Query 030940
Match_columns 169
No_of_seqs 26 out of 28
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:51:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030940hhsearch_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 36.5 25 0.00054 25.1 1.7 16 66-81 15-30 (57)
2 COG2886 Uncharacterized small 32.2 29 0.00064 26.2 1.5 18 64-81 54-71 (88)
3 PF13384 HTH_23: Homeodomain-l 20.8 33 0.00071 21.2 0.0 10 130-139 41-50 (50)
4 PF03013 Pyr_excise: Pyrimidin 19.3 69 0.0015 25.4 1.5 17 68-84 68-84 (130)
5 cd04465 S1_RPS1_repeat_ec2_hs2 16.8 37 0.00081 22.1 -0.4 12 133-144 21-32 (67)
6 KOG2578 Transcription factor E 14.0 1.2E+02 0.0026 28.5 1.9 16 63-80 90-105 (388)
7 PF00488 MutS_V: MutS domain V 13.7 2E+02 0.0043 23.9 3.0 27 46-76 88-114 (235)
8 PF11121 DUF2639: Protein of u 13.6 1.2E+02 0.0026 20.4 1.3 12 67-78 7-18 (40)
9 PF04368 DUF507: Protein of un 12.2 1.3E+02 0.0027 25.2 1.4 12 66-77 171-182 (183)
10 cd05694 S1_Rrp5_repeat_hs2_sc2 12.0 53 0.0012 22.7 -0.7 14 132-145 26-39 (74)
No 1
>PF14162 YozD: YozD-like protein
Probab=36.51 E-value=25 Score=25.10 Aligned_cols=16 Identities=44% Similarity=0.825 Sum_probs=13.6
Q ss_pred hhhHHHHHHcCCCCCC
Q 030940 66 SLFMKELKRRGMTPTS 81 (169)
Q Consensus 66 SLFmKELkRRGmaptS 81 (169)
.-|-+||-|||.-|+-
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=32.17 E-value=29 Score=26.21 Aligned_cols=18 Identities=28% Similarity=0.466 Sum_probs=14.2
Q ss_pred chhhhHHHHHHcCCCCCC
Q 030940 64 PESLFMKELKRRGMTPTS 81 (169)
Q Consensus 64 pESLFmKELkRRGmaptS 81 (169)
+=-.|+.||++||..+-+
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=20.78 E-value=33 Score=21.20 Aligned_cols=10 Identities=60% Similarity=0.890 Sum_probs=0.0
Q ss_pred hhccCcCCCc
Q 030940 130 LNSEGLEGRL 139 (169)
Q Consensus 130 LNSEGLEGLi 139 (169)
-|.+|+|||.
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=19.28 E-value=69 Score=25.42 Aligned_cols=17 Identities=41% Similarity=0.649 Sum_probs=9.6
Q ss_pred hHHHHHHcCCCCCCccc
Q 030940 68 FMKELKRRGMTPTSLLE 84 (169)
Q Consensus 68 FmKELkRRGmaptSl~~ 84 (169)
-|+|+++||..|.+...
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
>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=16.84 E-value=37 Score=22.13 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=10.2
Q ss_pred cCcCCCccHHHH
Q 030940 133 EGLEGRLTIPLI 144 (169)
Q Consensus 133 EGLEGLiPRa~l 144 (169)
+|++||||+..+
T Consensus 21 ~g~~gfip~s~~ 32 (67)
T cd04465 21 EGVRAFLPASQV 32 (67)
T ss_pred CCEEEEEEHHHC
Confidence 689999998854
No 6
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=13.97 E-value=1.2e+02 Score=28.47 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=11.2
Q ss_pred CchhhhHHHHHHcCCCCC
Q 030940 63 PPESLFMKELKRRGMTPT 80 (169)
Q Consensus 63 ~pESLFmKELkRRGmapt 80 (169)
-|-. |+||+.-||..+
T Consensus 90 iPra--l~eLqeEgvke~ 105 (388)
T KOG2578|consen 90 IPRA--LFELQEEGVKEG 105 (388)
T ss_pred hhHH--HHHHHHHHHhhc
Confidence 4444 569999999654
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=13.66 E-value=2e+02 Score=23.94 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=16.1
Q ss_pred EEEeeeccCCCCCCCCCCchhhhHHHHHHcC
Q 030940 46 KVCCGVQEGDKQSNGEEPPESLFMKELKRRG 76 (169)
Q Consensus 46 rV~c~~~eg~~~~~geE~pESLFmKELkRRG 76 (169)
++.++....|+..+ -.|.|+.|+++=.
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 3899999999854
No 8
>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=13.64 E-value=1.2e+02 Score=20.41 Aligned_cols=12 Identities=42% Similarity=0.816 Sum_probs=10.6
Q ss_pred hhHHHHHHcCCC
Q 030940 67 LFMKELKRRGMT 78 (169)
Q Consensus 67 LFmKELkRRGma 78 (169)
-|.+|||..|++
T Consensus 7 w~V~eLKk~GI~ 18 (40)
T PF11121_consen 7 WYVKELKKLGIR 18 (40)
T ss_pred HHHHHHHHhCcc
Confidence 589999999995
No 9
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=12.22 E-value=1.3e+02 Score=25.23 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=10.0
Q ss_pred hhhHHHHHHcCC
Q 030940 66 SLFMKELKRRGM 77 (169)
Q Consensus 66 SLFmKELkRRGm 77 (169)
-++..||++|||
T Consensus 171 k~yeeel~krGl 182 (183)
T PF04368_consen 171 KLYEEELRKRGL 182 (183)
T ss_pred HHHHHHHHHcCC
Confidence 466789999998
No 10
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=12.02 E-value=53 Score=22.72 Aligned_cols=14 Identities=21% Similarity=0.045 Sum_probs=11.0
Q ss_pred ccCcCCCccHHHHH
Q 030940 132 SEGLEGRLTIPLIK 145 (169)
Q Consensus 132 SEGLEGLiPRa~l~ 145 (169)
-.|++||+|+..+-
T Consensus 26 ~~gv~Gfl~~~~~~ 39 (74)
T cd05694 26 IPGTTGFLPKKDAG 39 (74)
T ss_pred CCCcEEEEEHHHCC
Confidence 35899999998653
Done!