Query 028165
Match_columns 212
No_of_seqs 55 out of 57
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:15:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028165hhsearch_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 5.4E-67 1.2E-71 427.4 15.4 137 64-200 1-139 (139)
2 PF02035 Coagulin: Coagulin; 85.4 0.81 1.8E-05 38.9 3.0 51 60-117 76-126 (174)
3 PF07490 Tir_receptor_N: Trans 47.9 26 0.00057 31.9 4.0 63 131-198 82-145 (266)
4 PF08624 CRC_subunit: Chromati 31.1 32 0.0007 28.9 1.8 48 85-142 15-69 (139)
5 KOG0288 WD40 repeat protein Ti 27.2 73 0.0016 31.6 3.6 55 41-97 394-455 (459)
6 PF10657 RC-P840_PscD: Photosy 22.5 58 0.0013 27.5 1.8 39 90-140 40-78 (144)
7 PF11814 DUF3335: Peptidase_C3 20.4 63 0.0014 28.8 1.7 42 129-196 151-192 (207)
8 KOG4718 Non-SMC (structural ma 17.6 1.3E+02 0.0028 27.5 3.0 47 154-205 61-111 (235)
9 PRK04179 rpl37e 50S ribosomal 17.4 38 0.00083 25.1 -0.3 15 102-116 41-55 (62)
10 PF13103 TonB_2: TonB C termin 16.1 84 0.0018 22.2 1.2 25 89-113 32-57 (85)
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=5.4e-67 Score=427.37 Aligned_cols=137 Identities=59% Similarity=1.002 Sum_probs=121.5
Q ss_pred eeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhhhcCCCCcceeeeCc
Q 028165 64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP 143 (212)
Q Consensus 64 sVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Llslg~~~s~EffHDP 143 (212)
+||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+++++++|||||||
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 cCcCCCccccceeeEEeeCCCC--ceEEEEEeecccCCCceeeeccchhHHHHHHHHHH
Q 028165 144 AMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACI 200 (212)
Q Consensus 144 ~~g~S~~G~v~K~LkIep~~dG--~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~ 200 (212)
+||+|++|+|+|+|||||+||| |||||+|+|++.|++++|+||||+|||||||++||
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 9999999999999999999996 99999999999999999999999999999999997
No 2
>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=85.44 E-value=0.81 Score=38.92 Aligned_cols=51 Identities=25% Similarity=0.541 Sum_probs=28.6
Q ss_pred eeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCccccccccee
Q 028165 60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117 (212)
Q Consensus 60 y~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~ 117 (212)
|+||+-|+..+-.+.+..-|.|.-.-+|.++ |++| ||.+|-||--|+.|-.
T Consensus 76 f~pf~hf~secpvstrdcepvfgyt~a~efr------vivq-apragfrqcvwqhkcr 126 (174)
T PF02035_consen 76 FPPFHHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKCR 126 (174)
T ss_dssp STT----SSB--EEEE----SEEE-TTS-EE------EE---BCCCTB-B---EEEET
T ss_pred CCCcccccccCCcccccccccccceecceEE------EEEe-CchhhHHHHHHHhhhc
Confidence 6999999999999999999999988888765 4555 9999999999999864
No 3
>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=47.94 E-value=26 Score=31.87 Aligned_cols=63 Identities=19% Similarity=0.305 Sum_probs=45.0
Q ss_pred cCCCCcceeeeCccCcCC-CccccceeeEEeeCCCCceEEEEEeecccCCCceeeeccchhHHHHHHHH
Q 028165 131 MGPRDSSEFFHDPAMLSS-NAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTA 198 (212)
Q Consensus 131 lg~~~s~EffHDP~~g~S-~~G~v~K~LkIep~~dG~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl 198 (212)
+.-.+.+|..||-.-.-. +..--.-+|.||.++||-++-+-.+|.+ -.+|-++..||+-|.++
T Consensus 82 i~L~ggfEVLHD~G~LDtLN~~IGss~FrvE~q~dG~h~AiGqk~gv-----EtsV~Ls~qE~~sLQai 145 (266)
T PF07490_consen 82 ITLHGGFEVLHDKGPLDTLNKQIGSSVFRVETQEDGSHVAIGQKNGV-----ETSVTLSEQELASLQAI 145 (266)
T ss_pred eeeccceEEeeccCchhhHHhhhCccceEEEeccCCceEeeeccCCe-----EEEEEeCHHHhhhhhcc
Confidence 455679999999542211 1111145899999999988778777654 56888999999988764
No 4
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=31.06 E-value=32 Score=28.93 Aligned_cols=48 Identities=35% Similarity=0.635 Sum_probs=33.6
Q ss_pred CCCCeeEeeeceEEEEeeecccCccccc-------ccceeEeeChhhhhhhhhcCCCCcceeeeC
Q 028165 85 DSGDLKVKRKGVILLTFAPAIGERKYDW-------AKKQHFALSPTEVGSLLTMGPRDSSEFFHD 142 (212)
Q Consensus 85 ~sG~~kv~R~G~vlLeFAPavG~RqYDW-------~kKq~FsLS~tEvG~Llslg~~~s~EffHD 142 (212)
+.|--||++.|-++ |.|+|-- .....|+|| +|+.-++ |.++|.+|||.
T Consensus 15 p~GE~KId~~G~Ll-------gGR~y~~~TFtl~~rg~~lymL~-td~ar~l--g~rDs~~ff~~ 69 (139)
T PF08624_consen 15 PKGEKKIDKNGRLL-------GGREYRFRTFTLPGRGNRLYMLS-TDPARCL--GFRDSYLFFRK 69 (139)
T ss_pred CCcCeEeCCCCccc-------CCCEEEEEEEEeCCCCCeEEEEe-HHHHHHh--ccccHHHHHHh
Confidence 45778999999874 5555521 116788887 5554444 99999999965
No 5
>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]
Probab=27.23 E-value=73 Score=31.56 Aligned_cols=55 Identities=20% Similarity=0.308 Sum_probs=36.1
Q ss_pred ccccccCccccCCCCCceeeeceeeeecceeEEEeecCC-------ceeecCCCCeeEeeeceE
Q 028165 41 GMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLP-------TFMKLDSGDLKVKRKGVI 97 (212)
Q Consensus 41 ~~st~~~~~~~~~~~~~rvy~~ysVYkgKaAls~~p~~P-------tF~~~~sG~~kv~R~G~v 97 (212)
-|| ....|.++|+...+||+ +.|++||....++-.-- .|.+.++|-+..+|++.+
T Consensus 394 vfS-pd~~YvaAGS~dgsv~i-W~v~tgKlE~~l~~s~s~~aI~s~~W~~sG~~Llsadk~~~v 455 (459)
T KOG0288|consen 394 VFS-PDGSYVAAGSADGSVYI-WSVFTGKLEKVLSLSTSNAAITSLSWNPSGSGLLSADKQKAV 455 (459)
T ss_pred EEC-CCCceeeeccCCCcEEE-EEccCceEEEEeccCCCCcceEEEEEcCCCchhhcccCCcce
Confidence 355 45568999999999998 89999998776653321 244444554444544443
No 6
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=22.51 E-value=58 Score=27.52 Aligned_cols=39 Identities=41% Similarity=0.566 Sum_probs=28.5
Q ss_pred eEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhhhcCCCCcceee
Q 028165 90 KVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFF 140 (212)
Q Consensus 90 kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Llslg~~~s~Eff 140 (212)
|.||.|.+-||++||.|-|+ |||++ .++...-+..+|+|
T Consensus 40 kRD~~g~Lql~i~pasGrrk----------Lspt~--emi~~l~~geIel~ 78 (144)
T PF10657_consen 40 KRDRYGKLQLTISPASGRRK----------LSPTP--EMIDKLISGEIELF 78 (144)
T ss_pred ecccCCceEEEEecCCCccc----------cCCcH--HHHHHHhcCceEEE
Confidence 56899999999999999887 56654 34544445566665
No 7
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=20.39 E-value=63 Score=28.78 Aligned_cols=42 Identities=24% Similarity=0.432 Sum_probs=28.7
Q ss_pred hhcCCCCcceeeeCccCcCCCccccceeeEEeeCCCCceEEEEEeecccCCCceeeeccchhHHHHHH
Q 028165 129 LTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMK 196 (212)
Q Consensus 129 lslg~~~s~EffHDP~~g~S~~G~v~K~LkIep~~dG~F~nLsV~n~~~~~~~~~~vPVt~aEfavlr 196 (212)
+..|.++.|-+.|||.-.. +.|+ ..-+...|||+.+||.-|.
T Consensus 151 ~v~g~d~~~vyihDP~~d~-~~~~-------------------------~~~d~~~lPi~~~~f~~m~ 192 (207)
T PF11814_consen 151 VVTGVDDDFVYIHDPDVDA-ERGE-------------------------SWVDCQHLPIPRADFDRMA 192 (207)
T ss_pred EEEEecCCEEEEeCCCCCc-ccCC-------------------------CchhhccCCccHHHHHHHH
Confidence 3457778888899998542 1111 1235788999999998764
No 8
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=17.55 E-value=1.3e+02 Score=27.50 Aligned_cols=47 Identities=21% Similarity=0.324 Sum_probs=35.4
Q ss_pred ceeeEEeeCCCC----ceEEEEEeecccCCCceeeeccchhHHHHHHHHHHHHHcc
Q 028165 154 RKSLSIKANADG----FFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASS 205 (212)
Q Consensus 154 ~K~LkIep~~dG----~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~f~l~~ 205 (212)
-+.+.+.-.+|| .|+||+.+ .+-.++.|.+.-|.+-||-++..||+|
T Consensus 61 ~~ikr~~~~~dgr~~lvyvNla~t-----p~SkmaT~f~~nEielfrkalE~im~s 111 (235)
T KOG4718|consen 61 QLIKRIKYPVDGREYLVYVNLAAT-----PDSKMATGFTANEIELFRKALEKIMSS 111 (235)
T ss_pred hhheeeeecCCCceEEEEEecCCC-----hhHHhcCCCCHHHHHHHHHHHHHHHhh
Confidence 345556666777 55566543 234589999999999999999999998
No 9
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=17.43 E-value=38 Score=25.12 Aligned_cols=15 Identities=27% Similarity=0.669 Sum_probs=11.8
Q ss_pred eecccCcccccccce
Q 028165 102 APAIGERKYDWAKKQ 116 (212)
Q Consensus 102 APavG~RqYDW~kKq 116 (212)
-|+.--|.|+|++|-
T Consensus 41 gps~k~R~YnWs~Ka 55 (62)
T PRK04179 41 GRSKRIRRYSWQNKK 55 (62)
T ss_pred CcccccccccHHHHh
Confidence 466668999999874
No 10
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=16.09 E-value=84 Score=22.21 Aligned_cols=25 Identities=16% Similarity=0.373 Sum_probs=16.9
Q ss_pred eeEeeeceE-EEEeeecccCcccccc
Q 028165 89 LKVKRKGVI-LLTFAPAIGERKYDWA 113 (212)
Q Consensus 89 ~kv~R~G~v-lLeFAPavG~RqYDW~ 113 (212)
+.++++|.| -.++..+.|+..+|-.
T Consensus 32 i~i~~dG~v~~~~i~~sSG~~~~D~a 57 (85)
T PF13103_consen 32 ITIDPDGRVISVRIVKSSGNPAFDAA 57 (85)
T ss_dssp EEE-TTSBEEEEEEEE--S-HHHHHH
T ss_pred EEECCCCCEEEEEEecCCCCHHHHHH
Confidence 456888988 7888899999999954
Done!