Query 017473
Match_columns 371
No_of_seqs 173 out of 906
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:52:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017473hhsearch_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 1.6E-39 3.5E-44 277.3 7.2 124 5-132 1-129 (129)
2 COG4868 Uncharacterized protei 33.8 16 0.00034 38.0 0.4 16 334-349 210-225 (493)
3 smart00265 BH4 BH4 Bcl-2 homol 19.5 1.2E+02 0.0026 20.5 2.4 18 15-32 6-23 (27)
4 PF03540 TFIID_30kDa: Transcri 16.3 99 0.0021 23.6 1.7 13 13-25 1-15 (51)
5 PHA00692 hypothetical protein 16.2 60 0.0013 25.9 0.5 8 5-12 37-44 (74)
6 PF08999 SP_C-Propep: Surfacta 14.5 66 0.0014 27.1 0.4 25 262-286 3-31 (93)
7 PRK13663 hypothetical protein; 13.2 70 0.0015 34.2 0.2 16 334-349 210-225 (493)
8 PF12593 McyA_C: Microcystin s 13.2 94 0.002 22.7 0.8 23 317-344 15-37 (40)
9 PF08338 DUF1731: Domain of un 12.3 1.3E+02 0.0029 22.1 1.4 15 7-21 31-47 (48)
10 smart00707 RPEL Repeat in Dros 11.7 75 0.0016 21.2 -0.1 13 7-19 5-18 (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=1.6e-39 Score=277.27 Aligned_cols=124 Identities=32% Similarity=0.600 Sum_probs=92.1
Q ss_pred CCCCceECCc-HHHHHHHHhhhhcCCCCCC-CCccccCCccCCCCCCccccCCCCCCCceEEEee-ccC-CCCCCCCccc
Q 017473 5 MREWYKSQPS-DELILCLLKKKRLDPHFSY-GPIKDIGHICSLEPWDLATESETDSEDQTCYFFY-KPR-YTKSNDAHRA 80 (371)
Q Consensus 5 LPPGfRF~PT-EELV~~YLr~KI~G~plp~-~vI~ev~DVY~~ePWdL~~~~pGk~~d~eWYFFS-R~r-y~~G~R~nRa 80 (371)
|||||||+|| +|||.+||++|+.|.+++. ++|.++ |||++|||+|+.. ....+++||||+ +.+ +.+|.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~-Diy~~~P~~L~~~--~~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDV-DIYSAHPWELPAK--FKGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHH--SSS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeec-ccCccChHHhhhh--ccCCCceEEEEEecccccCCccccccc
Confidence 8999999999 9999999999999999887 899999 9999999999732 233577999999 655 7789999999
Q ss_pred CCCceeeeeCCceeEee-CCceEEEEEEEeeeccCCCCCCCCcCeEEEEEEeC
Q 017473 81 TNAGSWKVTRKVSQIEA-RNGLTGTKKSLTFYLRGLPRKEAITEWGMHEYHVK 132 (371)
Q Consensus 81 tg~G~WKatG~dK~I~~-~g~vVG~KKtLvFY~gr~~r~p~KT~WvMhEYrL~ 132 (371)
+++|+||++|++++|.+ +|.+||+|++|+||.++.+ .+.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~-~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSP-NGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTT-S-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCC-CCCcCCeEEEEEEeC
Confidence 99999999999999999 8999999999999987521 344999999999984
No 2
>COG4868 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.80 E-value=16 Score=37.96 Aligned_cols=16 Identities=50% Similarity=1.126 Sum_probs=13.0
Q ss_pred ccccccCCcccccccC
Q 017473 334 EWQLPLHHPLEIHNSA 349 (371)
Q Consensus 334 ~~~~~~~~~~~~~~~~ 349 (371)
-|.||||||+.+--.|
T Consensus 210 vWNlPL~HPvNlAYEA 225 (493)
T COG4868 210 VWNLPLHHPVNLAYEA 225 (493)
T ss_pred ccccccCCchhhhhhh
Confidence 5999999999876544
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=19.49 E-value=1.2e+02 Score=20.47 Aligned_cols=18 Identities=17% Similarity=0.217 Sum_probs=14.9
Q ss_pred HHHHHHHHhhhhcCCCCC
Q 017473 15 DELILCLLKKKRLDPHFS 32 (371)
Q Consensus 15 EELV~~YLr~KI~G~plp 32 (371)
.|||.+|+.-|+.-...+
T Consensus 6 RelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 6 RELVVDYVTYKLSQNGYE 23 (27)
T ss_pred HHHHHHHHHHHHhhcCCC
Confidence 899999999999766443
No 4
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=16.32 E-value=99 Score=23.63 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=10.9
Q ss_pred Cc--HHHHHHHHhhh
Q 017473 13 PS--DELILCLLKKK 25 (371)
Q Consensus 13 PT--EELV~~YLr~K 25 (371)
|| +||+.|||.+-
T Consensus 1 P~IPD~v~~~yL~~~ 15 (51)
T PF03540_consen 1 PTIPDEVTDYYLERS 15 (51)
T ss_pred CCCCHHHHHHHHHHC
Confidence 77 99999999763
No 5
>PHA00692 hypothetical protein
Probab=16.20 E-value=60 Score=25.85 Aligned_cols=8 Identities=0% Similarity=-0.064 Sum_probs=6.8
Q ss_pred CCCCceEC
Q 017473 5 MREWYKSQ 12 (371)
Q Consensus 5 LPPGfRF~ 12 (371)
.||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 69999995
No 6
>PF08999 SP_C-Propep: Surfactant protein C, N terminal propeptide; InterPro: IPR015091 The N-terminal propeptide of surfactant protein C adopts an alpha-helical structure, with turn and extended regions. Its main function is the stabilisation of metastable surfactant protein C (SP-C), since the latter can irreversibly transform from its native alpha-helical structure to beta-sheet aggregates and form amyloid-like fibrils. The correct intracellular trafficking of proSP-C has also been reported to depend on the propeptide []. ; PDB: 1SPF_A 2YAD_F.
Probab=14.53 E-value=66 Score=27.14 Aligned_cols=25 Identities=28% Similarity=0.608 Sum_probs=3.3
Q ss_pred hhhcceecccCCCCCCCcc----cCCccc
Q 017473 262 IEQNMYLLKYLPNYSPAQQ----LPCDHF 286 (371)
Q Consensus 262 ~~~~~~~~~~~~~~~~~~~----~~~~~~ 286 (371)
+-+|.-|+.-||.||-+-+ ||||..
T Consensus 3 ~g~ke~lme~pp~ysa~p~~r~~iPc~p~ 31 (93)
T PF08999_consen 3 VGSKEVLMERPPDYSAAPRGRFGIPCCPV 31 (93)
T ss_dssp ------------------------SSS-S
T ss_pred ccchhhhhcCCCccccCCCCccCCCcccc
Confidence 4456677888999998776 999984
No 7
>PRK13663 hypothetical protein; Provisional
Probab=13.20 E-value=70 Score=34.20 Aligned_cols=16 Identities=44% Similarity=1.014 Sum_probs=12.7
Q ss_pred ccccccCCcccccccC
Q 017473 334 EWQLPLHHPLEIHNSA 349 (371)
Q Consensus 334 ~~~~~~~~~~~~~~~~ 349 (371)
-|.|||.||+.|---|
T Consensus 210 iWNlPLkHPVNlAYEA 225 (493)
T PRK13663 210 VWNLPLKHPVNLAYEA 225 (493)
T ss_pred ccCCcCCChHHHHHHH
Confidence 4999999999875443
No 8
>PF12593 McyA_C: Microcystin synthetase C terminal; InterPro: IPR022583 This domain of unknown function is found in cyanobacteria and is approximately 40 amino acids in length. It is found in association with PF00501 from PFAM, PF00668 from PFAM, PF00550 from PFAM, and PF08242 from PFAM and contains a conserved YAN motif. This region is found in microcystin synthetase, which is one of a number of proteins involved in microcystin toxin synthesis []. Microcystins form a large family of small cyclic heptapeptides harbouring extensive modifications in amino acid residue composition and functional group chemistry. These peptide hepatotoxins contain a range of non-proteinogenic amino acids and unusual peptide bonds, and are typically N-methylated. They are synthesized on large enzyme complexes consisting of non-ribosomal peptide synthetases and polyketide synthases [].
Probab=13.20 E-value=94 Score=22.67 Aligned_cols=23 Identities=43% Similarity=0.927 Sum_probs=18.5
Q ss_pred ccccCCCCCCcCCCCCcccccccCCccc
Q 017473 317 IEGFSPTNSLLPQNSNLEWQLPLHHPLE 344 (371)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 344 (371)
.--|+||+---| +||+=..|||.
T Consensus 15 l~~ft~T~q~kp-----dWq~YAN~PLq 37 (40)
T PF12593_consen 15 LRVFTPTHQAKP-----DWQLYANHPLQ 37 (40)
T ss_pred eeeeccccccCc-----hhhhhcCCCCC
Confidence 346899986655 99999999985
No 9
>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=12.31 E-value=1.3e+02 Score=22.14 Aligned_cols=15 Identities=20% Similarity=0.377 Sum_probs=8.1
Q ss_pred CCceEC-Cc-HHHHHHH
Q 017473 7 EWYKSQ-PS-DELILCL 21 (371)
Q Consensus 7 PGfRF~-PT-EELV~~Y 21 (371)
-||+|+ |+ ++-+.+-
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 88 7776653
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=11.74 E-value=75 Score=21.19 Aligned_cols=13 Identities=23% Similarity=0.325 Sum_probs=10.0
Q ss_pred CCceECCc-HHHHH
Q 017473 7 EWYKSQPS-DELIL 19 (371)
Q Consensus 7 PGfRF~PT-EELV~ 19 (371)
-...++|| +|||.
T Consensus 5 ~kl~~RP~~eeLv~ 18 (26)
T smart00707 5 RKLSQRPTREELEE 18 (26)
T ss_pred HHHHcCCCHHHHHH
Confidence 34568899 99986
Done!