Query 015998
Match_columns 397
No_of_seqs 196 out of 898
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:51:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015998hhsearch_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 7.9E-43 1.7E-47 301.9 6.9 128 5-135 1-129 (129)
2 PHA00692 hypothetical protein 18.4 49 0.0011 26.3 0.5 9 4-12 36-44 (74)
3 COG2326 Uncharacterized conser 13.7 1.4E+02 0.0029 30.2 2.4 37 3-39 97-137 (270)
4 KOG3238 Chloride ion current i 13.3 1.9E+02 0.0042 28.1 3.1 60 7-67 111-170 (216)
5 smart00265 BH4 BH4 Bcl-2 homol 13.3 2E+02 0.0044 19.3 2.4 20 14-33 4-23 (27)
6 PF07960 CBP4: CBP4; InterPro 13.2 99 0.0022 27.9 1.1 15 8-22 25-40 (128)
7 KOG4286 Dystrophin-like protei 12.4 1.3E+02 0.0027 34.7 1.8 49 104-152 613-675 (966)
8 cd07446 CRD_SFRP2 Cysteine-ric 12.2 87 0.0019 28.0 0.5 35 341-375 21-55 (128)
9 cd07453 CRD_crescent Cysteine- 10.6 1E+02 0.0022 27.8 0.5 34 341-374 19-52 (135)
10 cd00490 Met_repressor_MetJ Met 10.3 2.7E+02 0.0059 23.9 2.8 39 12-55 50-88 (103)
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=7.9e-43 Score=301.87 Aligned_cols=128 Identities=47% Similarity=0.875 Sum_probs=96.7
Q ss_pred CCCCcEECCChHHHHHHHHHHHHcCCCCCC-cceeccCcCCCCCCCCCCccCCCCCCCceEEEeeccccCCCCCCccccc
Q 015998 5 GVVGFRFHPTEEEIISYFLERKMCGLDFPA-HTIADVVDVCKYEPWDLPQRSRMPKEDRVWYFFNALVSKSPNSKLVNRQ 83 (397)
Q Consensus 5 LPpGFRF~PTDEELI~~YLr~Ki~G~pl~~-~~I~e~vDVY~~ePWdLP~~~~~g~~d~eWYFFspr~rKy~nG~R~nRa 83 (397)
|||||||+|||+|||.+||++|+.|.+++. .+|.+ +|||++|||+||+... +++.+||||+++++++.+|.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~-~Diy~~~P~~L~~~~~--~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHD-VDIYSAHPWELPAKFK--GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHSS--S-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceee-cccCccChHHhhhhcc--CCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999887 79999 9999999999995322 2477999999999999999999999
Q ss_pred cCCceEeecCCCeeEEcCCCceEeeEEEEEeeeCcCCCCCCcCeEEEEEEeC
Q 015998 84 TNSGFWKPTGKDRVIWDEQGKKIGFKKNLVFHTGRAKNGIRTNWVMHEYHSQ 135 (397)
Q Consensus 84 tggG~WKatG~~k~I~~~~g~~IG~KKtLvFy~Gr~p~G~KT~WvMhEYrL~ 135 (397)
+++|+||++|+.++|.+.++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999999976778999999999999888999999999999984
No 2
>PHA00692 hypothetical protein
Probab=18.38 E-value=49 Score=26.31 Aligned_cols=9 Identities=44% Similarity=0.619 Sum_probs=7.3
Q ss_pred CCCCCcEEC
Q 015998 4 HGVVGFRFH 12 (397)
Q Consensus 4 ~LPpGFRF~ 12 (397)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 469999995
No 3
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=13.71 E-value=1.4e+02 Score=30.20 Aligned_cols=37 Identities=19% Similarity=0.254 Sum_probs=28.0
Q ss_pred CCCCCCcEEC----CChHHHHHHHHHHHHcCCCCCCcceec
Q 015998 3 GHGVVGFRFH----PTEEEIISYFLERKMCGLDFPAHTIAD 39 (397)
Q Consensus 3 ~~LPpGFRF~----PTDEELI~~YLr~Ki~G~pl~~~~I~e 39 (397)
.--|.|+|-. |||+|+-..||.|-+.--|-...++--
T Consensus 97 ~lNPR~~rvval~aPt~~E~~qwY~qRy~~~lPa~GeiviF 137 (270)
T COG2326 97 ALNPRGARVVALPAPTDRERGQWYFQRYVAHLPAAGEIVIF 137 (270)
T ss_pred hcCCceeEEeecCCCChHhhccHHHHHHHHhCCCCCeEEEe
Confidence 3457788764 999999999999999887755554433
No 4
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=13.30 E-value=1.9e+02 Score=28.13 Aligned_cols=60 Identities=15% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCcEECCChHHHHHHHHHHHHcCCCCCCcceeccCcCCCCCCCCCCccCCCCCCCceEEEe
Q 015998 7 VGFRFHPTEEEIISYFLERKMCGLDFPAHTIADVVDVCKYEPWDLPQRSRMPKEDRVWYFF 67 (397)
Q Consensus 7 pGFRF~PTDEELI~~YLr~Ki~G~pl~~~~I~e~vDVY~~ePWdLP~~~~~g~~d~eWYFF 67 (397)
-+|||+|+|.--+.-.--..--...+-+....+ .|-|.-+=|+.-.....+++...||=+
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED-~~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDED-EDDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCcccc-ccccccchhhhhhhhccCCCCcccccc
Confidence 589999999876654222222233222222445 566666666665443333444555543
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=13.25 E-value=2e+02 Score=19.34 Aligned_cols=20 Identities=10% Similarity=0.315 Sum_probs=15.9
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 015998 14 TEEEIISYFLERKMCGLDFP 33 (397)
Q Consensus 14 TDEELI~~YLr~Ki~G~pl~ 33 (397)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999766543
No 6
>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=13.17 E-value=99 Score=27.90 Aligned_cols=15 Identities=33% Similarity=0.696 Sum_probs=11.0
Q ss_pred CcEE-CCChHHHHHHH
Q 015998 8 GFRF-HPTEEEIISYF 22 (397)
Q Consensus 8 GFRF-~PTDEELI~~Y 22 (397)
-|++ .||||||+..|
T Consensus 25 l~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 25 LVKYTTPTEEELFKRY 40 (128)
T ss_pred HheecCCCHHHHHHhc
Confidence 3444 49999999765
No 7
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=12.35 E-value=1.3e+02 Score=34.74 Aligned_cols=49 Identities=33% Similarity=0.579 Sum_probs=35.0
Q ss_pred ceEeeE-EEEE----------eeeCcCCCCCCcCeEEEEEEeCCCCC-CCCce--EEEEEEEc
Q 015998 104 KKIGFK-KNLV----------FHTGRAKNGIRTNWVMHEYHSQNASS-YSKEF--VLLRLKKK 152 (397)
Q Consensus 104 ~~IG~K-KtLv----------Fy~Gr~p~G~KT~WvMhEYrL~~~~~-~~~d~--VLCRVykK 152 (397)
.+||+| |+|+ |..|++.+|.|++.-|.||.....+. ...++ +||--|+.
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~ 675 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT 675 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhhHHHHHHHHHhhhcc
Confidence 358988 5554 66799999999999999999998771 11222 56666654
No 8
>cd07446 CRD_SFRP2 Cysteine-rich domain of the secreted frizzled-related protein 2 (SFRP2), a regulator of Wnt activity. The cysteine-rich-domain (CRD) is an essential part of the secreted frizzled related protein 2 (SFRP2), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. As a Wnt antagonist, SFRP2 regulates Nkx2.2 expression in the ventral spinal cord and anteroposterior axis elongation. SFRP2 also has a Wnt-independent function as an enhancer of procollagen cleavage by the TLD proteinases. SFRP2 binds both procollagen and TLD, thus facilitating the enzymatic reaction by bringing togeth
Probab=12.20 E-value=87 Score=27.98 Aligned_cols=35 Identities=20% Similarity=0.562 Sum_probs=28.0
Q ss_pred CCCCCCcccccchhhhhhccCcccchhhhhccchh
Q 015998 341 SDTDLPGIVGHKSVVDELQHTPKYHKYFEARCSTQ 375 (397)
Q Consensus 341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 375 (397)
..|.+|-++||.+..+-.+..-.|.-.....|+.+
T Consensus 21 n~T~~PN~lgH~sq~ea~~~~~~~~pLv~~~C~p~ 55 (128)
T cd07446 21 TNMRLPNLLGHETMKEVLQQAGSWIPLVQKQCHPD 55 (128)
T ss_pred CcccCCcccCCCCHHHHHHHHHHHHHHHhcCCChh
Confidence 56889999999998877777777777777788743
No 9
>cd07453 CRD_crescent Cysteine-rich domain of the crescent protein. The cysteine-rich domain (CRD) is an essential part of the crescent protein, a member of the secreted frizzled-related protein (SFRP) family, which regulates convergent extension movements (CEMs) during gastrulation and neurulation. Xenopus laevis crescent efficiently forms inhibitory complexes with Wnt5a and Wnt11, but this effect is cancelled in the presence of another member of the SFRP family, Frzb1. A potential role for Crescent in head formation is to regulate a non-canonical Wnt pathway positively in the adjacent posterior mesoderm, and negatively in the overlying anterior neuroectoderm.
Probab=10.64 E-value=1e+02 Score=27.84 Aligned_cols=34 Identities=15% Similarity=0.523 Sum_probs=28.2
Q ss_pred CCCCCCcccccchhhhhhccCcccchhhhhccch
Q 015998 341 SDTDLPGIVGHKSVVDELQHTPKYHKYFEARCST 374 (397)
Q Consensus 341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 374 (397)
..|.+|-++||.+.-+-.+....|.-..+..|+.
T Consensus 19 n~T~~PN~lgH~sq~ea~~~~~~~~pLv~~~C~p 52 (135)
T cd07453 19 SEMRIPNLLEHETMAEVIQQSSSWLPLLARECHP 52 (135)
T ss_pred CcccCCcccCCCCHHHHHHHHHHHHHHHhcCCCh
Confidence 4588999999999888777777888888888874
No 10
>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=10.33 E-value=2.7e+02 Score=23.89 Aligned_cols=39 Identities=21% Similarity=0.382 Sum_probs=31.9
Q ss_pred CCChHHHHHHHHHHHHcCCCCCCcceeccCcCCCCCCCCCCccC
Q 015998 12 HPTEEEIISYFLERKMCGLDFPAHTIADVVDVCKYEPWDLPQRS 55 (397)
Q Consensus 12 ~PTDEELI~~YLr~Ki~G~pl~~~~I~e~vDVY~~ePWdLP~~~ 55 (397)
|-|--||++.-...-..|+|+|.+ .|+-+..|..+|..+
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 457778888777788899999975 689999999999754
Done!