Query 023190
Match_columns 286
No_of_seqs 193 out of 981
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:06:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023190.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023190hhsearch_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 2E-33 4.3E-38 232.9 3.4 112 1-116 15-129 (129)
2 PF15471 TMEM171: Transmembran 17.6 93 0.002 30.1 2.2 14 132-145 176-189 (319)
3 KOG2675 Adenylate cyclase-asso 16.1 95 0.0021 31.8 2.0 13 106-118 171-183 (480)
4 PF01473 CW_binding_1: Putativ 12.0 1.5E+02 0.0033 16.4 1.3 8 44-51 7-14 (19)
5 KOG4280 Kinesin-like protein [ 10.2 1.2E+02 0.0027 31.9 0.9 19 214-236 203-221 (574)
6 KOG4816 Uncharacterized conser 9.5 1.3E+02 0.0029 24.3 0.6 16 205-221 10-25 (98)
7 PRK04235 hypothetical protein; 8.5 1.6E+02 0.0034 26.8 0.8 16 210-225 36-51 (196)
8 PF06214 SLAM: Signaling lymph 8.3 98 0.0021 26.2 -0.6 46 6-53 75-123 (126)
9 COG3100 Uncharacterized protei 7.8 2.8E+02 0.006 22.8 1.8 16 133-148 10-25 (103)
10 PF14983 DUF4513: Domain of un 7.3 2.9E+02 0.0063 23.5 1.8 33 207-241 4-37 (132)
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=99.97 E-value=2e-33 Score=232.91 Aligned_cols=112 Identities=47% Similarity=0.951 Sum_probs=85.7
Q ss_pred CccchhhHhccCCCCCCCCC-CCcccccCCCCCCCCCCccccCCCceEEEEeeccccCCCCCCCccccCCceEEecCCcc
Q 023190 1 MRSSLCTICAVNAFRSQSPF-RLSPKSIFTNLIPWDLPDLALYGEKEWYFFTPRDRKYPNGSRPNRAAGSGYWKATGADK 79 (286)
Q Consensus 1 V~hYL~rKi~G~pl~~~~~~-~~I~evDVY~~ePWdLP~~~~~ge~eWYFFs~r~rk~~nG~R~~Ratg~G~WK~tG~~k 79 (286)
|.+||++|+.|.++ +. ++|+++|||++|||+|++....++++||||+++++++.+|.|.+|++++|+||.+|+.+
T Consensus 15 i~~yL~~k~~g~~~----~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~ 90 (129)
T PF02365_consen 15 INHYLRPKILGEPL----PCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEK 90 (129)
T ss_dssp HHCTHHHHHTT-HH----CS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEECEEE
T ss_pred HHHHHHHHhcCCCC----CcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEeeccccc
Confidence 46999999999999 66 89999999999999999544446789999999999999999999999999999999999
Q ss_pred ccc--CCcceeeEEEEeeccCCCCCCCccCeEEeEEEec
Q 023190 80 PIG--QPKPVGIKKALVFYAGKAPKGEKTNWIMHEYRLA 116 (286)
Q Consensus 80 ~I~--~g~~VG~KktLvFy~gk~p~g~kT~WiMhEY~L~ 116 (286)
+|. ++++||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 91 ~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 91 PIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 885 4789999999999999888999999999999984
No 2
>PF15471 TMEM171: Transmembrane protein family 171
Probab=17.63 E-value=93 Score=30.07 Aligned_cols=14 Identities=7% Similarity=0.150 Sum_probs=9.1
Q ss_pred CEEEEEEEecCCCC
Q 023190 132 DWVLCRIYNKKGSI 145 (286)
Q Consensus 132 d~VLCRIy~Kk~~~ 145 (286)
=+||-.|.||..-.
T Consensus 176 FFVVAHvKKr~nln 189 (319)
T PF15471_consen 176 FFVVAHVKKRNNLN 189 (319)
T ss_pred hhheeeeeeccCCC
Confidence 46888887765443
No 3
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=16.11 E-value=95 Score=31.78 Aligned_cols=13 Identities=38% Similarity=0.642 Sum_probs=7.0
Q ss_pred cCeEEeEEEecCc
Q 023190 106 TNWIMHEYRLADV 118 (286)
Q Consensus 106 T~WiMhEY~L~~~ 118 (286)
||=+|.||+=.+.
T Consensus 171 ~NrvLkEyk~~D~ 183 (480)
T KOG2675|consen 171 TNRVLKEYKEKDP 183 (480)
T ss_pred HHHHHHHhccCCh
Confidence 3345666665544
No 4
>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=11.97 E-value=1.5e+02 Score=16.42 Aligned_cols=8 Identities=38% Similarity=1.448 Sum_probs=6.1
Q ss_pred CceEEEEe
Q 023190 44 EKEWYFFT 51 (286)
Q Consensus 44 e~eWYFFs 51 (286)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46899994
No 5
>KOG4280 consensus Kinesin-like protein [Cytoskeleton]
Probab=10.21 E-value=1.2e+02 Score=31.87 Aligned_cols=19 Identities=42% Similarity=0.679 Sum_probs=16.0
Q ss_pred ccccCCCCcccccCCCccceecc
Q 023190 214 KLNTDSSCSEHVVSPEFTCEVQS 236 (286)
Q Consensus 214 ~~~~~~s~~~~~~~~~~~~~~~s 236 (286)
.++.+||.| |++ |||.|.|
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 356689999 999 9999988
No 6
>KOG4816 consensus Uncharacterized conserved protein [Function unknown]
Probab=9.52 E-value=1.3e+02 Score=24.27 Aligned_cols=16 Identities=25% Similarity=0.694 Sum_probs=11.6
Q ss_pred eecCCCCCcccccCCCC
Q 023190 205 YFDTSDSVPKLNTDSSC 221 (286)
Q Consensus 205 ~~~~~~s~~~~~~~~s~ 221 (286)
.||.| -+-|+|.||-|
T Consensus 10 vynks-NFSrfh~dsvc 25 (98)
T KOG4816|consen 10 VYNKS-NFSRFHPDSVC 25 (98)
T ss_pred ccCcc-cccccCCCCcc
Confidence 45666 56688888888
No 7
>PRK04235 hypothetical protein; Provisional
Probab=8.50 E-value=1.6e+02 Score=26.75 Aligned_cols=16 Identities=38% Similarity=0.594 Sum_probs=12.9
Q ss_pred CCCcccccCCCCcccc
Q 023190 210 DSVPKLNTDSSCSEHV 225 (286)
Q Consensus 210 ~s~~~~~~~~s~~~~~ 225 (286)
-|.|.+-|.||||-.|
T Consensus 36 Ns~~~~~TTSSCSGRI 51 (196)
T PRK04235 36 NSLKNYYTTSSCSGRI 51 (196)
T ss_pred hCCCCeEEccCCcceE
Confidence 3677888999999765
No 8
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=8.32 E-value=98 Score=26.16 Aligned_cols=46 Identities=13% Similarity=0.008 Sum_probs=22.7
Q ss_pred hhHhccCCCCCCCCCCCcccccCCCCCCCCCCcc---ccCCCceEEEEeec
Q 023190 6 CTICAVNAFRSQSPFRLSPKSIFTNLIPWDLPDL---ALYGEKEWYFFTPR 53 (286)
Q Consensus 6 ~rKi~G~pl~~~~~~~~I~evDVY~~ePWdLP~~---~~~ge~eWYFFs~r 53 (286)
++||....++.++.++ .--|=|++++..|--. .+..+..|||-+-.
T Consensus 75 kkKIvSldl~eg~sp~--yledgY~FhlEnLsL~Il~SrkE~EGWYfmtlE 123 (126)
T PF06214_consen 75 KKKIVSLDLSEGGSPR--YLEDGYKFHLENLSLEILESRKEDEGWYFMTLE 123 (126)
T ss_dssp -EEEEEE-TTS-SS-E--ESSSSEEEETTTTEEEETT--GGG-EEEEEEEE
T ss_pred hheEEEeccccCCCcc--ccccccEEecccceeehhccccccCceEEEEee
Confidence 4566665552111111 1137888999888432 12234569998754
No 9
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=7.78 E-value=2.8e+02 Score=22.77 Aligned_cols=16 Identities=25% Similarity=0.378 Sum_probs=12.0
Q ss_pred EEEEEEEecCCCCccc
Q 023190 133 WVLCRIYNKKGSIEKQ 148 (286)
Q Consensus 133 ~VLCRIy~Kk~~~~k~ 148 (286)
-.||-||+++++..-.
T Consensus 10 ~mlCaIYkS~kk~~tY 25 (103)
T COG3100 10 SMLCAIYKSPKKDGTY 25 (103)
T ss_pred eeeeeeeecCcCCccE
Confidence 4899999987765543
No 10
>PF14983 DUF4513: Domain of unknown function (DUF4513)
Probab=7.31 E-value=2.9e+02 Score=23.50 Aligned_cols=33 Identities=30% Similarity=0.557 Sum_probs=22.5
Q ss_pred cCCCCCcccccCCCCcc-cccCCCccceeccccccc
Q 023190 207 DTSDSVPKLNTDSSCSE-HVVSPEFTCEVQSEPKMQ 241 (286)
Q Consensus 207 ~~~~s~~~~~~~~s~~~-~~~~~~~~~~~~s~p~~~ 241 (286)
||--.+|+| .++||+ ..--|...||+|.-|.|.
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 566678888 477774 333445567888888875
Done!