Query 026964
Match_columns 230
No_of_seqs 29 out of 31
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 03:05:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026964.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026964hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA03308 transcriptional regul 33.9 29 0.00064 37.4 2.4 40 114-154 1261-1301(1463)
2 PF08671 SinI: Anti-repressor 28.1 41 0.0009 21.9 1.5 14 132-145 15-28 (30)
3 PF15456 Uds1: Up-regulated Du 25.3 2E+02 0.0044 23.6 5.4 52 29-80 58-111 (124)
4 PF09510 Rtt102p: Rtt102p-like 25.0 38 0.00083 28.2 1.2 16 130-156 107-122 (130)
5 PF00072 Response_reg: Respons 24.7 58 0.0013 22.8 1.9 19 20-38 85-103 (112)
6 COG0329 DapA Dihydrodipicolina 23.2 1.3E+02 0.0027 27.5 4.2 43 14-56 85-127 (299)
7 COG3707 AmiR Response regulato 19.6 2.6E+02 0.0056 25.1 5.3 26 17-42 88-113 (194)
8 PF08285 DPM3: Dolichol-phosph 18.9 1.2E+02 0.0025 23.9 2.7 21 10-30 70-90 (91)
9 PF11129 EIAV_Rev: Rev protein 17.5 1.3E+02 0.0029 25.4 2.8 26 50-79 67-94 (134)
10 KOG4368 Predicted RNA binding 16.6 4.8E+02 0.01 27.7 7.0 55 25-86 556-611 (757)
No 1
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=33.88 E-value=29 Score=37.43 Aligned_cols=40 Identities=23% Similarity=0.186 Sum_probs=21.3
Q ss_pred cccCCCcccccC-CCCCCCCCCChHHHHHHHhhhccCCCCCC
Q 026964 114 ATASSSKRECES-NHSSENEGLRDEEVEVFLHSRVKRGRGAV 154 (230)
Q Consensus 114 ~~~sSS~~~~~s-s~~~~~~GL~DdEieeFL~SRvKRGRGAV 154 (230)
+|.|||+.++.+ |-.|+|+--. +|=-+.--+..||||-+.
T Consensus 1261 scsssssss~ssss~ed~d~~~~-~~dr~~~g~~KKRGRK~L 1301 (1463)
T PHA03308 1261 SCSSSSSSSDSSSSEEDGDEKNE-KEDRERAGGGKRRGRQRL 1301 (1463)
T ss_pred cccccCCCCCccccccccccccc-hhhhhcCCCccccCCCCC
Confidence 333333333333 3344444444 444455688999999764
No 2
>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=28.10 E-value=41 Score=21.85 Aligned_cols=14 Identities=43% Similarity=0.679 Sum_probs=10.3
Q ss_pred CCCChHHHHHHHhh
Q 026964 132 EGLRDEEVEVFLHS 145 (230)
Q Consensus 132 ~GL~DdEieeFL~S 145 (230)
-||+-+||.+||.+
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 3
>PF15456 Uds1: Up-regulated During Septation
Probab=25.31 E-value=2e+02 Score=23.65 Aligned_cols=52 Identities=15% Similarity=0.301 Sum_probs=40.5
Q ss_pred ceeeccCCccCCCCCcchhhhhhhhHhhhhhHHHH--HHHHHHHHHHHHHHHHh
Q 026964 29 VHVYLQQPKMRGRPNSRFLTATVLGVQQANRAVEM--NEMWRVRQKELELNEKL 80 (230)
Q Consensus 29 V~AyL~kP~vR~rPN~RFL~aTvrgVqqaNR~VE~--~EMWr~R~kelEl~~r~ 80 (230)
...|+..+..++......+--+--...++||.||. .++|.+-.+-.++..|+
T Consensus 58 l~~l~~~~~~~~~~~~~~~~~~eeel~~~~rk~ee~~~eL~~le~R~~~~~~rL 111 (124)
T PF15456_consen 58 LSRLYSSSSRRARFSRESSLKAEEELAESDRKCEELAQELWKLENRLAEVRQRL 111 (124)
T ss_pred HHHhcCCCccccCCCcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566666777888888888899999999987 99999887777766664
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=24.96 E-value=38 Score=28.23 Aligned_cols=16 Identities=38% Similarity=0.790 Sum_probs=13.8
Q ss_pred CCCCCChHHHHHHHhhhccCCCCCCCC
Q 026964 130 ENEGLRDEEVEVFLHSRVKRGRGAVGS 156 (230)
Q Consensus 130 ~~~GL~DdEieeFL~SRvKRGRGAVGS 156 (230)
.+++|..|+| |||||-
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
>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=24.73 E-value=58 Score=22.82 Aligned_cols=19 Identities=32% Similarity=0.387 Sum_probs=14.9
Q ss_pred HHHHHhhhcceeeccCCcc
Q 026964 20 LRQKAEKEGVHVYLQQPKM 38 (230)
Q Consensus 20 lr~~ae~eGV~AyL~kP~v 38 (230)
...++-+-||..||.||..
T Consensus 85 ~~~~~~~~g~~~~l~kp~~ 103 (112)
T PF00072_consen 85 EVQEALRAGADDYLSKPFS 103 (112)
T ss_dssp HHHHHHHTTESEEEESSSS
T ss_pred HHHHHHHCCCCEEEECCCC
Confidence 3455668999999999963
No 6
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=23.19 E-value=1.3e+02 Score=27.48 Aligned_cols=43 Identities=30% Similarity=0.330 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhhhcceeeccCCccCCCCCcchhhhhhhhHhh
Q 026964 14 LKEAAELRQKAEKEGVHVYLQQPKMRGRPNSRFLTATVLGVQQ 56 (230)
Q Consensus 14 l~EA~~lr~~ae~eGV~AyL~kP~vR~rPN~RFL~aTvrgVqq 56 (230)
++||.+|.+.|++-|+.+.|.=|+.=.+|+...|-.-++.|-+
T Consensus 85 t~eai~lak~a~~~Gad~il~v~PyY~k~~~~gl~~hf~~ia~ 127 (299)
T COG0329 85 TAEAIELAKHAEKLGADGILVVPPYYNKPSQEGLYAHFKAIAE 127 (299)
T ss_pred HHHHHHHHHHHHhcCCCEEEEeCCCCcCCChHHHHHHHHHHHH
Confidence 6899999999999999999999999999999998888888876
No 7
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=19.62 E-value=2.6e+02 Score=25.13 Aligned_cols=26 Identities=27% Similarity=0.372 Sum_probs=20.6
Q ss_pred HHHHHHHHhhhcceeeccCCccCCCC
Q 026964 17 AAELRQKAEKEGVHVYLQQPKMRGRP 42 (230)
Q Consensus 17 A~~lr~~ae~eGV~AyL~kP~vR~rP 42 (230)
...+=++|-.-||+||+.||---+|.
T Consensus 88 ~p~~i~~a~~~Gv~ayivkpi~~~rl 113 (194)
T COG3707 88 DPALIEAAIEAGVMAYIVKPLDESRL 113 (194)
T ss_pred ChHHHHHHHHcCCeEEEecCcchhhh
Confidence 44566788899999999999886554
No 8
>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=18.86 E-value=1.2e+02 Score=23.87 Aligned_cols=21 Identities=38% Similarity=0.425 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHhhhcce
Q 026964 10 AAILLKEAAELRQKAEKEGVH 30 (230)
Q Consensus 10 AalLl~EA~~lr~~ae~eGV~ 30 (230)
|..|++|+.+-+...+++||.
T Consensus 70 ~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 70 AKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred HHHHHHHHHHHHHHHHHcCCC
Confidence 678999999999999999985
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=17.45 E-value=1.3e+02 Score=25.37 Aligned_cols=26 Identities=38% Similarity=0.792 Sum_probs=18.3
Q ss_pred hhhhHhhhhhHHHH--HHHHHHHHHHHHHHHH
Q 026964 50 TVLGVQQANRAVEM--NEMWRVRQKELELNEK 79 (230)
Q Consensus 50 TvrgVqqaNR~VE~--~EMWr~R~kelEl~~r 79 (230)
.+|||||+-+-.|. .++|| ||....+
T Consensus 67 r~rgvqq~akel~~vnk~iwr----el~~~~~ 94 (134)
T PF11129_consen 67 RIRGVQQTAKELEKVNKEIWR----ELQYTRR 94 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHH----HHHhhHh
Confidence 47999998887754 68994 5554433
No 10
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=16.61 E-value=4.8e+02 Score=27.75 Aligned_cols=55 Identities=16% Similarity=0.230 Sum_probs=34.1
Q ss_pred hhhcceeeccCCcc-CCCCCcchhhhhhhhHhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccC
Q 026964 25 EKEGVHVYLQQPKM-RGRPNSRFLTATVLGVQQANRAVEMNEMWRVRQKELELNEKLKRRSKD 86 (230)
Q Consensus 25 e~eGV~AyL~kP~v-R~rPN~RFL~aTvrgVqqaNR~VE~~EMWr~R~kelEl~~r~k~rs~~ 86 (230)
-+..|.||..-|.+ +.++|+.++..-+--. .| ..|.+.|+++.|-.++...+|+-
T Consensus 556 l~~aveAfys~pshdrpr~segwe~~gLye~--~r-----~k~~aRKsk~~e~RdrsrskSRS 611 (757)
T KOG4368|consen 556 LLAAVEAFYSPPSHDRPRNSEGWEQNGLYEF--FR-----AKMRARRRKGQESRSRSRSKSRS 611 (757)
T ss_pred HHHHHHHhhccccccCCCCCchhhhcccHHH--HH-----HHHHHHhhccccccccccccccC
Confidence 34557788888877 8889988876544322 11 34556677777755554444443
Done!