Query 041697
Match_columns 230
No_of_seqs 143 out of 877
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:44:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041697hhsearch_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 5.7E-43 1.2E-47 279.8 5.9 129 8-144 1-129 (129)
2 PHA00692 hypothetical protein 35.7 15 0.00033 26.0 0.5 11 6-16 35-45 (74)
3 KOG1334 WD40 repeat protein [G 29.5 75 0.0016 31.5 4.1 74 45-127 341-435 (559)
4 PF07960 CBP4: CBP4; InterPro 28.8 30 0.00064 28.1 1.1 12 14-25 29-40 (128)
5 PF01473 CW_binding_1: Putativ 25.9 45 0.00097 17.6 1.2 8 67-74 7-14 (19)
6 COG1095 RPB7 DNA-directed RNA 24.2 49 0.0011 28.4 1.7 40 7-47 12-51 (183)
7 PF09174 Maf1: Maf1 regulator; 23.9 18 0.0004 30.6 -0.9 13 42-54 137-149 (179)
8 COG4741 Predicted secreted end 23.2 31 0.00068 29.0 0.3 17 3-20 94-110 (175)
9 smart00265 BH4 BH4 Bcl-2 homol 22.6 1.4E+02 0.0031 17.7 3.0 20 16-35 3-22 (27)
10 PF13822 ACC_epsilon: Acyl-CoA 22.3 45 0.00098 23.3 1.0 9 15-23 10-18 (62)
11 smart00707 RPEL Repeat in Dros 21.5 63 0.0014 19.1 1.3 13 11-23 6-18 (26)
12 PLN02417 dihydrodipicolinate s 21.4 48 0.001 29.6 1.2 19 7-26 102-120 (280)
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=5.7e-43 Score=279.83 Aligned_cols=129 Identities=35% Similarity=0.641 Sum_probs=94.9
Q ss_pred CCCCceeCCChHHHHHHHHHHHHhCCCCCcccceeeeccCCCCCCCcccccCCCCCCCCCCcEEEEecccccCCCCCccc
Q 041697 8 LPHGFQFRPSDEELVEHYLKKKVSGTLIPLAEYFIRDCNLYETKPSKIWDSHGGPFLNADEDLYFFTQLKKKSSKGSRID 87 (230)
Q Consensus 8 LPpGfRF~PTDeELI~~YL~~Ki~g~~~p~~~~vI~~~DvY~~ePw~L~~~~~~~~~~~~~~wYFFs~r~~k~~~g~R~~ 87 (230)
|||||||+|||+|||.+||++|+.|.++|.. .+|+++|||+++||+|+..+. .++.+||||++++++++++.|.+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~-~~i~~~Diy~~~P~~L~~~~~----~~~~~~yFF~~~~~~~~~~~r~~ 75 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCE-DVIHDVDIYSAHPWELPAKFK----GGDEEWYFFSPRKKKYPNGGRPN 75 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS-GGGCHHHSS----S-SSEEEEEEE----------S-
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcc-cceeecccCccChHHhhhhcc----CCCceEEEEEecccccCCccccc
Confidence 8999999999999999999999999987774 479999999999999995322 35679999999999999999999
Q ss_pred cccCCCCceeeeccCCceEEeCCCceEEEEEEEeecCcCCCCCCCCCCeEEEEEEeC
Q 041697 88 RKVGSSGGAWQGEDAGKDIVSGQSKIKIGSKKQFRYEKKDLPKNQATNYVLCRLRKN 144 (230)
Q Consensus 88 R~v~~~~G~Wk~~g~~k~I~~~~~g~~iG~Kk~l~fy~~~~~~~~kt~WvM~Ey~l~ 144 (230)
|+++ +|+||++|+.++|.+. ++.+||+|++|+||.+..+++.+|+|+|+||+|.
T Consensus 76 R~~~--~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 76 RVTG--GGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEET--TEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccc--ceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9888 9999999999999986 5689999999999988888889999999999983
No 2
>PHA00692 hypothetical protein
Probab=35.75 E-value=15 Score=25.97 Aligned_cols=11 Identities=36% Similarity=0.615 Sum_probs=8.3
Q ss_pred CCCCCCceeCC
Q 041697 6 PFLPHGFQFRP 16 (230)
Q Consensus 6 ~~LPpGfRF~P 16 (230)
...||||||--
T Consensus 35 veyppgfrfgg 45 (74)
T PHA00692 35 VEYPPGFRFGG 45 (74)
T ss_pred EecCCCccccc
Confidence 35799999953
No 3
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=29.47 E-value=75 Score=31.48 Aligned_cols=74 Identities=30% Similarity=0.396 Sum_probs=46.0
Q ss_pred ccCCCCCCCcccccCCCCCCCCCCcEEEEecccccC----------------CCCCccccccCCCCceeeeccCCceEEe
Q 041697 45 CNLYETKPSKIWDSHGGPFLNADEDLYFFTQLKKKS----------------SKGSRIDRKVGSSGGAWQGEDAGKDIVS 108 (230)
Q Consensus 45 ~DvY~~ePw~L~~~~~~~~~~~~~~wYFFs~r~~k~----------------~~g~R~~R~v~~~~G~Wk~~g~~k~I~~ 108 (230)
+=+|.++|-+|... ..+...|||.+-.... =+|.|-+|++++ .-+|=.. ..-|++
T Consensus 341 gl~Ysh~~sElLaS------YnDe~IYLF~~~~~~G~~p~~~s~~~~~~k~vYKGHrN~~TVKg-VNFfGPr--sEyVvS 411 (559)
T KOG1334|consen 341 GLVYSHDGSELLAS------YNDEDIYLFNKSMGDGSEPDPSSPREQYVKRVYKGHRNSRTVKG-VNFFGPR--SEYVVS 411 (559)
T ss_pred eEEecCCccceeee------ecccceEEeccccccCCCCCCCcchhhccchhhcccccccccce-eeeccCc--cceEEe
Confidence 34577777777643 3466789996432211 136777888876 7788753 345555
Q ss_pred C--CCceEEEEEEE---eecCcCC
Q 041697 109 G--QSKIKIGSKKQ---FRYEKKD 127 (230)
Q Consensus 109 ~--~~g~~iG~Kk~---l~fy~~~ 127 (230)
+ .+..+||.|++ +.|.+++
T Consensus 412 GSDCGhIFiW~K~t~eii~~MegD 435 (559)
T KOG1334|consen 412 GSDCGHIFIWDKKTGEIIRFMEGD 435 (559)
T ss_pred cCccceEEEEecchhHHHHHhhcc
Confidence 4 35567888864 5566654
No 4
>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=28.79 E-value=30 Score=28.12 Aligned_cols=12 Identities=42% Similarity=0.841 Sum_probs=10.1
Q ss_pred eCCChHHHHHHH
Q 041697 14 FRPSDEELVEHY 25 (230)
Q Consensus 14 F~PTDeELI~~Y 25 (230)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 379999999875
No 5
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=25.90 E-value=45 Score=17.55 Aligned_cols=8 Identities=25% Similarity=0.949 Sum_probs=6.6
Q ss_pred CCcEEEEe
Q 041697 67 DEDLYFFT 74 (230)
Q Consensus 67 ~~~wYFFs 74 (230)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899995
No 6
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=24.24 E-value=49 Score=28.43 Aligned_cols=40 Identities=25% Similarity=0.227 Sum_probs=31.0
Q ss_pred CCCCCceeCCChHHHHHHHHHHHHhCCCCCcccceeeeccC
Q 041697 7 FLPHGFQFRPSDEELVEHYLKKKVSGTLIPLAEYFIRDCNL 47 (230)
Q Consensus 7 ~LPpGfRF~PTDeELI~~YL~~Ki~g~~~p~~~~vI~~~Dv 47 (230)
.+||- .|.|--+++|...|+.|..|+.....+.+|...|+
T Consensus 12 ripP~-~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v 51 (183)
T COG1095 12 RIPPS-YFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDV 51 (183)
T ss_pred EeCHH-HcCccHHHHHHHHHHHHhcceEccccCEEEEEEEe
Confidence 46776 68888999999999999999766555556666555
No 7
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=23.90 E-value=18 Score=30.56 Aligned_cols=13 Identities=31% Similarity=1.071 Sum_probs=7.4
Q ss_pred eeeccCCCCCCCc
Q 041697 42 IRDCNLYETKPSK 54 (230)
Q Consensus 42 I~~~DvY~~ePw~ 54 (230)
+.+||||.+.|..
T Consensus 137 l~~C~iYsy~pd~ 149 (179)
T PF09174_consen 137 LKDCDIYSYNPDS 149 (179)
T ss_dssp GGG-EEEEE---G
T ss_pred ccCceEEEEccCC
Confidence 6689999999943
No 8
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=23.25 E-value=31 Score=29.04 Aligned_cols=17 Identities=35% Similarity=0.962 Sum_probs=12.0
Q ss_pred CCCCCCCCCceeCCChHH
Q 041697 3 EHIPFLPHGFQFRPSDEE 20 (230)
Q Consensus 3 ~~~~~LPpGfRF~PTDeE 20 (230)
++++-+| +|+|+|.|.-
T Consensus 94 qlaPffp-~f~ynPkD~R 110 (175)
T COG4741 94 QLAPFFP-EFKYNPKDAR 110 (175)
T ss_pred hhccccc-CCCcCCccce
Confidence 3444455 9999999953
No 9
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=22.64 E-value=1.4e+02 Score=17.73 Aligned_cols=20 Identities=30% Similarity=0.326 Sum_probs=15.8
Q ss_pred CChHHHHHHHHHHHHhCCCC
Q 041697 16 PSDEELVEHYLKKKVSGTLI 35 (230)
Q Consensus 16 PTDeELI~~YL~~Ki~g~~~ 35 (230)
.+-.|||.+|+.-|+.-+-.
T Consensus 3 ~~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred cchHHHHHHHHHHHHhhcCC
Confidence 35689999999999976533
No 10
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=22.25 E-value=45 Score=23.33 Aligned_cols=9 Identities=56% Similarity=0.940 Sum_probs=7.8
Q ss_pred CCChHHHHH
Q 041697 15 RPSDEELVE 23 (230)
Q Consensus 15 ~PTDeELI~ 23 (230)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999865
No 11
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=21.52 E-value=63 Score=19.07 Aligned_cols=13 Identities=46% Similarity=0.639 Sum_probs=11.0
Q ss_pred CceeCCChHHHHH
Q 041697 11 GFQFRPSDEELVE 23 (230)
Q Consensus 11 GfRF~PTDeELI~ 23 (230)
...++||-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 12
>PLN02417 dihydrodipicolinate synthase
Probab=21.41 E-value=48 Score=29.60 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=15.0
Q ss_pred CCCCCceeCCChHHHHHHHH
Q 041697 7 FLPHGFQFRPSDEELVEHYL 26 (230)
Q Consensus 7 ~LPpGfRF~PTDeELI~~YL 26 (230)
-+|| +.|.||++||+.||-
T Consensus 102 ~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 102 HINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EcCC-ccCCCCHHHHHHHHH
Confidence 4566 458999999999773
Done!