Query 013960
Match_columns 433
No_of_seqs 207 out of 975
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 00:29:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013960hhsearch_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 3.8E-42 8.2E-47 301.9 5.7 127 10-138 1-129 (129)
2 KOG3238 Chloride ion current i 19.3 1.1E+02 0.0024 29.9 3.2 63 10-72 109-171 (216)
3 PHA00692 hypothetical protein 17.4 52 0.0011 26.3 0.4 8 10-17 37-44 (74)
4 smart00265 BH4 BH4 Bcl-2 homol 15.7 1.6E+02 0.0035 19.9 2.4 20 19-38 4-23 (27)
5 PF05865 Cypo_polyhedrin: Cypo 14.4 1.4E+02 0.0031 28.5 2.6 28 90-117 140-168 (248)
6 TIGR01631 Trypano_RHS trypanos 11.7 69 0.0015 36.9 -0.4 72 298-374 638-730 (760)
7 PF08338 DUF1731: Domain of un 8.8 2.3E+02 0.0049 21.2 1.6 18 10-27 29-47 (48)
8 PF01473 CW_binding_1: Putativ 8.5 2E+02 0.0043 17.1 1.0 9 65-73 7-15 (19)
9 PF07960 CBP4: CBP4; InterPro 8.0 1.9E+02 0.0042 26.3 1.1 11 17-27 30-40 (128)
10 PTZ00209 retrotransposon hot s 8.0 1.6E+02 0.0035 33.7 0.7 68 298-370 533-628 (693)
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=3.8e-42 Score=301.91 Aligned_cols=127 Identities=53% Similarity=1.026 Sum_probs=96.9
Q ss_pred CCCCceeCCChHHHHHHHHHHHHcCCCCCC-CCeecCCCCCCCCCCCCccccccCCCcceeeeecccccCCCCCcccccc
Q 013960 10 LAPGFRFHPTDEELVRYYLKRKVCHRSLRF-NPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFSMLDKKYGNGSRTNRAT 88 (433)
Q Consensus 10 LPPGFRF~PTDEELV~~YL~rKi~G~pl~~-~~I~dvDvY~~ePwdLp~~~~~~~~d~eWYFFs~~~kK~~~G~R~nR~t 88 (433)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||.+|||+|++.. .+++.+||||+++++++.+|.|++|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc--cCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 68999999999999999432 235669999999999999999999999
Q ss_pred ccceeeecCCceeeec-CCeeEEEEEEEEeecCCCCCCCccCeEEEEEEeC
Q 013960 89 EKGYWKTTGKDRPVHH-NTRTVGMKKTLVYHMGRAPHGERTNWVMHEYRLT 138 (433)
Q Consensus 89 ~~GyWK~tG~~k~I~~-~g~vVG~KKtLvFy~Gr~p~G~rT~WvMhEY~L~ 138 (433)
++|+||.+|+.++|.. ++++||+||+|+||.++.+++.+|+|+||||+|.
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 9999999999999987 8999999999999998888999999999999984
No 2
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=19.30 E-value=1.1e+02 Score=29.90 Aligned_cols=63 Identities=19% Similarity=0.292 Sum_probs=37.9
Q ss_pred CCCCceeCCChHHHHHHHHHHHHcCCCCCCCCeecCCCCCCCCCCCCccccccCCCcceeeee
Q 013960 10 LAPGFRFHPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFS 72 (433)
Q Consensus 10 LPPGFRF~PTDEELV~~YL~rKi~G~pl~~~~I~dvDvY~~ePwdLp~~~~~~~~d~eWYFFs 72 (433)
.--+|||+|+|.--+..--.....+.-|.+....+.+-|.-+=|+.-.....++....||=+.
T Consensus 109 ~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred ccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCccccccc
Confidence 456899999998777663333334454544445566677777777755433344445555443
No 3
>PHA00692 hypothetical protein
Probab=17.39 E-value=52 Score=26.28 Aligned_cols=8 Identities=63% Similarity=1.323 Sum_probs=6.6
Q ss_pred CCCCceeC
Q 013960 10 LAPGFRFH 17 (433)
Q Consensus 10 LPPGFRF~ 17 (433)
.||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 58999985
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=15.74 E-value=1.6e+02 Score=19.92 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 013960 19 TDEELVRYYLKRKVCHRSLR 38 (433)
Q Consensus 19 TDEELV~~YL~rKi~G~pl~ 38 (433)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999755443
No 5
>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=14.43 E-value=1.4e+02 Score=28.53 Aligned_cols=28 Identities=29% Similarity=0.530 Sum_probs=18.2
Q ss_pred cceeeecC-CceeeecCCeeEEEEEEEEe
Q 013960 90 KGYWKTTG-KDRPVHHNTRTVGMKKTLVY 117 (433)
Q Consensus 90 ~GyWK~tG-~~k~I~~~g~vVG~KKtLvF 117 (433)
.--|.+|| +-|.|..+|.+||+...|..
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 34699999 66888889999999988765
No 6
>TIGR01631 Trypano_RHS trypanosome RHS (retrotransposon hot spot) family. This model describes full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position.
Probab=11.74 E-value=69 Score=36.89 Aligned_cols=72 Identities=21% Similarity=0.277 Sum_probs=46.6
Q ss_pred ccCCCCCCCCCCcc-eEeecC-----------CCCcccCCCcC---------chhHHHHhhcccCCCCCCcccccCcCcc
Q 013960 298 YLDATDNPQFSDGL-YLEAND-----------LSSTVEADSQG---------FDMVEEYLNFFDANDDNSEYLTFDASEI 356 (433)
Q Consensus 298 ~~da~~n~~~~dG~-fle~nd-----------ls~~~~~~~~~---------fd~~d~yl~~fda~~~~~~~~~fd~~~~ 356 (433)
|.=+..|+|++||+ |+|-|= -.-.++--+++ .-|.+-+-+||..=++-+|+|+. +|
T Consensus 638 Y~P~~~NFPlVDaFFFVes~~~~~~~~~~~~KTlVGLQmTtA~~HhTttstVrqFte~La~YF~gWeefSr~msW---Ei 714 (760)
T TIGR01631 638 YKPEVGNFPVVDAFFFVESPAIAEDKQRREKKTIVGLQYTVAGRHHTTTGTVRKFTEYLAAYFNGWDELSRQLVW---EI 714 (760)
T ss_pred EeeccCCCcceeEEEEecCccccccccccccceEEEEEEeccCCCCcchHHHHHHHHHHHHHHhhHHHHhhCCeE---EE
Confidence 34455699999999 888763 11111222333 55445556799999999999999 88
Q ss_pred ccCCCCCCCCCCCccccc
Q 013960 357 LGSGDNNSDQVPLTTEVT 374 (433)
Q Consensus 357 ~g~e~~~~~~~~~~~~~~ 374 (433)
|=.+-+.|- ||.--|.
T Consensus 715 IYVQh~Dst--pm~~wQr 730 (760)
T TIGR01631 715 IYVQHVDST--PITDWQR 730 (760)
T ss_pred EEEEccCCc--cccccee
Confidence 877666553 5553333
No 7
>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=8.81 E-value=2.3e+02 Score=21.23 Aligned_cols=18 Identities=50% Similarity=0.792 Sum_probs=10.3
Q ss_pred CCCCceeC-CChHHHHHHH
Q 013960 10 LAPGFRFH-PTDEELVRYY 27 (433)
Q Consensus 10 LPPGFRF~-PTDEELV~~Y 27 (433)
+--||+|+ ||=++-+.+-
T Consensus 29 ~~~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 29 LEAGFQFRYPTLEEALRDL 47 (48)
T ss_dssp HHTT---S-SSHHHHHHH-
T ss_pred HHCCCcccCCCHHHHHhcc
Confidence 34699998 8888777653
No 8
>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=8.54 E-value=2e+02 Score=17.12 Aligned_cols=9 Identities=33% Similarity=1.302 Sum_probs=6.5
Q ss_pred Ccceeeeec
Q 013960 65 DKEWYFFSM 73 (433)
Q Consensus 65 d~eWYFFs~ 73 (433)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 458999953
No 9
>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=8.05 E-value=1.9e+02 Score=26.30 Aligned_cols=11 Identities=55% Similarity=0.984 Sum_probs=9.5
Q ss_pred CCChHHHHHHH
Q 013960 17 HPTDEELVRYY 27 (433)
Q Consensus 17 ~PTDEELV~~Y 27 (433)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 39999999875
No 10
>PTZ00209 retrotransposon hot spot protein; Provisional
Probab=8.00 E-value=1.6e+02 Score=33.69 Aligned_cols=68 Identities=13% Similarity=0.263 Sum_probs=42.8
Q ss_pred ccCCCCCCCCCCcc-eEeecCCCC------------------cccCCCcC---------chhHHHHhhcccCCCCCCccc
Q 013960 298 YLDATDNPQFSDGL-YLEANDLSS------------------TVEADSQG---------FDMVEEYLNFFDANDDNSEYL 349 (433)
Q Consensus 298 ~~da~~n~~~~dG~-fle~ndls~------------------~~~~~~~~---------fd~~d~yl~~fda~~~~~~~~ 349 (433)
|.=+..|+|++||+ |+|-+---+ .++--+++ .-|-+-+-+||..=|+-+|+|
T Consensus 533 Y~P~~~NFPLVDgFFFVes~~~~~~~~~~~~~~~~~~pKTlVGLQmTtA~~HhTttStVrqFtE~LAaYFngWeefSrdM 612 (693)
T PTZ00209 533 YRSLEESKLFVDGFFFVEDCSRRVADMRDGFPQLGVASKTIVLIQITDNYRKEASVSELQEFMTNIARYFSDWDTFSRNM 612 (693)
T ss_pred EeecCCCCcceeeEEEeccchhccccccccccccCCCCceEEEEEEeccCCCCCcHHHHHHHHHHHHHHhccHHHHhhCC
Confidence 44566799999999 788531100 01111223 443355557999999999999
Q ss_pred ccCcCccccCCCCCCCCCCCc
Q 013960 350 TFDASEILGSGDNNSDQVPLT 370 (433)
Q Consensus 350 ~fd~~~~~g~e~~~~~~~~~~ 370 (433)
+. +||=.+-+.|- ||.
T Consensus 613 sW---EIIYVQhaDSt--pm~ 628 (693)
T PTZ00209 613 AW---EMIYVNAIYGG--VIK 628 (693)
T ss_pred ee---EEEEEEccCCc--ccc
Confidence 98 88766655553 444
Done!