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!