Query 048576
Match_columns 142
No_of_seqs 104 out of 828
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 10:49:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048576hhsearch_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 2.9E-39 6.2E-44 231.8 3.2 120 4-126 9-129 (129)
2 PF06214 SLAM: Signaling lymph 38.1 8.8 0.00019 27.1 -0.4 43 17-59 76-123 (126)
3 PF01473 CW_binding_1: Putativ 33.8 32 0.00069 15.9 1.3 8 50-57 7-14 (19)
4 PF05959 DUF884: Nucleopolyhed 24.0 90 0.002 23.8 3.0 41 9-62 78-123 (186)
5 cd00490 Met_repressor_MetJ Met 22.5 13 0.00028 25.2 -1.7 38 4-46 51-88 (103)
6 COG3060 MetJ Transcriptional r 22.2 5.5 0.00012 26.8 -3.5 38 4-46 52-89 (105)
7 PRK05264 transcriptional repre 20.3 14 0.00029 25.2 -1.9 38 4-46 52-89 (105)
8 PF06563 DUF1125: Protein of u 17.1 57 0.0012 19.8 0.5 15 6-20 21-35 (55)
9 KOG1334 WD40 repeat protein [G 11.1 4.7E+02 0.01 23.3 4.5 24 34-59 343-366 (559)
10 KOG3761 Choline transporter [L 10.7 1.4E+02 0.0031 25.5 1.2 21 113-133 299-319 (591)
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=2.9e-39 Score=231.75 Aligned_cols=120 Identities=45% Similarity=0.863 Sum_probs=91.1
Q ss_pred ccCCceecCCCccceecCCCCCC-CceeeccCCCCCCCCCCCcccCCCceEEEEeecCCCCCCCCCCeeeceecEEeeCC
Q 048576 4 VFDHDLICLPPCFRKVAGHRLSI-NIIAEIDLFKFEPWELPSKALFGDYEWYFFCPMDRKNPEASEPNRVIRVGYWEDAG 82 (142)
Q Consensus 4 ~~D~eli~~~yl~rKi~g~plp~-~~I~e~Dvy~~~PweL~~~~~~~~~~wyFFs~~~~~~~~g~r~~R~~~~G~Wk~~~ 82 (142)
-||+|||.+ ||.+||.|.++|. ++|.++|||++|||+|+.....++++||||+++.+++.++.|++|++++|+||+
T Consensus 9 PtD~ELi~~-yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~-- 85 (129)
T PF02365_consen 9 PTDEELINH-YLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKS-- 85 (129)
T ss_dssp --HHHHHHC-THHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEE--
T ss_pred CChHHHHHH-HHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEee--
Confidence 489999999 9999999999998 799999999999999995333357799999999999999999999999999999
Q ss_pred CCCceEEeCCCCeEEEEEEEEEeeecCCCCCCccCeEEEEEEeC
Q 048576 83 SGTDKIITTAGRKVVGIKNALVFHVGNAPNGTKTNWIMHEYRLF 126 (142)
Q Consensus 83 ~G~~~~I~~~~~~vvG~Kk~l~fy~~~~~~~~kt~W~M~EY~l~ 126 (142)
+|+++.|...++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 86 ~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 86 TGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999998767788999999999998888899999999999983
No 2
>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=38.13 E-value=8.8 Score=27.14 Aligned_cols=43 Identities=26% Similarity=0.300 Sum_probs=23.7
Q ss_pred ceecCCCCCCCceee--ccCCCCCCCCCCCc---ccCCCceEEEEeec
Q 048576 17 RKVAGHRLSINIIAE--IDLFKFEPWELPSK---ALFGDYEWYFFCPM 59 (142)
Q Consensus 17 rKi~g~plp~~~I~e--~Dvy~~~PweL~~~---~~~~~~~wyFFs~~ 59 (142)
+||....++..--++ -|=|.+|+.+|.=. ....++.|||.+-.
T Consensus 76 kKIvSldl~eg~sp~yledgY~FhlEnLsL~Il~SrkE~EGWYfmtlE 123 (126)
T PF06214_consen 76 KKIVSLDLSEGGSPRYLEDGYKFHLENLSLEILESRKEDEGWYFMTLE 123 (126)
T ss_dssp EEEEEE-TTS-SS-EESSSSEEEETTTTEEEETT--GGG-EEEEEEEE
T ss_pred heEEEeccccCCCccccccccEEecccceeehhccccccCceEEEEee
Confidence 577666665532222 27788888888432 12246789998754
No 3
>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=33.79 E-value=32 Score=15.90 Aligned_cols=8 Identities=38% Similarity=1.248 Sum_probs=6.4
Q ss_pred CceEEEEe
Q 048576 50 DYEWYFFC 57 (142)
Q Consensus 50 ~~~wyFFs 57 (142)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 4
>PF05959 DUF884: Nucleopolyhedrovirus protein of unknown function (DUF884); InterPro: IPR009235 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf146; it is a family of uncharacterised viral proteins.
Probab=24.03 E-value=90 Score=23.84 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=25.1
Q ss_pred eecCCCccceec-----CCCCCCCceeeccCCCCCCCCCCCcccCCCceEEEEeecCCC
Q 048576 9 LICLPPCFRKVA-----GHRLSINIIAEIDLFKFEPWELPSKALFGDYEWYFFCPMDRK 62 (142)
Q Consensus 9 li~~~yl~rKi~-----g~plp~~~I~e~Dvy~~~PweL~~~~~~~~~~wyFFs~~~~~ 62 (142)
++++|+|.+++. ..|+...++. .++..+ -+.||-|+-|+..
T Consensus 78 c~RlP~l~~~L~~~~~f~~p~~~~VVk--~~~~~~-----------~evWhVlgVrK~~ 123 (186)
T PF05959_consen 78 CFRLPFLLRNLVTHNKFTRPLGVVVVK--VVTKNE-----------TEVWHVLGVRKGR 123 (186)
T ss_pred EEechhhhHhHhhcccccCCcceEEEE--ecCCCC-----------ceEEEEEEEeccc
Confidence 588999999884 3444322222 223322 3789999988654
No 5
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=22.55 E-value=13 Score=25.18 Aligned_cols=38 Identities=26% Similarity=0.409 Sum_probs=27.2
Q ss_pred ccCCceecCCCccceecCCCCCCCceeeccCCCCCCCCCCCcc
Q 048576 4 VFDHDLICLPPCFRKVAGHRLSINIIAEIDLFKFEPWELPSKA 46 (142)
Q Consensus 4 ~~D~eli~~~yl~rKi~g~plp~~~I~e~Dvy~~~PweL~~~~ 46 (142)
+|.-||+|-- ...-..|+|||. +.|+-...|.++|...
T Consensus 51 ATNSELLCEA-FLHAfTGQPLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 51 ATNSELLCEA-FLHAFTGQPLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred cccHHHHHHH-HHHHhcCCCCCC----hhhhhhcCcccccHHH
Confidence 5666777762 334457999995 4588888999999763
No 6
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=22.18 E-value=5.5 Score=26.76 Aligned_cols=38 Identities=26% Similarity=0.437 Sum_probs=27.2
Q ss_pred ccCCceecCCCccceecCCCCCCCceeeccCCCCCCCCCCCcc
Q 048576 4 VFDHDLICLPPCFRKVAGHRLSINIIAEIDLFKFEPWELPSKA 46 (142)
Q Consensus 4 ~~D~eli~~~yl~rKi~g~plp~~~I~e~Dvy~~~PweL~~~~ 46 (142)
+|.-||+|-- ...-..|+|||. +.|+...-|.++|..+
T Consensus 52 atnsellcea-flhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 52 ATNSELLCEA-FLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhHHHHHHH-HHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 4566777762 334457999984 5688888999999764
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=20.30 E-value=14 Score=25.20 Aligned_cols=38 Identities=26% Similarity=0.392 Sum_probs=27.1
Q ss_pred ccCCceecCCCccceecCCCCCCCceeeccCCCCCCCCCCCcc
Q 048576 4 VFDHDLICLPPCFRKVAGHRLSINIIAEIDLFKFEPWELPSKA 46 (142)
Q Consensus 4 ~~D~eli~~~yl~rKi~g~plp~~~I~e~Dvy~~~PweL~~~~ 46 (142)
+|.-||+|-- ...-..|+|||. +.|+-...|.++|...
T Consensus 52 ATNSELLCEA-FLHA~TGQPLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 52 ATNSELLCEA-FLHAFTGQPLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred cccHHHHHHH-HHHHHcCCCCCC----hhhhhhcCcccchHHH
Confidence 5666777762 334457999995 4588888999998653
No 8
>PF06563 DUF1125: Protein of unknown function (DUF1125); InterPro: IPR009503 This entry is represented by Bacteriophage bIL285, Orf25. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short Lactococcus lactis and bacteriophage proteins. The function of this family is unknown.
Probab=17.14 E-value=57 Score=19.78 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=12.4
Q ss_pred CCceecCCCccceec
Q 048576 6 DHDLICLPPCFRKVA 20 (142)
Q Consensus 6 D~eli~~~yl~rKi~ 20 (142)
|-|.+...||+|||.
T Consensus 21 DieafS~~fL~rKIk 35 (55)
T PF06563_consen 21 DIEAFSFSFLFRKIK 35 (55)
T ss_pred ccceEEehheeeeEE
Confidence 667788889999986
No 9
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=11.07 E-value=4.7e+02 Score=23.30 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCcccCCCceEEEEeec
Q 048576 34 LFKFEPWELPSKALFGDYEWYFFCPM 59 (142)
Q Consensus 34 vy~~~PweL~~~~~~~~~~wyFFs~~ 59 (142)
+|.++|-||...+ .+...|||.+-
T Consensus 343 ~Ysh~~sElLaSY--nDe~IYLF~~~ 366 (559)
T KOG1334|consen 343 VYSHDGSELLASY--NDEDIYLFNKS 366 (559)
T ss_pred EecCCccceeeee--cccceEEeccc
Confidence 3556666665543 57789999543
No 10
>KOG3761 consensus Choline transporter [Lipid transport and metabolism]
Probab=10.65 E-value=1.4e+02 Score=25.48 Aligned_cols=21 Identities=24% Similarity=0.431 Sum_probs=17.5
Q ss_pred CCccCeEEEEEEeCCCCCCCC
Q 048576 113 GTKTNWIMHEYRLFEPPPNNG 133 (142)
Q Consensus 113 ~~kt~W~M~EY~l~~~~~~~~ 133 (142)
+..|+|.|..|.+.++.++..
T Consensus 299 ~~ntdw~~t~y~~~d~~tkve 319 (591)
T KOG3761|consen 299 AANTDWNMTAYGLPDNGTKVE 319 (591)
T ss_pred hccCcccccccCCCCCCcccc
Confidence 567999999999999976543
Done!