Query 046940
Match_columns 222
No_of_seqs 129 out of 923
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 06:04:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046940hhsearch_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 5E-42 1.1E-46 271.8 5.0 119 41-161 1-129 (129)
2 KOG3238 Chloride ion current i 44.9 36 0.00077 29.4 4.1 82 19-100 86-168 (216)
3 smart00265 BH4 BH4 Bcl-2 homol 41.2 32 0.0007 20.1 2.3 21 50-70 4-24 (27)
4 PHA00692 hypothetical protein 40.6 10 0.00023 26.4 0.3 11 38-48 34-44 (74)
5 PF02180 BH4: Bcl-2 homology r 25.3 69 0.0015 18.8 2.0 20 51-70 5-24 (27)
6 smart00707 RPEL Repeat in Dros 22.7 58 0.0013 18.9 1.3 13 44-56 6-18 (26)
7 PF01473 CW_binding_1: Putativ 22.3 65 0.0014 16.6 1.4 9 96-104 7-15 (19)
8 PF07960 CBP4: CBP4; InterPro 22.1 47 0.001 26.6 1.1 11 48-58 30-40 (128)
9 PF12672 DUF3793: Protein of u 20.7 61 0.0013 27.0 1.6 62 43-123 82-144 (176)
10 cd04497 hPOT1_OB1_like hPOT1_O 17.4 2.2E+02 0.0047 22.4 4.1 55 7-63 83-137 (138)
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=5e-42 Score=271.85 Aligned_cols=119 Identities=48% Similarity=0.990 Sum_probs=95.5
Q ss_pred CCCceeECCChHHHHHHHHHHhhcCCCCCC-CeeEeccCCCCCCCCCCccccccCCCCeEEEeecCCcc--------ccC
Q 046940 41 LPLGYRFSPRGNELITHYLIKKISGQQLPA-NIIREIDLYAFDPHQLPISEFKYGKPDEAYFFTRPGKR--------RRT 111 (222)
Q Consensus 41 LPpGfRF~PTDeELV~~YL~~Ki~g~pl~~-~~I~~~Dvy~~~PweLp~~~~~~g~~~~wYFFt~~~~k--------R~~ 111 (222)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|+. .... ++++||||++++++ |++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~-~~~~-~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPA-KFKG-GDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHH-HSSS--SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhh-hccC-CCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 799999999999999995 3322 37899999999864 788
Q ss_pred CCceeecCCCCeeeec-CCeeEEEEEEeeeecCCCCCCCCcCeEEEEEEeC
Q 046940 112 SSGYWKPTGRDLPILS-GKAIVGFKRILIFYKGKAPRGIKTPWVVHEFRVN 161 (222)
Q Consensus 112 ~~G~Wk~~g~~k~I~~-~g~~vG~kr~l~F~~~~~~~~~kT~W~M~EY~l~ 161 (222)
++|+||.+|+.+.|.+ +|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999998 9999999999999988888889999999999983
No 2
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=44.91 E-value=36 Score=29.36 Aligned_cols=82 Identities=13% Similarity=0.190 Sum_probs=48.3
Q ss_pred CCCCccccccCCCCCCCcC-ccCCCCceeECCChHHHHHHHHHHhhcCCCCCCCeeEeccCCCCCCCCCCccccccCCCC
Q 046940 19 NNLSAYSISAGRGSNQDDE-QYNLPLGYRFSPRGNELITHYLIKKISGQQLPANIIREIDLYAFDPHQLPISEFKYGKPD 97 (222)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~-~~~LPpGfRF~PTDeELV~~YL~~Ki~g~pl~~~~I~~~Dvy~~~PweLp~~~~~~g~~~ 97 (222)
-|-+-+...+.++.+.+.. ....--+|||+|+|.--...--.....++.+-+....+.|-|.-+=|+.-....+.|...
T Consensus 86 ~~~~e~~~~aa~~eee~sdddve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~ 165 (216)
T KOG3238|consen 86 WKFEESKEQAADEEEEDSDDDVEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSP 165 (216)
T ss_pred ecccccccccccccccCccccccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCc
Confidence 3444455556666655544 666667999999998777754444444444433335666777777777765333333334
Q ss_pred eEE
Q 046940 98 EAY 100 (222)
Q Consensus 98 ~wY 100 (222)
.||
T Consensus 166 ~~~ 168 (216)
T KOG3238|consen 166 NSY 168 (216)
T ss_pred ccc
Confidence 444
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=41.20 E-value=32 Score=20.15 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHhhcCCCCCC
Q 046940 50 RGNELITHYLIKKISGQQLPA 70 (222)
Q Consensus 50 TDeELV~~YL~~Ki~g~pl~~ 70 (222)
+-.|||.+|+.-|+.-+..+.
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 457999999999998776553
No 4
>PHA00692 hypothetical protein
Probab=40.59 E-value=10 Score=26.35 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=9.3
Q ss_pred ccCCCCceeEC
Q 046940 38 QYNLPLGYRFS 48 (222)
Q Consensus 38 ~~~LPpGfRF~ 48 (222)
-...||||||-
T Consensus 34 fveyppgfrfg 44 (74)
T PHA00692 34 FVEYPPGFRFG 44 (74)
T ss_pred eEecCCCcccc
Confidence 56899999995
No 5
>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=25.34 E-value=69 Score=18.78 Aligned_cols=20 Identities=25% Similarity=0.346 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHhhcCCCCCC
Q 046940 51 GNELITHYLIKKISGQQLPA 70 (222)
Q Consensus 51 DeELV~~YL~~Ki~g~pl~~ 70 (222)
-.|||.+|+.-|+.-+.++.
T Consensus 5 nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHTTSTS
T ss_pred HHHHHHHHHHHHhhhcCCCC
Confidence 47999999999998766543
No 6
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=22.73 E-value=58 Score=18.87 Aligned_cols=13 Identities=23% Similarity=0.207 Sum_probs=11.0
Q ss_pred ceeECCChHHHHH
Q 046940 44 GYRFSPRGNELIT 56 (222)
Q Consensus 44 GfRF~PTDeELV~ 56 (222)
...++|+.+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 7
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=22.32 E-value=65 Score=16.59 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=7.0
Q ss_pred CCeEEEeec
Q 046940 96 PDEAYFFTR 104 (222)
Q Consensus 96 ~~~wYFFt~ 104 (222)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 588999953
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=22.07 E-value=47 Score=26.57 Aligned_cols=11 Identities=36% Similarity=0.791 Sum_probs=9.4
Q ss_pred CCChHHHHHHH
Q 046940 48 SPRGNELITHY 58 (222)
Q Consensus 48 ~PTDeELV~~Y 58 (222)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 9
>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=20.65 E-value=61 Score=26.97 Aligned_cols=62 Identities=21% Similarity=0.366 Sum_probs=36.4
Q ss_pred CceeECCChHHHHHHHHHHhhcCCCCCCCeeEeccCC-CCCCCCCCccccccCCCCeEEEeecCCccccCCCceeecCCC
Q 046940 43 LGYRFSPRGNELITHYLIKKISGQQLPANIIREIDLY-AFDPHQLPISEFKYGKPDEAYFFTRPGKRRRTSSGYWKPTGR 121 (222)
Q Consensus 43 pGfRF~PTDeELV~~YL~~Ki~g~pl~~~~I~~~Dvy-~~~PweLp~~~~~~g~~~~wYFFt~~~~kR~~~~G~Wk~~g~ 121 (222)
-|| .+.+-+-+...|..|+....+| ||+=|+ +.++.|..+ +-... +.=|- ..|+||..|-
T Consensus 82 ~GY--~~~~~~~~L~~L~~R~~~~~FP----HEIGiFLGYPleDV~G-FI~~~--g~~~~----------~~GyWKVY~n 142 (176)
T PF12672_consen 82 YGY--PDSSLEDCLEHLKKRFESGEFP----HEIGIFLGYPLEDVKG-FIENK--GKNCK----------CCGYWKVYGN 142 (176)
T ss_pred CCc--CCCCHHHHHHHHHHHhcCCCCC----chhHhccCCCHHHHHH-HHhCC--CCCee----------EeccCccCCC
Confidence 377 5555555555799888555555 566554 677777766 32222 11122 2599998876
Q ss_pred Ce
Q 046940 122 DL 123 (222)
Q Consensus 122 ~k 123 (222)
..
T Consensus 143 ~~ 144 (176)
T PF12672_consen 143 PE 144 (176)
T ss_pred HH
Confidence 43
No 10
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=17.44 E-value=2.2e+02 Score=22.39 Aligned_cols=55 Identities=18% Similarity=0.172 Sum_probs=36.5
Q ss_pred eecccccccccCCCCCccccccCCCCCCCcCccCCCCceeECCChHHHHHHHHHHhh
Q 046940 7 VSYSQQTSATRNNNLSAYSISAGRGSNQDDEQYNLPLGYRFSPRGNELITHYLIKKI 63 (222)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpGfRF~PTDeELV~~YL~~Ki 63 (222)
.+|.....+..+...|+.++=.|+......-....++ |.|.+.|++.+. .|+.+.
T Consensus 83 ~~~~g~~~~~~~~~~ss~avf~~~~~~~~~p~~~~~~-~~~~~~e~~~~~-~Lr~w~ 137 (138)
T cd04497 83 QSYNGKPQGISNDRGSSWAVFRGDDGVVPIPQQSSKP-VEFGPEEEPSVE-ELRKWA 137 (138)
T ss_pred EEECCceEEEECCCceeEEEEcCCCCCCcCccccCCC-cccCcchHHHHH-HHHHhh
Confidence 4566666666666567777777776665433334444 889999988888 477653
Done!