Query 032364
Match_columns 142
No_of_seqs 24 out of 26
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 13:08:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032364hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14162 YozD: YozD-like prote 41.7 19 0.00041 25.0 1.7 16 66-81 15-30 (57)
2 COG2886 Uncharacterized small 37.2 22 0.00049 26.1 1.6 18 64-81 54-71 (88)
3 PF13384 HTH_23: Homeodomain-l 21.7 31 0.00066 20.8 0.0 10 130-139 41-50 (50)
4 PF03013 Pyr_excise: Pyrimidin 21.5 59 0.0013 25.1 1.5 17 68-84 68-84 (130)
5 PF11121 DUF2639: Protein of u 17.8 82 0.0018 20.6 1.3 12 67-78 7-18 (40)
6 PF04368 DUF507: Protein of un 14.7 1E+02 0.0022 25.2 1.4 12 66-77 171-182 (183)
7 PF00488 MutS_V: MutS domain V 13.9 2E+02 0.0043 23.3 3.0 27 46-76 88-114 (235)
8 TIGR02328 conserved hypothetic 13.4 1.4E+02 0.003 23.5 1.8 30 67-98 56-85 (120)
9 PF08970 Sda: Sporulation inhi 13.3 1.4E+02 0.0031 19.7 1.6 14 66-79 27-40 (46)
10 cd04465 S1_RPS1_repeat_ec2_hs2 12.3 49 0.0011 21.0 -0.8 9 133-141 21-29 (67)
No 1
>PF14162 YozD: YozD-like protein
Probab=41.71 E-value=19 Score=25.03 Aligned_cols=16 Identities=44% Similarity=0.825 Sum_probs=13.7
Q ss_pred hhhHHHHHHcCCCCCC
Q 032364 66 SLFMKELKRRGMTPTS 81 (142)
Q Consensus 66 SlFmKELkRRGmaptS 81 (142)
..|-+||-+||.-|+-
T Consensus 15 efFy~eL~kRGyvP~e 30 (57)
T PF14162_consen 15 EFFYHELVKRGYVPTE 30 (57)
T ss_pred HHHHHHHHHccCCCcH
Confidence 4699999999998864
No 2
>COG2886 Uncharacterized small protein [Function unknown]
Probab=37.25 E-value=22 Score=26.15 Aligned_cols=18 Identities=28% Similarity=0.466 Sum_probs=14.1
Q ss_pred chhhhHHHHHHcCCCCCC
Q 032364 64 PESLFMKELKRRGMTPTS 81 (142)
Q Consensus 64 pESlFmKELkRRGmaptS 81 (142)
+=-.|+.||++||..+-+
T Consensus 54 sl~ef~~eL~~R~i~l~~ 71 (88)
T COG2886 54 SLNEFEEELRKRGIPLYD 71 (88)
T ss_pred CHHHHHHHHHHhCCCccc
Confidence 345799999999996654
No 3
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.71 E-value=31 Score=20.79 Aligned_cols=10 Identities=40% Similarity=0.315 Sum_probs=0.0
Q ss_pred cccccccCcC
Q 032364 130 LNSEGLEVAG 139 (142)
Q Consensus 130 LNSEGLEGLi 139 (142)
-|.+|+|||.
T Consensus 41 ~~~~G~~gL~ 50 (50)
T PF13384_consen 41 YREEGLEGLL 50 (50)
T ss_dssp ----------
T ss_pred cccccccccC
Confidence 3678888874
No 4
>PF03013 Pyr_excise: Pyrimidine dimer DNA glycosylase; InterPro: IPR004260 Pyrimidine dimer DNA glycosylases are enzymes responsible for initiating the base excision repair pathway, excising pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond []. One such enzyme is T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway []. Bacteriophage T4 that are deficient in these enzymes are extremely sensitive to UV.; PDB: 2FCC_B 1ENJ_A 1ENI_A 1ENK_A 1VAS_A 2END_A.
Probab=21.54 E-value=59 Score=25.14 Aligned_cols=17 Identities=41% Similarity=0.649 Sum_probs=9.6
Q ss_pred hHHHHHHcCCCCCCccc
Q 032364 68 FMKELKRRGMTPTSLLE 84 (142)
Q Consensus 68 FmKELkRRGmaptS~~~ 84 (142)
-|+|+++||..|.+...
T Consensus 68 l~~EM~~RGY~~~~~~~ 84 (130)
T PF03013_consen 68 LMAEMQRRGYKPNSPWF 84 (130)
T ss_dssp HHHHHHHTT---S--S-
T ss_pred HHHHHHHcCCCCChhhh
Confidence 48999999999987763
No 5
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=17.82 E-value=82 Score=20.59 Aligned_cols=12 Identities=42% Similarity=0.816 Sum_probs=10.7
Q ss_pred hhHHHHHHcCCC
Q 032364 67 LFMKELKRRGMT 78 (142)
Q Consensus 67 lFmKELkRRGma 78 (142)
-|.+|||..|++
T Consensus 7 w~V~eLKk~GI~ 18 (40)
T PF11121_consen 7 WYVKELKKLGIR 18 (40)
T ss_pred HHHHHHHHhCcc
Confidence 589999999995
No 6
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=14.69 E-value=1e+02 Score=25.18 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=10.0
Q ss_pred hhhHHHHHHcCC
Q 032364 66 SLFMKELKRRGM 77 (142)
Q Consensus 66 SlFmKELkRRGm 77 (142)
-++..||++|||
T Consensus 171 k~yeeel~krGl 182 (183)
T PF04368_consen 171 KLYEEELRKRGL 182 (183)
T ss_pred HHHHHHHHHcCC
Confidence 456789999998
No 7
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 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. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. 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. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].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 the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=13.88 E-value=2e+02 Score=23.33 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=16.2
Q ss_pred EEEeeeccCCCCCCCCCCchhhhHHHHHHcC
Q 032364 46 KVCCGVQEGDKQSNGEEPPESLFMKELKRRG 76 (142)
Q Consensus 46 rV~c~~~eg~~~~~gee~pESlFmKELkRRG 76 (142)
++.++....|+..+ -.|.|+.||++-.
T Consensus 88 ~I~t~~~~~d~~~~----~~S~F~~E~~~~~ 114 (235)
T PF00488_consen 88 RIFTRIGDDDSIES----GLSTFMAEMKRLS 114 (235)
T ss_dssp EEEEEES---SSTT----SSSHHHHHHHHHH
T ss_pred EEEeeccccccccc----ccccHHHhHHHHH
Confidence 45555554444333 3899999999855
No 8
>TIGR02328 conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown.
Probab=13.37 E-value=1.4e+02 Score=23.51 Aligned_cols=30 Identities=20% Similarity=0.222 Sum_probs=18.8
Q ss_pred hhHHHHHHcCCCCCCccccCCCCCCCcchhhh
Q 032364 67 LFMKELKRRGMTPTSLLEDSSRTDSGLDDKTK 98 (142)
Q Consensus 67 lFmKELkRRGmaptS~~~~~~~~~~G~~~e~~ 98 (142)
+-|+|+++||-.|.-.-- ++...|-.-+..
T Consensus 56 lv~~EM~~RGY~~~~~W~--d~~yRG~~~~~y 85 (120)
T TIGR02328 56 LVMEEMATRGYHVSKQWL--DPNYRGQNCPNY 85 (120)
T ss_pred HHHHHHHHcCCCCChhhc--CccccCCcCCcc
Confidence 458999999998876432 233445444443
No 9
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=13.32 E-value=1.4e+02 Score=19.72 Aligned_cols=14 Identities=29% Similarity=0.584 Sum_probs=10.6
Q ss_pred hhhHHHHHHcCCCC
Q 032364 66 SLFMKELKRRGMTP 79 (142)
Q Consensus 66 SlFmKELkRRGmap 79 (142)
.|..+|+.|||+..
T Consensus 27 ~Ll~~Ei~rR~L~~ 40 (46)
T PF08970_consen 27 RLLEEEIQRRSLKH 40 (46)
T ss_dssp HHHHHHHHHCT-TT
T ss_pred HHHHHHHHHcCCcc
Confidence 57789999999854
No 10
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=12.31 E-value=49 Score=20.99 Aligned_cols=9 Identities=22% Similarity=0.161 Sum_probs=7.2
Q ss_pred ccccCcCCC
Q 032364 133 EGLEVAGRR 141 (142)
Q Consensus 133 EGLEGLiPR 141 (142)
+|++||||.
T Consensus 21 ~g~~gfip~ 29 (67)
T cd04465 21 EGVRAFLPA 29 (67)
T ss_pred CCEEEEEEH
Confidence 588888885
Done!