Query         gi|254780719|ref|YP_003065132.1| zinc uptake ABC transporter, permease protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 260
No_of_seqs    123 out of 2499
Neff          7.3 
Searched_HMMs 23785
Date          Tue May 31 17:46:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780719.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2nq2_A Hypothetical ABC transp  99.9 6.2E-22 2.6E-26  136.7  22.9  249   10-260    66-330 (337)
  2 2qi9_A Vitamin B12 import syst  99.9 1.1E-21 4.8E-26  135.3  19.2  247   11-260    61-324 (326)
  3 1tba_A TAFII230, transcription   8.8      57  0.0024   11.3  -0.1   14  109-122     7-20  (67)
  4 1td4_A Head decoration protein   8.4       8 0.00034   15.9  -4.6   14   30-43    100-113 (115)
  5 3io5_A Recombination and repai   7.7      79  0.0033   10.5   1.7   17  153-169    69-85  (333)
  6 2zr9_A Protein RECA, recombina   7.6      80  0.0033   10.5   1.8   16  153-168   100-115 (349)
  7 1veg_A NEDD8 ultimate buster-1   6.0      97  0.0041   10.0   1.9   17  146-162    33-49  (83)
  8 2qme_I CRIB domain of the seri   5.7      41  0.0017   12.1  -2.1   23  150-172    12-34  (36)
  9 2odb_B Serine/threonine-protei   5.4      43  0.0018   11.9  -2.1   23  150-172    12-34  (35)
 10 1xp8_A RECA protein, recombina   5.0 1.2E+02  0.0051    9.5   1.8   17  153-169   113-129 (366)

No 1  
>2nq2_A Hypothetical ABC transporter permease protein HI1471; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}
Probab=99.91  E-value=6.2e-22  Score=136.72  Aligned_cols=249  Identities=14%  Similarity=0.176  Sum_probs=180.0

Q ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHC-CCCCC
Q ss_conf             999999999987889999----998799964358999999999999950036---6799999999999986310-35765
Q gi|254780719|r   10 LFSGIGIVLSTGPLGCFI----IWQRIAYFGDTIAHSALLGVALSLIFQLPL---TICIFMIATLTSLVLLQIQ-KNEAL   81 (260)
Q Consensus        10 ll~~~~~~~~~~~lG~~v----v~rr~s~~~~alsH~a~~Gial~~~l~~~~---~~ga~~~~~l~al~i~~l~-~~~~~   81 (260)
                      .+++++.+...+.-|...    -.+=.+----+++..+-.|++++++++.+.   ......++.........+. ++++.
T Consensus        66 ~l~a~l~Ga~LavaG~llQ~~~rNpLA~P~iLGissGA~lg~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (337)
T 2nq2_A           66 ILTALCVGAGLALSGVVLQGIFRNPLVNPHIIGVTSGSAFGGTLAIFFGFSLYGLFTSTILFGFGTLALVFLFSFKFNQR  145 (337)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCTTCCTTTTSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999998657999990665489999999999999840022578999999999999999999964778


Q ss_pred             H--HHHHHHHHHHHHHHHHHHHHHH-CCC--CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             0--4569999999999999999962-132--0013334433324422876705899998999999984245665412888
Q gi|254780719|r   82 S--SDAILGVITHSTISLALVILSF-MKW--VNTDLTSFLFGDILAVNTTDILLIWGIGFLNIMILFKIWKPLLATTVNY  156 (260)
Q Consensus        82 ~--~da~igi~~s~~~alg~llls~-~~~--~~~~l~~~LfG~il~v~~~dv~~~~~~~~~~~~~l~~~~r~l~~~~fD~  156 (260)
                      +  +-..+|+..+..++....+..+ ..+  ...+...|++||....+|+|++.......+.....+...|++.....||
T Consensus       146 ~~~~liL~gi~~~~~~~a~~~~~~~l~~~~~~~~~~~~W~~Gs~~~~~w~~~~~~~~~~~~~~~~~~~~~~~l~~l~lG~  225 (337)
T 2nq2_A          146 SLLMLILIGMILSGLFSALVSLLQYISDTEEKLPSIVFWLMGSFATSNWEKLLFFFVPFLLCSSILLSLSWRLNLLSLDE  225 (337)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCTTTHHHHHHHHTTCCSTTCCHHHHHHHHHHHHHHHHHHHHTTTGGGGGGSCH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHCCCCHHCCCH
T ss_conf             72177876799999999999999997224889999999850143568843213311211478888888630056210793


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH-
Q ss_conf             9999808981067769999999999999999889999999999999999741998999999999999999999999999-
Q gi|254780719|r  157 ELAKAEGMQPEKIKLIFIMITSLMISVSIKFIGITLITSLLILPTVTARRFSTSPENMAILATIIGILGIIIGLYGSLI-  235 (260)
Q Consensus       157 ~~A~~~Gi~v~~~~~l~~~l~al~v~~~v~~vG~llv~allv~Paa~A~~l~~~~~~~~~~s~~~g~~~~~~G~~lS~~-  235 (260)
                      |.|++.|+|+++.+...+.+.++.++.++..+|.+.+.+ ++.|+.+.+...+++|+.++.|.+.|..-......++.. 
T Consensus       226 ~~A~sLGv~v~~~r~~~l~l~~llta~~vs~~G~I~FvG-Li~Phiar~l~g~~~~~~l~~s~l~Ga~lll~aD~i~r~l  304 (337)
T 2nq2_A          226 KEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSIGWVG-LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSL  304 (337)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHCCCCSST-THHHHHHHHHHCSCHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEHH-HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             889878997999999999999999999996377630387-4099999998188853399999999999999999998665


Q ss_pred             --HCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             --5588089999999999999987239
Q gi|254780719|r  236 --FDTPSGPSIIITSLFLFILSFFYKK  260 (260)
Q Consensus       236 --~~lp~g~~Iv~~~~~~f~~~~~~~k  260 (260)
                        +++|.|..+.++.+..|+ .+++||
T Consensus       305 ~p~elPvG~vtaliG~p~fl-~ll~r~  330 (337)
T 2nq2_A          305 SDAEIPISILTALIGAPLFG-VLVYKL  330 (337)
T ss_dssp             CSSCCCHHHHHHHHHHHHHH-HHHHCC
T ss_pred             CCCCEEHHHHHHHHHHHHHH-HHHHHH
T ss_conf             67773199999999999999-999985


No 2  
>2qi9_A Vitamin B12 import system permease protein BTUC; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_A*
Probab=99.90  E-value=1.1e-21  Score=135.28  Aligned_cols=247  Identities=14%  Similarity=0.121  Sum_probs=174.8

Q ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH------HHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999878899----9999879996435899999999999995003------667999999999999863103576
Q gi|254780719|r   11 FSGIGIVLSTGPLGC----FIIWQRIAYFGDTIAHSALLGVALSLIFQLP------LTICIFMIATLTSLVLLQIQKNEA   80 (260)
Q Consensus        11 l~~~~~~~~~~~lG~----~vv~rr~s~~~~alsH~a~~Gial~~~l~~~------~~~ga~~~~~l~al~i~~l~~~~~   80 (260)
                      +++++.|...+.-|.    ....+=.+----++++.+..|++++..++..      ....++..+...........+++.
T Consensus        61 l~a~l~Ga~LavsG~~lQ~~~rNpLA~P~iLGissGA~lg~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  140 (326)
T 2qi9_A           61 LAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHL  140 (326)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCSSCCGGGGTHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999999579887840222201699999999996302678999999999999999999998853556


Q ss_pred             CHH-HHHHHHHHHHHHHHHHHH-HHHCC-CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf             504-569999999999999999-96213-200133344333244228767058999989999999842456654128889
Q gi|254780719|r   81 LSS-DAILGVITHSTISLALVI-LSFMK-WVNTDLTSFLFGDILAVNTTDILLIWGIGFLNIMILFKIWKPLLATTVNYE  157 (260)
Q Consensus        81 ~~~-da~igi~~s~~~alg~ll-ls~~~-~~~~~l~~~LfG~il~v~~~dv~~~~~~~~~~~~~l~~~~r~l~~~~fD~~  157 (260)
                      .+. -...|+..+..++....+ ....+ +...++..|+.||....+|+|++........ ........|+++..+.|||
T Consensus       141 ~~~~liL~Gi~i~~~~~a~~~~l~~~~~~~~~~~~~~w~~Gs~~~~~~~~~~~~~~~~~~-~~~~~~~~~~L~~l~lG~~  219 (326)
T 2qi9_A          141 STSRLLLAGVALGIISSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPV-LLWISSQSRPMNMLALGEI  219 (326)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCCTTHHHHHHHHHTCCCTTCCGGGHHHHTTTHHH-HHHHTTCHHHHHHHHTCHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCHH
T ss_conf             505889999999999999999999816899999999997347778874677889999999-9999999988777636849


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH---
Q ss_conf             99980898106776999999999999999988999999999999999974199899999999999999999999999---
Q gi|254780719|r  158 LAKAEGMQPEKIKLIFIMITSLMISVSIKFIGITLITSLLILPTVTARRFSTSPENMAILATIIGILGIIIGLYGSL---  234 (260)
Q Consensus       158 ~A~~~Gi~v~~~~~l~~~l~al~v~~~v~~vG~llv~allv~Paa~A~~l~~~~~~~~~~s~~~g~~~~~~G~~lS~---  234 (260)
                      .|++.|+|+++.+...+.+.++.++.++..+|.+.+.+ ++.|+.+.+...+++|..++.|.++|.........++.   
T Consensus       220 ~A~sLGv~v~~~r~~~l~~~~ll~a~~va~~G~I~FvG-Li~PhiaR~~~g~~~~~~l~~s~l~Ga~lll~aD~i~r~i~  298 (326)
T 2qi9_A          220 SARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIG-LVIPHILRLSGLTDHRVLLPGCALAGASALLLADIVARLAL  298 (326)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCCCSST-THHHHHHHTTTCCSHHHHHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH-HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             88867985899889988688999999998515699999-98999999862777436999999999999999999996614


Q ss_pred             -HHCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             -95588089999999999999987239
Q gi|254780719|r  235 -IFDTPSGPSIIITSLFLFILSFFYKK  260 (260)
Q Consensus       235 -~~~lp~g~~Iv~~~~~~f~~~~~~~k  260 (260)
                       ..++|.|-.+.++.+..|+ .++.||
T Consensus       299 ~p~eiPvGvitaliG~P~fi-~Ll~r~  324 (326)
T 2qi9_A          299 AAAELPIGVVTATLGAPVFI-WLLLKA  324 (326)
T ss_dssp             TTCCCCHHHHHHHHHHHHHH-HHHSCC
T ss_pred             CCCCCHHHHHHHHHHHHHHH-HHHHHC
T ss_conf             66542199999999999999-977204


No 3  
>1tba_A TAFII230, transcription initiation factor IID 230K chain; complex (transcription factors), TAF, TAFII230, solution structure; NMR {Drosophila melanogaster} SCOP: a.15.1.1
Probab=8.83  E-value=57  Score=11.30  Aligned_cols=14  Identities=50%  Similarity=0.776  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             01333443332442
Q gi|254780719|r  109 NTDLTSFLFGDILA  122 (260)
Q Consensus       109 ~~~l~~~LfG~il~  122 (260)
                      ..++..+|||||-.
T Consensus         7 ~~~LtGfLFGNId~   20 (67)
T 1tba_A            7 GLDLTGILFGNIDS   20 (67)
T ss_dssp             SCCCTTHHHHCEET
T ss_pred             CCCEEEEEECCCCC
T ss_conf             72101224424377


No 4  
>1td4_A Head decoration protein; SHP, viral protein; 1.50A {Enterobacteria phage P21} SCOP: b.85.2.1 PDB: 1td3_A 1td0_A
Probab=8.40  E-value=8  Score=15.95  Aligned_cols=14  Identities=29%  Similarity=0.581  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             87999643589999
Q gi|254780719|r   30 QRIAYFGDTIAHSA   43 (260)
Q Consensus        30 rr~s~~~~alsH~a   43 (260)
                      |+-.|.|.++||++
T Consensus       100 K~~AF~Gs~vSh~~  113 (115)
T 1td4_A          100 KANAFAGSALSHAA  113 (115)
T ss_dssp             HHTTTTTSEEEEEC
T ss_pred             HHHHHHCCCCCCCC
T ss_conf             76666278542135


No 5  
>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}
Probab=7.66  E-value=79  Score=10.51  Aligned_cols=17  Identities=18%  Similarity=0.513  Sum_probs=13.0

Q ss_pred             CCCHHHHHHCCCCCCHH
Q ss_conf             28889999808981067
Q gi|254780719|r  153 TVNYELAKAEGMQPEKI  169 (260)
Q Consensus       153 ~fD~~~A~~~Gi~v~~~  169 (260)
                      ++||++|+..|+++..+
T Consensus        69 ~~~~~~a~~lGvd~~~l   85 (333)
T 3io5_A           69 GITPAYLRSMGVDPERV   85 (333)
T ss_dssp             CCCHHHHHHTTCCGGGE
T ss_pred             CCCHHHHHHCCCCCCCC
T ss_conf             78989999809881005


No 6  
>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, cytoplasm, DNA damage, DNA recombination; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...
Probab=7.61  E-value=80  Score=10.49  Aligned_cols=16  Identities=25%  Similarity=0.407  Sum_probs=13.1

Q ss_pred             CCCHHHHHHCCCCCCH
Q ss_conf             2888999980898106
Q gi|254780719|r  153 TVNYELAKAEGMQPEK  168 (260)
Q Consensus       153 ~fD~~~A~~~Gi~v~~  168 (260)
                      ++||++|+..|+++..
T Consensus       100 ~~~~~~a~~~GvD~~~  115 (349)
T 2zr9_A          100 ALDPEYAKKLGVDTDS  115 (349)
T ss_dssp             CCCHHHHHHTTCCGGG
T ss_pred             CCCHHHHHHCCCCHHH
T ss_conf             5899999983998899


No 7  
>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} SCOP: a.5.2.1
Probab=6.02  E-value=97  Score=10.03  Aligned_cols=17  Identities=18%  Similarity=0.139  Sum_probs=12.6

Q ss_pred             HHHHHHHCCCHHHHHHC
Q ss_conf             45665412888999980
Q gi|254780719|r  146 WKPLLATTVNYELAKAE  162 (260)
Q Consensus       146 ~r~l~~~~fD~~~A~~~  162 (260)
                      -.+++++.||+|.|++.
T Consensus        33 idqLvYMGF~~~~Ae~A   49 (83)
T 1veg_A           33 INQLVYMGFDTVVAEAA   49 (83)
T ss_dssp             HHHHHHHSCCHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHH
T ss_conf             99999834238889999


No 8  
>2qme_I CRIB domain of the serine/threonine-protein kinase PAK 1; GTPase RAC3, small GTP binding protein, P21 RAC; HET: GCP; 1.75A {Homo sapiens}
Probab=5.66  E-value=41  Score=12.09  Aligned_cols=23  Identities=13%  Similarity=0.208  Sum_probs=16.1

Q ss_pred             HHHCCCHHHHHHCCCCCCHHHHH
Q ss_conf             54128889999808981067769
Q gi|254780719|r  150 LATTVNYELAKAEGMQPEKIKLI  172 (260)
Q Consensus       150 ~~~~fD~~~A~~~Gi~v~~~~~l  172 (260)
                      .-++||++.-+..|+|..|-+++
T Consensus        12 ~HVg~D~~tG~f~GLP~~W~~ll   34 (36)
T 2qme_I           12 IHVGFDAVTGEFTGMPEQWARLL   34 (36)
T ss_dssp             EEECCBTTTTBCC----------
T ss_pred             EEEEECCCCCCEECCCHHHHHHH
T ss_conf             47418699981705999999985


No 9  
>2odb_B Serine/threonine-protein kinase PAK 6; small GTPase, CRIB, protein-protein complex, structural genomics, structural genomics consortium, SGC; HET: GCP; 2.40A {Homo sapiens}
Probab=5.40  E-value=43  Score=11.94  Aligned_cols=23  Identities=17%  Similarity=0.315  Sum_probs=15.7

Q ss_pred             HHHCCCHHHHHHCCCCCCHHHHH
Q ss_conf             54128889999808981067769
Q gi|254780719|r  150 LATTVNYELAKAEGMQPEKIKLI  172 (260)
Q Consensus       150 ~~~~fD~~~A~~~Gi~v~~~~~l  172 (260)
                      .-++||++.-+..|+|..|-+++
T Consensus        12 ~HVg~D~~tG~f~GLP~eW~~ll   34 (35)
T 2odb_B           12 VHTSFDPKEGKFVGLPPQWQNIL   34 (35)
T ss_dssp             EEEEEETTTTEEESCCHHHHHHH
T ss_pred             EEEEECCCCCCEECCCHHHHHHH
T ss_conf             47316699981845998999974


No 10 
>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA- binding protein, DNA binding protein; HET: SAP; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1
Probab=4.98  E-value=1.2e+02  Score=9.47  Aligned_cols=17  Identities=18%  Similarity=0.393  Sum_probs=13.4

Q ss_pred             CCCHHHHHHCCCCCCHH
Q ss_conf             28889999808981067
Q gi|254780719|r  153 TVNYELAKAEGMQPEKI  169 (260)
Q Consensus       153 ~fD~~~A~~~Gi~v~~~  169 (260)
                      +|||++++..|+++..+
T Consensus       113 ~~d~~~a~~~Gvd~d~l  129 (366)
T 1xp8_A          113 ALDPVYARALGVNTDEL  129 (366)
T ss_dssp             CCCHHHHHHTTCCGGGC
T ss_pred             CCCHHHHHHHCCCHHHE
T ss_conf             75999999718981107


Done!