Query 040245
Match_columns 271
No_of_seqs 170 out of 304
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:31:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03479 DUF296: Domain of unk 99.8 1.6E-18 3.5E-23 140.2 8.4 99 93-191 1-120 (120)
2 COG1661 Predicted DNA-binding 99.3 1.2E-11 2.6E-16 105.4 11.0 104 93-197 9-131 (141)
3 PF02178 AT_hook: AT hook moti 88.7 0.18 4E-06 27.8 0.6 13 66-78 1-13 (13)
4 COG4136 ABC-type uncharacteriz 76.4 0.93 2E-05 41.2 0.3 45 129-178 4-61 (213)
5 smart00384 AT_hook DNA binding 75.3 1.9 4.2E-05 28.0 1.5 15 66-80 1-15 (26)
6 PRK08179 prfH peptide chain re 32.1 96 0.0021 28.3 5.1 42 96-137 2-58 (200)
7 PF01582 TIR: TIR domain; Int 30.5 39 0.00085 27.3 2.1 36 92-127 28-65 (141)
8 cd04618 CBS_pair_5 The CBS dom 28.7 1.4E+02 0.003 22.3 4.7 36 97-132 52-88 (98)
9 TIGR03072 release_prfH putativ 27.4 1.3E+02 0.0027 27.6 5.0 41 97-137 2-57 (200)
10 PF00571 CBS: CBS domain CBS d 23.3 1.4E+02 0.003 19.8 3.5 39 93-131 5-43 (57)
No 1
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=99.76 E-value=1.6e-18 Score=140.20 Aligned_cols=99 Identities=34% Similarity=0.461 Sum_probs=85.9
Q ss_pred ceEEEEEecCCccHHHHHHHHHHhcCcccEEecccceeeeEEeeCCC--C---------CCcEEEEcC---------CCC
Q 040245 93 LRSHVMEVAGGADVAESVALFARRRQRGVCVLSGSGSVANVTLRQPA--A---------PGAVVALHG---------STG 152 (271)
Q Consensus 93 l~pHVIeV~~GeDV~e~I~~Farrr~raiCVLSasGtVsnVTLRqp~--s---------~g~ivTL~G---------~tg 152 (271)
||+|++++.+||||.++|.+||++.++..|++|+.|++++|+|+++. . +.+|++|.| ..|
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~~~g~~~~H 80 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISPEDGKPFVH 80 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEEETTEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEECCCCCCcce
Confidence 69999999999999999999999999988999999999999999962 1 346888888 349
Q ss_pred eEEEEeCCCCceeceeec-cceEecccEEEEEEecccccc
Q 040245 153 LTVYLAGGQGQVVGGSVV-GQLVAAGPVMVIAATFANATY 191 (271)
Q Consensus 153 LsVSLAg~qGQVvGG~V~-G~LiAAgpV~VIaaSF~n~~y 191 (271)
|||+|++.+|+|+||++. |.+.++..|.|+..++.+.+|
T Consensus 81 lHisl~~~~g~v~gGHl~~g~v~~t~Ev~i~~~~~~~~~~ 120 (120)
T PF03479_consen 81 LHISLADPDGQVFGGHLLEGTVFATAEVVITELSGINFTR 120 (120)
T ss_dssp EEEEEE-TTSEEEEEEEEEEEEEEEEEEEEEEETTEEEEE
T ss_pred EEEEEECCCCeEEeeEeCCCEEeEEEEEEEEEecCccccC
Confidence 999999999999999999 888888888888888877654
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.33 E-value=1.2e-11 Score=105.41 Aligned_cols=104 Identities=20% Similarity=0.268 Sum_probs=93.8
Q ss_pred ceEEEEEecCCccHHHHHHHHHHhcCcccEEecccceeeeEEeeCCCC------------CCcEEEEcC-------CCCe
Q 040245 93 LRSHVMEVAGGADVAESVALFARRRQRGVCVLSGSGSVANVTLRQPAA------------PGAVVALHG-------STGL 153 (271)
Q Consensus 93 l~pHVIeV~~GeDV~e~I~~Farrr~raiCVLSasGtVsnVTLRqp~s------------~g~ivTL~G-------~tgL 153 (271)
=|-+++++.+|+|+++.|.+||++......|.+|.|++++++||.-.. +.+|++|.| ..||
T Consensus 9 gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~p~~Hl 88 (141)
T COG1661 9 GRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDDPFVHL 88 (141)
T ss_pred ceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCCCcEEE
Confidence 467899999999999999999999999779999999999999998872 458999999 3799
Q ss_pred EEEEeCCCCceeceeeccceEecccEEEEEEeccccccccccCC
Q 040245 154 TVYLAGGQGQVVGGSVVGQLVAAGPVMVIAATFANATYERLPLE 197 (271)
Q Consensus 154 sVSLAg~qGQVvGG~V~G~LiAAgpV~VIaaSF~n~~yeRlpl~ 197 (271)
|++|++.+|+++|||+....+-. +++|+|-......+.|.+-+
T Consensus 89 Ha~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~el~~~~~~R~~d~ 131 (141)
T COG1661 89 HAALGDENGITLGGHLLEGEVFP-TAEVFIRELPGELFRREFDP 131 (141)
T ss_pred EEEEecCCCcEEeeeecccEEeE-EEEEEEEEccccceeEecCC
Confidence 99999999999999999988888 99999999888888887644
No 3
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=88.66 E-value=0.18 Score=27.80 Aligned_cols=13 Identities=46% Similarity=0.843 Sum_probs=4.2
Q ss_pred CCCCCCCCCCCCC
Q 040245 66 RRPRGRPPGSKNK 78 (271)
Q Consensus 66 rRpRGRPpGSknK 78 (271)
+|+||||+.+..|
T Consensus 1 ~r~RGRP~k~~~~ 13 (13)
T PF02178_consen 1 KRKRGRPRKNAKK 13 (13)
T ss_dssp S--SS--TT----
T ss_pred CCcCCCCccccCC
Confidence 5899999987654
No 4
>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=76.39 E-value=0.93 Score=41.23 Aligned_cols=45 Identities=33% Similarity=0.619 Sum_probs=29.5
Q ss_pred eeeeEEeeCCCC-----------CCcEEEEcCCC--CeEEEEeCCCCceeceeeccceEeccc
Q 040245 129 SVANVTLRQPAA-----------PGAVVALHGST--GLTVYLAGGQGQVVGGSVVGQLVAAGP 178 (271)
Q Consensus 129 tVsnVTLRqp~s-----------~g~ivTL~G~t--gLsVSLAg~qGQVvGG~V~G~LiAAgp 178 (271)
+++||+||+|.+ +|+||||.|.+ +=+-.|+ +++|++++.....+.
T Consensus 4 ~l~nvsl~l~g~cLLa~~n~Tia~GeivtlMGPSGcGKSTLls-----~~~G~La~~F~~~G~ 61 (213)
T COG4136 4 CLKNVSLRLPGSCLLANVNFTIAKGEIVTLMGPSGCGKSTLLS-----WMIGALAGQFSCTGE 61 (213)
T ss_pred eeeeeeecCCCceEEEeeeEEecCCcEEEEECCCCccHHHHHH-----HHHhhcccCcceeeE
Confidence 678999999974 68999999922 2222222 567777766554443
No 5
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=75.30 E-value=1.9 Score=27.99 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCCCCC
Q 040245 66 RRPRGRPPGSKNKPK 80 (271)
Q Consensus 66 rRpRGRPpGSknKpK 80 (271)
+|+||||+..++...
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 589999998777643
No 6
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=32.14 E-value=96 Score=28.30 Aligned_cols=42 Identities=14% Similarity=0.170 Sum_probs=34.7
Q ss_pred EEEEecCCc----------cHHHHHHHHHHhcCcccEEeccc-----ceeeeEEeeC
Q 040245 96 HVMEVAGGA----------DVAESVALFARRRQRGVCVLSGS-----GSVANVTLRQ 137 (271)
Q Consensus 96 HVIeV~~Ge----------DV~e~I~~Farrr~raiCVLSas-----GtVsnVTLRq 137 (271)
.+|+|.+|. |++.....||+++...+.|++.+ |.+.+|+|.-
T Consensus 2 ~~leI~aG~Gg~Ea~~fa~~L~~my~~~a~~~g~~~~ii~~~~~~~~gg~ksa~~~i 58 (200)
T PRK08179 2 ILLQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSL 58 (200)
T ss_pred EEEEEeCCCChHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEE
Confidence 378999986 88888999999999999998874 6688887754
No 7
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=30.46 E-value=39 Score=27.27 Aligned_cols=36 Identities=19% Similarity=0.294 Sum_probs=28.3
Q ss_pred CceEEEEE--ecCCccHHHHHHHHHHhcCcccEEeccc
Q 040245 92 SLRSHVME--VAGGADVAESVALFARRRQRGVCVLSGS 127 (271)
Q Consensus 92 al~pHVIe--V~~GeDV~e~I~~Farrr~raiCVLSas 127 (271)
.++..+-+ +.+|..+.+.|....++..+.|+|||..
T Consensus 28 g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~ 65 (141)
T PF01582_consen 28 GYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRN 65 (141)
T ss_dssp TS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHH
T ss_pred CeEEEEechhhcccccccchhhHhhhhceeeEEEeecc
Confidence 44444443 6789999999999999999999999953
No 8
>cd04618 CBS_pair_5 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=28.68 E-value=1.4e+02 Score=22.32 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=31.4
Q ss_pred EEEecCCccHHHHHHHHHHhcCcccEEeccc-ceeee
Q 040245 97 VMEVAGGADVAESVALFARRRQRGVCVLSGS-GSVAN 132 (271)
Q Consensus 97 VIeV~~GeDV~e~I~~Farrr~raiCVLSas-GtVsn 132 (271)
++.+.+.+++.+.+..|.+.+.+.++|+... |.+..
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~g 88 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGLY 88 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCceE
Confidence 7889999999999999999999999999876 65443
No 9
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=27.37 E-value=1.3e+02 Score=27.55 Aligned_cols=41 Identities=17% Similarity=0.222 Sum_probs=33.9
Q ss_pred EEEecCCc----------cHHHHHHHHHHhcCcccEEeccc-----ceeeeEEeeC
Q 040245 97 VMEVAGGA----------DVAESVALFARRRQRGVCVLSGS-----GSVANVTLRQ 137 (271)
Q Consensus 97 VIeV~~Ge----------DV~e~I~~Farrr~raiCVLSas-----GtVsnVTLRq 137 (271)
+|+|.+|. |++.....||++....+.|++.+ |.+.+|+|.-
T Consensus 2 ~leI~aG~GG~Ea~lfa~~L~~my~~~a~~~g~~~eii~~~~~~~~gg~ksa~~~i 57 (200)
T TIGR03072 2 LLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSL 57 (200)
T ss_pred EEEEECCCCcHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEE
Confidence 68888885 79999999999999999998874 5678877754
No 10
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=23.33 E-value=1.4e+02 Score=19.76 Aligned_cols=39 Identities=10% Similarity=0.253 Sum_probs=31.2
Q ss_pred ceEEEEEecCCccHHHHHHHHHHhcCcccEEecccceee
Q 040245 93 LRSHVMEVAGGADVAESVALFARRRQRGVCVLSGSGSVA 131 (271)
Q Consensus 93 l~pHVIeV~~GeDV~e~I~~Farrr~raiCVLSasGtVs 131 (271)
|++-++.|.+...+.+.+..|.+.+-..+.|+...|.+.
T Consensus 5 m~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~~~~~ 43 (57)
T PF00571_consen 5 MTPPPITVSPDDSLEEALEIMRKNGISRLPVVDEDGKLV 43 (57)
T ss_dssp SBSSSEEEETTSBHHHHHHHHHHHTSSEEEEESTTSBEE
T ss_pred CcCCCEEEcCcCcHHHHHHHHHHcCCcEEEEEecCCEEE
Confidence 444567888999999999999999888899986666554
Done!