Query         gi|254780946|ref|YP_003065359.1| hypothetical protein CLIBASIA_04225 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 98
No_of_seqs    114 out of 652
Neff          5.9 
Searched_HMMs 39220
Date          Mon May 30 02:57:58 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780946.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2938 Uncharacterized conser  99.9 6.2E-25 1.6E-29  164.9  11.0   86    1-87      7-92  (94)
  2 KOG3326 consensus               99.9 2.1E-21 5.3E-26  144.5   9.7   91    3-93     54-147 (154)
  3 pfam03937 Sdh5 Protein of unkn  99.7 1.5E-18 3.9E-23  127.9   4.7   51   14-64      1-51  (51)
  4 PRK10878 hypothetical protein;  99.7 2.6E-16 6.5E-21  115.0   8.2   68   21-88      1-68  (72)
  5 KOG2753 consensus               46.7      25 0.00064   16.7   3.6   84    6-89    160-253 (378)
  6 KOG3707 consensus               23.7      61  0.0016   14.5   2.9   82    7-89    137-244 (844)
  7 pfam03142 Chitin_synth_2 Chiti  19.5      57  0.0014   14.6   1.4   68   17-84    155-226 (536)
  8 PRK08558 adenine phosphoribosy  19.5      75  0.0019   14.0   4.3   41   44-84     26-66  (238)
  9 COG2908 Uncharacterized protei  19.1      77   0.002   13.9   4.3   53   33-86      5-66  (237)
 10 TIGR02668 moaA_archaeal probab  18.7      58  0.0015   14.6   1.3   48   31-82    102-150 (324)

No 1  
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=99.92  E-value=6.2e-25  Score=164.89  Aligned_cols=86  Identities=33%  Similarity=0.573  Sum_probs=81.5

Q ss_pred             CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             98658999999999997407899999999999998202999999999999468917999999488999806756999999
Q gi|254780946|r    1 MKKNMNLQCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKI   80 (98)
Q Consensus         1 M~~~ld~~~krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I   80 (98)
                      ++++.+.+++||.|||| |||+|||+|||+|+++++++||++++..|+.||+++|+|||+|++|+.+||+....+++.+|
T Consensus         7 ~~~~~d~~~~RL~~rsr-RGmrElDlil~~Fae~~~~~lsd~e~~~f~~LLe~~D~dL~~Wi~g~~~~~~~~~~~mv~~I   85 (94)
T COG2938           7 STEDDDARKARLRWRSR-RGMRELDLILGPFAEKEFDSLSDEELDEFERLLECEDNDLFNWIMGHGEPPDAELTPMVRKI   85 (94)
T ss_pred             CCCCCHHHHHHHHHHHH-HCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             66567799999999998-03099999989999999851999999999999858858999998589999837889999999


Q ss_pred             HHHHHHH
Q ss_conf             9999822
Q gi|254780946|r   81 YDYYSNN   87 (98)
Q Consensus        81 ~~f~~~~   87 (98)
                      +.+....
T Consensus        86 ~~~~~~~   92 (94)
T COG2938          86 QARRRIR   92 (94)
T ss_pred             HHHHHHC
T ss_conf             9986641


No 2  
>KOG3326 consensus
Probab=99.86  E-value=2.1e-21  Score=144.48  Aligned_cols=91  Identities=23%  Similarity=0.517  Sum_probs=85.8

Q ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC--CHHHHHHHHCCCCCCCHHHH-HHHHH
Q ss_conf             6589999999999974078999999999999982029999999999994689--17999999488999806756-99999
Q gi|254780946|r    3 KNMNLQCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEED--DSNLFKWFTGMEKPPEYLRT-PIFKK   79 (98)
Q Consensus         3 ~~ld~~~krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~--D~dL~~wl~~~~~~p~~~~~-~ii~~   79 (98)
                      +.+|.++.||+|||..|||+|+||+||.|+++++.+|+++++.+|+.||+.+  |+|||.|.++.++||+.+.+ +|++.
T Consensus        54 e~~etkraRLlYqSrKRGiLEnDLLLs~Fa~~~l~~m~e~~l~~YD~LiN~~~~dWDi~YWaTe~kp~Pe~~~s~~V~~~  133 (154)
T KOG3326          54 EPLETKRARLLYQSRKRGILENDLLLSNFAAKNLKKMSEEQLKEYDQLINEESNDWDIYYWATETKPPPEKVESSEVFKL  133 (154)
T ss_pred             CHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             60678899999998632346787998899999998679999999999964776783156563168799154403799999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999822776565
Q gi|254780946|r   80 IYDYYSNNLDRKNM   93 (98)
Q Consensus        80 I~~f~~~~~~~~~~   93 (98)
                      +++|+.++...+.+
T Consensus       134 L~e~v~n~~r~~~l  147 (154)
T KOG3326         134 LKEFVKNKERVHRL  147 (154)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999831001135


No 3  
>pfam03937 Sdh5 Protein of unknown function (DUF339). This family of uncharacterized proteins. Based on personal observation it was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true.
Probab=99.74  E-value=1.5e-18  Score=127.91  Aligned_cols=51  Identities=45%  Similarity=0.936  Sum_probs=50.2

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             999740789999999999999820299999999999946891799999948
Q gi|254780946|r   14 YRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTG   64 (98)
Q Consensus        14 ~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~   64 (98)
                      |||+||||||+|+|||+|+++++++++++++..|++||+++|+|||+|++|
T Consensus         1 ~rs~rRG~kElDlll~~F~~~~~~~l~~~e~~~f~~lL~~~D~dL~~w~~G   51 (51)
T pfam03937         1 WRSWRRGMLELDLLLGRFADAHLDTLSEEELDAFERLLDLEDPDLFDWLTG   51 (51)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf             997745389999989999999986599999999999984997899976647


No 4  
>PRK10878 hypothetical protein; Provisional
Probab=99.67  E-value=2.6e-16  Score=115.03  Aligned_cols=68  Identities=25%  Similarity=0.389  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999820299999999999946891799999948899980675699999999998227
Q gi|254780946|r   21 TREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKIYDYYSNNL   88 (98)
Q Consensus        21 ~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~~~~~   88 (98)
                      |+|+|++|.||++++|++||++++..|.+||+++|||||+|++|+..|++....+++..|++.++.+.
T Consensus         1 MlELDvll~PF~e~~y~~Ls~~dk~~F~rLL~~eD~dLf~Wfm~~~~P~D~el~~mV~~I~~r~~~~g   68 (72)
T PRK10878          1 MRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEQMVRLIQTRNRERG   68 (72)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             91699988999999981369999999999981778899999968999998789999999999875238


No 5  
>KOG2753 consensus
Probab=46.74  E-value=25  Score=16.72  Aligned_cols=84  Identities=12%  Similarity=0.206  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHCCHHHHH----------HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHH
Q ss_conf             99999999999740789999----------99999999982029999999999994689179999994889998067569
Q gi|254780946|r    6 NLQCRKIVYRCWRRGTREMD----------LILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTP   75 (98)
Q Consensus         6 d~~~krl~~Rs~rRG~kElD----------llL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~   75 (98)
                      +...+|-.+|+-|+.+++.+          -+||.|.+.+.+...++....-.+.+.-+-.-+||=+..-.++..-....
T Consensus       160 ~vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~  239 (378)
T KOG2753         160 SVEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL  239 (378)
T ss_pred             CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCEECCCHHCCCCHHHHHCCCH
T ss_conf             87889999999999998611042689999999988602336678999999999997098602142230582688862165


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999982277
Q gi|254780946|r   76 IFKKIYDYYSNNLD   89 (98)
Q Consensus        76 ii~~I~~f~~~~~~   89 (98)
                      |++.+.=|...+++
T Consensus       240 i~qLL~IF~s~~L~  253 (378)
T KOG2753         240 IHQLLKIFVSGKLD  253 (378)
T ss_pred             HHHHHHHHHHCCHH
T ss_conf             99999999853249


No 6  
>KOG3707 consensus
Probab=23.74  E-value=61  Score=14.47  Aligned_cols=82  Identities=16%  Similarity=0.317  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHCCHHHH--------------HHHHHHHHHHHHCCCCHHHHHHHHHHHCCC-------CHHHHHHHHCC
Q ss_conf             999999999974078999--------------999999999982029999999999994689-------17999999488
Q gi|254780946|r    7 LQCRKIVYRCWRRGTREM--------------DLILGSFVDHFILELSSVELTMLESIIEED-------DSNLFKWFTGM   65 (98)
Q Consensus         7 ~~~krl~~Rs~rRG~kEl--------------DllL~~F~~~~~~~l~~~el~~f~~LL~~~-------D~dL~~wl~~~   65 (98)
                      .+-+|+.|+-.+ --++.              -+-+|.|.+..+.+++++|....++|++.+       |++...=+-.+
T Consensus       137 trs~r~~~~~sk-~a~dfLP~~Pv~~~iepWWr~~~g~~le~d~k~Lse~E~~~iD~l~d~~A~pagl~d~~Vv~sLY~r  215 (844)
T KOG3707         137 TRSKRIMWKLSK-IAKDFLPTLPVDFPIEPWWRVCLGNFLEEDFKKLSEDEMATIDKLCDEEANPAGLFDPEVVKSLYQR  215 (844)
T ss_pred             CCCCHHHHHCCC-CHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHC
T ss_conf             356246662254-6677556787674135266542466319988743998888899997327884445698999999877


Q ss_pred             C----CCCCH-HHHHHHHHHHHHHHHHHH
Q ss_conf             9----99806-756999999999982277
Q gi|254780946|r   66 E----KPPEY-LRTPIFKKIYDYYSNNLD   89 (98)
Q Consensus        66 ~----~~p~~-~~~~ii~~I~~f~~~~~~   89 (98)
                      .    .+|.. .+.--+..+..|++|+.-
T Consensus       216 GLiYfDVPvy~~Dri~v~pL~gFvmNRv~  244 (844)
T KOG3707         216 GLIYFDVPVYQDDRIKVSPLEGFVMNRVY  244 (844)
T ss_pred             CEEEEECCCCCCCEEEECCHHHHHHHCCC
T ss_conf             73898335456873640530334540232


No 7  
>pfam03142 Chitin_synth_2 Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <= UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).
Probab=19.53  E-value=57  Score=14.65  Aligned_cols=68  Identities=16%  Similarity=0.308  Sum_probs=46.4

Q ss_pred             HHCCHHHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHCCC--CHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             740789999999999999--82029999999999994689--179999994889998067569999999999
Q gi|254780946|r   17 WRRGTREMDLILGSFVDH--FILELSSVELTMLESIIEED--DSNLFKWFTGMEKPPEYLRTPIFKKIYDYY   84 (98)
Q Consensus        17 ~rRG~kElDllL~~F~~~--~~~~l~~~el~~f~~LL~~~--D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~   84 (98)
                      -.||=+.--+++.+|+.+  +-.-+++-+.+.|..+....  ++|.|+.+.+-..--......+...+....
T Consensus       155 GNRGKRDSqiilmsFl~kv~~~~rmt~le~e~~~~i~~~~Gv~pd~ye~~l~vDADT~V~pdsl~~mv~~~~  226 (536)
T pfam03142       155 GNRGKRDSQIILMSFLQKVHFDERMTPLEYEMFHQIWNVTGVSPDFYETVLMVDADTKVFPDSLTRMVAAMV  226 (536)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCEECCHHHHHHHHHHH
T ss_conf             877650378999998878750786770269999999987388901578999966886288068999999981


No 8  
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=19.53  E-value=75  Score=13.95  Aligned_cols=41  Identities=27%  Similarity=0.354  Sum_probs=33.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999994689179999994889998067569999999999
Q gi|254780946|r   44 LTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKIYDYY   84 (98)
Q Consensus        44 l~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~   84 (98)
                      ..++..++..+-+.|..+..|+.-|..+.-.+|+++|....
T Consensus        26 ykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~~~   66 (238)
T PRK08558         26 YEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKPYY   66 (238)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999887979999850534887875899999999842114


No 9  
>COG2908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=19.10  E-value=77  Score=13.90  Aligned_cols=53  Identities=13%  Similarity=0.318  Sum_probs=38.3

Q ss_pred             HHHHCCCCHHHHHHHHHHHCCCCH---------HHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             998202999999999999468917---------999999488999806756999999999982
Q gi|254780946|r   33 DHFILELSSVELTMLESIIEEDDS---------NLFKWFTGMEKPPEYLRTPIFKKIYDYYSN   86 (98)
Q Consensus        33 ~~~~~~l~~~el~~f~~LL~~~D~---------dL~~wl~~~~~~p~~~~~~ii~~I~~f~~~   86 (98)
                      |-|+..-.....+.|.++|....+         |||+...|...||+. .+.++.+|+...+.
T Consensus         5 DlHL~~~~p~~t~~fl~Fl~~~a~~ad~lyilGDifd~w~g~~~~~~~-~~~V~~~l~~~a~~   66 (237)
T COG2908           5 DLHLGPKRPALTAFFLDFLREEAAQADALYILGDIFDGWIGDDEPPQL-HRQVAQKLLRLARK   66 (237)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHCCCCCCHH-HHHHHHHHHHHHHC
T ss_conf             002589970789999999983535675799950016666268760389-99999999999865


No 10 
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485    This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=18.74  E-value=58  Score=14.61  Aligned_cols=48  Identities=15%  Similarity=0.273  Sum_probs=30.4

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCC-CCCCCHHHHHHHHHHHH
Q ss_conf             99998202999999999999468917999999488-99980675699999999
Q gi|254780946|r   31 FVDHFILELSSVELTMLESIIEEDDSNLFKWFTGM-EKPPEYLRTPIFKKIYD   82 (98)
Q Consensus        31 F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~-~~~p~~~~~~ii~~I~~   82 (98)
                      .+.++-.+|.++-|+--.-=|+--|++.|.+|||. ....+    .+++=|.+
T Consensus       102 LL~~~A~~Lk~AGLdRVNVSLdtld~e~Y~kITG~~~~~~~----~Vi~GI~~  150 (324)
T TIGR02668       102 LLEKLAKKLKEAGLDRVNVSLDTLDPEKYKKITGQSRDALD----RVIEGIES  150 (324)
T ss_pred             HHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCHHH----HHHHHHHH
T ss_conf             48989999998285613120267886788864489986078----99999999


Done!