Query         gi|254780513|ref|YP_003064926.1| hypothetical protein CLIBASIA_02000 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 66
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 22:54:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780513.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam07065 D123 D123. This fami  30.5     7.3 0.00019   20.2  -1.5   51    9-60    161-223 (297)
  2 PRK10632 putative DNA-binding   26.3      48  0.0012   15.8   2.1   44    1-46      1-48  (309)
  3 COG5478 Predicted small integr  18.4      66  0.0017   15.1   1.5   46    3-50     79-124 (141)
  4 KOG3259 consensus               18.4      91  0.0023   14.4   2.4   26   21-46     75-100 (163)
  5 pfam00372 Hemocyanin_M Hemocya  17.5      78   0.002   14.7   1.7   21   33-53    172-192 (278)
  6 pfam06363 Picorna_P3A Picornav  13.1      96  0.0024   14.3   1.2   28    7-34     27-54  (100)
  7 pfam11593 Med3 Mediator comple  12.8 1.1E+02  0.0027   14.1   1.3   16   27-42     23-38  (381)
  8 COG2077 Tpx Peroxiredoxin [Pos  12.4 1.2E+02   0.003   13.8   1.5   51    6-57     33-85  (158)
  9 pfam12188 STAT2_C Signal trans  11.9      97  0.0025   14.3   0.9   30    3-32     12-41  (56)
 10 KOG2983 consensus               11.5      39 0.00099   16.3  -1.2   52    9-60    176-239 (334)

No 1  
>pfam07065 D123 D123. This family contains a number of eukaryotic D123 proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate. D123 proteins are regulators of eIF2, the central regulator of translational initiation.
Probab=30.55  E-value=7.3  Score=20.16  Aligned_cols=51  Identities=25%  Similarity=0.600  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHCCCCCCCH-----------HHHHHHHHHHH-HHHHHHHHCCCCEEEEEEEEEEC
Q ss_conf             688899985211012670-----------27789999998-99999720030003766543503
Q gi|254780513|r    9 TKEFKCFLKNSRKKHITP-----------SKDVVAKSIKK-YEDRIRSSIDKKTFLTLSVYFEN   60 (66)
Q Consensus         9 tkefkcflknsrkkhitp-----------skdvvaksikk-yedrirssidkktfltlsvyfen   60 (66)
                      .-||.||.++.+---|.+           -++-+...|.. +++.|+....-..| +.-||...
T Consensus       161 ~~EFRcFVr~~~li~IsQRd~nyy~~L~~~~~~i~~~I~~Ff~~~i~~~fp~~~y-vfDVYi~~  223 (297)
T pfam07065       161 ALEFRCFVKNNKLVGISQRDLNYYEYLAELKEDIKDAIQEFFEEKILPHFPDDDY-VFDVYIPR  223 (297)
T ss_pred             CCEEEEEEECCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE-EEEEEECC
T ss_conf             6278899987889998436450777788779999999999999998743788887-99999649


No 2  
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=26.31  E-value=48  Score=15.83  Aligned_cols=44  Identities=23%  Similarity=0.527  Sum_probs=30.6

Q ss_pred             CCHHHHCCH----HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             951443176----8889998521101267027789999998999997200
Q gi|254780513|r    1 MDKLDELNT----KEFKCFLKNSRKKHITPSKDVVAKSIKKYEDRIRSSI   46 (66)
Q Consensus         1 mdkldelnt----kefkcflknsrkkhitpskdvvaksikkyedrirssi   46 (66)
                      ||+|+.|.+    -|-.-|-+-+++-++++|  .|.+.|+.-|+++....
T Consensus         1 Md~L~~L~~F~~Vae~gSfs~AA~~L~~s~s--aVSr~I~~LE~~LG~~L   48 (309)
T PRK10632          1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVS--SISQTVSKLEDELQVKL   48 (309)
T ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHCCCHH--HHHHHHHHHHHHHCCCC
T ss_conf             9767899999999980999999999795988--99999999999979956


No 3  
>COG5478 Predicted small integral membrane protein [Function unknown]
Probab=18.41  E-value=66  Score=15.13  Aligned_cols=46  Identities=22%  Similarity=0.182  Sum_probs=25.1

Q ss_pred             HHHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             144317688899985211012670277899999989999972003000
Q gi|254780513|r    3 KLDELNTKEFKCFLKNSRKKHITPSKDVVAKSIKKYEDRIRSSIDKKT   50 (66)
Q Consensus         3 kldelntkefkcflknsrkkhitpskdvvaksikkyedrirssidkkt   50 (66)
                      ||||+--+-++---.----+|.+|+  -+.+.+..|||.+.+..++-+
T Consensus        79 KLDElir~~~e~~n~~VgIEh~~~~--~i~~~~~~~e~~a~~~~g~~~  124 (141)
T COG5478          79 KLDELIRSLREARNDVVGIEHLKPE--EIEEIRDRLEDEAGTGDGVPT  124 (141)
T ss_pred             HHHHHHHHHCCCCCCEEEECCCCHH--HHHHHHHHHHHHHCCCCCCCC
T ss_conf             9999999712366762101038888--999999999998267988433


No 4  
>KOG3259 consensus
Probab=18.39  E-value=91  Score=14.39  Aligned_cols=26  Identities=27%  Similarity=0.429  Sum_probs=22.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             01267027789999998999997200
Q gi|254780513|r   21 KKHITPSKDVVAKSIKKYEDRIRSSI   46 (66)
Q Consensus        21 kkhitpskdvvaksikkyedrirssi   46 (66)
                      ..|||-||+-.-.-+|-|+..|.+.-
T Consensus        75 ~~~it~skeeA~~llk~~~~~l~~g~  100 (163)
T KOG3259          75 SENITRSKEEALDLLKGYHEDLKSGS  100 (163)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             43220139999999987688760574


No 5  
>pfam00372 Hemocyanin_M Hemocyanin, copper containing domain. This family includes arthropod hemocyanins and insect larval storage proteins.
Probab=17.47  E-value=78  Score=14.74  Aligned_cols=21  Identities=24%  Similarity=0.498  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHCCCCEEEE
Q ss_conf             999989999972003000376
Q gi|254780513|r   33 KSIKKYEDRIRSSIDKKTFLT   53 (66)
Q Consensus        33 ksikkyedrirssidkktflt   53 (66)
                      .-++.||+||+..||..-+.+
T Consensus       172 ~~i~~~e~Ri~~aId~G~~~~  192 (278)
T pfam00372       172 RDMDRWEERILDAIQKGYIEA  192 (278)
T ss_pred             HHHHHHHHHHHHHHHCCCEEC
T ss_conf             999999999999998097898


No 6  
>pfam06363 Picorna_P3A Picornaviridae P3A protein. This family consists of the P3A protein of picornaviridae. P3A has been identified as a genome-linked protein (VPg) and is involved in replication.
Probab=13.14  E-value=96  Score=14.27  Aligned_cols=28  Identities=32%  Similarity=0.360  Sum_probs=19.7

Q ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             1768889998521101267027789999
Q gi|254780513|r    7 LNTKEFKCFLKNSRKKHITPSKDVVAKS   34 (66)
Q Consensus         7 lntkefkcflknsrkkhitpskdvvaks   34 (66)
                      -..--|+||--.-+.+--|.++.|++-.
T Consensus        27 P~~S~F~CF~~~~~~~~~~a~~kV~~w~   54 (100)
T pfam06363        27 PRPSVFKCFASKLPHKPKTASRKVKAWV   54 (100)
T ss_pred             CCCCCHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             8998322213458986224789999999


No 7  
>pfam11593 Med3 Mediator complex subunit 3 fungal. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator subunit Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor.
Probab=12.85  E-value=1.1e+02  Score=14.05  Aligned_cols=16  Identities=50%  Similarity=0.613  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             2778999999899999
Q gi|254780513|r   27 SKDVVAKSIKKYEDRI   42 (66)
Q Consensus        27 skdvvaksikkyedri   42 (66)
                      +||+|+..|++-+|+|
T Consensus        23 ~kd~V~~~I~ea~d~I   38 (381)
T pfam11593        23 TKDEVADKIKEAKDAI   38 (381)
T ss_pred             CHHHHHHHHHHHHCCC
T ss_conf             0899999999865332


No 8  
>COG2077 Tpx Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=12.39  E-value=1.2e+02  Score=13.82  Aligned_cols=51  Identities=22%  Similarity=0.387  Sum_probs=36.0

Q ss_pred             HCCHHHHHHHHHHCCCCCCCHHHH--HHHHHHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             317688899985211012670277--8999999899999720030003766543
Q gi|254780513|r    6 ELNTKEFKCFLKNSRKKHITPSKD--VVAKSIKKYEDRIRSSIDKKTFLTLSVY   57 (66)
Q Consensus         6 elntkefkcflknsrkkhitpskd--vvaksikkyedrirssidkktfltlsvy   57 (66)
                      .|+-..+.||.-..+--.|-||-|  |.+.+.+++.++.. +.+.-.+|++|.-
T Consensus        33 dL~~v~l~~~~gk~~vi~v~PSiDT~VC~~qvr~Fn~~aa-~~~~~~Vl~IS~D   85 (158)
T COG2077          33 DLNDVSLADFAGKKKVISVFPSIDTPVCATQVRKFNEEAA-KLGNTVVLCISMD   85 (158)
T ss_pred             CCCCEECCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-CCCCCEEEEEECC
T ss_conf             4101022335885699998258987344688999999984-2599279999678


No 9  
>pfam12188 STAT2_C Signal transducer and activator of transcription 2 C terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam02865, pfam00017, pfam01017, pfam02864. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules.
Probab=11.86  E-value=97  Score=14.25  Aligned_cols=30  Identities=33%  Similarity=0.508  Sum_probs=23.8

Q ss_pred             HHHHCCHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf             144317688899985211012670277899
Q gi|254780513|r    3 KLDELNTKEFKCFLKNSRKKHITPSKDVVA   32 (66)
Q Consensus         3 kldelntkefkcflknsrkkhitpskdvva   32 (66)
                      .|..|||.|.+-|-.+-+-..|+|..|-+-
T Consensus        12 DL~~lnteemeifrN~~~ie~ImpngdPlL   41 (56)
T pfam12188        12 DLQQLNTEEMEIFRNNINIEEIMPNGDPLL   41 (56)
T ss_pred             HHHHHCHHHHHHHHCCCCHHHHCCCCCCCC
T ss_conf             788738788998826545866146899521


No 10 
>KOG2983 consensus
Probab=11.47  E-value=39  Score=16.33  Aligned_cols=52  Identities=25%  Similarity=0.441  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHCCCCCCCH-----HHHHHHHHHHHHHHHHHHHCCCC---EE----EEEEEEEEC
Q ss_conf             688899985211012670-----27789999998999997200300---03----766543503
Q gi|254780513|r    9 TKEFKCFLKNSRKKHITP-----SKDVVAKSIKKYEDRIRSSIDKK---TF----LTLSVYFEN   60 (66)
Q Consensus         9 tkefkcflknsrkkhitp-----skdvvaksikkyedrirssidkk---tf----ltlsvyfen   60 (66)
                      .-||.||.|+.+--.|+.     --|+..+.+.-|++-|..-.+++   +|    .++.||...
T Consensus       176 ~~EFRcFVKsn~lvg~~QRd~tnyYd~l~e~kd~~k~lI~eff~d~i~~kF~dedfvfDVYi~k  239 (334)
T KOG2983         176 EMEFRCFVKSNELVGICQRDVTNYYDVLLEEKDLLKGLIEEFFKDKILFKFPDEDFVFDVYITK  239 (334)
T ss_pred             CCEEEEEEECCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             7368999732606666411202488999887899999999998752112478977268999637


Done!