Query 016542
Match_columns 387
No_of_seqs 227 out of 992
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:47:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016542hhsearch_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 8.5E-44 1.8E-48 307.2 7.3 128 18-151 1-129 (129)
2 PF02083 Urotensin_II: Urotens 42.3 8 0.00017 21.3 -0.1 7 381-387 4-10 (12)
3 PHA00692 hypothetical protein 32.4 17 0.00036 28.7 0.3 11 15-25 34-44 (74)
4 smart00265 BH4 BH4 Bcl-2 homol 22.0 92 0.002 20.9 2.3 20 27-46 4-23 (27)
5 cd00490 Met_repressor_MetJ Met 14.8 1.4E+02 0.0031 25.4 2.4 40 25-68 50-89 (103)
6 COG3060 MetJ Transcriptional r 14.5 1E+02 0.0022 26.1 1.5 40 25-68 51-90 (105)
7 PRK05264 transcriptional repre 13.0 1.6E+02 0.0034 25.3 2.2 40 25-68 51-90 (105)
8 PF07960 CBP4: CBP4; InterPro 11.9 1.1E+02 0.0024 27.5 1.1 17 25-41 30-49 (128)
9 KOG4286 Dystrophin-like protei 11.7 90 0.0019 35.7 0.5 35 119-153 612-657 (966)
10 PF02180 BH4: Bcl-2 homology r 11.0 2.1E+02 0.0045 19.2 1.8 20 28-47 5-24 (27)
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=8.5e-44 Score=307.19 Aligned_cols=128 Identities=55% Similarity=1.096 Sum_probs=97.8
Q ss_pred CCCCceeCCCHHHHHHHHHHHHHcCCCCCc-cceeeccCCCCCCCCCcccccCCCceEEEeeccCccCCCCCCceeecCC
Q 016542 18 LPPGFRFHPTDEEIITHYLTEKVMNTSFSA-CAIGEVDLNKSEPWDLPSKAKMGEKEFYFFCQRDRKYPTGMRTNRATEA 96 (387)
Q Consensus 18 LPPGFRF~PTDEELI~~YL~~Ki~g~pl~~-~~I~evDVy~~ePWdLP~~~k~gekeWYFFs~r~rKy~~G~R~nRat~~ 96 (387)
|||||||+|||||||.+||++|+.+.+++. .+|+++|||.+|||+||...+.++++||||+++.+++.+|.|++|++++
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 899999999999999999999999999877 7899999999999999965555778999999999999999999999999
Q ss_pred ceEEeccCCceeeeCCCCCCCCCceeEEEEEEEeeecCCCCCCCcCeEEEEEEeC
Q 016542 97 GYWKATGKDKEIYKGNKGGVGGGGLVGMKKTLVFYKGRAPKGEKTNWVMHEYRLE 151 (387)
Q Consensus 97 GyWKatGkdk~I~~~~~gg~g~g~lVG~KKtLvFY~GrapkG~KT~WvMhEYrL~ 151 (387)
|+||++|++++|.... +.+||+||+|+||.++.+++.||+|+||||+|+
T Consensus 81 G~Wk~~g~~~~i~~~~------g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPG------GKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-T------TCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeeccccccccccc------ceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999853 799999999999999889999999999999984
No 2
>PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=42.32 E-value=8 Score=21.30 Aligned_cols=7 Identities=43% Similarity=1.436 Sum_probs=5.6
Q ss_pred cccccCC
Q 016542 381 LDSFWDY 387 (387)
Q Consensus 381 ~~~~w~~ 387 (387)
-+|||+|
T Consensus 4 ~~CFWKY 10 (12)
T PF02083_consen 4 SECFWKY 10 (12)
T ss_pred cchhhhh
Confidence 5789987
No 3
>PHA00692 hypothetical protein
Probab=32.45 E-value=17 Score=28.74 Aligned_cols=11 Identities=55% Similarity=1.361 Sum_probs=9.1
Q ss_pred CCCCCCCceeC
Q 016542 15 VIDLPPGFRFH 25 (387)
Q Consensus 15 ~~~LPPGFRF~ 25 (387)
-.+.||||||-
T Consensus 34 fveyppgfrfg 44 (74)
T PHA00692 34 FVEYPPGFRFG 44 (74)
T ss_pred eEecCCCcccc
Confidence 35789999995
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=21.96 E-value=92 Score=20.86 Aligned_cols=20 Identities=20% Similarity=0.541 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHcCCCCC
Q 016542 27 TDEEIITHYLTEKVMNTSFS 46 (387)
Q Consensus 27 TDEELI~~YL~~Ki~g~pl~ 46 (387)
.-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999876554
No 5
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=14.79 E-value=1.4e+02 Score=25.43 Aligned_cols=40 Identities=23% Similarity=0.422 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCCccccc
Q 016542 25 HPTDEEIITHYLTEKVMNTSFSACAIGEVDLNKSEPWDLPSKAK 68 (387)
Q Consensus 25 ~PTDEELI~~YL~~Ki~g~pl~~~~I~evDVy~~ePWdLP~~~k 68 (387)
|-|.-||++.-...-..|+|+|. +.||-+..|..+|..++
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ak 89 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAAK 89 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHHH
Confidence 57778888766666788999985 68999999999998753
No 6
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=14.48 E-value=1e+02 Score=26.08 Aligned_cols=40 Identities=23% Similarity=0.430 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCCccccc
Q 016542 25 HPTDEEIITHYLTEKVMNTSFSACAIGEVDLNKSEPWDLPSKAK 68 (387)
Q Consensus 25 ~PTDEELI~~YL~~Ki~g~pl~~~~I~evDVy~~ePWdLP~~~k 68 (387)
|.|.-||++.-...-..|+|+|. +.|+.+..|.++|+.++
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~ak 90 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAAK 90 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHHH
Confidence 56777888766666788999984 68999999999998764
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=12.99 E-value=1.6e+02 Score=25.29 Aligned_cols=40 Identities=23% Similarity=0.405 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCCccccc
Q 016542 25 HPTDEEIITHYLTEKVMNTSFSACAIGEVDLNKSEPWDLPSKAK 68 (387)
Q Consensus 25 ~PTDEELI~~YL~~Ki~g~pl~~~~I~evDVy~~ePWdLP~~~k 68 (387)
|-|.-||++.-...-..|+|+|. +.||-+..|.++|..++
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ak 90 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAAK 90 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHHH
Confidence 67778888766666788999985 67999999999997653
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=11.89 E-value=1.1e+02 Score=27.46 Aligned_cols=17 Identities=35% Similarity=0.811 Sum_probs=13.1
Q ss_pred CCCHHHHHHHH---HHHHHc
Q 016542 25 HPTDEEIITHY---LTEKVM 41 (387)
Q Consensus 25 ~PTDEELI~~Y---L~~Ki~ 41 (387)
.||||||+..| |+++.+
T Consensus 30 tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred CCCHHHHHHhcCHHHHHHHH
Confidence 49999999987 555554
No 9
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=11.72 E-value=90 Score=35.68 Aligned_cols=35 Identities=34% Similarity=0.614 Sum_probs=28.5
Q ss_pred CceeEEEEE-EE----------eeecCCCCCCCcCeEEEEEEeCCC
Q 016542 119 GGLVGMKKT-LV----------FYKGRAPKGEKTNWVMHEYRLEGK 153 (387)
Q Consensus 119 g~lVG~KKt-Lv----------FY~GrapkG~KT~WvMhEYrL~~~ 153 (387)
..|||+|-. |+ |..|++.+|.|++.-|.||.....
T Consensus 612 ~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tt 657 (966)
T KOG4286|consen 612 CPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTT 657 (966)
T ss_pred CccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCC
Confidence 578999753 43 566999999999999999998754
No 10
>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=10.98 E-value=2.1e+02 Score=19.25 Aligned_cols=20 Identities=15% Similarity=0.448 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHcCCCCCc
Q 016542 28 DEEIITHYLTEKVMNTSFSA 47 (387)
Q Consensus 28 DEELI~~YL~~Ki~g~pl~~ 47 (387)
-.|||.+|+.-|+.-+.+++
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 47999999999998665543
Done!