Query 045827
Match_columns 227
No_of_seqs 147 out of 950
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:53:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045827hhsearch_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 1.3E-41 2.8E-46 271.1 7.2 120 52-171 1-129 (129)
2 PHA00692 hypothetical protein 34.3 15 0.00032 25.9 0.2 10 50-59 35-44 (74)
3 KOG3038 Histone acetyltransfer 33.9 47 0.001 29.9 3.4 27 194-220 144-170 (264)
4 PF10571 UPF0547: Uncharacteri 30.3 26 0.00057 20.4 0.8 18 19-36 8-25 (26)
5 KOG0349 Putative DEAD-box RNA 26.0 48 0.001 32.6 2.2 45 14-59 211-255 (725)
6 PF04700 Baculo_gp41: Structur 22.9 72 0.0016 27.3 2.5 20 61-80 6-27 (186)
7 PF07960 CBP4: CBP4; InterPro 22.6 47 0.001 26.8 1.3 17 53-69 23-40 (128)
8 KOG4286 Dystrophin-like protei 20.4 22 0.00047 36.7 -1.3 72 140-225 613-700 (966)
9 smart00265 BH4 BH4 Bcl-2 homol 19.9 1.3E+02 0.0029 17.7 2.5 19 61-79 4-22 (27)
10 smart00707 RPEL Repeat in Dros 18.8 79 0.0017 18.5 1.3 14 55-68 6-19 (26)
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=1.3e-41 Score=271.08 Aligned_cols=120 Identities=44% Similarity=0.853 Sum_probs=95.9
Q ss_pred CCCceeEcCCHHHHHHHHhhhhhhCCCCCC-CceeeCCCCCCCCCCcccccccCCCeEEEEeecc--------CCccccC
Q 045827 52 LPPGFKFLPTDEELVLHFLYPKASLLPCHP-NIIPELNPQLHDPWQLNGRALCSGNRWYFFSQIE--------DKRVTGN 122 (227)
Q Consensus 52 LPpGfRF~PTDeELI~~YL~~Ki~g~pl~~-~~I~~~DVy~~~P~eLp~~~~~~~~~wyFFs~~~--------~~R~~~~ 122 (227)
|||||||+|||+|||.+||.+|+.|.+++. .+|+++|||++|||+|++....++++||||++++ .+|++++
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 899999999999999999999999998876 7999999999999999954444667999999996 4578899
Q ss_pred cEEeeccccceEECCCCeEEEEEEEEEeeecCCCCCCccCeEEEEEEeC
Q 045827 123 GYWKQLDFEEPVINSAGKKIGMKKYFVFCVGEAPLGVETNWIMQEYHLC 171 (227)
Q Consensus 123 G~Wk~~g~~k~I~~~~g~~iG~Kk~l~Fy~~~~~~~~kT~WvM~EY~l~ 171 (227)
|+||.+|+.+.|.+.+|.+||+|++|+||.++.+.+.+|+|+||||+|.
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 9999999999998878999999999999998888889999999999984
No 2
>PHA00692 hypothetical protein
Probab=34.32 E-value=15 Score=25.92 Aligned_cols=10 Identities=50% Similarity=1.268 Sum_probs=8.7
Q ss_pred CCCCCceeEc
Q 045827 50 INLPPGFKFL 59 (227)
Q Consensus 50 ~~LPpGfRF~ 59 (227)
+..||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4899999995
No 3
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=33.92 E-value=47 Score=29.90 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=23.3
Q ss_pred CCcEEEEEEEEecCCCCCCcCCCCCCC
Q 045827 194 CCKWVLCRVYEEDGNSKGFCHGDDDDD 220 (227)
Q Consensus 194 ~~~~VLCkIy~k~~~~~~~~~~~~~~~ 220 (227)
+++|.||.|-+-++..+..|+..|++-
T Consensus 144 dg~WIlaeVv~~~~~~~ye~ev~D~Ep 170 (264)
T KOG3038|consen 144 DGDWILAEVVKVSSETRYEFEVVDPEP 170 (264)
T ss_pred CCCEEEEEEEEEecCCceEeEecCCCc
Confidence 477999999999888888999888775
No 4
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.32 E-value=26 Score=20.36 Aligned_cols=18 Identities=22% Similarity=0.108 Sum_probs=13.1
Q ss_pred cccccccccCCCChhhhc
Q 045827 19 HIVPVKYINSPSLSYIRS 36 (227)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~ 36 (227)
..||++...||.|.+.+.
T Consensus 8 ~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 8 AEVPESAKFCPHCGYDFE 25 (26)
T ss_pred CCchhhcCcCCCCCCCCc
Confidence 456777888888887764
No 5
>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]
Probab=26.03 E-value=48 Score=32.60 Aligned_cols=45 Identities=31% Similarity=0.536 Sum_probs=37.6
Q ss_pred cCCcccccccccccCCCChhhhcccceeeeecccCCCCCCCceeEc
Q 045827 14 KASTFHIVPVKYINSPSLSYIRSRKKYLIINMCDRTINLPPGFKFL 59 (227)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M~~~~~~LPpGfRF~ 59 (227)
.-+.|.| |++|.++--..-.+=.++.|+++.+...+.+|||-.|.
T Consensus 211 lg~AF~i-p~~~kn~~lfPAvvlkNael~fNFG~~~FKfpPgngFv 255 (725)
T KOG0349|consen 211 LGAAFSI-PVKYKNSNLFPAVVLKNAELSFNFGSQPFKFPPGNGFV 255 (725)
T ss_pred cceeEEc-ChhhcccccchheeeccceEEEecCCCccccCCCCceE
Confidence 4566777 88888887777777788999999999999999999995
No 6
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=22.90 E-value=72 Score=27.33 Aligned_cols=20 Identities=30% Similarity=0.242 Sum_probs=15.0
Q ss_pred CHHHHHHHH--hhhhhhCCCCC
Q 045827 61 TDEELVLHF--LYPKASLLPCH 80 (227)
Q Consensus 61 TDeELI~~Y--L~~Ki~g~pl~ 80 (227)
+|||||.|| |.++..|...+
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~ 27 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVP 27 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCC
Confidence 899999999 66677665443
No 7
>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=22.58 E-value=47 Score=26.80 Aligned_cols=17 Identities=41% Similarity=0.751 Sum_probs=12.9
Q ss_pred CCceeE-cCCHHHHHHHH
Q 045827 53 PPGFKF-LPTDEELVLHF 69 (227)
Q Consensus 53 PpGfRF-~PTDeELI~~Y 69 (227)
|.-|++ .||||||+..|
T Consensus 23 ~~l~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 23 PALVKYTTPTEEELFKRY 40 (128)
T ss_pred hHHheecCCCHHHHHHhc
Confidence 344555 69999999986
No 8
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=20.39 E-value=22 Score=36.69 Aligned_cols=72 Identities=18% Similarity=0.215 Sum_probs=48.4
Q ss_pred eEEEEEE-EEE----------eeecCCCCCCccCeEEEEEEeCCCCCCCcccccccCCcccccCCCCcEEEEEEEE----
Q 045827 140 KKIGMKK-YFV----------FCVGEAPLGVETNWIMQEYHLCSCGASANKSYKRRGNRILVSEGCCKWVLCRVYE---- 204 (227)
Q Consensus 140 ~~iG~Kk-~l~----------Fy~~~~~~~~kT~WvM~EY~l~~~~~~~~~~~~~~~~~~l~~~~~~~~VLCkIy~---- 204 (227)
-+||+|= .++ |..|...++.+++.-|.||-....+...- ..---+||--|+
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d~--------------rdfak~L~nkfr~~~~ 678 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGEDV--------------RDFAKVLKNKFRTKRY 678 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhhH--------------HHHHHHHHhhhccchh
Confidence 5888883 333 45577788999999999999987753210 001125555555
Q ss_pred -ecCCCCCCcCCCCCCCCCCCC
Q 045827 205 -EDGNSKGFCHGDDDDDDNGTE 225 (227)
Q Consensus 205 -k~~~~~~~~~~~~~~~~~~~~ 225 (227)
.+...+|+|--+.+...+|.|
T Consensus 679 ~a~~~rrGylpvq~~~e~~~~e 700 (966)
T KOG4286|consen 679 FAKHPRRGYLPVQTVLEGDNME 700 (966)
T ss_pred hhcccccCCccchhcccccccc
Confidence 577889999887776666643
No 9
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=19.90 E-value=1.3e+02 Score=17.74 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=15.0
Q ss_pred CHHHHHHHHhhhhhhCCCC
Q 045827 61 TDEELVLHFLYPKASLLPC 79 (227)
Q Consensus 61 TDeELI~~YL~~Ki~g~pl 79 (227)
+-.|||.+|+.-|+.-...
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 5689999999999974433
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=18.77 E-value=79 Score=18.54 Aligned_cols=14 Identities=36% Similarity=0.313 Sum_probs=11.3
Q ss_pred ceeEcCCHHHHHHH
Q 045827 55 GFKFLPTDEELVLH 68 (227)
Q Consensus 55 GfRF~PTDeELI~~ 68 (227)
...++|+.+|||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45679999999973
Done!