Query 025156
Match_columns 257
No_of_seqs 187 out of 889
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:11:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025156.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025156hhsearch_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 8E-25 1.7E-29 178.1 4.7 86 2-87 42-129 (129)
2 PF01473 CW_binding_1: Putativ 17.2 87 0.0019 17.3 1.2 8 15-22 7-14 (19)
3 KOG2675 Adenylate cyclase-asso 15.5 1E+02 0.0022 31.3 2.0 13 77-89 171-183 (480)
4 PF15471 TMEM171: Transmembran 12.8 1.6E+02 0.0034 28.3 2.4 13 103-115 176-188 (319)
5 KOG4280 Kinesin-like protein [ 9.6 1.4E+02 0.0031 31.0 1.1 19 185-207 203-221 (574)
6 PRK04235 hypothetical protein; 8.9 1.6E+02 0.0034 26.4 0.9 16 181-196 36-51 (196)
7 COG3350 Uncharacterized conser 7.5 2.5E+02 0.0055 20.4 1.3 18 5-23 15-32 (53)
8 KOG4816 Uncharacterized conser 6.8 2.2E+02 0.0047 23.0 0.7 16 176-192 10-25 (98)
9 PF14983 DUF4513: Domain of un 6.8 3.1E+02 0.0068 23.2 1.7 33 178-212 4-37 (132)
10 COG3100 Uncharacterized protei 6.5 3.2E+02 0.007 22.3 1.6 17 103-119 9-25 (103)
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=99.90 E-value=8e-25 Score=178.14 Aligned_cols=86 Identities=56% Similarity=1.122 Sum_probs=64.5
Q ss_pred CCcccccccccCCCceEEEeccCCCCCCCCCCCcccccCccccccCCccccc--CCcceEEEEEEeeeeccCCCCcccCe
Q 025156 2 IFIREISDLALYGEKEWYFFTPRDRKYPNGSRPNRAAGSGYWKATGADKPIG--QPKPVGIKKALVFYAGKAPKGEKTNW 79 (257)
Q Consensus 2 ~~P~dLPg~al~gekeWYFFSpr~rKy~nG~R~nRatg~GyWK~tG~~k~I~--~gk~VG~KKtLvFY~Gk~p~g~KT~W 79 (257)
.+||+||+....++++||||+++.+++.+|.|.+|++++|+||.+|++++|. ++++||+|++|+||.++.+++.+|+|
T Consensus 42 ~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W 121 (129)
T PF02365_consen 42 AHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGW 121 (129)
T ss_dssp S-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEE
T ss_pred cChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCe
Confidence 4799999543446779999999999999999999999999999999999996 57899999999999998899999999
Q ss_pred EEeEEEec
Q 025156 80 IMHEYRLA 87 (257)
Q Consensus 80 vMhEYrL~ 87 (257)
+||||+|.
T Consensus 122 ~M~EY~L~ 129 (129)
T PF02365_consen 122 VMHEYSLE 129 (129)
T ss_dssp EEEEEEE-
T ss_pred EEEEEEeC
Confidence 99999983
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=17.23 E-value=87 Score=17.33 Aligned_cols=8 Identities=38% Similarity=1.448 Sum_probs=6.4
Q ss_pred CceEEEec
Q 025156 15 EKEWYFFT 22 (257)
Q Consensus 15 ekeWYFFS 22 (257)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899995
No 3
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=15.51 E-value=1e+02 Score=31.29 Aligned_cols=13 Identities=38% Similarity=0.642 Sum_probs=7.3
Q ss_pred cCeEEeEEEecCc
Q 025156 77 TNWIMHEYRLADV 89 (257)
Q Consensus 77 T~WvMhEYrL~~~ 89 (257)
||=+|.||+=.+.
T Consensus 171 ~NrvLkEyk~~D~ 183 (480)
T KOG2675|consen 171 TNRVLKEYKEKDP 183 (480)
T ss_pred HHHHHHHhccCCh
Confidence 4456667765443
No 4
>PF15471 TMEM171: Transmembrane protein family 171
Probab=12.76 E-value=1.6e+02 Score=28.31 Aligned_cols=13 Identities=8% Similarity=0.232 Sum_probs=8.3
Q ss_pred CeEEEEEEeeCCC
Q 025156 103 DWVLCRIYNKKGS 115 (257)
Q Consensus 103 dwVLCRIy~Kk~~ 115 (257)
=+||-+|.||..-
T Consensus 176 FFVVAHvKKr~nl 188 (319)
T PF15471_consen 176 FFVVAHVKKRNNL 188 (319)
T ss_pred hhheeeeeeccCC
Confidence 4688888665433
No 5
>KOG4280 consensus Kinesin-like protein [Cytoskeleton]
Probab=9.65 E-value=1.4e+02 Score=31.03 Aligned_cols=19 Identities=42% Similarity=0.679 Sum_probs=15.9
Q ss_pred ccccCCCCcceecCCCccceecc
Q 025156 185 KLNTDSSCSEHVVSPEFTCEVQS 207 (257)
Q Consensus 185 ~~~~dss~~~~~~s~~~~~~v~s 207 (257)
.+|.+||.| |++ |||.|.|
T Consensus 203 ~mn~~SsRS-H~i---ft~~i~~ 221 (574)
T KOG4280|consen 203 SMNEESSRS-HAI---FTIHIES 221 (574)
T ss_pred cCCcccccc-eEE---EEEEEEe
Confidence 456689999 999 9999888
No 6
>PRK04235 hypothetical protein; Provisional
Probab=8.92 E-value=1.6e+02 Score=26.43 Aligned_cols=16 Identities=38% Similarity=0.594 Sum_probs=13.0
Q ss_pred CCCcccccCCCCccee
Q 025156 181 DSVPKLNTDSSCSEHV 196 (257)
Q Consensus 181 ~s~p~~~~dss~~~~~ 196 (257)
-|.|.+-|.||||-.|
T Consensus 36 Ns~~~~~TTSSCSGRI 51 (196)
T PRK04235 36 NSLKNYYTTSSCSGRI 51 (196)
T ss_pred hCCCCeEEccCCcceE
Confidence 3778888999999755
No 7
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=7.47 E-value=2.5e+02 Score=20.42 Aligned_cols=18 Identities=28% Similarity=0.580 Sum_probs=10.5
Q ss_pred ccccccccCCCceEEEecc
Q 025156 5 REISDLALYGEKEWYFFTP 23 (257)
Q Consensus 5 ~dLPg~al~gekeWYFFSp 23 (257)
..-.-+..|++++ ||||-
T Consensus 15 ~~a~~k~~Y~Gkt-YYFcs 32 (53)
T COG3350 15 ENAEYKSSYGGKT-YYFCS 32 (53)
T ss_pred cccceeEEeCCEE-EEEeC
Confidence 3344455677777 55664
No 8
>KOG4816 consensus Uncharacterized conserved protein [Function unknown]
Probab=6.83 E-value=2.2e+02 Score=22.97 Aligned_cols=16 Identities=25% Similarity=0.694 Sum_probs=11.4
Q ss_pred cccCCCCCcccccCCCC
Q 025156 176 YFDTSDSVPKLNTDSSC 192 (257)
Q Consensus 176 ~~~~s~s~p~~~~dss~ 192 (257)
-||.| -+-|+|.||-|
T Consensus 10 vynks-NFSrfh~dsvc 25 (98)
T KOG4816|consen 10 VYNKS-NFSRFHPDSVC 25 (98)
T ss_pred ccCcc-cccccCCCCcc
Confidence 35666 56688888888
No 9
>PF14983 DUF4513: Domain of unknown function (DUF4513)
Probab=6.83 E-value=3.1e+02 Score=23.18 Aligned_cols=33 Identities=30% Similarity=0.557 Sum_probs=22.1
Q ss_pred cCCCCCcccccCCCCcc-eecCCCccceeccccccc
Q 025156 178 DTSDSVPKLNTDSSCSE-HVVSPEFTCEVQSEPKMQ 212 (257)
Q Consensus 178 ~~s~s~p~~~~dss~~~-~~~s~~~~~~v~s~p~~~ 212 (257)
||--.+|+| .++||+ ..--|...||+|.-|.|+
T Consensus 4 dt~p~~pkl--~~~~s~e~~~k~~~k~~~iHlPrFS 37 (132)
T PF14983_consen 4 DTCPTLPKL--TNNCSDENSYKPANKYEEIHLPRFS 37 (132)
T ss_pred CcCCcCccc--ccccccccccCCcccccccccchhh
Confidence 455577888 477774 333445567888888875
No 10
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=6.53 E-value=3.2e+02 Score=22.30 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=12.7
Q ss_pred CeEEEEEEeeCCCCccc
Q 025156 103 DWVLCRIYNKKGSIEKQ 119 (257)
Q Consensus 103 dwVLCRIy~Kk~~~ek~ 119 (257)
--.||-||+++++..-+
T Consensus 9 ~~mlCaIYkS~kk~~tY 25 (103)
T COG3100 9 KSMLCAIYKSPKKDGTY 25 (103)
T ss_pred eeeeeeeeecCcCCccE
Confidence 35799999887766554
Done!