Query 025667
Match_columns 249
No_of_seqs 177 out of 855
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 08:14:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025667hhsearch_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 99.9 1.7E-22 3.6E-27 163.4 6.5 74 5-78 54-129 (129)
2 PF01473 CW_binding_1: Putativ 18.6 81 0.0018 17.5 1.3 8 6-13 7-14 (19)
3 COG3100 Uncharacterized protei 9.2 2.1E+02 0.0045 23.4 1.6 22 94-115 9-30 (103)
4 PRK04235 hypothetical protein; 8.5 1.6E+02 0.0035 26.3 0.8 15 164-178 37-51 (196)
5 PF10983 DUF2793: Protein of u 7.8 1.8E+02 0.0038 22.9 0.7 15 2-16 52-66 (87)
6 PHA02123 hypothetical protein 7.5 2.2E+02 0.0048 24.0 1.2 42 148-191 21-63 (146)
7 cd08398 C2_PI3K_class_I_alpha 7.2 2E+02 0.0043 24.6 0.7 8 191-198 53-60 (158)
8 PF06587 DUF1137: Protein of u 6.5 1.2E+02 0.0027 26.3 -0.8 23 169-192 71-94 (159)
9 PF10872 DUF2740: Protein of u 5.9 2.5E+02 0.0054 19.7 0.5 10 233-242 3-12 (48)
10 PF15471 TMEM171: Transmembran 5.5 6.9E+02 0.015 24.1 3.4 13 94-106 176-188 (319)
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=99.87 E-value=1.7e-22 Score=163.39 Aligned_cols=74 Identities=64% Similarity=1.310 Sum_probs=56.9
Q ss_pred CCceEEEEeecCCCCCCCCCCcccccCceeeecCCccccc--CCceeeEEEEEEeeecCCCCCcccceEEEEeeeC
Q 025667 5 GEKEWYFFSPRDRKYPNGSRPNRAAGSGYWKATGADKPIG--KPKTLGIKKALVFYAGKAPKGIKTNWIMHEYRPA 78 (249)
Q Consensus 5 gEkeWYFFSpr~rK~~nG~R~nRatg~GyWKatG~~K~I~--~gkvVG~KKtLvFY~Gk~p~g~KT~WvMhEYrL~ 78 (249)
++++|||||++++++.+|.|.+|++++|+||++|+.++|. ++++||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 54 ~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 54 GDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred CCceEEEEEecccccCCcccccccccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 5679999999999999999999999999999999999996 5889999999999999888999999999999983
No 2
>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=18.60 E-value=81 Score=17.48 Aligned_cols=8 Identities=38% Similarity=1.468 Sum_probs=6.4
Q ss_pred CceEEEEe
Q 025667 6 EKEWYFFS 13 (249)
Q Consensus 6 EkeWYFFS 13 (249)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 3
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=9.24 E-value=2.1e+02 Score=23.43 Aligned_cols=22 Identities=14% Similarity=0.310 Sum_probs=16.2
Q ss_pred ceEEEEEEEeCCCCCcCCCCCC
Q 025667 94 DWVLCRLYNKKGRMEKHYPSDQ 115 (249)
Q Consensus 94 d~VLCRIY~Kk~~~ek~~~~~~ 115 (249)
--.||-||+++++..-+--+..
T Consensus 9 ~~mlCaIYkS~kk~~tYLYV~k 30 (103)
T COG3100 9 KSMLCAIYKSPKKDGTYLYVEK 30 (103)
T ss_pred eeeeeeeeecCcCCccEEEEec
Confidence 3479999999888776655533
No 4
>PRK04235 hypothetical protein; Provisional
Probab=8.50 E-value=1.6e+02 Score=26.30 Aligned_cols=15 Identities=40% Similarity=0.567 Sum_probs=12.2
Q ss_pred CCcccccCCCCcccc
Q 025667 164 SVPRLQTDSSCSEHV 178 (249)
Q Consensus 164 s~~~~h~dss~~~~~ 178 (249)
|.|.+-|.||||--|
T Consensus 37 s~~~~~TTSSCSGRI 51 (196)
T PRK04235 37 SLKNYYTTSSCSGRI 51 (196)
T ss_pred CCCCeEEccCCcceE
Confidence 677888999999754
No 5
>PF10983 DUF2793: Protein of unknown function (DUF2793); InterPro: IPR021251 This entry is represented by Bacteriophage D3112, Orf54. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=7.82 E-value=1.8e+02 Score=22.86 Aligned_cols=15 Identities=33% Similarity=0.911 Sum_probs=12.6
Q ss_pred CccCCceEEEEeecC
Q 025667 2 ARYGEKEWYFFSPRD 16 (249)
Q Consensus 2 al~gEkeWYFFSpr~ 16 (249)
|.+-++.|.||+|+.
T Consensus 52 A~~~~g~W~f~~P~~ 66 (87)
T PF10983_consen 52 AAWQDGAWRFLTPRP 66 (87)
T ss_pred EEEECCeEEEeCCCC
Confidence 566788999999996
No 6
>PHA02123 hypothetical protein
Probab=7.52 E-value=2.2e+02 Score=23.97 Aligned_cols=42 Identities=26% Similarity=0.438 Sum_probs=27.2
Q ss_pred CCCCcccCcccccCCCCCcccccCCCCc-ccccCCccccCccccc
Q 025667 148 SPVPMMNDLLNMDTSDSVPRLQTDSSCS-EHVLSPEIACDKEVQS 191 (249)
Q Consensus 148 ~~~~~~~~~~~~~~s~s~~~~h~dss~~-~~~~~~~~~~~~evqs 191 (249)
|-++.+|++|+|---.-|-+-.||-..- |.+|| ..|++||.-
T Consensus 21 pvtan~nemf~fp~ksgvi~eftdeng~yesals--~scd~~~~~ 63 (146)
T PHA02123 21 PVTANVNEMFHFPQKSGVIQEFTDENGTYESALS--ASCDREVRE 63 (146)
T ss_pred ccccChhhhccccccccchhhhhcCCCcEeehhc--ccccHHHHh
Confidence 3355689999985433444444776554 77775 579988744
No 7
>cd08398 C2_PI3K_class_I_alpha C2 domain present in class I alpha phosphatidylinositol 3-kinases (PI3Ks). PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. The members here are class I, alpha isoform PI3Ks and contain both a Ras-binding domain and a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a c
Probab=7.18 E-value=2e+02 Score=24.61 Aligned_cols=8 Identities=50% Similarity=1.261 Sum_probs=6.2
Q ss_pred cccccccc
Q 025667 191 SVPKWNDL 198 (249)
Q Consensus 191 s~pk~~~~ 198 (249)
+.++||||
T Consensus 53 ~~~~WnEw 60 (158)
T cd08398 53 SNPRWNEW 60 (158)
T ss_pred CCCcccee
Confidence 45789998
No 8
>PF06587 DUF1137: Protein of unknown function (DUF1137); InterPro: IPR010564 This family consists of several hypothetical proteins specific to Chlamydia species. The function of this family is unknown.
Probab=6.54 E-value=1.2e+02 Score=26.31 Aligned_cols=23 Identities=39% Similarity=0.641 Sum_probs=14.7
Q ss_pred ccCCCCcc-cccCCccccCcccccc
Q 025667 169 QTDSSCSE-HVLSPEIACDKEVQSV 192 (249)
Q Consensus 169 h~dss~~~-~~~~~~~~~~~evqs~ 192 (249)
|.|-||=| |.-...++| ||+-|.
T Consensus 71 ~idKScmELh~s~~~~~C-kE~LS~ 94 (159)
T PF06587_consen 71 TIDKSCMELHFSDASYSC-KELLSR 94 (159)
T ss_pred eeechheeEeecCCChHH-HHHHHH
Confidence 35777877 444446788 577664
No 9
>PF10872 DUF2740: Protein of unknown function (DUF2740); InterPro: IPR022626 This entry is represented by Bacteriophage P22, Orf48. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Probab=5.85 E-value=2.5e+02 Score=19.72 Aligned_cols=10 Identities=70% Similarity=1.036 Sum_probs=7.7
Q ss_pred CCCCchhhhH
Q 025667 233 DQLSPYQDLF 242 (249)
Q Consensus 233 ~~~~~~qd~~ 242 (249)
.|+||.||-+
T Consensus 3 kqlsp~qdk~ 12 (48)
T PF10872_consen 3 KQLSPYQDKI 12 (48)
T ss_pred cccCccHHHH
Confidence 3789999864
No 10
>PF15471 TMEM171: Transmembrane protein family 171
Probab=5.49 E-value=6.9e+02 Score=24.14 Aligned_cols=13 Identities=8% Similarity=0.197 Sum_probs=8.2
Q ss_pred ceEEEEEEEeCCC
Q 025667 94 DWVLCRLYNKKGR 106 (249)
Q Consensus 94 d~VLCRIY~Kk~~ 106 (249)
=+|+-+|.||..-
T Consensus 176 FFVVAHvKKr~nl 188 (319)
T PF15471_consen 176 FFVVAHVKKRNNL 188 (319)
T ss_pred hhheeeeeeccCC
Confidence 3677888665543
Done!