Query 040617
Match_columns 247
No_of_seqs 162 out of 982
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 10:07:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040617.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040617hhsearch_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 8.7E-45 1.9E-49 292.5 7.6 127 6-134 1-129 (129)
2 PHA00692 hypothetical protein 42.5 9.3 0.0002 26.9 0.3 10 4-13 35-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 28.6 66 0.0014 19.1 2.3 20 15-34 4-23 (27)
4 cd00933 barnase Barnase, a mem 25.6 2.3E+02 0.005 22.3 5.6 23 15-40 2-24 (107)
5 KOG3238 Chloride ion current i 24.7 99 0.0022 27.1 3.7 63 5-67 108-170 (216)
6 smart00707 RPEL Repeat in Dros 23.3 56 0.0012 19.2 1.3 14 9-22 6-19 (26)
7 PF07960 CBP4: CBP4; InterPro 22.6 45 0.00098 27.1 1.1 11 13-23 30-40 (128)
8 PF08338 DUF1731: Domain of un 22.2 63 0.0014 21.5 1.6 16 8-23 31-47 (48)
9 PF05865 Cypo_polyhedrin: Cypo 19.8 1E+02 0.0023 26.3 2.8 28 86-113 140-168 (248)
10 PF01473 CW_binding_1: Putativ 17.1 82 0.0018 16.4 1.1 9 61-69 7-15 (19)
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=8.7e-45 Score=292.53 Aligned_cols=127 Identities=57% Similarity=1.145 Sum_probs=97.0
Q ss_pred CCCCceeCCChHHHHHHHHHhhHcCCCCCc-CceeecCCCCCCcccchhhcCCCCCCCceEEeccccccCCCCCcccccc
Q 040617 6 LPPGFRFHPTDEELVNYYLKRKINGQEIEL-DIIPEVDLYKCEPWELAEKSFLPSRDPEWYFFGPRDRKYPNGFRTNRAT 84 (247)
Q Consensus 6 LPpGfrF~PTDeELI~~YL~~Ki~g~~l~~-~~I~evDvy~~~PwdL~~~~~~~~~d~~wYFFt~r~~k~~~g~R~~R~t 84 (247)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|++. ...++.+||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~--~~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAK--FKGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHH--SSS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhh--ccCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 7899999999999999953 2346679999999999999999999999
Q ss_pred ccceeeecCCceeEee-cCceeeEEEEEEeecCCCCCCCCcCeEEEEEEeC
Q 040617 85 RAGYWKSTGKDRRVTY-QSRAIGMKKTLVYYRGRAPQGIRTDWVMHEYRLD 134 (247)
Q Consensus 85 ~gG~Wk~~G~~~~I~~-~g~~iG~Krtl~Fy~g~~~~g~rT~WvM~EY~l~ 134 (247)
++|+||.+|+.++|.+ ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999998 8999999999999998888899999999999984
No 2
>PHA00692 hypothetical protein
Probab=42.47 E-value=9.3 Score=26.91 Aligned_cols=10 Identities=70% Similarity=1.388 Sum_probs=8.0
Q ss_pred CCCCCCceeC
Q 040617 4 VGLPPGFRFH 13 (247)
Q Consensus 4 ~~LPpGfrF~ 13 (247)
+..||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4579999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=28.62 E-value=66 Score=19.07 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=15.5
Q ss_pred ChHHHHHHHHHhhHcCCCCC
Q 040617 15 TDEELVNYYLKRKINGQEIE 34 (247)
Q Consensus 15 TDeELI~~YL~~Ki~g~~l~ 34 (247)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999755443
No 4
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=25.58 E-value=2.3e+02 Score=22.29 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHhhHcCCCCCcCceee
Q 040617 15 TDEELVNYYLKRKINGQEIELDIIPE 40 (247)
Q Consensus 15 TDeELI~~YL~~Ki~g~~l~~~~I~e 40 (247)
|++|-|..||.. .+ .||..+|.-
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK 24 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITK 24 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeH
Confidence 455666678887 33 377777754
No 5
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=24.75 E-value=99 Score=27.07 Aligned_cols=63 Identities=21% Similarity=0.316 Sum_probs=34.9
Q ss_pred CCCCCceeCCChHHHHHHHHHhhHcCCCCCcCceeecCCCCCCcccchhhcCCCCCCCceEEe
Q 040617 5 GLPPGFRFHPTDEELVNYYLKRKINGQEIELDIIPEVDLYKCEPWELAEKSFLPSRDPEWYFF 67 (247)
Q Consensus 5 ~LPpGfrF~PTDeELI~~YL~~Ki~g~~l~~~~I~evDvy~~~PwdL~~~~~~~~~d~~wYFF 67 (247)
...-+|||+|+|.--+...---...++.+-+.-..+.+-|.-+=|+.-......++...||=+
T Consensus 108 e~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 108 EPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred cccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCcccccc
Confidence 345689999999887775333444444332222455566666666665543333344444433
No 6
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=23.26 E-value=56 Score=19.20 Aligned_cols=14 Identities=36% Similarity=0.404 Sum_probs=11.2
Q ss_pred CceeCCChHHHHHH
Q 040617 9 GFRFHPTDEELVNY 22 (247)
Q Consensus 9 GfrF~PTDeELI~~ 22 (247)
...++||.+|||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45689999999973
No 7
>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=22.62 E-value=45 Score=27.08 Aligned_cols=11 Identities=55% Similarity=0.927 Sum_probs=9.4
Q ss_pred CCChHHHHHHH
Q 040617 13 HPTDEELVNYY 23 (247)
Q Consensus 13 ~PTDeELI~~Y 23 (247)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 8
>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=22.17 E-value=63 Score=21.45 Aligned_cols=16 Identities=44% Similarity=0.717 Sum_probs=9.3
Q ss_pred CCceeC-CChHHHHHHH
Q 040617 8 PGFRFH-PTDEELVNYY 23 (247)
Q Consensus 8 pGfrF~-PTDeELI~~Y 23 (247)
-||+|+ |+=++-+.+.
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 499998 8888777654
No 9
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=19.76 E-value=1e+02 Score=26.25 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=18.0
Q ss_pred cceeeecC-CceeEeecCceeeEEEEEEe
Q 040617 86 AGYWKSTG-KDRRVTYQSRAIGMKKTLVY 113 (247)
Q Consensus 86 gG~Wk~~G-~~~~I~~~g~~iG~Krtl~F 113 (247)
.--|.++| +-|+|..+|++||+...|..
T Consensus 140 shpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred cCCccccCceEEEeeccceEeeeeeeeec
Confidence 34699998 56778889999999988765
No 10
>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=17.07 E-value=82 Score=16.42 Aligned_cols=9 Identities=33% Similarity=1.335 Sum_probs=6.8
Q ss_pred CCceEEecc
Q 040617 61 DPEWYFFGP 69 (247)
Q Consensus 61 d~~wYFFt~ 69 (247)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 468999953
Done!