk-----fgslisdfhr   71 (93)
                      ...|++||.+     +...+||||-
T Consensus       235 ~~~l~~yl~~~~~~~~~~~~sdFHl  259 (306)
T pfam05021       235 LRALAKYLKSHKPKPFLERLSDFHL  259 (306)
T ss_pred             HHHHHHHHHHHCCCCHHHHHCCHHH
T ss_conf             9999999986079726661024131


No 5  
>PRK09293 fructose-1,6-bisphosphatase; Provisional
Probab=25.61  E-value=35  Score=16.25  Aligned_cols=14  Identities=36%  Similarity=0.589  Sum_probs=10.8

Q ss_pred             HHHHHHHHHCCCCH
Q ss_conf             99898786207701
Q gi|254781081|r   62 FGSLISDFHRNSES   75 (93)
Q Consensus        62 fgslisdfhrnses   75 (93)
                      .||++.||||+-.-
T Consensus       238 ~gslVaD~hr~L~~  251 (328)
T PRK09293        238 IGSMVADVHRILLK  251 (328)
T ss_pred             ECCHHHHHHHHHHC
T ss_conf             23224888999761


No 6  
>cd04418 NDPk5 Nucleoside diphosphate kinase homolog 5 (NDP kinase homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is almost exclusively found in testis, especially in the flagella of spermatids and spermatozoa, in association with axoneme microtubules, and may play a role in spermatogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species.  It belongs to the nm23 Group II genes and appears to differ from the other human NDPks in that it lacks two important catalytic site residues, and thus does not appear to possess NDP kinase activity. NDPk5 confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes, including glutathione peroxidase 5 (Gpx5).
Probab=25.45  E-value=31  Score=16.52  Aligned_cols=29  Identities=28%  Similarity=0.188  Sum_probs=23.3

Q ss_pred             HHHHHHHHHCCCCHHEEEECCCCHHHHHH
Q ss_conf             99898786207701323204542056652
Q gi|254781081|r   62 FGSLISDFHRNSESELVRCSDSESEEAKE   90 (93)
Q Consensus        62 fgslisdfhrnseselvrcsdseseeake   90 (93)
                      -||+-.+|-.......|.||||.....+|
T Consensus        98 P~siR~~fg~~~~~N~vH~Sds~e~A~~E  126 (132)
T cd04418          98 PDSLRAIYGTDDLRNAVHGSDSFSSAERE  126 (132)
T ss_pred             CCCHHHHHCCCCCCCCEECCCCHHHHHHH
T ss_conf             99859983899776795888999999999


No 7  
>pfam00316 FBPase Fructose-1-6-bisphosphatase.
Probab=23.59  E-value=42  Score=15.85  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHH----------------HHHHHHHHHCCCC
Q ss_conf             6366889879999999----------------9989878620770
Q gi|254781081|r   46 LNKHLLVDNLKSYLDK----------------FGSLISDFHRNSE   74 (93)
Q Consensus        46 lnkhllvdnlksyldk----------------fgslisdfhrnse   74 (93)
                      .|..-.-+.++.|++.                .||++.||||+--
T Consensus       204 ~n~~~w~~~~~~yi~~~~~~~~~~~k~y~~Ry~GsmVaD~HR~L~  248 (325)
T pfam00316       204 GNYRHWDPPVRKYIDDCKAGAEGPRRPYNMRYIGSMVADVHRILL  248 (325)
T ss_pred             CCHHHCCHHHHHHHHHHHCCCCCCCCCCCEEEECCHHHHHHHHHH
T ss_conf             003323688999999986557677887433442321588999987


No 8  
>cd04414 NDPk6 Nucleoside diphosphate kinase 6 (NDP kinase 6, NDPk6, NM23-H6; NME6; Inhibitor of p53-induced apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding NDPk6 is expressed mainly in mitochondria, but also found at a lower level in most tissues. NDPk6 has all nine residues considered crucial for enzyme structure and activity, and has been found to have NDP kinase activity. It may play a role in cell growth and cell cycle progression. The nm23-H6 gene locus has been implicated in a variety of malignant tumors.
Probab=22.27  E-value=38  Score=16.04  Aligned_cols=29  Identities=17%  Similarity=0.138  Sum_probs=23.2

Q ss_pred             HHHHHHHHHCCCCHHEEEECCCCHHHHHH
Q ss_conf             99898786207701323204542056652
Q gi|254781081|r   62 FGSLISDFHRNSESELVRCSDSESEEAKE   90 (93)
Q Consensus        62 fgslisdfhrnseselvrcsdseseeake   90 (93)
                      -||+-.+|-.+.-...|.||||..+-.+|
T Consensus       101 P~tIR~~fg~~~~~N~vHgSds~e~A~rE  129 (135)
T cd04414         101 PDSIRGLYGLTDTRNATHGSDSPASAQRE  129 (135)
T ss_pred             CCCHHHHHCCCCCCCCEECCCCHHHHHHH
T ss_conf             99719984787766084388999999999


No 9  
>cd04416 NDPk_TX NDP kinase domain of thioredoxin domain-containing proteins  (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin IC1 (intermediate chain-1) protein, a component of the sperm axonemal outer dynein arm complex. Txl-2 is mainly represented in close association with microtubules within tissues with cilia and flagella such as seminiferous epithelium (spermatids) and lung airway epithelium, suggesting possible role in control of microtubule stability and maintenance.
Probab=19.43  E-value=41  Score=15.89  Aligned_cols=29  Identities=38%  Similarity=0.365  Sum_probs=22.8

Q ss_pred             HHHHHHHHHCCCCHHEEEECCCCHHHHHH
Q ss_conf             99898786207701323204542056652
Q gi|254781081|r   62 FGSLISDFHRNSESELVRCSDSESEEAKE   90 (93)
Q Consensus        62 fgslisdfhrnseselvrcsdseseeake   90 (93)
                      -||+-.+|-.+.....|.||||...-.+|
T Consensus        99 P~siR~~fg~~~~~N~vH~SDs~e~A~rE  127 (132)
T cd04416          99 PDSLRAQFARDHLSNAVHGSSSAEEAEKE  127 (132)
T ss_pred             CCCCHHHHCCCCCCCCEECCCCHHHHHHH
T ss_conf             99878885688675695889999999999


No 10 
>cd04413 NDPk_I Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4),  and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that 
Probab=18.71  E-value=59  Score=15.03  Aligned_cols=30  Identities=27%  Similarity=0.347  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHCCCCHHEEEECCCCHHHHHH
Q ss_conf             999898786207701323204542056652
Q gi|254781081|r   61 KFGSLISDFHRNSESELVRCSDSESEEAKE   90 (93)
Q Consensus        61 kfgslisdfhrnseselvrcsdseseeake   90 (93)
                      +-||+-.+|-.+.....|.||||...-.+|
T Consensus        96 ~p~siR~~fg~~~~~NavHgSDs~e~A~~E  125 (130)
T cd04413          96 APGTIRGDFALSIGRNIVHGSDSVESAERE  125 (130)
T ss_pred             CCCCHHHHHCCCCCCCCEECCCCHHHHHHH
T ss_conf             973146773787564794788999999999


Done!