Query 013077
Match_columns 450
No_of_seqs 183 out of 900
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 00:10:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013077.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013077hhsearch_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 1.4E-42 3E-47 304.7 7.6 128 5-135 1-129 (129)
2 cd07446 CRD_SFRP2 Cysteine-ric 16.3 58 0.0013 29.6 0.5 35 394-428 21-55 (128)
3 cd00490 Met_repressor_MetJ Met 14.1 1.7E+02 0.0037 25.6 2.7 39 12-55 50-88 (103)
4 PHA00692 hypothetical protein 14.1 72 0.0016 25.9 0.5 9 4-12 36-44 (74)
5 cd07453 CRD_crescent Cysteine- 14.0 72 0.0016 29.4 0.5 34 394-427 19-52 (135)
6 PRK05264 transcriptional repre 12.6 1.8E+02 0.0039 25.6 2.5 39 12-55 51-89 (105)
7 KOG3238 Chloride ion current i 12.6 2E+02 0.0043 28.6 3.1 62 6-68 110-171 (216)
8 cd07463 CRD_FZ9 Cysteine-rich 12.3 78 0.0017 28.8 0.2 33 395-427 20-52 (127)
9 cd07462 CRD_FZ10 Cysteine-rich 11.5 81 0.0018 28.7 0.1 34 395-428 20-53 (127)
10 cd07442 CRD_SFRP4 Cysteine-ric 11.0 95 0.0021 28.3 0.3 35 394-428 19-53 (127)
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=1.4e-42 Score=304.75 Aligned_cols=128 Identities=48% Similarity=0.863 Sum_probs=97.0
Q ss_pred CCCceeECCChHHHHHHHHHHHHCCCCCCC-CceeccCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCCCCCCCcccc
Q 013077 5 GVVGFRFHPTDEEIVTYFLERKMCGLDFPA-HTIADVVDVCKYEPWELPQRSSMPKEDRVWYFFNAPVPKYANSKRINRT 83 (450)
Q Consensus 5 LPpGfRF~PTDEELV~~YL~~Ki~G~plp~-~vI~e~vDVY~~ePWdLP~~~~~g~~e~eWYFFs~r~rKy~nG~R~nRa 83 (450)
|||||||+|||+|||.+||++|+.|.+++. .+|.+ +|||+++||+||+.... .+.+||||+++++++++|.|++|+
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-VDIYSAHPWELPAKFKG--GDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHSSS---SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceee-cccCccChHHhhhhccC--CCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999887 78999 99999999999953322 377999999999999999999999
Q ss_pred CCCcEEEeeccCeeEEcCCCceEEEEEEEEeeeCcCCCCCccCeEEEEEEeC
Q 013077 84 TNSGFWKSTCKDREIWDERGKKIGLKKNLVFHEGRVPNGIRTKWVMHEYHSL 135 (450)
Q Consensus 84 tggGyWKatG~~K~I~~~~g~vVG~KKtLvFY~Gr~p~G~KT~WVMHEYrL~ 135 (450)
+++|+||++|+.++|.+.++.+||+||+|+||.++.+++.+|+|+||||+|.
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 9999999999999999976679999999999999888999999999999984
No 2
>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=16.32 E-value=58 Score=29.63 Aligned_cols=35 Identities=23% Similarity=0.584 Sum_probs=27.8
Q ss_pred CCCCCCccccchhhhhhhccCcccchhhhhccchh
Q 013077 394 SDTDLPGIVGHESVVDELQHTPKYHKYFEARCSTQ 428 (450)
Q Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (450)
..|.+|-++||++..+-++..-.|.-.....|+.+
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 46789999999998877777777777777788743
No 3
>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=14.12 E-value=1.7e+02 Score=25.61 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=32.9
Q ss_pred CCChHHHHHHHHHHHHCCCCCCCCceeccCCCCCCCCCCCCccC
Q 013077 12 HPTDEEIVTYFLERKMCGLDFPAHTIADVVDVCKYEPWELPQRS 55 (450)
Q Consensus 12 ~PTDEELV~~YL~~Ki~G~plp~~vI~e~vDVY~~ePWdLP~~~ 55 (450)
|-|-.||++.-...-..|+|||.+ .|+-+..|..+|+..
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 568889999888888999999975 688888999998643
No 4
>PHA00692 hypothetical protein
Probab=14.09 E-value=72 Score=25.89 Aligned_cols=9 Identities=44% Similarity=0.619 Sum_probs=7.0
Q ss_pred CCCCceeEC
Q 013077 4 HGVVGFRFH 12 (450)
Q Consensus 4 ~LPpGfRF~ 12 (450)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 368999985
No 5
>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=14.03 E-value=72 Score=29.39 Aligned_cols=34 Identities=18% Similarity=0.547 Sum_probs=28.1
Q ss_pred CCCCCCccccchhhhhhhccCcccchhhhhccch
Q 013077 394 SDTDLPGIVGHESVVDELQHTPKYHKYFEARCST 427 (450)
Q Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 427 (450)
..|.+|-++||++..+-++....|.-..+..|+.
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 3578999999999888777777888888888874
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=12.64 E-value=1.8e+02 Score=25.57 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHHHCCCCCCCCceeccCCCCCCCCCCCCccC
Q 013077 12 HPTDEEIVTYFLERKMCGLDFPAHTIADVVDVCKYEPWELPQRS 55 (450)
Q Consensus 12 ~PTDEELV~~YL~~Ki~G~plp~~vI~e~vDVY~~ePWdLP~~~ 55 (450)
|-|-.||++.-...-..|+|||.+ .|+-+..|..+|+..
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 568889999888888999999975 688888999998643
No 7
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=12.57 E-value=2e+02 Score=28.55 Aligned_cols=62 Identities=15% Similarity=0.258 Sum_probs=35.9
Q ss_pred CCceeECCChHHHHHHHHHHHHCCCCCCCCceeccCCCCCCCCCCCCccCCCCCCCceEEEEe
Q 013077 6 VVGFRFHPTDEEIVTYFLERKMCGLDFPAHTIADVVDVCKYEPWELPQRSSMPKEDRVWYFFN 68 (450)
Q Consensus 6 PpGfRF~PTDEELV~~YL~~Ki~G~plp~~vI~e~vDVY~~ePWdLP~~~~~g~~e~eWYFFs 68 (450)
-.+|||+|+|.--+.-.-.-..-+..+-+....+ .+-|.-+=|+.-+....+++...||=+.
T Consensus 110 i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED-~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 110 ITEFRFVPSDKSALEAMFTQFCECQELNPDPDED-EDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred cccceecCCchhHHHHHHHHHHhhhhcCCCcccc-ccccccchhhhhhhhccCCCCccccccc
Confidence 4589999999876653333333343332222445 6667777777765544445555665443
No 8
>cd07463 CRD_FZ9 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 9 (Fz9) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 9 (Fz9) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz9 may play a signaling role in lymphoid development and maturation, particularly at points where B cells undergo self-renewal prior to further differentiation.
Probab=12.32 E-value=78 Score=28.78 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=27.1
Q ss_pred CCCCCccccchhhhhhhccCcccchhhhhccch
Q 013077 395 DTDLPGIVGHESVVDELQHTPKYHKYFEARCST 427 (450)
Q Consensus 395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 427 (450)
.|.+|-++||++..+-.+....|+......||.
T Consensus 20 ~T~~PN~lgh~sq~ea~~~~~~f~pLv~~~Csp 52 (127)
T cd07463 20 LTRMPNFLGHDSQREAAIKLNEFAPLVEYGCHV 52 (127)
T ss_pred cccCCcccCCcCHHHHHHHHHHHHHHHhcCCCh
Confidence 478999999999877777777788888888884
No 9
>cd07462 CRD_FZ10 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 10 (Fz10) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 10 (Fz10) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. The cellular functon of Fz10 is unknown.
Probab=11.55 E-value=81 Score=28.71 Aligned_cols=34 Identities=21% Similarity=0.450 Sum_probs=25.7
Q ss_pred CCCCCccccchhhhhhhccCcccchhhhhccchh
Q 013077 395 DTDLPGIVGHESVVDELQHTPKYHKYFEARCSTQ 428 (450)
Q Consensus 395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (450)
.|.+|-++||++..+-.+....|+...+..|+..
T Consensus 20 ~T~~PN~lgH~~q~ea~~~~~~f~pLv~~~C~p~ 53 (127)
T cd07462 20 MTRMPNLMGHENQREAAIQLHEFAPLVEYGCHSH 53 (127)
T ss_pred ceeCCcccCCcCHHHHHHHHHHHHHHhccCCChh
Confidence 4779999999997766666666777777777753
No 10
>cd07442 CRD_SFRP4 Cysteine-rich domain of the secreted frizzled-related protein 4 (SFRP4), a Wnt antagonist. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 4 (SFRP4), 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 the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs.
Probab=10.99 E-value=95 Score=28.30 Aligned_cols=35 Identities=17% Similarity=0.370 Sum_probs=27.9
Q ss_pred CCCCCCccccchhhhhhhccCcccchhhhhccchh
Q 013077 394 SDTDLPGIVGHESVVDELQHTPKYHKYFEARCSTQ 428 (450)
Q Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (450)
..|.+|-++||++.-+-.+..-.|+-..+..||..
T Consensus 19 n~T~~PN~lgH~~q~ea~~~~~~f~pLv~~~Csp~ 53 (127)
T cd07442 19 NITRMPNHLHHSTQENAVLAIEQYEELVDTGCSPV 53 (127)
T ss_pred CcccCcCccCCCCHHHHHHHHHHHHHHHcCCCCcc
Confidence 45789999999998877767777888888888743
Done!