Query 046218
Match_columns 437
No_of_seqs 180 out of 960
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:51:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046218.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046218hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 6.6E-43 1.4E-47 303.4 5.5 124 19-142 1-129 (129)
2 PHA00692 hypothetical protein 24.1 29 0.00063 28.3 0.3 12 15-26 33-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 20.4 1E+02 0.0022 21.3 2.3 20 28-47 4-23 (27)
4 COG4598 HisP ABC-type histidin 13.0 2.2E+02 0.0047 28.6 3.4 42 2-43 153-200 (256)
5 COG1126 GlnQ ABC-type polar am 12.5 2.4E+02 0.0053 28.5 3.7 44 2-45 137-186 (240)
6 PF12672 DUF3793: Protein of u 11.6 1.3E+02 0.0029 28.4 1.5 60 22-103 83-143 (176)
7 PF02180 BH4: Bcl-2 homology r 11.1 2.1E+02 0.0045 20.0 1.9 19 29-47 5-23 (27)
8 PF07960 CBP4: CBP4; InterPro 10.0 1.5E+02 0.0032 27.4 1.2 14 23-36 26-40 (128)
9 PHA03357 Alkaline exonuclease; 10.0 1.2E+02 0.0026 25.8 0.6 37 391-435 29-65 (81)
10 PF08338 DUF1731: Domain of un 9.6 2E+02 0.0044 21.8 1.6 16 21-36 31-47 (48)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=6.6e-43 Score=303.37 Aligned_cols=124 Identities=46% Similarity=0.998 Sum_probs=96.2
Q ss_pred CCCCceeCCCHHHHHHHHHHhhhcCCCCCC-CceeecCCCCCCCCCcccc---cCceEEeecCccccCCCCCCCcccccc
Q 046218 19 FPPGYRFCPTDKELVLDYLKNKAMNKPLPP-NKIMDINLYNHGPQDLSEQ---EEKTLYFFTPRDRKYPKGTRPNRAAGR 94 (437)
Q Consensus 19 LPPGFRF~PTDEELV~~YLrrKi~G~Plp~-~iI~EvDVY~~dPWELp~~---ge~EWYFFSpR~rKy~nG~R~nRatGg 94 (437)
|||||||+|||||||.+||++|+.|.+++. .+|+++|||++|||+|+.. ++++||||+++++++.+|.|.+|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 899999999999999999999999999888 7999999999999999943 677999999999999999999999999
Q ss_pred ceeEecCCCeeecC-CCCceeEEEEEEEeeCCCCCCCCcCeEEEEEEeC
Q 046218 95 GYWKATGVDNIIGR-KENPIGYRKSLVYYQGYPKKSKKTNWIMHEYRID 142 (437)
Q Consensus 95 GyWKatG~dK~I~s-~g~vVG~KKtLvFY~GkaprG~KTgWVMhEYrL~ 142 (437)
|+||.+|++++|.+ .+++||+||+|+||.++.+++.||+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999998 6899999999999999888999999999999984
No 2
>PHA00692 hypothetical protein
Probab=24.13 E-value=29 Score=28.28 Aligned_cols=12 Identities=50% Similarity=1.373 Sum_probs=9.9
Q ss_pred hcccCCCCceeC
Q 046218 15 YLNSFPPGYRFC 26 (437)
Q Consensus 15 ~~~~LPPGFRF~ 26 (437)
++-..||||||-
T Consensus 33 yfveyppgfrfg 44 (74)
T PHA00692 33 YFVEYPPGFRFG 44 (74)
T ss_pred EeEecCCCcccc
Confidence 456899999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=20.37 E-value=1e+02 Score=21.34 Aligned_cols=20 Identities=30% Similarity=0.512 Sum_probs=15.8
Q ss_pred CHHHHHHHHHHhhhcCCCCC
Q 046218 28 TDKELVLDYLKNKAMNKPLP 47 (437)
Q Consensus 28 TDEELV~~YLrrKi~G~Plp 47 (437)
+-.|||.+|+.-|+.....+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999765443
No 4
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=13.04 E-value=2.2e+02 Score=28.61 Aligned_cols=42 Identities=43% Similarity=0.427 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHHhhcccCCCCceeC-CC---HHHHHHHHHH--hhhcC
Q 046218 2 VSVEQQQRVAMLKYLNSFPPGYRFC-PT---DKELVLDYLK--NKAMN 43 (437)
Q Consensus 2 ~~~~~~q~~am~~~~~~LPPGFRF~-PT---DEELV~~YLr--rKi~G 43 (437)
.|+-|||+.+++--+.--|-=.=|+ || |-|||..-|+ ++++.
T Consensus 153 LSGGQQQR~aIARaLameP~vmLFDEPTSALDPElVgEVLkv~~~LAe 200 (256)
T COG4598 153 LSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVMQDLAE 200 (256)
T ss_pred cCchHHHHHHHHHHHhcCCceEeecCCcccCCHHHHHHHHHHHHHHHH
Confidence 4788999999986666666667787 77 7899998887 44543
No 5
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=12.48 E-value=2.4e+02 Score=28.53 Aligned_cols=44 Identities=39% Similarity=0.380 Sum_probs=32.7
Q ss_pred ccHHHHHHHHHHhhcccCCCCceeC-CC---HHHHHHHHHH--hhhcCCC
Q 046218 2 VSVEQQQRVAMLKYLNSFPPGYRFC-PT---DKELVLDYLK--NKAMNKP 45 (437)
Q Consensus 2 ~~~~~~q~~am~~~~~~LPPGFRF~-PT---DEELV~~YLr--rKi~G~P 45 (437)
.|+-||||+|++--+.==|.=.=|+ || |=|||...|. +.++.+.
T Consensus 137 LSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eG 186 (240)
T COG1126 137 LSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEG 186 (240)
T ss_pred cCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcC
Confidence 5889999999996665556666788 87 7899988877 4444443
No 6
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=11.61 E-value=1.3e+02 Score=28.41 Aligned_cols=60 Identities=25% Similarity=0.469 Sum_probs=34.2
Q ss_pred CceeCCCHHHHHHHHHHhhhcCCCCCCCceeecCCC-CCCCCCcccccCceEEeecCccccCCCCCCCccccccceeEec
Q 046218 22 GYRFCPTDKELVLDYLKNKAMNKPLPPNKIMDINLY-NHGPQDLSEQEEKTLYFFTPRDRKYPKGTRPNRAAGRGYWKAT 100 (437)
Q Consensus 22 GFRF~PTDEELV~~YLrrKi~G~Plp~~iI~EvDVY-~~dPWELp~~ge~EWYFFSpR~rKy~nG~R~nRatGgGyWKat 100 (437)
|| .+.+-|-+...|+.|+.+..+| ||+-|+ ++...|.-+ |.... .......||||..
T Consensus 83 GY--~~~~~~~~L~~L~~R~~~~~FP----HEIGiFLGYPleDV~G-------FI~~~---------g~~~~~~GyWKVY 140 (176)
T PF12672_consen 83 GY--PDSSLEDCLEHLKKRFESGEFP----HEIGIFLGYPLEDVKG-------FIENK---------GKNCKCCGYWKVY 140 (176)
T ss_pred Cc--CCCCHHHHHHHHHHHhcCCCCC----chhHhccCCCHHHHHH-------HHhCC---------CCCeeEeccCccC
Confidence 77 5555554556788888666565 555555 444444332 33211 1223457999987
Q ss_pred CCC
Q 046218 101 GVD 103 (437)
Q Consensus 101 G~d 103 (437)
|-.
T Consensus 141 ~n~ 143 (176)
T PF12672_consen 141 GNP 143 (176)
T ss_pred CCH
Confidence 654
No 7
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=11.15 E-value=2.1e+02 Score=19.95 Aligned_cols=19 Identities=32% Similarity=0.487 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhhhcCCCCC
Q 046218 29 DKELVLDYLKNKAMNKPLP 47 (437)
Q Consensus 29 DEELV~~YLrrKi~G~Plp 47 (437)
-.|||.+|+.-|+.....+
T Consensus 5 nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHTTST
T ss_pred HHHHHHHHHHHHhhhcCCC
Confidence 4799999999998655443
No 8
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=9.97 E-value=1.5e+02 Score=27.37 Aligned_cols=14 Identities=36% Similarity=0.793 Sum_probs=10.6
Q ss_pred cee-CCCHHHHHHHH
Q 046218 23 YRF-CPTDKELVLDY 36 (437)
Q Consensus 23 FRF-~PTDEELV~~Y 36 (437)
|++ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 444 49999999865
No 9
>PHA03357 Alkaline exonuclease; Provisional
Probab=9.97 E-value=1.2e+02 Score=25.79 Aligned_cols=37 Identities=41% Similarity=0.751 Sum_probs=27.8
Q ss_pred ccccccccccccccchhHHHHHHhhhccccceeecCCCCCCCCCC
Q 046218 391 NVMLDQQFFHDYDYTSSLFEEVWNNCLVDLPVIEFPPSNFDDVKD 435 (437)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (437)
=|-||..+|.||+ |+|-|+. +-|.| .||.-||-|+|.
T Consensus 29 tvaLdad~FEdF~-----lDE~~~e-~~~~~--~~~~~~~~~~~~ 65 (81)
T PHA03357 29 TLALNADCFEDFD-----FDENTNE-AADKP--DFPKPNFIDPKN 65 (81)
T ss_pred EEEeChhhhhccc-----cccccCc-cccCc--CCCCCcccCCCc
Confidence 3668999999998 4677865 34544 688889999875
No 10
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=9.57 E-value=2e+02 Score=21.75 Aligned_cols=16 Identities=38% Similarity=0.673 Sum_probs=9.2
Q ss_pred CCceeC-CCHHHHHHHH
Q 046218 21 PGYRFC-PTDKELVLDY 36 (437)
Q Consensus 21 PGFRF~-PTDEELV~~Y 36 (437)
-||+|+ |+=++-+.+-
T Consensus 31 ~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDL 47 (48)
T ss_dssp TT---S-SSHHHHHHH-
T ss_pred CCCcccCCCHHHHHhcc
Confidence 599998 8888876653
Done!