Query 009388
Match_columns 536
No_of_seqs 224 out of 983
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 12:31:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009388hhsearch_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 5.8E-41 1.3E-45 302.2 5.2 127 9-140 1-128 (129)
2 PHA00692 hypothetical protein 14.5 66 0.0014 26.5 0.4 9 8-16 36-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 12.8 1.9E+02 0.0042 20.2 2.2 20 18-37 4-23 (27)
4 PLN03105 TCP24 transcription f 11.1 1.9E+02 0.0041 30.0 2.5 34 466-499 38-72 (324)
5 PF03831 PhnA: PhnA protein; 9.7 1.3E+02 0.0029 24.5 0.7 14 485-498 30-43 (56)
6 PF07960 CBP4: CBP4; InterPro 9.5 1.5E+02 0.0033 27.8 1.1 17 10-26 23-40 (128)
7 PF04771 CAV_VP3: Chicken anae 9.3 96 0.0021 28.3 -0.3 37 461-497 62-121 (121)
8 KOG3238 Chloride ion current i 8.9 2.8E+02 0.006 28.1 2.7 45 11-55 111-155 (216)
9 PLN02417 dihydrodipicolinate s 8.3 2.2E+02 0.0048 29.2 1.8 18 9-27 103-120 (280)
10 TIGR02313 HpaI-NOT-DapA 2,4-di 7.6 2.5E+02 0.0054 29.1 1.9 18 9-27 102-119 (294)
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=5.8e-41 Score=302.21 Aligned_cols=127 Identities=57% Similarity=1.113 Sum_probs=95.9
Q ss_pred CCCcceEcCChHHHHHHHHHHHhCCCCCCc-eeeecccCCCCCCCCCCCcCcccCCCCceEEeccCCCcCCCCCCccccc
Q 009388 9 LPLGFRFRPTDEELINHYLRLKINGRDSEV-EVIPEIDVCKLEPWDLPGLSVIKTEDPEWFFFCPRDRKYPNGLRSNRAT 87 (536)
Q Consensus 9 LPpGfRF~PTDEELV~~YL~~Ki~G~p~~~-~~I~evDVY~~ePWdLp~~s~~k~~d~eWYFFspr~rKy~nG~R~nRat 87 (536)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||.+|||+||. ....++.+||||+++.+++++|.|++|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~--~~~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPA--KFKGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHH--HSSS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhh--hccCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 789999999999999994 22346779999999999999999999999
Q ss_pred CCCeeeecCccceEeecCCCCceeeeeEEEEEEeecCCCCCCCcCeEEEEEec
Q 009388 88 EAGYWKATGKDRTIRSRKAGTNACIGMKKTLVFYRGRAPKGERTNWIMHEYRP 140 (536)
Q Consensus 88 g~G~WKatGk~k~I~s~~sggg~vIG~KKtLvFY~grapkg~KT~WvMhEYrl 140 (536)
++|+||++|+.++|... ++.+||+||+|+||.++.+++.+|+|+||||+|
T Consensus 79 ~~G~Wk~~g~~~~i~~~---~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L 128 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDP---GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSL 128 (129)
T ss_dssp TTEEEEEECEEEEEEE----TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE
T ss_pred cceEEeecccccccccc---cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEe
Confidence 99999999999999975 467999999999999888889999999999997
No 2
>PHA00692 hypothetical protein
Probab=14.55 E-value=66 Score=26.48 Aligned_cols=9 Identities=56% Similarity=1.102 Sum_probs=7.3
Q ss_pred CCCCcceEc
Q 009388 8 SLPLGFRFR 16 (536)
Q Consensus 8 ~LPpGfRF~ 16 (536)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=12.80 E-value=1.9e+02 Score=20.25 Aligned_cols=20 Identities=25% Similarity=0.482 Sum_probs=15.6
Q ss_pred ChHHHHHHHHHHHhCCCCCC
Q 009388 18 TDEELINHYLRLKINGRDSE 37 (536)
Q Consensus 18 TDEELV~~YL~~Ki~G~p~~ 37 (536)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999655443
No 4
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=11.05 E-value=1.9e+02 Score=30.05 Aligned_cols=34 Identities=26% Similarity=0.319 Sum_probs=25.0
Q ss_pred cceEEEcccCC-CCCCCCCCccccccccceeeeee
Q 009388 466 GTGIKIRTRQP-QQRPNSFNSVNQGTAQRRLRLQV 499 (536)
Q Consensus 466 gTGIkiRtRqp-q~~~~~~n~~~QGtA~RRIRLq~ 499 (536)
.+-|.+.+|-. .--.++-.++.||.--|||||.+
T Consensus 38 ssrivrvsRa~g~KDRHSKI~TAqGpRDRRvRLSv 72 (324)
T PLN03105 38 SSRIIRVSRASGGKDRHSKVLTSKGLRDRRIRLSV 72 (324)
T ss_pred cceEEEeeccCCCCCcccceecccCCcccceecCH
Confidence 45566666654 33345667899999999999998
No 5
>PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A.
Probab=9.67 E-value=1.3e+02 Score=24.48 Aligned_cols=14 Identities=29% Similarity=0.646 Sum_probs=9.9
Q ss_pred ccccccccceeeee
Q 009388 485 SVNQGTAQRRLRLQ 498 (536)
Q Consensus 485 ~~~QGtA~RRIRLq 498 (536)
..-|||+-|.|||-
T Consensus 30 ~~K~GTkvknIrL~ 43 (56)
T PF03831_consen 30 TIKRGTKVKNIRLV 43 (56)
T ss_dssp EE-TT-EEECEEE-
T ss_pred cccCceEEEeEEec
Confidence 36799999999995
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=9.51 E-value=1.5e+02 Score=27.81 Aligned_cols=17 Identities=41% Similarity=0.860 Sum_probs=12.1
Q ss_pred CCcceE-cCChHHHHHHH
Q 009388 10 PLGFRF-RPTDEELINHY 26 (536)
Q Consensus 10 PpGfRF-~PTDEELV~~Y 26 (536)
|.-|++ .||||||+..|
T Consensus 23 ~~l~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 23 PALVKYTTPTEEELFKRY 40 (128)
T ss_pred hHHheecCCCHHHHHHhc
Confidence 334444 49999999876
No 7
>PF04771 CAV_VP3: Chicken anaemia virus VP-3 protein; InterPro: IPR006858 Chicken anaemia virus (CAV) is a circovirus which can cause severe depletion of some cell types, such as lymphocytes, by the induction of apoptosis []. Studies indicate that expression of the viral VP3 protein, also known as apoptin, is sufficient to induce apoptosis in susceptible cells and to produce the doughnut-shaped apoptosis body formations observed in cells during CAV infections. This protein induces apoptosis in tumor cells and transformed cells, but is incapable of inducing apoptosis in normal cells unless tranforming signals are supplied which induce its phosphorylation. Cell death occurs in a p53- and Bcl-2-independent manner []. Apoptin contains putative nuclear localisation and nuclear export domains, and has a positively charged C terminus which is thought to allow direct interaction with nucleic acids. Localisation to the nucleus appears to be necessary for apoptosis, but is not sufficient on its own. The biologically active form of the protein appears to be large complexes of 30-40 molecules which form distinct superstructures upon DNA binding. A number of cellular factors including Nmi, and several death domain superfamily proteins, have been shown to interact apoptin. It has been suggested that in the nucleus, it this binding of phosphorylated apoptin to DNA and other factors which starts the apoptotic machinery, triggering cell death.; GO: 0019051 induction by virus of host apoptosis, 0042025 host cell nucleus
Probab=9.25 E-value=96 Score=28.29 Aligned_cols=37 Identities=32% Similarity=0.460 Sum_probs=22.6
Q ss_pred CCCCCcceEE----EcccCCCCCCCCCCcc--------------c-----cccccceeee
Q 009388 461 GDFAVGTGIK----IRTRQPQQRPNSFNSV--------------N-----QGTAQRRLRL 497 (536)
Q Consensus 461 ~~~~~gTGIk----iRtRqpq~~~~~~n~~--------------~-----QGtA~RRIRL 497 (536)
.|.++-||.| .|+|+|+.-+....++ + --||.|||||
T Consensus 62 Ad~s~~TGsrr~~D~~hrrPrrtS~~~~~~~~~~ke~~qKEnlIT~~~~~p~~~~~~~~~ 121 (121)
T PF04771_consen 62 ADDSGVTGSRRLPDLSHRRPRRTSSPESYVGSEAKESQQKENLITLRPSRPRTARRRIRL 121 (121)
T ss_pred cCCCccccccccccccccCCCCCCCCcccchhhhhHHHhhhhheeccCCCcchhhhhccC
Confidence 3455667766 4788887654433211 1 2489999997
No 8
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=8.93 E-value=2.8e+02 Score=28.10 Aligned_cols=45 Identities=18% Similarity=0.264 Sum_probs=23.9
Q ss_pred CcceEcCChHHHHHHHHHHHhCCCCCCceeeecccCCCCCCCCCC
Q 009388 11 LGFRFRPTDEELINHYLRLKINGRDSEVEVIPEIDVCKLEPWDLP 55 (536)
Q Consensus 11 pGfRF~PTDEELV~~YL~~Ki~G~p~~~~~I~evDVY~~ePWdLp 55 (536)
-+|||+|+|.--+...-........+.+.-..+.+-|.-+=|+.-
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~me 155 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDME 155 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhh
Confidence 489999999876654333333333222211344444555555543
No 9
>PLN02417 dihydrodipicolinate synthase
Probab=8.29 E-value=2.2e+02 Score=29.22 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=14.5
Q ss_pred CCCcceEcCChHHHHHHHH
Q 009388 9 LPLGFRFRPTDEELINHYL 27 (536)
Q Consensus 9 LPpGfRF~PTDEELV~~YL 27 (536)
+|| |-|.|+++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 566 458999999999884
No 10
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=7.57 E-value=2.5e+02 Score=29.08 Aligned_cols=18 Identities=22% Similarity=0.508 Sum_probs=14.4
Q ss_pred CCCcceEcCChHHHHHHHH
Q 009388 9 LPLGFRFRPTDEELINHYL 27 (536)
Q Consensus 9 LPpGfRF~PTDEELV~~YL 27 (536)
+||-| |.|++++|+.||-
T Consensus 102 ~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred cCccC-CCCCHHHHHHHHH
Confidence 46655 8899999999873
Done!