Query         gi|254781127|ref|YP_003065540.1| hypothetical protein CLIBASIA_05145 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 48
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 05:38:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781127.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01070 mutS1 DNA mismatch r  46.4      14 0.00035   19.4   2.0   29    7-46    664-695 (863)
  2 COG3965 Predicted Co/Zn/Cd cat  37.1      38 0.00096   17.1   3.0   47    2-48    217-264 (314)
  3 COG4073 Uncharacterized protei  23.1      79   0.002   15.4   2.8   29    3-31    166-194 (198)
  4 pfam09385 HisK_N Histidine kin  22.1      52  0.0013   16.4   1.6   39    1-48     46-85  (133)
  5 smart00302 GED Dynamin GTPase   20.1      92  0.0024   15.1   3.0   27    1-28      9-35  (92)
  6 TIGR00342 TIGR00342 thiamine b  19.9      73  0.0019   15.6   2.0   23    1-23     10-33  (391)
  7 pfam06793 UPF0262 Uncharacteri  17.5 1.1E+02  0.0027   14.7   2.4   28    2-29     87-116 (159)
  8 pfam02212 GED Dynamin GTPase e  16.8 1.1E+02  0.0028   14.7   3.2   27    1-28      9-35  (92)
  9 pfam04416 consensus             15.3 1.2E+02  0.0031   14.4   2.2   17   14-30     25-41  (129)
 10 pfam11792 Baculo_LEF5_C Baculo  15.3      44  0.0011   16.8  -0.1   16   21-36     20-36  (43)

No 1  
>TIGR01070 mutS1 DNA mismatch repair protein MutS; InterPro: IPR005748   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents a family of MutS proteins.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair.
Probab=46.43  E-value=14  Score=19.37  Aligned_cols=29  Identities=45%  Similarity=0.727  Sum_probs=22.2

Q ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             778865546---6999999999987876987666431146535
Q gi|254781127|r    7 DYFKIEITE---NIKQATEKALRAFDEFHFLRDKHKANVGRGE   46 (48)
Q Consensus         7 dyfkieite---nikqatekalrafdefhflrdkhkanvgrge   46 (48)
                      --|-+|.+|   -|++||+..|--|||           ||||-
T Consensus       664 STFMVEM~E~aNil~~AT~~SLvL~DE-----------~GRGT  695 (863)
T TIGR01070       664 STFMVEMTEAANILHNATENSLVLLDE-----------IGRGT  695 (863)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHC-----------CCCCC
T ss_conf             430067899999999866510223310-----------34530


No 2  
>COG3965 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=37.15  E-value=38  Score=17.10  Aligned_cols=47  Identities=28%  Similarity=0.369  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCC
Q ss_conf             3676777886554669999999999878769876664-3114653549
Q gi|254781127|r    2 KSLVRDYFKIEITENIKQATEKALRAFDEFHFLRDKH-KANVGRGEFI   48 (48)
Q Consensus         2 kslvrdyfkieitenikqatekalrafdefhflrdkh-kanvgrgefi   48 (48)
                      ||-+||-.-+.-.|-+.+....+-+.-+++.|..-.+ -|.||||-||
T Consensus       217 k~al~eiLlmtP~el~q~ies~~~~~v~k~~f~~~~~yvArVGr~l~I  264 (314)
T COG3965         217 KSALREILLMTPNELQQSIESHAHEIVEKYGFPSYHVYVARVGRGLFI  264 (314)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCEEE
T ss_conf             999999995193788999999999999986585278899984662289


No 3  
>COG4073 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.12  E-value=79  Score=15.42  Aligned_cols=29  Identities=38%  Similarity=0.501  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67677788655466999999999987876
Q gi|254781127|r    3 SLVRDYFKIEITENIKQATEKALRAFDEF   31 (48)
Q Consensus         3 slvrdyfkieitenikqatekalrafdef   31 (48)
                      |..|+-|--+...-.-.++|||++-|.+|
T Consensus       166 s~tReE~ie~Lr~rfPeq~ekA~e~fr~f  194 (198)
T COG4073         166 SRTREEFIEELRRRFPEQTEKALEYFRSF  194 (198)
T ss_pred             CCCHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_conf             46489999999867859899999999987


No 4  
>pfam09385 HisK_N Histidine kinase N terminal. This domain is found at the N terminal of sensor histidine kinase proteins.
Probab=22.08  E-value=52  Score=16.35  Aligned_cols=39  Identities=28%  Similarity=0.503  Sum_probs=19.8

Q ss_pred             CHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9367677788655466-99999999998787698766643114653549
Q gi|254781127|r    1 MKSLVRDYFKIEITEN-IKQATEKALRAFDEFHFLRDKHKANVGRGEFI   48 (48)
Q Consensus         1 mkslvrdyfkieiten-ikqatekalrafdefhflrdkhkanvgrgefi   48 (48)
                      |-+||..|+..++.+. |++-.+|-         -+..-.||++-|||+
T Consensus        46 m~~lv~~~l~~~~s~~~i~~la~Ki---------A~ER~eA~~NIgeFV   85 (133)
T pfam09385        46 LLELFIEALLEELSEEYIQRLAEKI---------AKERAEADVNIGEFV   85 (133)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHH---------HHHHHHCCCCHHHHH
T ss_conf             9999999985657699999999999---------999865125799999


No 5  
>smart00302 GED Dynamin GTPase effector domain.
Probab=20.05  E-value=92  Score=15.07  Aligned_cols=27  Identities=33%  Similarity=0.652  Sum_probs=20.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9367677788655466999999999987
Q gi|254781127|r    1 MKSLVRDYFKIEITENIKQATEKALRAF   28 (48)
Q Consensus         1 mkslvrdyfkieitenikqatekalraf   28 (48)
                      +++++..||.| +..+|.....|+...|
T Consensus         9 i~~lv~sYf~i-v~k~i~D~VPKaI~~~   35 (92)
T smart00302        9 IKSLVKSYFTI-VSKTLADQVPKAIMYL   35 (92)
T ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_conf             99999999999-9999998726999999


No 6  
>TIGR00342 TIGR00342 thiamine biosynthesis/tRNA modification protein ThiI; InterPro: IPR003720 Thiamine pyrophosphate (TPP) is synthesized de novo in many bacteria and is a required cofactor for many enzymes in the cell. ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway . Almost all the proteins in this group have an N-terminal THUMP domain (see IPR004114 from INTERPRO).; GO: 0009228 thiamin biosynthetic process.
Probab=19.87  E-value=73  Score=15.58  Aligned_cols=23  Identities=35%  Similarity=0.502  Sum_probs=19.3

Q ss_pred             CHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             9367-6777886554669999999
Q gi|254781127|r    1 MKSL-VRDYFKIEITENIKQATEK   23 (48)
Q Consensus         1 mksl-vrdyfkieitenikqatek   23 (48)
                      .||- +|.+|--..++|||+|..+
T Consensus        10 ~Kg~s~R~~F~~~L~~NIk~~lk~   33 (391)
T TIGR00342        10 IKGKSNRKRFEKKLKKNIKKALKK   33 (391)
T ss_pred             ECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             058656789999999999998610


No 7  
>pfam06793 UPF0262 Uncharacterized protein family (UPF0262).
Probab=17.45  E-value=1.1e+02  Score=14.74  Aligned_cols=28  Identities=36%  Similarity=0.634  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHH--HHHHHHHHHHHHHHHHH
Q ss_conf             36767778865--54669999999999878
Q gi|254781127|r    2 KSLVRDYFKIE--ITENIKQATEKALRAFD   29 (48)
Q Consensus         2 kslvrdyfkie--itenikqatekalrafd   29 (48)
                      +.+++|||-|-  --+.||.++..-+.|.|
T Consensus        87 RriikDYf~iCeSYy~AIk~~~p~qIEaID  116 (159)
T pfam06793        87 RRIIKDYFMICESYYEAIRTATPSQIEAID  116 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             999999999999999999609998877877


No 8  
>pfam02212 GED Dynamin GTPase effector domain.
Probab=16.81  E-value=1.1e+02  Score=14.66  Aligned_cols=27  Identities=30%  Similarity=0.589  Sum_probs=18.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9367677788655466999999999987
Q gi|254781127|r    1 MKSLVRDYFKIEITENIKQATEKALRAF   28 (48)
Q Consensus         1 mkslvrdyfkieitenikqatekalraf   28 (48)
                      +++++..||+|- ..++.....|+.-.|
T Consensus         9 i~~ll~sYf~iv-~k~i~D~VPK~I~~~   35 (92)
T pfam02212         9 IRRLLKSYFNIV-RKRIADQIPKAIMYF   35 (92)
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_conf             999999999999-999998887999999


No 9  
>pfam04416 consensus
Probab=15.32  E-value=1.2e+02  Score=14.45  Aligned_cols=17  Identities=41%  Similarity=0.511  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             46699999999998787
Q gi|254781127|r   14 TENIKQATEKALRAFDE   30 (48)
Q Consensus        14 tenikqatekalrafde   30 (48)
                      -+.+..|+.+|+|||.+
T Consensus        25 ~~hl~~A~~~A~ra~~~   41 (129)
T pfam04416        25 EEHVIFAAIKALKAFKR   41 (129)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             99999999999999884


No 10 
>pfam11792 Baculo_LEF5_C Baculoviridae late expression factor 5 C-terminal domain. This C-terminal domain is likely to be a zinc-binding domain.
Probab=15.31  E-value=44  Score=16.76  Aligned_cols=16  Identities=50%  Similarity=0.584  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHH-HHHHH
Q ss_conf             99999987876-98766
Q gi|254781127|r   21 TEKALRAFDEF-HFLRD   36 (48)
Q Consensus        21 tekalrafdef-hflrd   36 (48)
                      .|+-+||.||- .|.+-
T Consensus        20 ~E~Q~RAGDE~VSFi~y   36 (43)
T pfam11792        20 VEKQLRAGDEAVSFIKY   36 (43)
T ss_pred             EEHHHHCCCHHHHHHHH
T ss_conf             00343030078999999


Done!