Query         gi|254780688|ref|YP_003065101.1| putative flagellar motor switch protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 147
No_of_seqs    169 out of 872
Neff          5.6 
Searched_HMMs 13730
Date          Wed Jun  1 09:05:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780688.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 d1o6aa_ b.139.1.1 (A:) Putativ  99.8 3.5E-19 2.5E-23  126.7   9.9   77   67-146     2-78  (87)
  2 d1o9ya_ b.139.1.1 (A:) Structu  99.8 1.3E-18 9.8E-23  123.4  11.4   71   71-144     1-71  (71)
  3 d2gcxa1 b.34.1.2 (A:1-75) Ferr  58.7     5.1 0.00037   17.4   4.6   31   94-124    29-61  (75)
  4 d3bwud1 b.167.1.1 (D:2-122) Ou  47.3     7.8 0.00057   16.4   4.3   36   91-130    16-52  (121)
  5 d2h3ja1 b.34.1.2 (A:1-75) Hypo  37.8     6.7 0.00049   16.7   1.6   31   94-124    30-62  (75)
  6 d1ywua1 b.45.2.1 (A:1-125) Hyp  27.1      17  0.0012   14.5   6.4   57   84-143    25-90  (125)
  7 d1g7sa1 b.43.3.1 (A:228-328) I  22.0      10 0.00076   15.6   0.4   45   98-142     6-52  (101)
  8 d1k8wa3 b.122.1.1 (A:251-312)   19.0      25  0.0018   13.5   4.8   42   85-126     3-47  (62)
  9 d1u1za_ d.38.1.6 (A:) (3R)-hyd  18.9      25  0.0018   13.5   3.6   50   78-129    85-142 (145)
 10 d1d3ba_ b.38.1.1 (A:) D3 core   16.8      28   0.002   13.2   3.9   38  104-144     7-44  (72)

No 1  
>d1o6aa_ b.139.1.1 (A:) Putative flagelar motor switch protein FliN {Thermotoga maritima [TaxId: 2336]}
Probab=99.78  E-value=3.5e-19  Score=126.73  Aligned_cols=77  Identities=39%  Similarity=0.797  Sum_probs=73.6

Q ss_pred             HHHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECC
Q ss_conf             00234305513899999213442999945797889984777888069999998999999999568887055899973167
Q gi|254780688|r   67 DNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA  146 (147)
Q Consensus        67 ~~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~  146 (147)
                      .+++.++|+|++++|+||++++++++|++|++||||+|++.++++++++|||+++|+|+++.+|+   ++||||+++++.
T Consensus         2 ~~l~~i~dipv~l~~~Lg~~~l~l~el~~L~~Gdvi~L~~~~~~~v~l~v~g~~~~~g~lg~~~~---~~av~I~~~i~~   78 (87)
T d1o6aa_           2 DKLELLLDIPLKVTVELGRTRMTLKRVLEMIHGSIIELDKLTGEPVDILVNGKLIARGEVVVIDE---NFGVRITEIVSP   78 (87)
T ss_dssp             HHHHHHTTCEEEEEEEEEEEEEEHHHHHHCCTTCEEEEEEETTCCEEEEETTEEEEEEEEEEETT---EEEEEEEEECCH
T ss_pred             CCHHHHCCCCEEEEEEEEEEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEECCC
T ss_conf             43023326717999999300845999857999999991898999799999999999999999999---999999981595


No 2  
>d1o9ya_ b.139.1.1 (A:) Structural protein HrcQ2, C-terminal domain {Pseudomonas syringae [TaxId: 317]}
Probab=99.77  E-value=1.3e-18  Score=123.38  Aligned_cols=71  Identities=14%  Similarity=0.347  Sum_probs=68.3

Q ss_pred             HHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf             43055138999992134429999457978899847778880699999989999999995688870558999731
Q gi|254780688|r   71 LIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL  144 (147)
Q Consensus        71 ~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii  144 (147)
                      .+.++|++++|+||++++++++|++|++|++|+|++.++++|++++||+++|+|+++.+|+   +||||||+++
T Consensus         1 al~~i~v~l~~~lg~~~~~l~el~~L~~G~vl~l~~~~~~~V~l~v~g~~i~~G~l~~~~~---~~av~It~li   71 (71)
T d1o9ya_           1 ALDSLALDLTLRCGELRLTLAELRRLDAGTILEVTGISPGHATLCHGEQVVAEGELVDVEG---RLGLQITRLV   71 (71)
T ss_dssp             CCTTCEEEEEEEEEEEEEEHHHHHTCCTTCEEEECSSCTTEEEEEETTEEEEEEEEEEETT---EEEEEEEEEC
T ss_pred             CCCCEEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECC---EEEEEEEEEC
T ss_conf             9542068999999200838999853589999991877899799999988999999999999---9999999919


No 3  
>d2gcxa1 b.34.1.2 (A:1-75) Ferrous iron transport protein A, FeoA {Klebsiella pneumoniae [TaxId: 573]}
Probab=58.72  E-value=5.1  Score=17.44  Aligned_cols=31  Identities=13%  Similarity=0.266  Sum_probs=26.8

Q ss_pred             HCCCCCCEEECCCCC--CCCEEEEECCEEEEEE
Q ss_conf             457978899847778--8806999999899999
Q gi|254780688|r   94 VNLSKGDVITLDKRV--GESVDITINNQKIAKG  124 (147)
Q Consensus        94 l~L~~G~Vi~Ld~~~--~epV~i~vng~~ia~G  124 (147)
                      +.+.+|..+.+-+.+  ++|+.+.|+|..+|-+
T Consensus        29 mGl~pG~~V~v~~~ap~g~P~~i~v~~~~iaLr   61 (75)
T d2gcxa1          29 LGMLPGSSFHVVRVAPLGDPVHIETRRVSLVLR   61 (75)
T ss_dssp             TTCCSSEEEEECCCCSSCCEEEEEETTEEEEEE
T ss_pred             CCCCCCCEEEEEEECCCCCCEEEEECCEEEEEC
T ss_conf             699999899999978999989999999999978


No 4  
>d3bwud1 b.167.1.1 (D:2-122) Outer membrane usher protein FimD {Escherichia coli [TaxId: 562]}
Probab=47.30  E-value=7.8  Score=16.37  Aligned_cols=36  Identities=28%  Similarity=0.465  Sum_probs=25.3

Q ss_pred             HHHHCCCCCCEEECCCCCCC-CEEEEECCEEEEEEEEEEEC
Q ss_conf             99945797889984777888-06999999899999999956
Q gi|254780688|r   91 SNLVNLSKGDVITLDKRVGE-SVDITINNQKIAKGEITIME  130 (147)
Q Consensus        91 ~dll~L~~G~Vi~Ld~~~~e-pV~i~vng~~ia~GElv~v~  130 (147)
                      .||..+..|.-+    .+|. .|+|+|||+.+++.++..+.
T Consensus        16 ~Dls~F~~~n~~----~pG~Y~vdI~vN~~~~~~~~i~F~~   52 (121)
T d3bwud1          16 ADLSRFENGQEL----PPGTYRVDIYLNNGYMATRDVTFNT   52 (121)
T ss_dssp             HHHHHHHTTCSS----CSEEEEEEEEETTEEEEEEEEEEEE
T ss_pred             EEHHHHCCCCCC----CCEEEEEEEEECCEEEEEEEEEEEE
T ss_conf             217876258987----9838899999999684558999983


No 5  
>d2h3ja1 b.34.1.2 (A:1-75) Hypothetical protein PA4359 {Pseudomonas aeruginosa [TaxId: 287]}
Probab=37.83  E-value=6.7  Score=16.74  Aligned_cols=31  Identities=13%  Similarity=0.352  Sum_probs=25.9

Q ss_pred             HCCCCCCEEECCCC--CCCCEEEEECCEEEEEE
Q ss_conf             45797889984777--88806999999899999
Q gi|254780688|r   94 VNLSKGDVITLDKR--VGESVDITINNQKIAKG  124 (147)
Q Consensus        94 l~L~~G~Vi~Ld~~--~~epV~i~vng~~ia~G  124 (147)
                      +.+.+|..+.+-+.  .+.|+.+.++|..+|-+
T Consensus        30 mG~~~G~~v~v~~~~p~g~p~~v~v~~~~iaLr   62 (75)
T d2h3ja1          30 MGLLPGAALRVVRIAPLGDPIQVETRQTSLALR   62 (75)
T ss_dssp             HTCCTTCEEEEEECCTTSCCCEEESSSSEECCC
T ss_pred             CCCCCCCEEEEEEECCCCCCEEEEECCEEEEEC
T ss_conf             699999899999978999989999999999948


No 6  
>d1ywua1 b.45.2.1 (A:1-125) Hypothetical protein PA4608 {Pseudomonas aeruginosa [TaxId: 287]}
Probab=27.08  E-value=17  Score=14.45  Aligned_cols=57  Identities=9%  Similarity=0.091  Sum_probs=32.9

Q ss_pred             EEEEECHHHHHCCCCCCEE-----ECCCCCCCCEEEEE----CCEEEEEEEEEEECCCCCEEEEEEEEE
Q ss_conf             2134429999457978899-----84777888069999----998999999999568887055899973
Q gi|254780688|r   84 GSCCMQISNLVNLSKGDVI-----TLDKRVGESVDITI----NNQKIAKGEITIMEEDDTHFGVRVIEI  143 (147)
Q Consensus        84 G~~~i~i~dll~L~~G~Vi-----~Ld~~~~epV~i~v----ng~~ia~GElv~v~e~~~~~gvrIt~i  143 (147)
                      |...+. ..+..+..|-+.     .+....+.++.|.+    ....-+.|++|...+  +.+|++++.+
T Consensus        25 ~~~~~~-~~~~DiS~~G~~i~~~~~~~~~~~~~v~l~l~l~~~~~i~~~~~Vv~~~~--~~~Gl~f~~i   90 (125)
T d1ywua1          25 GERRWE-VLLHDVSLHGILVGQPQDWNGDPQRPFEARLYLGLDVLIRMEISLAWARD--GLLGFECQHI   90 (125)
T ss_dssp             TTEEEE-EEEEEECSSEEEEECSSCCCCCTTSEEEEEEESSSSCEEEEEEEEEEEET--TEEEEEEEEE
T ss_pred             CCEEEE-EEEEEECCCCEEEECCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEEECC--CEEEEEEEEC
T ss_conf             999999-99998217848997488778899987999998699959999999999749--9999999866


No 7  
>d1g7sa1 b.43.3.1 (A:228-328) Initiation factor IF2/eIF5b, domains 2 and 4 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=21.95  E-value=10  Score=15.64  Aligned_cols=45  Identities=16%  Similarity=0.370  Sum_probs=20.1

Q ss_pred             CCCEEEC--CCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEE
Q ss_conf             7889984--77788806999999899999999956888705589997
Q gi|254780688|r   98 KGDVITL--DKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIE  142 (147)
Q Consensus        98 ~G~Vi~L--d~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~  142 (147)
                      .|.||+-  ++-.|--.++.+..=.+-.|..+++|...|+.-.+|-.
T Consensus         6 ~G~VlEs~~dkg~G~~atviv~~GtLk~GD~iv~g~~~G~i~~~ira   52 (101)
T d1g7sa1           6 RGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRS   52 (101)
T ss_dssp             EEEEEEEEEETTEEEEEEEEEEESEEETTCEEEEEBSSSEEEEECCE
T ss_pred             EEEEEEEEECCCCCEEEEEEEECCEECCCCEEEEECCCCCEEEEEEC
T ss_conf             79999999737998069999976878359999990674779987440


No 8  
>d1k8wa3 b.122.1.1 (A:251-312) Pseudouridine synthase II TruB, C-terminal domain {Escherichia coli [TaxId: 562]}
Probab=19.03  E-value=25  Score=13.51  Aligned_cols=42  Identities=21%  Similarity=0.311  Sum_probs=32.3

Q ss_pred             EEEECHHHHHCCCCCCEEECCCC-CCCCEEEEE--CCEEEEEEEE
Q ss_conf             13442999945797889984777-888069999--9989999999
Q gi|254780688|r   85 SCCMQISNLVNLSKGDVITLDKR-VGESVDITI--NNQKIAKGEI  126 (147)
Q Consensus        85 ~~~i~i~dll~L~~G~Vi~Ld~~-~~epV~i~v--ng~~ia~GEl  126 (147)
                      +..++-.+...+..|.-+.+... ....|.||.  +++-++-||+
T Consensus         3 ~v~L~~~~~~~~~~GQ~V~~~~~~~~g~vRvy~~~~~~FlGiGei   47 (62)
T d1k8wa3           3 VVNLPLTSSVYFKNGNPVRTSGAPLEGLVRVTEGENGKFIGMGEI   47 (62)
T ss_dssp             EEEECHHHHHHHTTTCCBCCSSCCSSSEEEEEETTTTEEEEEEEE
T ss_pred             EEEECHHHHHHHHCCCEEECCCCCCCCEEEEEECCCCEEEEEEEE
T ss_conf             599899999786687996358999776899998899869999998


No 9  
>d1u1za_ d.38.1.6 (A:) (3R)-hydroxymyristoyl ACP dehydrase FabZ {Pseudomonas aeruginosa [TaxId: 287]}
Probab=18.85  E-value=25  Score=13.49  Aligned_cols=50  Identities=16%  Similarity=0.273  Sum_probs=29.5

Q ss_pred             EEEEEEEEEEECHHHHHCCCCCCEEECCCCC--------CCCEEEEECCEEEEEEEEEEE
Q ss_conf             8999992134429999457978899847778--------880699999989999999995
Q gi|254780688|r   78 KMQIILGSCCMQISNLVNLSKGDVITLDKRV--------GESVDITINNQKIAKGEITIM  129 (147)
Q Consensus        78 ~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~--------~epV~i~vng~~ia~GElv~v  129 (147)
                      .+-+-++-.+...  .....+|+.+.+.-..        --...+++||++++.||++-.
T Consensus        85 ~~~~l~~i~~~kf--~~~v~PGd~L~i~v~~~~~~~~~~~~~~~~~v~~~~v~~a~l~~a  142 (145)
T d1u1za_          85 TLYYFVGSDKLRF--RQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICA  142 (145)
T ss_dssp             CEEEEEEEEEEEE--CSCCCTTCEEEEEEEEEEEETTEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             CEEEEEECEEEEE--CCCCCCCCEEEEEEEEEEEECCEEEEEEEEEECCEEEEEEEEEEE
T ss_conf             5999970408999--455579989999999999658999999999999999999999999


No 10 
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}
Probab=16.76  E-value=28  Score=13.20  Aligned_cols=38  Identities=18%  Similarity=0.344  Sum_probs=29.1

Q ss_pred             CCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEE
Q ss_conf             47778880699999989999999995688870558999731
Q gi|254780688|r  104 LDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL  144 (147)
Q Consensus       104 Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~ii  144 (147)
                      |.+..+.+|.+...+-...+|.+.-+|.   ++-+.+.+..
T Consensus         7 L~~~~g~~V~VeLkng~~~~G~L~~~D~---~mNi~L~~~~   44 (72)
T d1d3ba_           7 LHEAEGHIVTCETNTGEVYRGKLIEAED---NMNCQMSNIT   44 (72)
T ss_dssp             HHHTTTSEEEEEETTSCEEEEEEEEECT---TCCEEEEEEE
T ss_pred             HHHCCCCEEEEEECCCEEEEEEEEEECC---CEEEEEEEEE
T ss_conf             9860899999998998399998999948---7258997999


Done!