Query 041622
Match_columns 205
No_of_seqs 14 out of 16
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 09:03:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041622.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041622hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01624 MutS_I: MutS domain I 39.6 3.9 8.4E-05 30.5 -2.1 18 94-111 15-32 (113)
2 PF04001 Vhr1: Transcription f 31.8 47 0.001 26.5 2.7 39 65-115 50-88 (95)
3 KOG4100 Uncharacterized conser 24.0 56 0.0012 27.2 1.9 24 61-84 24-48 (125)
4 PF07240 Turandot: Stress-indu 21.5 42 0.00091 25.9 0.7 30 105-136 18-59 (85)
5 PF15114 UPF0640: Uncharacteri 13.8 1.4E+02 0.003 22.8 1.8 16 104-119 50-65 (69)
6 PF06850 PHB_depo_C: PHB de-po 13.3 96 0.0021 27.3 1.1 11 102-112 84-94 (202)
7 PF08137 DVL: DVL family; Int 11.2 63 0.0014 19.3 -0.5 7 101-107 3-9 (19)
8 COG4785 NlpI Lipoprotein NlpI, 9.9 97 0.0021 28.8 -0.0 16 97-112 66-81 (297)
9 PF02939 UcrQ: UcrQ family; I 9.8 1.8E+02 0.004 21.8 1.4 16 108-123 60-75 (80)
10 PF02781 G6PD_C: Glucose-6-pho 8.7 1.9E+02 0.0041 26.1 1.4 18 97-114 30-47 (293)
No 1
>PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 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 N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. 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 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....
Probab=39.59 E-value=3.9 Score=30.53 Aligned_cols=18 Identities=39% Similarity=0.816 Sum_probs=15.3
Q ss_pred CCCccccccchhhHHHHH
Q 041622 94 ANSSPLFERGRFYEEYAA 111 (205)
Q Consensus 94 ~nSspLFeRGRfYd~YSA 111 (205)
+++--||++|-||+.|..
T Consensus 15 ~d~i~lf~~G~fYe~y~~ 32 (113)
T PF01624_consen 15 PDTIVLFQVGDFYEAYGE 32 (113)
T ss_dssp TTSEEEEEETTEEEEECH
T ss_pred CCeEEEEEcCCEEEEEcc
Confidence 567889999999999863
No 2
>PF04001 Vhr1: Transcription factor Vhr1; InterPro: IPR007147 This is a family of proteins of unknown function found in yeast.
Probab=31.78 E-value=47 Score=26.52 Aligned_cols=39 Identities=28% Similarity=0.394 Sum_probs=29.8
Q ss_pred hHHHHHHHHhHhhhcCCCCCCCCCCccccCCCccccccchhhHHHHHHHHH
Q 041622 65 CELRALARMVQDEFGTNDTNKGGIGKSLCANSSPLFERGRFYEEYAARRNE 115 (205)
Q Consensus 65 ~elRAlA~mV~dEf~~~~s~~~~~~~~l~~nSspLFeRGRfYd~YSARRNE 115 (205)
.+++-+|.+++.|||-+. .+++.||+==---.-|.|||.
T Consensus 50 ~~I~~iA~iLR~Ef~Yp~------------~~~~~FeKLV~aavQSVRRNR 88 (95)
T PF04001_consen 50 DNIRQIAEILRTEFGYPE------------SYSSEFEKLVTAAVQSVRRNR 88 (95)
T ss_pred HHHHHHHHHHHHHhCCCh------------hhHHHHHHHHHHHHHHHHHhh
Confidence 578999999999999873 346677765445567888885
No 3
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.01 E-value=56 Score=27.16 Aligned_cols=24 Identities=46% Similarity=0.699 Sum_probs=19.4
Q ss_pred cccchHHHHHH-HHhHhhhcCCCCC
Q 041622 61 RSISCELRALA-RMVQDEFGTNDTN 84 (205)
Q Consensus 61 ~sis~elRAlA-~mV~dEf~~~~s~ 84 (205)
+-+|.|+|||. .+|+|||-.-.+.
T Consensus 24 r~lp~~~R~lGD~YVkdEFrrHk~v 48 (125)
T KOG4100|consen 24 RGLPAELRALGDQYVKDEFRRHKTV 48 (125)
T ss_pred ccCChHHHHHHHHHHHHHHHHhccC
Confidence 34588999999 5999999987554
No 4
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=21.51 E-value=42 Score=25.93 Aligned_cols=30 Identities=40% Similarity=0.712 Sum_probs=20.0
Q ss_pred hhHHHHHH---------HHHHHhhhcCc---cCCCCCcccCcce
Q 041622 105 FYEEYAAR---------RNERLKRKKSE---ACSGEKTPYNLGV 136 (205)
Q Consensus 105 fYd~YSAR---------RNERLkRKkg~---~v~~~~~~~~lgV 136 (205)
||+.|+.+ |.+|+-+++-. .|||. |.+-|+
T Consensus 18 fY~ky~~~~~L~~~~r~~~d~~i~~y~~~~~lVDGv--PaQGG~ 59 (85)
T PF07240_consen 18 FYEKYSPRLPLTPQDRQRIDRFIRRYKEENNLVDGV--PAQGGF 59 (85)
T ss_pred HHHHcCccCCCCHHHHHHHHHHHHHHHHHhhcccCc--CCCCCc
Confidence 89999877 66666655542 37776 666664
No 5
>PF15114 UPF0640: Uncharacterised protein family UPF0640
Probab=13.75 E-value=1.4e+02 Score=22.76 Aligned_cols=16 Identities=38% Similarity=0.746 Sum_probs=13.3
Q ss_pred hhhHHHHHHHHHHHhh
Q 041622 104 RFYEEYAARRNERLKR 119 (205)
Q Consensus 104 RfYd~YSARRNERLkR 119 (205)
-|||.|-.|+-||+-+
T Consensus 50 ~FY~tykrrqae~~~e 65 (69)
T PF15114_consen 50 NFYDTYKRRQAERQVE 65 (69)
T ss_pred eHHHHHHHHHHHHHHH
Confidence 3999999999988753
No 6
>PF06850 PHB_depo_C: PHB de-polymerase C-terminus; InterPro: IPR009656 This entry represents the C terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid.
Probab=13.29 E-value=96 Score=27.34 Aligned_cols=11 Identities=55% Similarity=0.981 Sum_probs=8.8
Q ss_pred cchhhHHHHHH
Q 041622 102 RGRFYEEYAAR 112 (205)
Q Consensus 102 RGRfYd~YSAR 112 (205)
.-+|||||-|-
T Consensus 84 ~~~FydEY~av 94 (202)
T PF06850_consen 84 HRRFYDEYLAV 94 (202)
T ss_pred HHHHHHHHHHH
Confidence 34899999874
No 7
>PF08137 DVL: DVL family; InterPro: IPR012552 This family consists of the DVL family of proteins. In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, DEVIL (DVL) gene was identified. DVL is a small protein and over expression of the protein results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. DVL family is a novel class of small polypeptides and the over expression phenotypes suggest that these polypeptides may have a role in plant development [].
Probab=11.21 E-value=63 Score=19.27 Aligned_cols=7 Identities=43% Similarity=0.890 Sum_probs=5.0
Q ss_pred ccchhhH
Q 041622 101 ERGRFYE 107 (205)
Q Consensus 101 eRGRfYd 107 (205)
+|||||=
T Consensus 3 qr~r~YI 9 (19)
T PF08137_consen 3 QRARLYI 9 (19)
T ss_pred cceEEEe
Confidence 5788874
No 8
>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]
Probab=9.86 E-value=97 Score=28.84 Aligned_cols=16 Identities=44% Similarity=0.802 Sum_probs=12.9
Q ss_pred ccccccchhhHHHHHH
Q 041622 97 SPLFERGRFYEEYAAR 112 (205)
Q Consensus 97 spLFeRGRfYd~YSAR 112 (205)
.-|||||-+||----|
T Consensus 66 ~l~fERGvlYDSlGL~ 81 (297)
T COG4785 66 QLLFERGVLYDSLGLR 81 (297)
T ss_pred HHHHHhcchhhhhhHH
Confidence 5699999999976544
No 9
>PF02939 UcrQ: UcrQ family; InterPro: IPR004205 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multi-enzyme complex [], which recognises a mitochondrial targeting presequence. The bc1 complex contains 11 subunits: 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 9.5 kDa subunit of the complex. This subunit together with cytochrome B binds to ubiquinone.; GO: 0008121 ubiquinol-cytochrome-c reductase activity; PDB: 1L0N_G 1SQQ_G 1PP9_G 1PPJ_T 2FYU_G 2BCC_G 1BCC_G 2A06_G 1NTZ_G 2YBB_g ....
Probab=9.80 E-value=1.8e+02 Score=21.83 Aligned_cols=16 Identities=38% Similarity=0.609 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhhhcCc
Q 041622 108 EYAARRNERLKRKKSE 123 (205)
Q Consensus 108 ~YSARRNERLkRKkg~ 123 (205)
.+.-.+||+|+||.|-
T Consensus 60 ~Wa~~~~~~~~rK~p~ 75 (80)
T PF02939_consen 60 DWANEENEYLNRKNPA 75 (80)
T ss_dssp HHHHHHHHHHTSCCGC
T ss_pred HHHHHHHHHHcCCCHH
Confidence 4578899999999984
No 10
>PF02781 G6PD_C: Glucose-6-phosphate dehydrogenase, C-terminal domain; InterPro: IPR022675 Glucose-6-phosphate dehydrogenase (1.1.1.49 from EC) (G6PDH) is a ubiquitous protein, present in bacteria and all eukaryotic cell types []. The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells []. Deficiency of G6PDH is a common genetic abnormality affecting millions of people worldwide. Many sequence variants, most caused by single point mutations, are known, exhibiting a wide variety of phenotypes []. This entry represents the C-terminal domain of glucose-6-phosphate dehydrogenase.; GO: 0004345 glucose-6-phosphate dehydrogenase activity, 0050661 NADP binding, 0006006 glucose metabolic process, 0055114 oxidation-reduction process; PDB: 1QKI_E 2BH9_A 2BHL_A 4EM5_C 4E9I_A 2DPG_A 1E77_A 1E7M_A 1H9B_A 1E7Y_A ....
Probab=8.74 E-value=1.9e+02 Score=26.11 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=13.8
Q ss_pred ccccccchhhHHHHHHHH
Q 041622 97 SPLFERGRFYEEYAARRN 114 (205)
Q Consensus 97 spLFeRGRfYd~YSARRN 114 (205)
--+-.||.|||.|-|-|.
T Consensus 30 ~Gve~R~~yYD~~GaiRD 47 (293)
T PF02781_consen 30 LGVEGRGGYYDQSGAIRD 47 (293)
T ss_dssp S-STSTHHHHHHHHHHHH
T ss_pred cccccccccccccchHHH
Confidence 345689999999988773
Done!