Query 008837
Match_columns 551
No_of_seqs 96 out of 117
Neff 2.6
Searched_HMMs 46136
Date Thu Mar 28 17:12:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008837.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008837hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03759 PRONE: PRONE (Plant-s 100.0 1E-202 2E-207 1498.6 25.4 364 96-473 2-365 (365)
2 smart00546 CUE Domain that may 77.4 2.8 6.1E-05 30.9 3.1 34 408-441 3-36 (43)
3 PF02845 CUE: CUE domain; Int 71.1 5 0.00011 29.6 3.0 34 408-441 2-35 (42)
4 PF09539 DUF2385: Protein of u 60.2 1.4 3.1E-05 39.3 -1.9 31 137-167 10-41 (96)
5 TIGR02301 conserved hypothetic 45.9 3.3 7.2E-05 38.4 -2.0 31 137-167 35-66 (121)
6 PF05823 Gp-FAR-1: Nematode fa 45.8 74 0.0016 29.9 6.8 95 306-448 1-96 (154)
7 KOG2379 Endonuclease MUS81 [Re 38.9 72 0.0016 35.9 6.3 81 268-360 356-450 (501)
8 KOG0938 Adaptor complexes medi 30.7 37 0.00081 37.0 2.6 39 140-203 261-299 (446)
9 PF10236 DAP3: Mitochondrial r 30.2 60 0.0013 33.1 3.8 74 281-354 80-159 (309)
10 cd08812 CARD_RIG-I_like Caspas 23.2 84 0.0018 27.0 2.9 38 393-430 31-77 (88)
11 PF06584 DIRP: DIRP; InterPro 22.2 96 0.0021 28.3 3.2 37 274-317 55-91 (109)
12 PF02169 LPP20: LPP20 lipoprot 21.7 42 0.0009 27.3 0.8 31 115-145 14-44 (92)
No 1
>PF03759 PRONE: PRONE (Plant-specific Rop nucleotide exchanger); InterPro: IPR005512 In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop proteins (Rho of plants, Rac-like and atRac in Arabidopsis thaliana (Mouse-ear cress)) belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factor that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop [, , ]. The PRONE domain can be divided into three highly conserved subdomains separated by two short stretches of variable amino acid residues [, ]. It is approximately 370 residues in length and displays an almost all alpha-helical structure except for a beta-turn that protrudes from the main body of the molecule. The overall structure of the PRONE domain can be divided into two subdomains, the first one including helices alpha1-5 and alpha13, the second alpha6-12 [].; GO: 0005089 Rho guanyl-nucleotide exchange factor activity; PDB: 2NTX_B 2NTY_B 2WBL_A.
Probab=100.00 E-value=1.1e-202 Score=1498.61 Aligned_cols=364 Identities=67% Similarity=1.087 Sum_probs=290.0
Q ss_pred hhHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHhHhHHhhhccccccCcCcHHHhhhhhhhccccccccceeEEee
Q 008837 96 LSEIELMKERFAKLLLGEDMSGGGKGVCTALAISNAITNLSASVFGELWKLEPLALRKKMMWQREMEWLLCVSDSIVELI 175 (551)
Q Consensus 96 ~se~E~MKErFaKLLLGEDMSGggKGV~tALAiSNAITNL~AtVFGelwrLEPL~~ekK~mWrREmdwLLsVsD~IVElv 175 (551)
.+|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
T Consensus 2 ~se~e~mKErFaKLLLGEDmSG~gkGV~tAlAiSNAITNL~AtvFGe~~rLEPl~~ekk~~WrrEm~wLLsv~d~iVE~v 81 (365)
T PF03759_consen 2 PSEVEMMKERFAKLLLGEDMSGGGKGVCTALAISNAITNLAATVFGELWRLEPLSPEKKAMWRREMDWLLSVTDYIVELV 81 (365)
T ss_dssp HHHHHHHHHHHHHHHTTTBTTSSS-S--HHHHHHHHHHHHHHHHHTT--SSS---HHHHHHHHHHHHHHHGGGGG-EEEE
T ss_pred chHHHHHHHHHHHHhccCCCCCCCCcccHHHHHHHHHHHHHHHHhhhhhccCCCChHHHHHHHHhcceeecchhhhhhcc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccCCCcEEEeeecccccccccCchhhHHHhHHHHHHHhccCCCeeEeeeCCcccCCCCCCCCCCCCCCCCCCCCCC
Q 008837 176 PSLQEFPGGGTFEVMVTRPRSDLYVNLPALKKLDTMLVNILEGFREAEFCYVDRGLIVGGGGDDTKTFPSCSSSSRPFAG 255 (551)
Q Consensus 176 Ps~Q~~~dG~~~EvM~~rpRsDl~~NLPALrKLD~MLle~LDsF~dtEFWYvd~g~~~~~~~~~~~~~~~s~s~r~~~~R 255 (551)
|++|++|||+++|||+||||+|||||||||||||+||||+||||+|||||||++|+++ +.+ + ++++|+..+|
T Consensus 82 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLie~LDsf~dtEFwYv~~g~~~-~~~-~------~~~~~~~~~r 153 (365)
T PF03759_consen 82 PSKQTFPDGTTMEVMTTRPRSDLYMNLPALRKLDAMLIEILDSFKDTEFWYVDQGIVA-DSD-S------SSSFRRSSQR 153 (365)
T ss_dssp EEEEE-TTS-EEEEEEEEE-HHHHTHHHHHHHHHHHHHHHHHTTCS-SSEE--TT--------S------HHHHT-----
T ss_pred cceeecCCCceEEEEecCccchhhcCcHHHHHHHHHHHHHHHhCCCCeeEEecCCccc-ccc-c------CccccCcccc
Confidence 9999999999999999999999999999999999999999999999999999999998 332 2 6789999999
Q ss_pred CCCcccccCCcCCCCCCCHHHHHHHhHhhHHHHHHHHHHHHhhhhhhhcCCCchHHHhhcccCCccchhhHHHHhhhcCC
Q 008837 256 PEEKWWLPFPMVPPNGLSENMRERLQQARECTSQILKAAMAINSNVLAEMEIPNAYLESLPKSGKECLGEIMYNYITADQ 335 (551)
Q Consensus 256 ~eeKWWLP~P~VPp~GLSe~~RK~L~~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~esLPKnGrasLGD~iYr~iT~d~ 335 (551)
|++|||||+|||||+||||++||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+||+|+
T Consensus 154 ~~~KWWLP~p~VP~~GLse~~rK~L~~~rd~~~QilKAAmaIN~~vL~EMeiP~~y~esLPKnGrasLGd~iYr~it~~~ 233 (365)
T PF03759_consen 154 QEEKWWLPVPRVPPNGLSEESRKWLQHQRDCVNQILKAAMAINSQVLAEMEIPESYLESLPKNGRASLGDSIYRYITSEQ 233 (365)
T ss_dssp -CCCTTS--EE--TT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---HHHHHCS-SSHHHHHHHHHHHHCTSSS
T ss_pred cCCcccCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcccccHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHhhhcCCCchhhHHHHhhhhHHHHHHHHHHhhccccccCCCccCCCccccccccchhHHHHHHHHHHHHHHHHHH
Q 008837 336 FSPESLLAYLDLSSEYTTLEIANRIEAAVHIWRQKYQNKRIIRTKSGRSSWGGKVKGFVSDIERSKLLAHRADTILQNLK 415 (551)
Q Consensus 336 Fspe~lL~~ldLssEH~aLe~aNRiEAai~vWrrK~~~k~~~~~~~~ksSWg~~Vkd~~~d~dK~e~laeRAEtlL~~LK 415 (551)
|||||||+||||||||+|||+||||||||||||||+++++ +|+|||++|||++++.|||++|++|||+||+|||
T Consensus 234 Fspe~ll~~ldlssEH~~le~~NRvEAai~vWrrK~~~k~------~ksSWg~~vkdl~~~~dK~e~l~eRAEtlL~~LK 307 (365)
T PF03759_consen 234 FSPEQLLDCLDLSSEHKALELANRVEAAIYVWRRKICEKD------SKSSWGSMVKDLMSDGDKRELLAERAETLLLCLK 307 (365)
T ss_dssp --HHHHHHTS--SSHHHHHHHHHHHHHHHHHHCH---------------------------HHHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhcCCC------CccchhhhcccccccchHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999997 8999999999999999999999999999999999
Q ss_pred hhCCCCCcchhhhhhhhhcchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccch
Q 008837 416 LRFPSLPQTALDMNKIQYNKDVGQSILESYSRVMESLAFNIMARIDDLLYVDDATKQR 473 (551)
Q Consensus 416 qRfPgLpQT~LD~sKIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~l~~~~ 473 (551)
|||||||||+||++|||||||||||||||||||||||||||++|||||||+|++++++
T Consensus 308 ~RfPgl~QT~LD~~KIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~~~~~~ 365 (365)
T PF03759_consen 308 QRFPGLPQTSLDISKIQYNKDVGQAILESYSRVLESLAFNILSRIDDVLYADDLTKNS 365 (365)
T ss_dssp HHSTT----HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HhCCCCCchHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Confidence 9999999999999999999999999999999999999999999999999999999863
No 2
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=77.40 E-value=2.8 Score=30.92 Aligned_cols=34 Identities=29% Similarity=0.393 Sum_probs=29.2
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHH
Q 008837 408 DTILQNLKLRFPSLPQTALDMNKIQYNKDVGQSI 441 (551)
Q Consensus 408 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aI 441 (551)
+..+..|++-||.++...+-..=.++|.||..+|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i 36 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATI 36 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3467889999999999999888888999998876
No 3
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=71.07 E-value=5 Score=29.64 Aligned_cols=34 Identities=26% Similarity=0.424 Sum_probs=29.3
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHH
Q 008837 408 DTILQNLKLRFPSLPQTALDMNKIQYNKDVGQSI 441 (551)
Q Consensus 408 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aI 441 (551)
+..+..|+.-||+++...+-..=.++|.||-.+|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai 35 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAI 35 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 4567899999999999999999999999998876
No 4
>PF09539 DUF2385: Protein of unknown function (DUF2385); InterPro: IPR012645 Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function is unknown.
Probab=60.22 E-value=1.4 Score=39.27 Aligned_cols=31 Identities=29% Similarity=0.462 Sum_probs=27.6
Q ss_pred HhhhccccccCcCcH-HHhhhhhhhccccccc
Q 008837 137 ASVFGELWKLEPLAL-RKKMMWQREMEWLLCV 167 (551)
Q Consensus 137 AtVFGelwrLEPL~~-ekK~mWrREmdwLLsV 167 (551)
|-|+|+++-|.+|+. +....||.+|.=||-+
T Consensus 10 AeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~~ 41 (96)
T PF09539_consen 10 AEILGALHYLRNLCGGNEDQYWRDRMQALLDA 41 (96)
T ss_pred HHHHHHHHHHHHHhCCCCcchHHHHHHHHHHh
Confidence 679999999999999 8899999999877754
No 5
>TIGR02301 conserved hypothetical protein TIGR02301. Members of this uncharacterized protein family are found in a number of alphaProteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function is unknown.
Probab=45.93 E-value=3.3 Score=38.39 Aligned_cols=31 Identities=29% Similarity=0.430 Sum_probs=26.5
Q ss_pred HhhhccccccCcCcHHHh-hhhhhhccccccc
Q 008837 137 ASVFGELWKLEPLALRKK-MMWQREMEWLLCV 167 (551)
Q Consensus 137 AtVFGelwrLEPL~~ekK-~mWrREmdwLLsV 167 (551)
|.|+|+++-|..|+.... ..||.+|.=|+-+
T Consensus 35 AeiLG~lHyLR~LC~~~~~~~WR~~M~~Ll~a 66 (121)
T TIGR02301 35 AEILGSLHYLRNLCGSKGDDYWRSRMQALIDA 66 (121)
T ss_pred HHHHHHHHHHHHHhCCCcchHHHHHHHHHHHh
Confidence 578999999999998665 8999999877754
No 6
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=45.83 E-value=74 Score=29.94 Aligned_cols=95 Identities=20% Similarity=0.285 Sum_probs=54.3
Q ss_pred CCchHHHhhcccCCccchhhHHHHhhhcCCCChHHHhhhcCCCchhhHHHHhhhhHHHHHHHHHHhhccccccCCCccCC
Q 008837 306 EIPNAYLESLPKSGKECLGEIMYNYITADQFSPESLLAYLDLSSEYTTLEIANRIEAAVHIWRQKYQNKRIIRTKSGRSS 385 (551)
Q Consensus 306 eIPe~y~esLPKnGrasLGD~iYr~iT~d~Fspe~lL~~ldLssEH~aLe~aNRiEAai~vWrrK~~~k~~~~~~~~ksS 385 (551)
+||+.|.|-+|..-. ++++.|.-.....+.|+++.- . + -++
T Consensus 1 ~i~~~~k~~iP~ev~-------------------~~~~~Lt~eeK~~lkev~~~~-------~-----~--------~~~ 41 (154)
T PF05823_consen 1 DIPEEYKELIPSEVV-------------------EFYKNLTPEEKAELKEVAKNY-------A-----K--------FKN 41 (154)
T ss_dssp -S-HHHHTT--HHHH-------------------HHHHH--TTTHHHHHHHHTT--------------------------
T ss_pred CchHHHHHhCcHHHH-------------------HHHHcCCHHHHHHHHHHHHHc-------c-----c--------cCC
Confidence 488899988886533 234444444566777777661 1 1 125
Q ss_pred Cccccccccchh-HHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHHHHHHHHH
Q 008837 386 WGGKVKGFVSDI-ERSKLLAHRADTILQNLKLRFPSLPQTALDMNKIQYNKDVGQSILESYSRV 448 (551)
Q Consensus 386 Wg~~Vkd~~~d~-dK~e~laeRAEtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aILESYSRV 448 (551)
| .|++... +|..-|.++++.+...+|.+|=+|...+- +|=+.|....+.-|...
T Consensus 42 ~----de~i~~LK~ksP~L~~k~~~l~~~~k~ki~~L~peak-----~Fv~~li~~~~~l~~~~ 96 (154)
T PF05823_consen 42 E----DEMIAALKEKSPSLYEKAEKLRDKLKKKIDKLSPEAK-----AFVKELIAKARSLYAQY 96 (154)
T ss_dssp -----TTHHHHHHHH-HHHHHHHHHHHHHHHHTTTT--HHHH-----HHHHHHHHHHHHHHHHH
T ss_pred H----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHHHHHHHh
Confidence 6 4445454 68899999999999999999999966553 45555555555555553
No 7
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=38.92 E-value=72 Score=35.86 Aligned_cols=81 Identities=23% Similarity=0.324 Sum_probs=61.9
Q ss_pred CCCCCCHHHHHHHhHhhHHHHHHHHHHHHhh-------hhhhhcCCCch-------HHHhhcccCCccchhhHHHHhhhc
Q 008837 268 PPNGLSENMRERLQQARECTSQILKAAMAIN-------SNVLAEMEIPN-------AYLESLPKSGKECLGEIMYNYITA 333 (551)
Q Consensus 268 Pp~GLSe~~RK~L~~qrd~~nQIlKAAmAIN-------s~vL~EMeIPe-------~y~esLPKnGrasLGD~iYr~iT~ 333 (551)
-..||-+..+|-=--+|. .-||.+-.+-=+ .|..-+|.+|. ++.+-++|++.-++||..++.
T Consensus 356 RT~~l~et~s~l~y~tr~-~~~~~~~~~~~~~d~~~~~~q~~~~~~~p~~~~~~f~~F~~~~~K~~~~TV~evf~~q--- 431 (501)
T KOG2379|consen 356 RTRDLGETVSKLAYLTRG-LLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQ--- 431 (501)
T ss_pred EecChhHHHHHHHHHhHH-HHHHHHHhhccccccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHH---
Confidence 356676776665334444 467777777655 78999999995 889999999999999999995
Q ss_pred CCCChHHHhhhcCCCchhhHHHHhhhh
Q 008837 334 DQFSPESLLAYLDLSSEYTTLEIANRI 360 (551)
Q Consensus 334 d~Fspe~lL~~ldLssEH~aLe~aNRi 360 (551)
|+.+..+|-| .|.+|++|-
T Consensus 432 -------LMqvkg~S~e-rAiAI~d~Y 450 (501)
T KOG2379|consen 432 -------LMQVKGMSLE-RAIAIADRY 450 (501)
T ss_pred -------HHhccCccHH-HHHHHHHhc
Confidence 6777788877 677777764
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.72 E-value=37 Score=36.97 Aligned_cols=39 Identities=36% Similarity=0.761 Sum_probs=30.7
Q ss_pred hccccccCcCcHHHhhhhhhhccccccccceeEEeecCccccCCCcEEEeeecccccccccCch
Q 008837 140 FGELWKLEPLALRKKMMWQREMEWLLCVSDSIVELIPSLQEFPGGGTFEVMVTRPRSDLYVNLP 203 (551)
Q Consensus 140 FGelwrLEPL~~ekK~mWrREmdwLLsVsD~IVElvPs~Q~~~dG~~~EvM~~rpRsDl~~NLP 203 (551)
|-||-||--.. +.|+++||| ||| .||.|--|-+.+| |||
T Consensus 261 FHqCV~L~kFn-----------------~eh~IsFvP-----PDG-e~ELMkYr~~enI--nlP 299 (446)
T KOG0938|consen 261 FHQCVRLDKFN-----------------SEHIISFVP-----PDG-EFELMKYRVTENI--NLP 299 (446)
T ss_pred hheeecccccc-----------------ccceEEEeC-----CCC-ceEeEeeeeccCc--ccc
Confidence 99999986443 469999999 677 5899999888765 665
No 9
>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=30.18 E-value=60 Score=33.13 Aligned_cols=74 Identities=16% Similarity=0.188 Sum_probs=53.2
Q ss_pred hHhhHHHHHHHHHHHHhhhhhhhcCCCchHHHhh--cccCCccchhhHHHHhhhcCCCChHH---HhhhcCCCch-hhHH
Q 008837 281 QQARECTSQILKAAMAINSNVLAEMEIPNAYLES--LPKSGKECLGEIMYNYITADQFSPES---LLAYLDLSSE-YTTL 354 (551)
Q Consensus 281 ~~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~es--LPKnGrasLGD~iYr~iT~d~Fspe~---lL~~ldLssE-H~aL 354 (551)
=.|-..+.++||.-.+.|..+|..|.+...|.-+ -+..+..+|-|.+=..|....+++++ |++.|...++ ..+|
T Consensus 80 ~~qP~~a~~~L~~~~~~N~~~L~~i~~s~~~~~~~~~~~~~g~tL~dLv~~g~~~~~~a~~~~~~l~~EL~~~~~~~PVL 159 (309)
T PF10236_consen 80 YDQPMYAAKWLKKFLKANEELLKKIKLSKDYKWSKRESTPKGSTLLDLVEQGINDPKYAWDVFQALIRELKAQSKRPPVL 159 (309)
T ss_pred eecHHHHHHHHHHHHHHhHHHHHhccccccccccccccCCCCCCHHHHHHhhcccchhHHHHHHHHHHHHHhcccCCceE
Confidence 4566778888889999999999999999998776 34445568888777777777777754 3444555555 4444
No 10
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mec
Probab=23.22 E-value=84 Score=26.98 Aligned_cols=38 Identities=26% Similarity=0.398 Sum_probs=28.9
Q ss_pred ccchhHHHHHHHH--------HHHHHHHHHHh-hCCCCCcchhhhhh
Q 008837 393 FVSDIERSKLLAH--------RADTILQNLKL-RFPSLPQTALDMNK 430 (551)
Q Consensus 393 ~~~d~dK~e~lae--------RAEtlL~~LKq-RfPgLpQT~LD~sK 430 (551)
...+.+|-++.++ .|+.||.+|.+ |=||-.+.++|+=.
T Consensus 31 ~L~~~~~e~I~a~~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl~AL~ 77 (88)
T cd08812 31 CLTDEDKEQILAEERNKGNIAAAEELLDRLERCDKPGWFQAFLDALR 77 (88)
T ss_pred HcCHHHHHHHHHHHhccChHHHHHHHHHHHHHhccCCcHHHHHHHHH
Confidence 4445556555554 48899999998 99999999998743
No 11
>PF06584 DIRP: DIRP; InterPro: IPR010561 DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of Drosophila melanogaster and mustard weed. Studies of lin-9 and aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway.
Probab=22.18 E-value=96 Score=28.35 Aligned_cols=37 Identities=30% Similarity=0.491 Sum_probs=25.4
Q ss_pred HHHHHHHhHhhHHHHHHHHHHHHhhhhhhhcCCCchHHHhhccc
Q 008837 274 ENMRERLQQARECTSQILKAAMAINSNVLAEMEIPNAYLESLPK 317 (551)
Q Consensus 274 e~~RK~L~~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~esLPK 317 (551)
+++|..|.++|+.+.|+-+ .-+.+-+....+++.||+
T Consensus 55 ~eER~~Le~~R~~iR~lQ~-------~~~~~~~~~~~~~~~lP~ 91 (109)
T PF06584_consen 55 EEEREELERKRQKIRQLQQ-------RKFHDTELNSDLLEDLPD 91 (109)
T ss_pred HHHHHHHHHHHHHHHHHhh-------ccccccccchhhhhcCch
Confidence 5799999999999999733 233333445566666654
No 12
>PF02169 LPP20: LPP20 lipoprotein; InterPro: IPR002217 A major antigen has been recognised in Helicobacter pylori, a protein with an apparent molecular weight of 20,000 and mass 18,283 kDa []. DNA sequence analysis revealed a 525 bp gene, encoding a 175-amino acid residue product with a typical 21-residue lipoprotein signal peptide and consensus prolipoprotein processing site []. Results of experimental work with Lpp20 are consistent with it being a nonessential lipoprotein []. Prokaryotic membrane lipoproteins are synthesised with precursor signal peptides that are cleaved by specific peptidases (signal peptidase II). The enzyme recognises a conserved sequence, cutting upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [].; GO: 0009279 cell outer membrane
Probab=21.67 E-value=42 Score=27.30 Aligned_cols=31 Identities=19% Similarity=0.233 Sum_probs=25.7
Q ss_pred CCCCCcchhHHHHHHHHHhHhHHhhhccccc
Q 008837 115 MSGGGKGVCTALAISNAITNLSASVFGELWK 145 (551)
Q Consensus 115 MSGggKGV~tALAiSNAITNL~AtVFGelwr 145 (551)
+.|-|.|-..-.|.-||..||+..|+|..-.
T Consensus 14 l~a~G~~~~~~~A~~~A~~~la~~i~~~v~~ 44 (92)
T PF02169_consen 14 LYAVGSGSSREQAKQDALANLAEQISVVVIS 44 (92)
T ss_pred EEEEEcccChHHHHHHHHHHHHHheeEEEEe
Confidence 5566777777899999999999999998643
Done!