Query 024467
Match_columns 267
No_of_seqs 59 out of 61
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:48:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024467.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024467hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08536 Whirly: Whirly transc 100.0 8E-63 1.7E-67 414.6 17.0 139 90-228 1-139 (139)
2 PRK12301 bssS biofilm formatio 59.9 2.8 6E-05 33.7 -0.2 16 1-16 27-42 (84)
3 PF02035 Coagulin: Coagulin; 50.4 17 0.00037 32.0 3.1 51 85-142 75-125 (174)
4 cd00139 PIPKc Phosphatidylinos 37.6 30 0.00066 33.1 3.0 47 189-241 96-154 (313)
5 PF13991 BssS: BssS protein fa 27.7 28 0.00061 27.3 0.8 16 1-16 17-32 (73)
6 PF07490 Tir_receptor_N: Trans 25.0 89 0.0019 29.4 3.6 60 160-226 85-145 (266)
7 PF01690 PLRV_ORF5: Potato lea 24.4 2.2E+02 0.0048 29.3 6.6 36 89-130 33-68 (465)
8 PLN03185 phosphatidylinositol 24.2 63 0.0014 34.9 2.9 47 188-240 443-500 (765)
9 PF11314 DUF3117: Protein of u 23.1 1.8E+02 0.0039 21.6 4.2 40 111-156 6-45 (51)
10 cd07703 Ig2_Nectin-2_like Seco 22.5 1.2E+02 0.0025 24.0 3.4 38 178-215 56-93 (95)
11 KOG1892 Actin filament-binding 20.7 91 0.002 35.4 3.2 59 92-154 312-385 (1629)
No 1
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=100.00 E-value=8e-63 Score=414.63 Aligned_cols=139 Identities=74% Similarity=1.128 Sum_probs=123.6
Q ss_pred eEEeCceeEEEeecCCceeecCCcceEEeeeceEEEEEeecCcccccccccceEEEEehhhhhhhhhccccccceeeecC
Q 024467 90 SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDP 169 (267)
Q Consensus 90 sVYKgKAALsv~pi~P~F~~~~sG~~kv~R~G~ILLeFAPa~g~rqYDW~kKq~FsLS~tEvG~LLsl~~~~s~EffHdP 169 (267)
+||||||||+|+|++|+|+.+++|+++++|+|+|||||||++|+|||||+|||+|+|||+|||+||+|+++++|||||||
T Consensus 1 sVYk~kaAl~v~p~~P~f~~~~sg~~kv~R~G~vlLefapa~g~r~YDW~kKq~FsLS~tEvG~ll~l~~~~s~effHdP 80 (139)
T PF08536_consen 1 SVYKGKAALSVRPIKPTFTSLDSGYFKVSREGSVLLEFAPAVGPRQYDWSKKQTFSLSPTEVGSLLSLGARESCEFFHDP 80 (139)
T ss_dssp EEEESSEEEEEEEE--EEEE-TTSCEEEEC--EEEEEEEEBCSTTEB-GGG-EEEEE-HHHHHHHHT--TT--EEEEE-T
T ss_pred CccccceeEEEEecCCccEECCCCcEEEeeccEEEEEEccccCCcccccccceEEEEcHHHhhhhhhhccCCceEEEecc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceeeEEEEeeCCCCCcceEEEeEeecccCCCcceeeeecHhHHHHHHHHHH
Q 024467 170 FKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228 (267)
Q Consensus 170 ~~g~s~eG~v~K~LkIeP~pdgsG~F~nLsV~nk~~~~de~i~IPVT~gEfaVlrsl~~ 228 (267)
+||+|++|+++|+|||||+|||+|+||||+|+|+.++++++|+||||+|||+|||++|+
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfavl~s~f~ 139 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAVLRSAFN 139 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHHHHHHHH
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccccceEEEechHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999986
No 2
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=59.93 E-value=2.8 Score=33.71 Aligned_cols=16 Identities=31% Similarity=0.565 Sum_probs=14.1
Q ss_pred CceeeeeccccCCCCC
Q 024467 1 MMLQLQCLSSQTLNPK 16 (267)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (267)
||++||.|||+.|.|.
T Consensus 27 mmirlhyLss~~Q~~e 42 (84)
T PRK12301 27 LMLRLHYQSPNDQEPE 42 (84)
T ss_pred HHHhhhhcCCCCCCcc
Confidence 7999999999988764
No 3
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=50.39 E-value=17 Score=32.03 Aligned_cols=51 Identities=25% Similarity=0.425 Sum_probs=26.5
Q ss_pred eeecceEEeCceeEEEeecCCceeecCCcceEEeeeceEEEEEeecCcccccccccce
Q 024467 85 VYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQ 142 (267)
Q Consensus 85 vy~~ysVYKgKAALsv~pi~P~F~~~~sG~~kv~R~G~ILLeFAPa~g~rqYDW~kKq 142 (267)
-|++|.-|+..+-.+.+..-|.|.---+|-+. |++ =||.+|-||--|+.|-
T Consensus 75 nf~pf~hf~secpvstrdcepvfgyt~a~efr------viv-qapragfrqcvwqhkc 125 (174)
T PF02035_consen 75 NFPPFHHFKSECPVSTRDCEPVFGYTVAGEFR------VIV-QAPRAGFRQCVWQHKC 125 (174)
T ss_dssp GSTT----SSB--EEEE----SEEE-TTS-EE------EE---BCCCTB-B---EEEE
T ss_pred cCCCcccccccCCcccccccccccceecceEE------EEE-eCchhhHHHHHHHhhh
Confidence 46789999999999999999999876666654 344 4899999999999774
No 4
>cd00139 PIPKc Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs.
Probab=37.64 E-value=30 Score=33.08 Aligned_cols=47 Identities=26% Similarity=0.436 Sum_probs=35.7
Q ss_pred CCCCcceEEEeEeecccCCCcceeeeecHhHHHHHHHHH------------Hhhhhhhhchhhhh
Q 024467 189 PDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAF------------NFILPYLLGWHAYA 241 (267)
Q Consensus 189 pdgsG~F~nLsV~nk~~~~de~i~IPVT~gEfaVlrsl~------------~ysLP~LLGWda~~ 241 (267)
++.||.||..|-.++- -|. .|+..|+.+|+.++ +.+||+++|-+++.
T Consensus 96 ~GKSGs~F~~T~D~rf-----iIK-ti~~~E~~~l~~~Lp~Y~~~~~~n~~~TLL~k~~Gl~~i~ 154 (313)
T cd00139 96 GGKSGSFFYKTLDDRF-----IIK-TVSHSEIESLLKFLPNYYEYITQNPQNTLLPKFFGLYRVK 154 (313)
T ss_pred CCCCCCEEEEecCCcE-----EEE-ecCHHHHHHHHHHHHHHHHHHHhCCCCcchhhheEEEEEE
Confidence 4557888887742221 123 78999999999998 89999999998874
No 5
>PF13991 BssS: BssS protein family
Probab=27.69 E-value=28 Score=27.33 Aligned_cols=16 Identities=44% Similarity=0.663 Sum_probs=13.6
Q ss_pred CceeeeeccccCCCCC
Q 024467 1 MMLQLQCLSSQTLNPK 16 (267)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (267)
||++||.|+++.|.+.
T Consensus 17 l~lrl~yls~~~q~~e 32 (73)
T PF13991_consen 17 LMLRLHYLSSPDQPPE 32 (73)
T ss_pred eEEEecccCCCCCCcc
Confidence 7999999999977754
No 6
>PF07490 Tir_receptor_N: Translocated intimin receptor (Tir) N-terminus; InterPro: IPR022633 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Enteropathogenic and entero- haemorrhagic Escherichia coli secrete the bacterial adhesion mediation molecule intimin [], which targets the translocated intimin receptor, Tir. Tir is secreted by the bacteria and is embedded in the target cell's plasma membrane []. This facilitates bacterial cell attachment to the host.
Probab=25.00 E-value=89 Score=29.43 Aligned_cols=60 Identities=20% Similarity=0.247 Sum_probs=39.4
Q ss_pred cccceeeecCCCCCC-CCCceeeEEEEeeCCCCCcceEEEeEeecccCCCcceeeeecHhHHHHHHHH
Q 024467 160 RESCEFFHDPFKGKS-EEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSA 226 (267)
Q Consensus 160 ~~s~EffHdP~~g~s-~eG~v~K~LkIeP~pdgsG~F~nLsV~nk~~~~de~i~IPVT~gEfaVlrsl 226 (267)
.+.+|..||-.-... +..--.-+++||-++||+ +.-+-.+|+++ .+|.++..||+-|++|
T Consensus 85 ~ggfEVLHD~G~LDtLN~~IGss~FrvE~q~dG~--h~AiGqk~gvE-----tsV~Ls~qE~~sLQai 145 (266)
T PF07490_consen 85 HGGFEVLHDKGPLDTLNKQIGSSVFRVETQEDGS--HVAIGQKNGVE-----TSVTLSEQELASLQAI 145 (266)
T ss_pred ccceEEeeccCchhhHHhhhCccceEEEeccCCc--eEeeeccCCeE-----EEEEeCHHHhhhhhcc
Confidence 457899998433111 111223589999999996 35555555554 6889999999987654
No 7
>PF01690 PLRV_ORF5: Potato leaf roll virus readthrough protein; InterPro: IPR002929 This family consists mainly of the Potato leafroll virus (PLrV) read through protein otherwise known as the minor capsid protein. This is generated via a readthrough of open reading frame 3, the coat protein, allowing transcription of open reading frame 5 to give an extended coat protein with a large C-terminal addition or read through domain []. The read through protein is essential for the circulative aphid transmission of PLrV [] and Beet western yellows virus []. The N-terminal region of the luteovirus readthrough domain determines virus binding to Buchnera GroEL and is essential for virus persistence in the aphid [].; GO: 0019028 viral capsid
Probab=24.36 E-value=2.2e+02 Score=29.33 Aligned_cols=36 Identities=8% Similarity=0.202 Sum_probs=27.1
Q ss_pred ceEEeCceeEEEeecCCceeecCCcceEEeeeceEEEEEeec
Q 024467 89 HSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPA 130 (267)
Q Consensus 89 ysVYKgKAALsv~pi~P~F~~~~sG~~kv~R~G~ILLeFAPa 130 (267)
|-+|-|-....|..+- +|.++.|..-|.+-+.+..-
T Consensus 33 F~~Y~G~p~~~I~tr~------n~d~I~v~~l~~q~~~yiEd 68 (465)
T PF01690_consen 33 FIGYEGVPQTKISTRE------NDDSISVRSLNSQRMRYIED 68 (465)
T ss_pred eEEEecccceeeeccc------cccceEeeccCceeEEEEec
Confidence 3458898888888776 66678888888888777754
No 8
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=24.16 E-value=63 Score=34.91 Aligned_cols=47 Identities=28% Similarity=0.485 Sum_probs=36.6
Q ss_pred CCCCCcceEEEeEeecccCCCcceeeeecHhHHHHHHHHH-----------Hhhhhhhhchhhh
Q 024467 188 LPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAF-----------NFILPYLLGWHAY 240 (267)
Q Consensus 188 ~pdgsG~F~nLsV~nk~~~~de~i~IPVT~gEfaVlrsl~-----------~ysLP~LLGWda~ 240 (267)
-++.||-||..|-.++- -|. .|+..|+.+|+.++ +.+|++++|-+++
T Consensus 443 S~GKSGS~Fy~S~D~rF-----iIK-TI~k~E~~~l~~iLp~Y~~hv~~n~~TLL~kf~Gl~~i 500 (765)
T PLN03185 443 SPGKSGSVFFLSQDDRF-----MIK-TLRKSEVKVLLRMLPDYHHHVKTYENTLITKFFGLHRI 500 (765)
T ss_pred CCCCcCCeEEEecCCcE-----EEE-ecCHHHHHHHHHHHHHHHHHHhhCCCcchhhheEEEEE
Confidence 36778889998843222 133 88999999999998 6789999999987
No 9
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.12 E-value=1.8e+02 Score=21.59 Aligned_cols=40 Identities=23% Similarity=0.362 Sum_probs=34.2
Q ss_pred CCcceEEeeeceEEEEEeecCcccccccccceEEEEehhhhhhhhh
Q 024467 111 DSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVA 156 (267)
Q Consensus 111 ~sG~~kv~R~G~ILLeFAPa~g~rqYDW~kKq~FsLS~tEvG~LLs 156 (267)
+||-+.+.|+|.=++==+|..| .-+.+..|++.|...|-+
T Consensus 6 GdGPlEv~kEgR~ivmRvPleG------GGRLVvEl~~~Ea~~L~~ 45 (51)
T PF11314_consen 6 GDGPLEVTKEGRGIVMRVPLEG------GGRLVVELNPDEAKELGE 45 (51)
T ss_pred CCCCcEEeecCceEEEEEecCC------CcEEEEEeCHHHHHHHHH
Confidence 7888999999998888899866 457899999999998865
No 10
>cd07703 Ig2_Nectin-2_like Second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112) and similar proteins. Ig2_Nectin-2_like: domain similar to the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112). Nectin-2 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through 4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development.
Probab=22.49 E-value=1.2e+02 Score=24.01 Aligned_cols=38 Identities=13% Similarity=0.287 Sum_probs=29.0
Q ss_pred ceeeEEEEeeCCCCCcceEEEeEeecccCCCcceeeee
Q 024467 178 KVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPV 215 (267)
Q Consensus 178 ~v~K~LkIeP~pdgsG~F~nLsV~nk~~~~de~i~IPV 215 (267)
.+.-.|.+.|.++++|+.+.|.|.+.....+..+.+.+
T Consensus 56 tv~S~l~~~P~~~d~Gk~ltC~v~h~al~~~~~~~~~l 93 (95)
T cd07703 56 TVTSEYSLVPTPEANGKEVTCKVEHETLQEPQLLPVTL 93 (95)
T ss_pred EEEEEEEEecCHHHCCCEEEEEEeCcccCCCeEEEEEE
Confidence 56779999999999999999999887754444444433
No 11
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=20.74 E-value=91 Score=35.44 Aligned_cols=59 Identities=29% Similarity=0.390 Sum_probs=42.8
Q ss_pred EeCceeEEEeecCCcee-----------ecCCcceEEe----eeceEEEEEeecCcccccccccceEEEEehhhhhhh
Q 024467 92 YKGKAALTVEPRGPEFV-----------SLDSGAVKLS----REGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSL 154 (267)
Q Consensus 92 YKgKAALsv~pi~P~F~-----------~~~sG~~kv~----R~G~ILLeFAPa~g~rqYDW~kKq~FsLS~tEvG~L 154 (267)
=||..+|.++-++|.+- ...+|.+.-+ ++|-||+|..|... |-.+++...++|+|||+=
T Consensus 312 ~~g~~~f~~kRrP~D~qP~~~kk~P~g~~~~~~~v~g~~~~~~~lPvLve~s~dG~----~s~~ri~L~~~vtEVGs~ 385 (1629)
T KOG1892|consen 312 DKGILVFQLKRRPPDHQPKKTKKTPKGKERADGSVYGSTLPPEKLPVLVELSPDGS----DSRKRIRLQLSVTEVGSE 385 (1629)
T ss_pred ccceEEEEEccCCcccCccccccCccccccCCCcccCCCCCcccCcEEEEEcCCCC----CcceeEEeccCceecccc
Confidence 35566666666655553 3455566656 88999999999864 444899999999999974
Done!