Query 028984
Match_columns 200
No_of_seqs 110 out of 137
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 05:38:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028984.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028984hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02234 CDI: Cyclin-dependent 99.7 3.4E-19 7.3E-24 122.8 2.2 46 151-196 5-51 (51)
2 KOG4743 Cyclin-dependent kinas 98.8 5.5E-09 1.2E-13 89.7 5.4 47 152-198 26-74 (195)
3 TIGR01878 cas_Csa5 CRISPR-asso 55.2 16 0.00035 29.0 3.4 24 147-170 60-83 (97)
4 PF09702 Cas_Csa5: CRISPR-asso 49.2 20 0.00043 28.9 3.1 23 147-169 68-90 (105)
5 PF04244 DPRP: Deoxyribodipyri 38.4 11 0.00024 32.7 0.2 18 174-191 171-188 (224)
6 PF12983 DUF3867: Protein of u 34.1 25 0.00053 30.8 1.6 15 167-181 62-76 (186)
7 cd08002 WGR_PARP3_like WGR dom 22.6 1.4E+02 0.0031 22.9 3.9 14 183-196 86-99 (100)
8 COG3200 AroG 3-deoxy-D-arabino 20.7 93 0.002 30.4 2.9 42 150-191 147-200 (445)
9 cd07997 WGR_PARP WGR domain of 19.3 2E+02 0.0044 21.6 4.1 34 163-196 65-101 (102)
10 PF14420 Clr5: Clr5 domain 18.8 50 0.0011 22.6 0.6 18 161-179 36-53 (54)
No 1
>PF02234 CDI: Cyclin-dependent kinase inhibitor; InterPro: IPR003175 Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.; GO: 0004861 cyclin-dependent protein kinase inhibitor activity, 0007050 cell cycle arrest, 0005634 nucleus; PDB: 1H27_E 1JSU_C.
Probab=99.75 E-value=3.4e-19 Score=122.77 Aligned_cols=46 Identities=43% Similarity=0.928 Sum_probs=39.0
Q ss_pred CCC-hHHHHHHHHHHHHHHHHHHHhhhCCcccCCccCCCccceEEcC
Q 028984 151 IPS-AAEIDEFFTAAEKREQERFAEKYNYDIVNDLPLEGRYQWVRLN 196 (200)
Q Consensus 151 ~Pt-~~E~eeFFa~aEke~q~rF~~KyNFDf~~d~PLeGRYEW~~v~ 196 (200)
.|+ .+||+.||++++++++++|++||||||++|+||+|||+|++|+
T Consensus 5 gp~d~~e~~~~~~~~l~~~~e~~~~kWNFDF~~~~PL~GryeWe~v~ 51 (51)
T PF02234_consen 5 GPVDHEELERFFQEELQEQREEFSEKWNFDFVNDTPLPGRYEWERVD 51 (51)
T ss_dssp ----HHHHHHHHHHHHTTTTHHHHHHHTEETTTTEE-SSSS--EEEE
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCccCCCCeEeEeCC
Confidence 366 8999999999999999999999999999999999999999985
No 2
>KOG4743 consensus Cyclin-dependent kinase inhibitor [Signal transduction mechanisms]
Probab=98.81 E-value=5.5e-09 Score=89.73 Aligned_cols=47 Identities=26% Similarity=0.516 Sum_probs=41.7
Q ss_pred CChHHHHHHHHHHHHHHHHHHHhhhCCcccCCccCCC--ccceEEcCCC
Q 028984 152 PSAAEIDEFFTAAEKREQERFAEKYNYDIVNDLPLEG--RYQWVRLNEA 198 (200)
Q Consensus 152 Pt~~E~eeFFa~aEke~q~rF~~KyNFDf~~d~PLeG--RYEW~~v~~~ 198 (200)
|..+|+---|.+.=+++++..++||||||..++||+| +|+|+.|+-+
T Consensus 26 vd~EElSR~l~s~l~~m~~e~~~KWnFDFq~~~PL~g~g~y~we~V~~~ 74 (195)
T KOG4743|consen 26 VDHEELSRDLNSRLERMNEEDQQKWNFDFQQGTPLEGSGDYEWEEVSSD 74 (195)
T ss_pred CCHHHHhHHHHHHHHHHHHHHHhccCcccccCCcccCCCCceeEEccCC
Confidence 6777787778888789999999999999999999997 9999999754
No 3
>TIGR01878 cas_Csa5 CRISPR-associated protein, Csa5 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents a minor family of Cas protein found in the (all archaeal) APERN subtype of CRISPR/Cas locus, so the family is designated Csa5, for CRISPR/Cas Subtype Protein 5.
Probab=55.20 E-value=16 Score=29.00 Aligned_cols=24 Identities=13% Similarity=0.303 Sum_probs=20.6
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHH
Q 028984 147 EEEKIPSAAEIDEFFTAAEKREQE 170 (200)
Q Consensus 147 ~~~~~Pt~~E~eeFFa~aEke~q~ 170 (200)
..+.+|+++|++.||..+++++..
T Consensus 60 ~~~~lptdeeVe~f~r~~~~di~~ 83 (97)
T TIGR01878 60 LVGYLPTDKEVEDFLRDVREDIRY 83 (97)
T ss_pred ecCCCCcHHHHHHHHHHhHHHHHH
Confidence 355899999999999999988764
No 4
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=49.17 E-value=20 Score=28.91 Aligned_cols=23 Identities=17% Similarity=0.387 Sum_probs=20.4
Q ss_pred ccCCCCChHHHHHHHHHHHHHHH
Q 028984 147 EEEKIPSAAEIDEFFTAAEKREQ 169 (200)
Q Consensus 147 ~~~~~Pt~~E~eeFFa~aEke~q 169 (200)
..+.+|+.+|++.|....|+++.
T Consensus 68 ~~g~lPt~~eVe~Fl~~v~~di~ 90 (105)
T PF09702_consen 68 IVGYLPTDEEVEDFLDDVERDIY 90 (105)
T ss_pred ecCCCCChHHHHHHHHHHHHHHH
Confidence 46789999999999999999864
No 5
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=38.36 E-value=11 Score=32.73 Aligned_cols=18 Identities=28% Similarity=0.348 Sum_probs=7.2
Q ss_pred hhhCCcccCCccCCCccc
Q 028984 174 EKYNYDIVNDLPLEGRYQ 191 (200)
Q Consensus 174 ~KyNFDf~~d~PLeGRYE 191 (200)
-|||||-.|-.|+|+...
T Consensus 171 GkWnfD~eNRk~~p~~~~ 188 (224)
T PF04244_consen 171 GKWNFDAENRKKLPKGIP 188 (224)
T ss_dssp GSS--GGGS-------TT
T ss_pred CcCCCChhhccCCCCCCC
Confidence 399999999999997653
No 6
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=34.06 E-value=25 Score=30.84 Aligned_cols=15 Identities=33% Similarity=0.694 Sum_probs=13.6
Q ss_pred HHHHHHHhhhCCccc
Q 028984 167 REQERFAEKYNYDIV 181 (200)
Q Consensus 167 e~q~rF~~KyNFDf~ 181 (200)
.||+.|.+||.||+.
T Consensus 62 niQkk~mERYGfd~~ 76 (186)
T PF12983_consen 62 NIQKKFMERYGFDPS 76 (186)
T ss_pred HHHHHHHHHhCCCHH
Confidence 799999999999964
No 7
>cd08002 WGR_PARP3_like WGR domain of poly(ADP-ribose) polymerase 3 and similar proteins. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-3 and similar proteins, including Arabidopsis thaliana PARP-
Probab=22.64 E-value=1.4e+02 Score=22.89 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=11.8
Q ss_pred CccCCCccceEEcC
Q 028984 183 DLPLEGRYQWVRLN 196 (200)
Q Consensus 183 d~PLeGRYEW~~v~ 196 (200)
..|.||+|-|..++
T Consensus 86 f~k~~gky~~ie~d 99 (100)
T cd08002 86 FVPHPGKYTLIEMD 99 (100)
T ss_pred CCcCCCcceEEEec
Confidence 45889999999876
No 8
>COG3200 AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=20.71 E-value=93 Score=30.37 Aligned_cols=42 Identities=24% Similarity=0.454 Sum_probs=32.7
Q ss_pred CCCChHHHHHHH--HHHHHHHHHHHH----------hhhCCcccCCccCCCccc
Q 028984 150 KIPSAAEIDEFF--TAAEKREQERFA----------EKYNYDIVNDLPLEGRYQ 191 (200)
Q Consensus 150 ~~Pt~~E~eeFF--a~aEke~q~rF~----------~KyNFDf~~d~PLeGRYE 191 (200)
.+|.++-|..=| ++|-..+-+.|. .+||-+|+++-|+--||+
T Consensus 147 R~pdP~R~l~aY~qsaAtlNLlRafa~gG~A~L~~vh~W~l~Fv~~sp~~~rY~ 200 (445)
T COG3200 147 REPDPERLLKAYAQSAATLNLLRAFASGGLADLENVHRWNLGFVKNSPQGARYE 200 (445)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHhhhcCCchHHHHH
Confidence 467777666666 445557778887 589999999999999996
No 9
>cd07997 WGR_PARP WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins and histones. Higher eukaryotes contain several PARPs and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. Poly-ADP-ribosylation was thought to be a reversible post-translational covalent modification that serves as a regulator
Probab=19.33 E-value=2e+02 Score=21.64 Aligned_cols=34 Identities=24% Similarity=0.277 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHhhhCCc---ccCCccCCCccceEEcC
Q 028984 163 AAEKREQERFAEKYNYD---IVNDLPLEGRYQWVRLN 196 (200)
Q Consensus 163 ~aEke~q~rF~~KyNFD---f~~d~PLeGRYEW~~v~ 196 (200)
.|.++-++.|.+|=.-+ -.+..+.+|.|.|+.++
T Consensus 65 ~A~~~F~k~f~~Kt~~~w~~r~~f~k~~~ky~~i~~d 101 (102)
T cd07997 65 SAIKEFEKKFKDKTGNEWENRPLFKKQPGKYALVELD 101 (102)
T ss_pred HHHHHHHHHHHHHHCCccccccccccCCCceeEEeec
Confidence 34444445555554333 35677888999999876
No 10
>PF14420 Clr5: Clr5 domain
Probab=18.81 E-value=50 Score=22.61 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHhhhCCc
Q 028984 161 FTAAEKREQERFAEKYNYD 179 (200)
Q Consensus 161 Fa~aEke~q~rF~~KyNFD 179 (200)
|.+.+++...+|. +|+|.
T Consensus 36 F~at~rqy~~r~~-~Wg~~ 53 (54)
T PF14420_consen 36 FKATKRQYKRRFK-KWGFR 53 (54)
T ss_pred CCcCHHHHHHHHH-HcCCC
Confidence 4445777777776 77774
Done!