Query         gi|254780514|ref|YP_003064927.1| type II restriction endonuclease [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 110
No_of_seqs    7 out of 9
Neff          1.7 
Searched_HMMs 13730
Date          Wed Jun  1 10:01:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780514.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1na6a2 c.52.1.22 (A:179-398)   97.5 1.2E-05 8.7E-10   51.4   1.7   31   61-91     75-105 (220)
  2 d1xsza1 a.118.3.1 (A:1-197) Ra  25.8      16  0.0012   15.5   1.9   79   11-91     58-145 (197)
  3 d1r8se_ a.118.3.1 (E:) Exchang  23.0      19  0.0014   15.1   1.9   79   11-91     50-137 (187)
  4 d1gg2g_ a.137.3.1 (G:) Transdu  14.0      38  0.0028   13.4   2.8   35   18-53      5-39  (54)
  5 d1hyua3 c.47.1.2 (A:1-102) Alk  11.0      47  0.0034   12.8   2.1   16   73-88     82-97  (102)
  6 d1v54e_ a.118.11.1 (E:) Cytoch  10.8      48  0.0035   12.8   1.5   50    8-59     29-81  (105)
  7 d1rq6a_ a.4.15.1 (A:) ribosoma  10.8      48  0.0035   12.8   1.7   35   41-100    28-62  (62)
  8 d1a6sa_ a.61.1.4 (A:) GAG poly  10.0      51  0.0037   12.6   1.9   24   38-61      2-25  (87)
  9 d1dqna_ c.61.1.1 (A:) Guanine    9.3      22  0.0016   14.7  -0.8   22   54-75    193-216 (230)
 10 d1d0xa2 c.37.1.9 (A:2-33,A:80-   9.1      49  0.0036   12.7   0.9   38   42-79     91-141 (712)

No 1  
>d1na6a2 c.52.1.22 (A:179-398) Restriction endonuclease EcoRII, C-terminal domain {Escherichia coli [TaxId: 562]}
Probab=97.54  E-value=1.2e-05  Score=51.43  Aligned_cols=31  Identities=23%  Similarity=0.321  Sum_probs=28.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6310322355433045799999999739999
Q gi|254780514|r   61 EWVLSNTQSRRSRDGQEFEYIIYSLYNINTF   91 (110)
Q Consensus        61 ~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~   91 (110)
                      .+.||++|+|+||||+.||.+++.|++-+..
T Consensus        75 ~~slSv~nrRKSRAG~sfE~hl~~if~~~gi  105 (220)
T d1na6a2          75 ALANSVSNRRKSRAGKSLELHLEHLFIEHGL  105 (220)
T ss_dssp             HHHHHHHHHHHHHSSSHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC
T ss_conf             9999998877503305699999999996699


No 2  
>d1xsza1 a.118.3.1 (A:1-197) RalF, N-terminal domain {Legionella pneumophila [TaxId: 446]}
Probab=25.79  E-value=16  Score=15.51  Aligned_cols=79  Identities=11%  Similarity=0.129  Sum_probs=43.3

Q ss_pred             HHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH--HCC---CC----HHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             77641036999999999637964200157999999996321--201---10----4457631032235543304579999
Q gi|254780514|r   11 ISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDY--MSK---IT----PYLYEWVLSNTQSRRSRDGQEFEYI   81 (110)
Q Consensus        11 i~k~~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY--~~~---i~----P~iy~l~lsntqsrrsrag~~fe~i   81 (110)
                      ||..+-.|+.+-..++.+.++.-+++++.+-+++|.+|+..  ||+   |-    -+--.|+..|...-.|.+  .--.+
T Consensus        58 iGeyLg~~~~~n~~vl~~y~~~f~f~~~~id~ALR~~l~~f~LpgE~Q~IdRile~Fa~~y~~~Np~~~~~~d--~v~~L  135 (197)
T d1xsza1          58 VGDYLSSPEAENQQVLKAFTSQMNFNGQSFVEGLRTFLKTFKLPGEAQKIDRLVQSFSGAYFQQNPDVVSNAD--AAYLL  135 (197)
T ss_dssp             HHHHHTCCSHHHHHHHHHHHHTSCCTTSCHHHHHHHHHHTSCBCSSHHHHHHHHHHHHHHHHHHCTTTSSSHH--HHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC--HHHHH
T ss_conf             9999818966789999999984785799789999999984208860899999999999999985929999965--88999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999739999
Q gi|254780514|r   82 IYSLYNINTF   91 (110)
Q Consensus        82 iY~~Yn~~t~   91 (110)
                      .||+-=|||=
T Consensus       136 ~~siimLnTD  145 (197)
T d1xsza1         136 AFQTIMLNTD  145 (197)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHCC
T ss_conf             9999998112


No 3  
>d1r8se_ a.118.3.1 (E:) Exchange factor ARNO {Human (Homo sapiens) [TaxId: 9606]}
Probab=22.99  E-value=19  Score=15.09  Aligned_cols=79  Identities=16%  Similarity=0.161  Sum_probs=42.1

Q ss_pred             HHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH--C---CCC----HHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             776410369999999996379642001579999999963212--0---110----4457631032235543304579999
Q gi|254780514|r   11 ISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYM--S---KIT----PYLYEWVLSNTQSRRSRDGQEFEYI   81 (110)
Q Consensus        11 i~k~~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY~--~---~i~----P~iy~l~lsntqsrrsrag~~fe~i   81 (110)
                      ||..+.-|+.+-.+++.+.++.-.++++.+-+++|.+|+...  |   .|-    -+--.|+..|...-.|  -..--.+
T Consensus        50 ige~Lg~~~~~~~~vl~~y~~~f~f~~~~i~~ALR~~l~~f~lpgE~Q~Idrile~Fs~~y~~~Np~~~~~--~d~v~~l  127 (187)
T d1r8se_          50 IGDYLGEREELNLAVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGKAQKIDRMMEAFAQRYCLCNPGVFQS--TDTCYVL  127 (187)
T ss_dssp             HHHHHTCCSHHHHHHHHHHHHTCCCTTCCHHHHHHHHHHSSCCCSSHHHHHHHHHHHHHHHHHHSTTSSSC--HHHHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHH
T ss_conf             99997156678999999998724768994999999999846189718999999999999999869886788--7799999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999739999
Q gi|254780514|r   82 IYSLYNINTF   91 (110)
Q Consensus        82 iY~~Yn~~t~   91 (110)
                      .||+-=+||=
T Consensus       128 ~~siimLnTd  137 (187)
T d1r8se_         128 SYSVIMLNTD  137 (187)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
T ss_conf             9999999765


No 4  
>d1gg2g_ a.137.3.1 (G:) Transducin (heterotrimeric G protein), gamma chain {Cow (Bos taurus) [TaxId: 9913]}
Probab=14.02  E-value=38  Score=13.35  Aligned_cols=35  Identities=9%  Similarity=-0.057  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             699999999963796420015799999999632120
Q gi|254780514|r   18 PKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMS   53 (110)
Q Consensus        18 PK~ll~~llselin~~t~K~~e~~etir~~~gdY~~   53 (110)
                      -|+..+ .|..-.+.++.|-+...+.+.++|.+|+.
T Consensus         5 ~rk~Ve-qLr~e~~~~RikvS~aa~~l~~y~e~~~~   39 (54)
T d1gg2g_           5 ARKLVE-QLKMEANIDRIKVSKAAADLMAYCEAHAK   39 (54)
T ss_dssp             HHHHHH-HHHHHHSSCCCCHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHH-HHHHHHCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999-99999687420499999999999996276


No 5  
>d1hyua3 c.47.1.2 (A:1-102) Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain {Salmonella typhimurium [TaxId: 90371]}
Probab=11.01  E-value=47  Score=12.80  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             3045799999999739
Q gi|254780514|r   73 RDGQEFEYIIYSLYNI   88 (110)
Q Consensus        73 rag~~fe~iiY~~Yn~   88 (110)
                      -+|.||-+.|-+|||.
T Consensus        82 P~GhEF~Slilail~v   97 (102)
T d1hyua3          82 PLGHEFTSLVLALLWT   97 (102)
T ss_dssp             CCGGGHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHC
T ss_conf             8851088999999841


No 6  
>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}
Probab=10.79  E-value=48  Score=12.75  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=26.3

Q ss_pred             HHHHHH--HHCCHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             999776--41036999999999-63796420015799999999632120110445
Q gi|254780514|r    8 LKNISN--NYEVPKMLITELST-ELFNLKTANQNFFHNTLTKKFGDYMSKITPYL   59 (110)
Q Consensus         8 ~~~i~k--~~EtPK~ll~~lls-elin~~t~K~~e~~etir~~~gdY~~~i~P~i   59 (110)
                      ||++.-  ++--||-+.-++-- -++| --+--.-+.|+||.+||+- ..|.|||
T Consensus        29 mN~l~~~DlVPeP~Ii~aALrAcRRvN-D~alAVR~lE~vK~K~~~~-k~~y~yi   81 (105)
T d1v54e_          29 MNTLVGYDLVPEPKIIDAALRACRRLN-DFASAVRILEVVKDKAGPH-KEIYPYV   81 (105)
T ss_dssp             HHHHTTSSBCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHTTTC-TTHHHHH
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCC-HHHHHHH
T ss_conf             999851566899099999999998840-0799999999999873470-8899999


No 7  
>d1rq6a_ a.4.15.1 (A:) ribosomal protein S17e {Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=10.78  E-value=48  Score=12.75  Aligned_cols=35  Identities=17%  Similarity=0.437  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999963212011044576310322355433045799999999739999999974220
Q gi|254780514|r   41 HNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKK  100 (110)
Q Consensus        41 ~etir~~~gdY~~~i~P~iy~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~~~~~~~~~~  100 (110)
                      .++=++.|.|++-             .+|.+-|.            .|-.||||||...|
T Consensus        28 F~~NK~~v~e~a~-------------i~SKklRN------------~IAGYvTrl~k~~k   62 (62)
T d1rq6a_          28 FDTNKKLVEEFST-------------VSTKHLRN------------KIAGYITRIISQQK   62 (62)
T ss_dssp             HHHHHHHHHTTCC-------------CSSTTHHH------------HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHC-------------CCCHHHHH------------HHHHHHHHHHHHCC
T ss_conf             8887899999813-------------88665767------------99989999998229


No 8  
>d1a6sa_ a.61.1.4 (A:) GAG polyprotein M-domain {Rous sarcoma virus [TaxId: 11886]}
Probab=10.02  E-value=51  Score=12.59  Aligned_cols=24  Identities=17%  Similarity=0.223  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             579999999963212011044576
Q gi|254780514|r   38 NFFHNTLTKKFGDYMSKITPYLYE   61 (110)
Q Consensus        38 ~e~~etir~~~gdY~~~i~P~iy~   61 (110)
                      .-+..-+..+|-+|-|+.+|---+
T Consensus         2 e~VikVl~~~ck~~~gk~spskKe   25 (87)
T d1a6sa_           2 EAVIKVISSACKTYCGKTSPSKKE   25 (87)
T ss_dssp             HHHHHHHHHHHHHHHTTTSSCSSH
T ss_pred             CHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             069999999999874778983889


No 9  
>d1dqna_ c.61.1.1 (A:) Guanine PRTase {Giardia lamblia [TaxId: 5741]}
Probab=9.34  E-value=22  Score=14.69  Aligned_cols=22  Identities=23%  Similarity=0.158  Sum_probs=13.7

Q ss_pred             CCCHHHHHHHHCCC--HHHHHHHH
Q ss_conf             11044576310322--35543304
Q gi|254780514|r   54 KITPYLYEWVLSNT--QSRRSRDG   75 (110)
Q Consensus        54 ~i~P~iy~l~lsnt--qsrrsrag   75 (110)
                      |=.|+||.+..|+.  +++|+|+-
T Consensus       193 RnLp~Iy~l~~~~~~~~~~~~~~~  216 (230)
T d1dqna_         193 RGWAHLFDINLSESEVTEFRRRLT  216 (230)
T ss_dssp             TTCCSEEESSSCHHHHHHHHHHHH
T ss_pred             CCCCCEEEECCCCCCCHHHHHHCH
T ss_conf             898916997520123424442053


No 10 
>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}
Probab=9.10  E-value=49  Score=12.69  Aligned_cols=38  Identities=11%  Similarity=0.097  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCC-------------CHHHHHHHHHHHH
Q ss_conf             9999996321201104457631032-------------2355433045799
Q gi|254780514|r   42 NTLTKKFGDYMSKITPYLYEWVLSN-------------TQSRRSRDGQEFE   79 (110)
Q Consensus        42 etir~~~gdY~~~i~P~iy~l~lsn-------------tqsrrsrag~~fe   79 (110)
                      +.++.+.+.-.+...||||.++.+-             --|-.|-|||+.-
T Consensus        91 ~~~~~y~~~~~~~~~PHifaiA~~Ay~~m~~~~~nQsIiisGeSGaGKTe~  141 (712)
T d1d0xa2          91 EMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTEN  141 (712)
T ss_dssp             HHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHH
T ss_pred             HHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
T ss_conf             999997188768899859999999999999738991699967998888999


Done!