Query 026981
Match_columns 230
No_of_seqs 98 out of 110
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:18:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026981.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026981hhsearch_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 3.9E-18 8.4E-23 119.8 1.4 45 185-229 6-51 (51)
2 KOG4743 Cyclin-dependent kinas 98.4 4.4E-07 9.4E-12 79.6 5.0 45 185-229 26-72 (195)
3 TIGR01878 cas_Csa5 CRISPR-asso 49.0 22 0.00048 28.8 3.3 22 181-202 61-82 (97)
4 PF09702 Cas_Csa5: CRISPR-asso 38.9 34 0.00074 28.1 3.0 22 180-201 68-89 (105)
5 PF07583 PSCyt2: Protein of un 32.8 30 0.00066 30.6 2.0 25 173-197 28-52 (208)
6 PF04244 DPRP: Deoxyribodipyri 24.5 25 0.00055 31.3 0.1 18 207-224 171-188 (224)
7 PF13169 Poxvirus_B22R_N: Poxv 15.4 1.4E+02 0.003 23.6 2.4 23 191-213 32-54 (92)
8 PF12983 DUF3867: Protein of u 15.2 90 0.0019 28.0 1.4 15 200-214 62-76 (186)
9 cd08002 WGR_PARP3_like WGR dom 13.8 3.1E+02 0.0067 21.5 4.0 15 215-229 85-99 (100)
10 PF05689 DUF823: Salmonella re 13.4 1.2E+02 0.0026 26.1 1.7 24 10-33 1-26 (184)
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=99.69 E-value=3.9e-18 Score=119.82 Aligned_cols=45 Identities=47% Similarity=1.047 Sum_probs=38.8
Q ss_pred CC-hHHHHHHHHHHHHHHHHHHhhhhCCCCCCCCCCCCccceeecC
Q 026981 185 PT-AHEMDKFFADTEEEQQRQFIEKYNYDPVNDKPLPGHFKWQKVD 229 (230)
Q Consensus 185 Pt-~~E~eeFFa~aE~~~~~rF~~KyNfD~~~d~PL~GRyEW~~~~ 229 (230)
|+ .+||+.||++++++++++|++||||||++|+||+|||+|++|+
T Consensus 6 p~d~~e~~~~~~~~l~~~~e~~~~kWNFDF~~~~PL~GryeWe~v~ 51 (51)
T PF02234_consen 6 PVDHEELERFFQEELQEQREEFSEKWNFDFVNDTPLPGRYEWERVD 51 (51)
T ss_dssp ---HHHHHHHHHHHHTTTTHHHHHHHTEETTTTEE-SSSS--EEEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCccCCCCeEeEeCC
Confidence 66 7999999999999999999999999999999999999999984
No 2
>KOG4743 consensus Cyclin-dependent kinase inhibitor [Signal transduction mechanisms]
Probab=98.37 E-value=4.4e-07 Score=79.65 Aligned_cols=45 Identities=22% Similarity=0.483 Sum_probs=36.9
Q ss_pred CChHHHHHHHHHHHHHHHHHHhhhhCCCCCCCCCCCC--ccceeecC
Q 026981 185 PTAHEMDKFFADTEEEQQRQFIEKYNYDPVNDKPLPG--HFKWQKVD 229 (230)
Q Consensus 185 Pt~~E~eeFFa~aE~~~~~rF~~KyNfD~~~d~PL~G--RyEW~~~~ 229 (230)
|..+|+---|.+.=+..++.-++||||||..|+||+| +|+|..|+
T Consensus 26 vd~EElSR~l~s~l~~m~~e~~~KWnFDFq~~~PL~g~g~y~we~V~ 72 (195)
T KOG4743|consen 26 VDHEELSRDLNSRLERMNEEDQQKWNFDFQQGTPLEGSGDYEWEEVS 72 (195)
T ss_pred CCHHHHhHHHHHHHHHHHHHHHhccCcccccCCcccCCCCceeEEcc
Confidence 3556666667777667777788999999999999977 99999885
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=49.00 E-value=22 Score=28.77 Aligned_cols=22 Identities=27% Similarity=0.628 Sum_probs=19.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHH
Q 026981 181 CSLIPTAHEMDKFFADTEEEQQ 202 (230)
Q Consensus 181 ~~~~Pt~~E~eeFFa~aE~~~~ 202 (230)
.+.+|+++|||.||..++++..
T Consensus 61 ~~~lptdeeVe~f~r~~~~di~ 82 (97)
T TIGR01878 61 VGYLPTDKEVEDFLRDVREDIR 82 (97)
T ss_pred cCCCCcHHHHHHHHHHhHHHHH
Confidence 4589999999999999998874
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=38.91 E-value=34 Score=28.08 Aligned_cols=22 Identities=27% Similarity=0.594 Sum_probs=19.8
Q ss_pred cCCCCCChHHHHHHHHHHHHHH
Q 026981 180 ACSLIPTAHEMDKFFADTEEEQ 201 (230)
Q Consensus 180 ~~~~~Pt~~E~eeFFa~aE~~~ 201 (230)
..+.+|+.+|+|.|....|.++
T Consensus 68 ~~g~lPt~~eVe~Fl~~v~~di 89 (105)
T PF09702_consen 68 IVGYLPTDEEVEDFLDDVERDI 89 (105)
T ss_pred ecCCCCChHHHHHHHHHHHHHH
Confidence 3578999999999999999987
No 5
>PF07583 PSCyt2: Protein of unknown function (DUF1549); InterPro: IPR011444 The function is not known. It is found associated with IPR022655 from INTERPRO. It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=32.83 E-value=30 Score=30.62 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=21.2
Q ss_pred hhhhhcccCCCCCChHHHHHHHHHH
Q 026981 173 NREAQISACSLIPTAHEMDKFFADT 197 (230)
Q Consensus 173 ~~r~~~~~~~~~Pt~~E~eeFFa~a 197 (230)
-||+..-..+.+||.+|+++|.+.-
T Consensus 28 lRRv~LDL~G~~PT~eEv~~Fl~d~ 52 (208)
T PF07583_consen 28 LRRVYLDLTGLPPTPEEVRAFLADP 52 (208)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHhCC
Confidence 4667777789999999999999754
No 6
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=24.49 E-value=25 Score=31.28 Aligned_cols=18 Identities=39% Similarity=0.632 Sum_probs=7.2
Q ss_pred hhhCCCCCCCCCCCCccc
Q 026981 207 EKYNYDPVNDKPLPGHFK 224 (230)
Q Consensus 207 ~KyNfD~~~d~PL~GRyE 224 (230)
-|||||..|-.|+|+-..
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 399999999999987653
No 7
>PF13169 Poxvirus_B22R_N: Poxvirus B22R protein N-terminal
Probab=15.41 E-value=1.4e+02 Score=23.64 Aligned_cols=23 Identities=17% Similarity=0.442 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCC
Q 026981 191 DKFFADTEEEQQRQFIEKYNYDP 213 (230)
Q Consensus 191 eeFFa~aE~~~~~rF~~KyNfD~ 213 (230)
=.+|.-|++.++.+|..+.|++.
T Consensus 32 ~kyl~i~~~~E~~~l~~~fnWt~ 54 (92)
T PF13169_consen 32 YKYLDIAEKREKERLESKFNWTS 54 (92)
T ss_pred HHHHHHHHHHHHHHHHhcCChHH
Confidence 46899999999999999999874
No 8
>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=15.21 E-value=90 Score=27.95 Aligned_cols=15 Identities=40% Similarity=1.028 Sum_probs=13.0
Q ss_pred HHHHHHhhhhCCCCC
Q 026981 200 EQQRQFIEKYNYDPV 214 (230)
Q Consensus 200 ~~~~rF~~KyNfD~~ 214 (230)
.+|+.|.++|-||+.
T Consensus 62 niQkk~mERYGfd~~ 76 (186)
T PF12983_consen 62 NIQKKFMERYGFDPS 76 (186)
T ss_pred HHHHHHHHHhCCCHH
Confidence 479999999999964
No 9
>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=13.76 E-value=3.1e+02 Score=21.54 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=12.2
Q ss_pred CCCCCCCccceeecC
Q 026981 215 NDKPLPGHFKWQKVD 229 (230)
Q Consensus 215 ~d~PL~GRyEW~~~~ 229 (230)
+..|.||+|-|+.++
T Consensus 85 ~f~k~~gky~~ie~d 99 (100)
T cd08002 85 NFVPHPGKYTLIEMD 99 (100)
T ss_pred CCCcCCCcceEEEec
Confidence 345889999999876
No 10
>PF05689 DUF823: Salmonella repeat of unknown function (DUF823); InterPro: IPR008541 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with IPR008542 from INTERPRO. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=13.37 E-value=1.2e+02 Score=26.12 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=18.9
Q ss_pred cccCc--eeEeeeccCCCcccchhhh
Q 026981 10 TAAGE--VAVMEVTQSSPLGVRTRAK 33 (230)
Q Consensus 10 ~~~ge--Vavmevsq~~~lGVRTRar 33 (230)
|+||+ .+.+.|+|...+||+|-=.
T Consensus 1 G~T~~~G~~~~~vtq~~~~G~kT~l~ 26 (184)
T PF05689_consen 1 GVTGADGTATFTVTQPNGPGLKTPLT 26 (184)
T ss_pred CccCCCCcEEEEEEcCCCCCEeeeEE
Confidence 45666 7889999977899999654
Done!