Query 016095
Match_columns 395
No_of_seqs 161 out of 951
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:44:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016095hhsearch_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 2.4E-42 5.3E-47 299.1 7.7 128 25-152 1-129 (129)
2 PF07960 CBP4: CBP4; InterPro 20.6 67 0.0015 28.9 1.9 16 32-47 30-48 (128)
3 smart00265 BH4 BH4 Bcl-2 homol 17.0 1.4E+02 0.0031 20.0 2.3 20 34-53 4-23 (27)
4 PHA00692 hypothetical protein 16.4 56 0.0012 25.9 0.4 9 24-32 36-44 (74)
5 cd00933 barnase Barnase, a mem 14.9 4.4E+02 0.0095 23.1 5.5 24 34-60 2-25 (107)
6 cd00490 Met_repressor_MetJ Met 11.8 2.4E+02 0.0051 24.2 2.9 39 32-74 50-88 (103)
7 PF12522 UL73_N: Cytomegalovir 10.5 1.4E+02 0.003 20.0 0.9 14 310-323 10-23 (27)
8 KOG4286 Dystrophin-like protei 10.3 59 0.0013 37.1 -1.5 54 121-174 613-677 (966)
9 PRK05264 transcriptional repre 10.2 3E+02 0.0065 23.7 3.0 39 32-74 51-89 (105)
10 TIGR03874 4cys_cytochr c-type 10.1 2.2E+02 0.0048 26.0 2.4 27 24-50 90-119 (143)
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=2.4e-42 Score=299.07 Aligned_cols=128 Identities=53% Similarity=1.071 Sum_probs=97.9
Q ss_pred CCCCceEcCChHHHHHHHHHHHHcCCCCCc-cceeeccCCCCCCCChhhhhccCceeEEEEeeccccCCCCCCCcccccc
Q 016095 25 VMPGFRFHPTEEELVEFYLRRKVEGKRFNV-ELITFLDLYRYDPWELPALAAVGEKEWFFYVPRDRKYRNGDRPNRVTTS 103 (395)
Q Consensus 25 LPPGfRF~PTDEELI~~YLrrKi~G~plp~-~~I~evDVY~~ePwdLP~~~~~ge~eWYFFtpr~rK~~nG~R~~R~tgg 103 (395)
|||||||+|||||||.+||++|+.|.+++. .+|+++|||.+|||+|++....++++||||+++.+++.+|.|.+|++++
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 799999999999999999999999999887 7999999999999999964445677999999999999999999999999
Q ss_pred ceEeecCCCceEEcCCCceEEEEEEEEEeeCCCCCCCCcCcEEEEEecC
Q 016095 104 GYWKATGADRMIKSENSRSIGLKKTLVFYSGKAPKGIRTSWIMNEYRLP 152 (395)
Q Consensus 104 G~WK~tG~~k~I~~~~G~vIG~KktL~Fy~Gk~pkg~kT~WvMhEY~L~ 152 (395)
|+||.+|+.+.|.+.+|.+||+|++|+||.++.+++.+|+|+||||+|.
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 9999999999999877899999999999999888999999999999983
No 2
>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=20.58 E-value=67 Score=28.91 Aligned_cols=16 Identities=56% Similarity=0.906 Sum_probs=12.6
Q ss_pred cCChHHHHHHH---HHHHH
Q 016095 32 HPTEEELVEFY---LRRKV 47 (395)
Q Consensus 32 ~PTDEELI~~Y---LrrKi 47 (395)
.||||||+..| |+++.
T Consensus 30 tPTeEeL~~r~sPELrkr~ 48 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRY 48 (128)
T ss_pred CCCHHHHHHhcCHHHHHHH
Confidence 69999999887 55554
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=17.01 E-value=1.4e+02 Score=20.02 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 016095 34 TEEELVEFYLRRKVEGKRFN 53 (395)
Q Consensus 34 TDEELI~~YLrrKi~G~plp 53 (395)
.-.|||++|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999998755433
No 4
>PHA00692 hypothetical protein
Probab=16.39 E-value=56 Score=25.86 Aligned_cols=9 Identities=56% Similarity=0.966 Sum_probs=7.2
Q ss_pred CCCCCceEc
Q 016095 24 VVMPGFRFH 32 (395)
Q Consensus 24 ~LPPGfRF~ 32 (395)
-.||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 359999994
No 5
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=14.90 E-value=4.4e+02 Score=23.10 Aligned_cols=24 Identities=25% Similarity=0.094 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHHHcCCCCCccceeec
Q 016095 34 TEEELVEFYLRRKVEGKRFNVELITFL 60 (395)
Q Consensus 34 TDEELI~~YLrrKi~G~plp~~~I~ev 60 (395)
|+.|-|..||.. .+ .||..+|.-.
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK~ 25 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITKS 25 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeHH
Confidence 455666778987 33 3788777643
No 6
>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=11.82 E-value=2.4e+02 Score=24.17 Aligned_cols=39 Identities=26% Similarity=0.293 Sum_probs=31.8
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCChhhhh
Q 016095 32 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 74 (395)
Q Consensus 32 ~PTDEELI~~YLrrKi~G~plp~~~I~evDVY~~ePwdLP~~~ 74 (395)
|-|..||++.-...-..|+|||.+ .|+-+..|.++|...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHHH
Confidence 567889998888888899999864 588888899998754
No 7
>PF12522 UL73_N: Cytomegalovirus glycoprotein N terminal; InterPro: IPR021003 This domain family is found in viruses, and is approximately 30 amino acids in length. The signature is found in association with PF03554 from PFAM. This family is an envelope glycoprotein of (Human herpesvirus 5) [].
Probab=10.49 E-value=1.4e+02 Score=19.99 Aligned_cols=14 Identities=43% Similarity=0.143 Sum_probs=5.9
Q ss_pred ccccCCCCcCCccc
Q 016095 310 ALSSSSSSSLIYSD 323 (395)
Q Consensus 310 ~~s~~~~~~~~~~~ 323 (395)
++|++.++|+++++
T Consensus 10 ~gSs~n~sSTsts~ 23 (27)
T PF12522_consen 10 AGSSGNNSSTSTSA 23 (27)
T ss_pred eccccCCccccccc
Confidence 33444444444443
No 8
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=10.26 E-value=59 Score=37.11 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=38.0
Q ss_pred ceEEEEEE-EE----------EeeCCCCCCCCcCcEEEEEecCCCCcccccCCCeEEEEEEecCC
Q 016095 121 RSIGLKKT-LV----------FYSGKAPKGIRTSWIMNEYRLPQHETERYQKAEISLCRVHKRPG 174 (395)
Q Consensus 121 ~vIG~Kkt-L~----------Fy~Gk~pkg~kT~WvMhEY~L~~~~~~~~~~~d~VLCRIykk~g 174 (395)
-|||+|-+ ++ |..|++.++.+++.-|.||..+........+-.-+||--|+.++
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~~~ 677 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR 677 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhhHHHHHHHHHhhhccch
Confidence 47897743 32 56689999999999999999986544333223348888887543
No 9
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=10.24 E-value=3e+02 Score=23.71 Aligned_cols=39 Identities=26% Similarity=0.279 Sum_probs=31.7
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCChhhhh
Q 016095 32 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 74 (395)
Q Consensus 32 ~PTDEELI~~YLrrKi~G~plp~~~I~evDVY~~ePwdLP~~~ 74 (395)
|-|-.||++.-...-..|+|||.+ -|+-+..|.++|...
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D----~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD----EDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh----hhhhhcCcccchHHH
Confidence 567889998888888899999864 588888899998754
No 10
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=10.15 E-value=2.2e+02 Score=25.97 Aligned_cols=27 Identities=33% Similarity=0.444 Sum_probs=21.2
Q ss_pred CCCCCceEcCChH-HH--HHHHHHHHHcCC
Q 016095 24 VVMPGFRFHPTEE-EL--VEFYLRRKVEGK 50 (395)
Q Consensus 24 ~LPPGfRF~PTDE-EL--I~~YLrrKi~G~ 50 (395)
..+|+|.-..+|+ || |..||+.+..|.
T Consensus 90 ~~MPaF~~~LsD~~eIa~L~~YLR~~~~g~ 119 (143)
T TIGR03874 90 NVMPAFGDNPNVMCYLDDLYVYLRARGTDA 119 (143)
T ss_pred CCCCCccccCCcHHHHHHHHHHHHhccCCC
Confidence 5799999999987 44 455799888774
Done!