Query         gi|254781198|ref|YP_003065611.1| guanylate kinase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 117
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 06:04:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781198.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam05278 PEARLI-4 Arabidopsis  26.4      44  0.0011   15.8   1.9   77   11-98     29-109 (234)
  2 pfam09943 DUF2175 Uncharacteri  23.3      61  0.0016   15.0   2.2   27   21-47     73-99  (101)
  3 TIGR02079 THD1 threonine dehyd  15.5      41   0.001   16.0  -0.2   37   22-68      8-44  (415)
  4 TIGR00366 TIGR00366 conserved   12.9      85  0.0022   14.2   0.9   21   21-41    227-250 (463)
  5 COG2854 Ttg2D ABC-type transpo  12.8      83  0.0021   14.2   0.8   95    8-105    78-178 (202)
  6 pfam07798 DUF1640 Protein of u  12.0 1.3E+02  0.0033   13.2   3.1   78   23-100    66-162 (177)
  7 pfam04701 Pox_D2 Pox virus D2   10.6   1E+02  0.0026   13.7   0.7   49   17-65     15-73  (143)
  8 pfam09068 efhand_1 EF hand. Me  10.5 1.5E+02  0.0037   12.9   1.9   19   96-114    90-108 (125)
  9 COG4127 Uncharacterized conser  10.5 1.4E+02  0.0036   12.9   1.4   13   34-46    295-307 (318)
 10 pfam07600 DUF1564 Protein of u  10.2 1.1E+02  0.0029   13.5   0.8   12   94-105   100-111 (167)

No 1  
>pfam05278 PEARLI-4 Arabidopsis phospholipase-like protein (PEARLI 4). This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4.
Probab=26.39  E-value=44  Score=15.81  Aligned_cols=77  Identities=22%  Similarity=0.326  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHEEEEEEEEEEEEEHHHHHHHHH---
Q ss_conf             04567789986785100122025525217998776667689999999507432110256874357750143689888---
Q gi|254781198|r   11 DTNHKGSNLPPEEIKNIQDHRITLLEKNYERLSDKVEASHTKLMEAILDNREDIANVRIEVANVRIEVANVRTEMLG---   87 (117)
Q Consensus        11 dtnhkgsnlppeeikniqdhritlleknyerlsdkveashtklmeaildnredianvrievanvrievanvrtemlg---   87 (117)
                      +..+++++-|||-     +-...+-+------.-+|.+|-.....+|+|...|||      ||-+.+-+..|+-.|-   
T Consensus        29 ~~~~~~~~ep~eL-----e~~sviSds~VSVgkY~VRasvss~Lq~IidKhGDIA------a~~kL~S~s~Rs~yLe~l~   97 (234)
T pfam05278        29 DDEENNNEEPVEL-----DLQSVMSDSYVSVGKYRVRASVSTTLQAIIDKHGDIA------SNSKLQSLSTRSYYLECLA   97 (234)
T ss_pred             CCHHCCCCCCEEE-----HHHHHHHHHHEEHEHEEEHHHHHHHHHHHHHHCCCCC------CCCCCCCHHHHHHHHHHHH
T ss_conf             8200177667020-----1677651321201110011349999999998606311------1674442788999999999


Q ss_pred             -HHHHCCHHHHH
Q ss_conf             -88760025776
Q gi|254781198|r   88 -LIWKIPATAIG   98 (117)
Q Consensus        88 -liwkipataig   98 (117)
                       ++.....|..+
T Consensus        98 ~vv~eLqsTpl~  109 (234)
T pfam05278        98 SVVQELQSTPLR  109 (234)
T ss_pred             HHHHHHCCCHHH
T ss_conf             999998057177


No 2  
>pfam09943 DUF2175 Uncharacterized protein conserved in archaea (DUF2175). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=23.27  E-value=61  Score=15.00  Aligned_cols=27  Identities=37%  Similarity=0.406  Sum_probs=21.6

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             678510012202552521799877666
Q gi|254781198|r   21 PEEIKNIQDHRITLLEKNYERLSDKVE   47 (117)
Q Consensus        21 peeikniqdhritlleknyerlsdkve   47 (117)
                      .||+|.+-+.++..+||+-..|+.+++
T Consensus        73 ~ee~k~~i~q~~k~~Ek~Aa~lT~~i~   99 (101)
T pfam09943        73 SEEIKKVIRQVRKDLEKLAAKLTRKIE   99 (101)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             488999999999999999999999987


No 3  
>TIGR02079 THD1 threonine dehydratase; InterPro: IPR011820    This entry represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases are described by IPR005787 from INTERPRO and IPR005789 from INTERPRO. The sequences described by this entry are exclusively found in species containing the rest of the isoleucine pathway and which are generally lacking in members of the other two clades of threonine dehydratases. The sequences associated with this entry are often cluster with other elements of the isoleucine pathway.; GO: 0004794 L-threonine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0009097 isoleucine biosynthetic process.
Probab=15.45  E-value=41  Score=16.01  Aligned_cols=37  Identities=51%  Similarity=0.702  Sum_probs=24.6

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHEEE
Q ss_conf             78510012202552521799877666768999999950743211025
Q gi|254781198|r   22 EEIKNIQDHRITLLEKNYERLSDKVEASHTKLMEAILDNREDIANVR   68 (117)
Q Consensus        22 eeikniqdhritlleknyerlsdkveashtklmeaildnredianvr   68 (117)
                      ++||.|-.|  |-|++| ++||.+-.|+       |+=.|||...||
T Consensus         8 ~~~~~vv~~--TPL~~n-~~LS~~Y~a~-------i~LKREDLq~VR   44 (415)
T TIGR02079         8 KRIKEVVKH--TPLQKN-ERLSEKYGAN-------IYLKREDLQEVR   44 (415)
T ss_pred             HHHHHHCCC--CCCCCC-HHHHHHHCCC-------EEEEECCCCCCC
T ss_conf             998630589--878701-3555776861-------677510367331


No 4  
>TIGR00366 TIGR00366 conserved hypothetical protein TIGR00366; InterPro: IPR006161    This is a family of conserved hypothetical proteins of no clearly defined function, although they may act as short chain fatty acid transporters.; GO: 0015635 short-chain fatty acid transporter activity, 0015912 short-chain fatty acid transport, 0016020 membrane.
Probab=12.87  E-value=85  Score=14.17  Aligned_cols=21  Identities=48%  Similarity=0.594  Sum_probs=15.7

Q ss_pred             HHHHHCCHH---HHHHHHHHHHHH
Q ss_conf             678510012---202552521799
Q gi|254781198|r   21 PEEIKNIQD---HRITLLEKNYER   41 (117)
Q Consensus        21 peeikniqd---hritlleknyer   41 (117)
                      ++|+|.|..   |-|.|+.+.++.
T Consensus       227 ~~e~~~ID~vaPhiikL~~~e~~~  250 (463)
T TIGR00366       227 KGEIKSIDPVAPHIIKLLKKEKEE  250 (463)
T ss_pred             CCCCCCCCCCCHHHHHHHCCCHHH
T ss_conf             777332365307899972247257


No 5  
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=12.75  E-value=83  Score=14.24  Aligned_cols=95  Identities=17%  Similarity=0.217  Sum_probs=50.3

Q ss_pred             HHHCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHEEEEEEEEE-----EEEEHHHH
Q ss_conf             5430456778998678510012202552521799877666768999999950743211025687435-----77501436
Q gi|254781198|r    8 SVMDTNHKGSNLPPEEIKNIQDHRITLLEKNYERLSDKVEASHTKLMEAILDNREDIANVRIEVANV-----RIEVANVR   82 (117)
Q Consensus         8 svmdtnhkgsnlppeeikniqdhritlleknyerlsdkveashtklmeaildnredianvrievanv-----rievanvr   82 (117)
                      .||..+  -+.+.||.++-..+---++|++.|...--....-+-+.-..-..+..++..||.+|.+-     ..+.-.-.
T Consensus        78 ~vLGk~--~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q~~~v~~~~~~~~~~~v~V~~~Ii~~~~~PV~l~f~~r~  155 (202)
T COG2854          78 LVLGKY--YKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQTLKVKPSRPLGDGTDVIVRVEIIDPGQKPVKLDFLWRK  155 (202)
T ss_pred             HHHCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEEE
T ss_conf             973445--120899999999999999999999999997069875137875469998489999871589998578998733


Q ss_pred             HHHHHHHHHCCHH-HHHHHHHHHH
Q ss_conf             8988888760025-7769999999
Q gi|254781198|r   83 TEMLGLIWKIPAT-AIGISICLRF  105 (117)
Q Consensus        83 temlgliwkipat-aigisiclrf  105 (117)
                      ..--|- ||+--- +-|||+.--|
T Consensus       156 ~~~~G~-WKv~Dvi~eGiSlv~t~  178 (202)
T COG2854         156 NNQTGK-WKVYDVIIEGVSLVTTY  178 (202)
T ss_pred             CCCCCC-EEEEEEEECCHHHHHHH
T ss_conf             587687-25888642441389989


No 6  
>pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Probab=11.98  E-value=1.3e+02  Score=13.15  Aligned_cols=78  Identities=19%  Similarity=0.401  Sum_probs=50.0

Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------------HHHHHEEEEEE--EE--EEEEEHHHHH
Q ss_conf             85100122025525217998776667689999999507---------------43211025687--43--5775014368
Q gi|254781198|r   23 EIKNIQDHRITLLEKNYERLSDKVEASHTKLMEAILDN---------------REDIANVRIEV--AN--VRIEVANVRT   83 (117)
Q Consensus        23 eikniqdhritlleknyerlsdkveashtklmeaildn---------------redianvriev--an--vrievanvrt   83 (117)
                      |+.+.+.+-+..+..-.++|-..++.-..+|.+-|..-               ||..+.....+  .|  ...|+++.|+
T Consensus        66 el~~~~~~e~~~lr~e~e~L~~dve~L~~~L~~ei~k~~a~~klDlNleK~riree~~~~e~ki~e~~~kId~ei~~lrt  145 (177)
T pfam07798        66 ELQSLEKSEFSNLQAENEKLKNDLEKLKNRLRDEIDKVTAGVRLDLNLEKGRIREELAEQELKIKETDTKIDTEIAGLKT  145 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99987775899999999999999999999999999986152576545552077899987999999999899999999999


Q ss_pred             HHHHHHHHCCHHHHHHH
Q ss_conf             98888876002577699
Q gi|254781198|r   84 EMLGLIWKIPATAIGIS  100 (117)
Q Consensus        84 emlgliwkipataigis  100 (117)
                      ++=.+-|..---++|+.
T Consensus       146 ~iEs~K~~~ir~l~g~~  162 (177)
T pfam07798       146 QLESVKLDTIKYLIGVV  162 (177)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999


No 7  
>pfam04701 Pox_D2 Pox virus D2 protein.
Probab=10.65  E-value=1e+02  Score=13.73  Aligned_cols=49  Identities=24%  Similarity=0.438  Sum_probs=30.6

Q ss_pred             CCCCHHHHHCCHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             8998678510012202552521----------799877666768999999950743211
Q gi|254781198|r   17 SNLPPEEIKNIQDHRITLLEKN----------YERLSDKVEASHTKLMEAILDNREDIA   65 (117)
Q Consensus        17 snlppeeikniqdhritllekn----------yerlsdkveashtklmeaildnredia   65 (117)
                      .-+-|.++.+|-..|-.+||++          |++.+---..+--+....+..||+|+-
T Consensus        15 ~ivf~~di~~i~~e~~I~le~~~~g~~~~iHiyd~~aRFDN~ti~~~vK~vy~nr~~il   73 (143)
T pfam04701        15 NIVFPNDVNKILNEKYILLEKGDNGKPFRIHIYDRAARFDNKTIYRVVKFVYKNRPDIL   73 (143)
T ss_pred             CCCCHHHHHHHHHCCEEEEEECCCCCEEEEEEECCHHHCCCHHHHHHHHHHHHCCHHHH
T ss_conf             81361789998434679999669996687655121330264619999999980879899


No 8  
>pfam09068 efhand_1 EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
Probab=10.50  E-value=1.5e+02  Score=12.86  Aligned_cols=19  Identities=32%  Similarity=0.600  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             7769999999999863210
Q gi|254781198|r   96 AIGISICLRFLANVMDKGI  114 (117)
Q Consensus        96 aigisiclrflanvmdkgi  114 (117)
                      ..-++.|+.||-||.|.+-
T Consensus        90 ~~~~dl~lNwLlnvYD~~r  108 (125)
T pfam09068        90 ELAVDLLLNWLLNVYDPGR  108 (125)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             8999999999999848889


No 9  
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=10.49  E-value=1.4e+02  Score=12.94  Aligned_cols=13  Identities=54%  Similarity=0.741  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             5252179987766
Q gi|254781198|r   34 LLEKNYERLSDKV   46 (117)
Q Consensus        34 lleknyerlsdkv   46 (117)
                      -|-.||++|||.+
T Consensus       295 ALf~nY~qlsdEt  307 (318)
T COG4127         295 ALFENYEQLSDET  307 (318)
T ss_pred             HHHHHHHHHCHHH
T ss_conf             9986565526787


No 10 
>pfam07600 DUF1564 Protein of unknown function (DUF1564). A family of paralogous proteins in Leptospira interrogans. Several have been annotated as possible CopG-like transcriptional regulators (see pfam01402).
Probab=10.23  E-value=1.1e+02  Score=13.47  Aligned_cols=12  Identities=50%  Similarity=0.805  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             257769999999
Q gi|254781198|r   94 ATAIGISICLRF  105 (117)
Q Consensus        94 ataigisiclrf  105 (117)
                      |.+-|+|.|.-|
T Consensus       100 A~~hGVSrC~LF  111 (167)
T pfam07600       100 AAAHGVSRCYLF  111 (167)
T ss_pred             HHHCCCHHHHHH
T ss_conf             998183189999


Done!