Query 025986
Match_columns 245
No_of_seqs 32 out of 34
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 11:51:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025986.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025986hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12100 DUF3576: Domain of un 36.9 38 0.00081 28.0 3.0 32 7-38 66-103 (103)
2 PHA03308 transcriptional regul 33.0 32 0.0007 37.4 2.5 20 19-38 1128-1147(1463)
3 PF08671 SinI: Anti-repressor 26.1 47 0.001 21.8 1.5 14 147-160 15-28 (30)
4 PF09510 Rtt102p: Rtt102p-like 24.7 39 0.00084 28.4 1.2 16 145-171 107-122 (130)
5 PF08285 DPM3: Dolichol-phosph 17.8 1.2E+02 0.0027 23.9 2.6 22 24-45 69-90 (91)
6 COG3707 AmiR Response regulato 17.5 4.1E+02 0.0089 24.1 6.1 25 32-56 88-112 (194)
7 PF00072 Response_reg: Respons 17.2 1.1E+02 0.0023 21.6 2.0 19 35-53 85-103 (112)
8 PF15456 Uds1: Up-regulated Du 17.1 3.6E+02 0.0078 22.4 5.3 50 46-95 60-111 (124)
9 PF11129 EIAV_Rev: Rev protein 16.3 1.4E+02 0.0031 25.4 2.8 19 65-83 67-87 (134)
10 PF08672 APC2: Anaphase promot 15.6 1.1E+02 0.0023 22.5 1.7 22 145-166 29-50 (60)
No 1
>PF12100 DUF3576: Domain of unknown function (DUF3576); InterPro: IPR021959 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Probab=36.86 E-value=38 Score=27.96 Aligned_cols=32 Identities=28% Similarity=0.365 Sum_probs=26.4
Q ss_pred cccccccC------cCChHHHHHHHHHHHHHHHHHHHH
Q 025986 7 YLEPSLQG------QMDLETENRIAAILLKEAAELRQK 38 (245)
Q Consensus 7 ~~~~s~~~------~mD~etE~rlAaLLlkEA~~lr~~ 38 (245)
.|+|...+ .++.+|-+-|...||.-|+|||.+
T Consensus 66 vf~q~~~~~~W~d~~v~~~t~~~ie~~ILtRARqLr~~ 103 (103)
T PF12100_consen 66 VFRQVRQGGQWVDAPVSPETARDIEDAILTRARQLRIQ 103 (103)
T ss_pred EEEeeccCCcceeccCCHHHHHHHHHHHHHHHHHHhcC
Confidence 35555555 789999999999999999999853
No 2
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=33.04 E-value=32 Score=37.44 Aligned_cols=20 Identities=15% Similarity=0.203 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 025986 19 ETENRIAAILLKEAAELRQK 38 (245)
Q Consensus 19 etE~rlAaLLlkEA~~lr~~ 38 (245)
-.+++||.|+.--|++.-++
T Consensus 1128 ps~a~~~~lftgpaaerler 1147 (1463)
T PHA03308 1128 PSHAYLVKLFTGPAAERLER 1147 (1463)
T ss_pred chHHHHHHhccchHHHHHhc
Confidence 36899999999888765544
No 3
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=26.14 E-value=47 Score=21.80 Aligned_cols=14 Identities=43% Similarity=0.679 Sum_probs=10.3
Q ss_pred CCCChHHHHHHHhh
Q 025986 147 EGLRDEEVEVFLHS 160 (245)
Q Consensus 147 ~GL~DdEieeFL~S 160 (245)
-||+-+||.+||.+
T Consensus 15 ~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 15 SGLSKEEIREFLEF 28 (30)
T ss_dssp TT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHHh
Confidence 58999999999975
No 4
>PF09510 Rtt102p: Rtt102p-like transcription regulator protein; InterPro: IPR018304 Rtt102p (Regulator of Ty1 Transposition Protein 102) is a transcription regulator protein found in fungi that appears to be integrally associated with both the Swi-Snf and the RSC chromatin remodelling complexes, []. RSC is involved in transcription regulation and nucleosome positioning, and is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodelling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signalling pathway, for organisation of the cellular cytoskeleton. It is a probable component of the SWI/SNF complex, an ATP-dependent chromatin-remodelling complex, is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors.
Probab=24.65 E-value=39 Score=28.44 Aligned_cols=16 Identities=38% Similarity=0.790 Sum_probs=13.8
Q ss_pred CCCCCChHHHHHHHhhhccCCCCCCCC
Q 025986 145 ENEGLRDEEVEVFLHSRVKRGRGAVGS 171 (245)
Q Consensus 145 ~~~GL~DdEieeFL~SRvKRGRGAVGS 171 (245)
.+++|..|+| |||||-
T Consensus 107 ~~~~LT~dDI-----------RGAVGg 122 (130)
T PF09510_consen 107 NGDSLTVDDI-----------RGAVGG 122 (130)
T ss_pred CCCCCCHHHh-----------hhcccC
Confidence 5689999999 899984
No 5
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=17.81 E-value=1.2e+02 Score=23.93 Aligned_cols=22 Identities=36% Similarity=0.394 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHhhccee
Q 025986 24 IAAILLKEAAELRQKAEKEGVH 45 (245)
Q Consensus 24 lAaLLlkEA~~lr~~ae~~GV~ 45 (245)
=|..|++|+.+-+....++||.
T Consensus 69 A~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 69 AAKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred HHHHHHHHHHHHHHHHHHcCCC
Confidence 4788999999999999999985
No 6
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=17.53 E-value=4.1e+02 Score=24.10 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=19.6
Q ss_pred HHHHHHHHhhcceeeeccCCccCCC
Q 025986 32 AAELRQKAEKEGVHVYLQQPKMRGR 56 (245)
Q Consensus 32 A~~lr~~ae~~GV~AyL~kP~~r~r 56 (245)
....-+++-..||+||+.||---++
T Consensus 88 ~p~~i~~a~~~Gv~ayivkpi~~~r 112 (194)
T COG3707 88 DPALIEAAIEAGVMAYIVKPLDESR 112 (194)
T ss_pred ChHHHHHHHHcCCeEEEecCcchhh
Confidence 3456678889999999999987543
No 7
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=17.23 E-value=1.1e+02 Score=21.65 Aligned_cols=19 Identities=32% Similarity=0.387 Sum_probs=14.5
Q ss_pred HHHHHhhcceeeeccCCcc
Q 025986 35 LRQKAEKEGVHVYLQQPKM 53 (245)
Q Consensus 35 lr~~ae~~GV~AyL~kP~~ 53 (245)
...++-+-|+.+||.||..
T Consensus 85 ~~~~~~~~g~~~~l~kp~~ 103 (112)
T PF00072_consen 85 EVQEALRAGADDYLSKPFS 103 (112)
T ss_dssp HHHHHHHTTESEEEESSSS
T ss_pred HHHHHHHCCCCEEEECCCC
Confidence 3345558999999999964
No 8
>PF15456 Uds1: Up-regulated During Septation
Probab=17.13 E-value=3.6e+02 Score=22.39 Aligned_cols=50 Identities=16% Similarity=0.302 Sum_probs=38.0
Q ss_pred eeccCCccCCCCCccchhhhhhhhhhhhhHHHH--HHHHHHHHHHHHHHHHh
Q 025986 46 VYLQQPKMRGRPNSRFLTATVLGVQQANRAVEM--NEMWRVRQKELELNEKL 95 (245)
Q Consensus 46 AyL~kP~~r~rpN~RFL~atvRGVq~aNR~VE~--~EmWr~R~kelEl~~r~ 95 (245)
.|+..+..++......+--+--...++|+.||. +++|.+-.+-.+...|+
T Consensus 60 ~l~~~~~~~~~~~~~~~~~~eeel~~~~rk~ee~~~eL~~le~R~~~~~~rL 111 (124)
T PF15456_consen 60 RLYSSSSRRARFSRESSLKAEEELAESDRKCEELAQELWKLENRLAEVRQRL 111 (124)
T ss_pred HhcCCCccccCCCcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555677777788888888899999987 99999887777766664
No 9
>PF11129 EIAV_Rev: Rev protein of equine infectious anaemia virus; InterPro: IPR021311 The sequence of this family is highly conserved and carries a nuclear export signal from residues 31-55, and RNA binding/nuclear localisation signals of RRDR at residue 76 and KRRRK at residue 159. Rev is an essential regulatory protein required for nucleocytoplasmic transport of incompletely spliced viral mRNAs that encode structural proteins. Rev has been shown to down-regulate the expression of viral late genes and alter sensitivity to Gag-specific cytotoxic-T-lymphocytes (CTL). Equine infectious anaemia virus (EIAV) exhibits a high rate of genetic variation in vivo, and results in a clinically variable disease in infected horses.
Probab=16.32 E-value=1.4e+02 Score=25.39 Aligned_cols=19 Identities=42% Similarity=0.858 Sum_probs=15.5
Q ss_pred hhhhhhhhhhHHHH--HHHHH
Q 025986 65 TVLGVQQANRAVEM--NEMWR 83 (245)
Q Consensus 65 tvRGVq~aNR~VE~--~EmWr 83 (245)
-||||||+-+-+|. .++||
T Consensus 67 r~rgvqq~akel~~vnk~iwr 87 (134)
T PF11129_consen 67 RIRGVQQTAKELEKVNKEIWR 87 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 48999999888865 68994
No 10
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=15.61 E-value=1.1e+02 Score=22.47 Aligned_cols=22 Identities=27% Similarity=0.421 Sum_probs=15.7
Q ss_pred CCCCCChHHHHHHHhhhccCCC
Q 025986 145 ENEGLRDEEVEVFLHSRVKRGR 166 (245)
Q Consensus 145 ~~~GL~DdEieeFL~SRvKRGR 166 (245)
+.-..+.+|++.||...|+-|+
T Consensus 29 ~~~~~s~~eL~~fL~~lv~e~~ 50 (60)
T PF08672_consen 29 GGYDISLEELQEFLDRLVEEGK 50 (60)
T ss_dssp --TT--HHHHHHHHHHHHHTTS
T ss_pred CCCCCCHHHHHHHHHHHHHCCc
Confidence 3445789999999999998875
Done!