Query 008192
Match_columns 574
No_of_seqs 96 out of 121
Neff 2.5
Searched_HMMs 46136
Date Thu Mar 28 20:39:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008192.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008192hhsearch_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 4E-202 9E-207 1499.2 23.7 364 93-469 2-365 (365)
2 smart00546 CUE Domain that may 78.0 2.7 5.9E-05 31.2 3.1 34 404-437 3-36 (43)
3 PF02845 CUE: CUE domain; Int 72.2 4.7 0.0001 29.9 3.1 34 404-437 2-35 (42)
4 PF09539 DUF2385: Protein of u 59.4 1.2 2.5E-05 40.0 -2.6 31 134-164 10-41 (96)
5 TIGR02301 conserved hypothetic 46.1 2.7 5.9E-05 39.1 -2.5 31 134-164 35-66 (121)
6 KOG2379 Endonuclease MUS81 [Re 29.5 1.2E+02 0.0027 34.3 6.2 80 265-356 357-450 (501)
7 PF10236 DAP3: Mitochondrial r 28.9 58 0.0013 33.4 3.5 61 276-336 79-141 (309)
8 PF05823 Gp-FAR-1: Nematode fa 28.4 1.7E+02 0.0037 27.7 6.2 96 302-445 1-97 (154)
9 cd08812 CARD_RIG-I_like Caspas 23.1 57 0.0012 28.1 1.9 39 389-427 31-78 (88)
10 PF05408 Peptidase_C28: Foot-a 20.4 20 0.00044 35.9 -1.5 82 286-368 12-102 (193)
11 PF02169 LPP20: LPP20 lipoprot 20.1 47 0.001 27.1 0.8 31 112-142 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=4.1e-202 Score=1499.20 Aligned_cols=364 Identities=74% Similarity=1.162 Sum_probs=290.2
Q ss_pred hhHHHHHHHHHHHhhhccCCCCCCcchhhHHHHHHHHhHhHHhhhccccccCCCchhHHhhhhhhcceeeeccceeEEee
Q 008192 93 LSEVEMMKERFAKLLLGEDMSGGGKGVCTALAISNAITNLSATVFGELWRLEPLAPQKKAMWRREMQWLLCVSDSIVELV 172 (574)
Q Consensus 93 ~se~E~MKERFaKLLLGEDMSGggKGV~tALAiSNAITNL~AtVFGelwrLEPL~~ekK~mWrREmdwLLSVsD~IVElv 172 (574)
.+|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccCCCceEEeeccccccccccCchhHHHHHHHHHHHhhccCCCeeEEEeCCccccCCCCCCCCCCCCCCCCCcccc
Q 008192 173 PSIQQFPGGGTYEVMATRPRSDLYMNLPALKKLDAMLIGMLDGFCETEFWYVDRGIVVGDGGDRDAFSSMVPSGRPSVRH 252 (574)
Q Consensus 173 Ps~Q~~~dG~~~EVM~~rpRsDl~~NLPALrKLD~MLle~LDsF~dtEFWYvd~g~~a~~~~~~~~~~~s~s~r~~~~R~ 252 (574)
|++|++|||+++|||+||||+|||||||||||||+||||+||||+|||||||++|+++ ++++ ++++|+..+||
T Consensus 82 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLie~LDsf~dtEFwYv~~g~~~-~~~~------~~~~~~~~~r~ 154 (365)
T PF03759_consen 82 PSKQTFPDGTTMEVMTTRPRSDLYMNLPALRKLDAMLIEILDSFKDTEFWYVDQGIVA-DSDS------SSSFRRSSQRQ 154 (365)
T ss_dssp EEEEE-TTS-EEEEEEEEE-HHHHTHHHHHHHHHHHHHHHHHTTCS-SSEE--TT-------S------HHHHT------
T ss_pred cceeecCCCceEEEEecCccchhhcCcHHHHHHHHHHHHHHHhCCCCeeEEecCCccc-cccc------CccccCccccc
Confidence 9999999999999999999999999999999999999999999999999999999988 4443 67899999999
Q ss_pred CccccccCCCCCCCCCCHHHHHHhhhhhhhHHHHHHHHHHhhhhhhccCCCcHHHHhhcccCCccchhHHHHHHhhcCCC
Q 008192 253 EEKWWLPCPKVPQNGLSEDVRKKLQQCRDCTNQILKAAMAINSSVLAEMEIPAAYLETLPKNGKACLGDIIYRYITADQF 332 (574)
Q Consensus 253 eeKWWLP~P~VPp~GLSe~~RK~L~~qrd~~nQIlKAAmAINs~vL~EMeVPe~y~esLPKnGrasLGD~iYr~iT~d~F 332 (574)
++|||||+|||||+||||++||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+||+|+|
T Consensus 155 ~~KWWLP~p~VP~~GLse~~rK~L~~~rd~~~QilKAAmaIN~~vL~EMeiP~~y~esLPKnGrasLGd~iYr~it~~~F 234 (365)
T PF03759_consen 155 EEKWWLPVPRVPPNGLSEESRKWLQHQRDCVNQILKAAMAINSQVLAEMEIPESYLESLPKNGRASLGDSIYRYITSEQF 234 (365)
T ss_dssp CCCTTS--EE--TT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---HHHHHCS-SSHHHHHHHHHHHHCTSSS-
T ss_pred CCcccCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcccccHHHHHHHHhccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHhhhcCCCchhhHHHHhhhhHHHHHHHHHhhhcccccCCCCCCCCccccccccccchhhHHHHHHHHHHHHHHHHh
Q 008192 333 SPECLLDCLDLSSEHHTLEVANRIEAAVHVWKQKDQRKHLSHSKSRRSSWGGKVKGLVADSEKNHSLAHRAETLLHSLRL 412 (574)
Q Consensus 333 spe~lL~~ldLssEH~aLe~aNRiEAai~vWrrK~~~k~~~~~~~~ksSWg~~Vkd~~~d~dK~e~laeRAEtlL~~LKq 412 (574)
||||||+||||||||+|||+||||||||||||||++++ ++|+|||++|||++++.|||++|++|||+||+||||
T Consensus 235 spe~ll~~ldlssEH~~le~~NRvEAai~vWrrK~~~k------~~ksSWg~~vkdl~~~~dK~e~l~eRAEtlL~~LK~ 308 (365)
T PF03759_consen 235 SPEQLLDCLDLSSEHKALELANRVEAAIYVWRRKICEK------DSKSSWGSMVKDLMSDGDKRELLAERAETLLLCLKQ 308 (365)
T ss_dssp -HHHHHHTS--SSHHHHHHHHHHHHHHHHHHCH---------------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhcCC------CCccchhhhcccccccchHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999987 579999999999999999999999999999999999
Q ss_pred hCCCCCcchhhhhhhhhcchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccc
Q 008192 413 RFPGLPQTALDMNKIQYNKDVGQSILESYSRVMESLAFNIMARIDDVLFVDDATKRC 469 (574)
Q Consensus 413 RfPgLpQT~LD~sKIQyNKDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~l~k~~ 469 (574)
||||||||+||++|||||||||||||||||||||||||||++|||||||+|++++++
T Consensus 309 RfPgl~QT~LD~~KIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~~~~~~ 365 (365)
T PF03759_consen 309 RFPGLPQTSLDISKIQYNKDVGQAILESYSRVLESLAFNILSRIDDVLYADDLTKNS 365 (365)
T ss_dssp HSTT----HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred hCCCCCchHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Confidence 999999999999999999999999999999999999999999999999999999863
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=78.03 E-value=2.7 Score=31.16 Aligned_cols=34 Identities=26% Similarity=0.390 Sum_probs=29.4
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHH
Q 008192 404 ETLLHSLRLRFPGLPQTALDMNKIQYNKDVGQSI 437 (574)
Q Consensus 404 EtlL~~LKqRfPgLpQT~LD~sKIQyNKDVG~aI 437 (574)
+..+..|++-||.++...+-..=.++|.||..+|
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 3467889999999999999888888999999876
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=72.20 E-value=4.7 Score=29.94 Aligned_cols=34 Identities=26% Similarity=0.412 Sum_probs=29.5
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHH
Q 008192 404 ETLLHSLRLRFPGLPQTALDMNKIQYNKDVGQSI 437 (574)
Q Consensus 404 EtlL~~LKqRfPgLpQT~LD~sKIQyNKDVG~aI 437 (574)
+..+..|+.-||+++...+...=.++|.||-.+|
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=59.44 E-value=1.2 Score=39.96 Aligned_cols=31 Identities=35% Similarity=0.550 Sum_probs=27.4
Q ss_pred HhhhccccccCCCch-hHHhhhhhhcceeeec
Q 008192 134 ATVFGELWRLEPLAP-QKKAMWRREMQWLLCV 164 (574)
Q Consensus 134 AtVFGelwrLEPL~~-ekK~mWrREmdwLLSV 164 (574)
|-|+|+++-|.+||. +....||.+|.=||-+
T Consensus 10 AeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~~ 41 (96)
T PF09539_consen 10 AEILGALHYLRNLCGGNEDQYWRDRMQALLDA 41 (96)
T ss_pred HHHHHHHHHHHHHhCCCCcchHHHHHHHHHHh
Confidence 679999999999999 8899999999877643
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=46.14 E-value=2.7 Score=39.09 Aligned_cols=31 Identities=35% Similarity=0.538 Sum_probs=26.3
Q ss_pred HhhhccccccCCCchhHH-hhhhhhcceeeec
Q 008192 134 ATVFGELWRLEPLAPQKK-AMWRREMQWLLCV 164 (574)
Q Consensus 134 AtVFGelwrLEPL~~ekK-~mWrREmdwLLSV 164 (574)
|.|+|+++-|..||.... ..||.+|.=||-+
T Consensus 35 AeiLG~lHyLR~LC~~~~~~~WR~~M~~Ll~a 66 (121)
T TIGR02301 35 AEILGSLHYLRNLCGSKGDDYWRSRMQALIDA 66 (121)
T ss_pred HHHHHHHHHHHHHhCCCcchHHHHHHHHHHHh
Confidence 578999999999998665 8999999877653
No 6
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=29.49 E-value=1.2e+02 Score=34.27 Aligned_cols=80 Identities=25% Similarity=0.368 Sum_probs=59.5
Q ss_pred CCCCCHHHHHHhhhhhhhHHHHHHHHHHhh-------hhhhccCCCcH-------HHHhhcccCCccchhHHHHHHhhcC
Q 008192 265 QNGLSEDVRKKLQQCRDCTNQILKAAMAIN-------SSVLAEMEIPA-------AYLETLPKNGKACLGDIIYRYITAD 330 (574)
Q Consensus 265 p~GLSe~~RK~L~~qrd~~nQIlKAAmAIN-------s~vL~EMeVPe-------~y~esLPKnGrasLGD~iYr~iT~d 330 (574)
..||-+..+|-=.-+|. .-||.+-.|-=+ .+..-+|.+|. ++.+-++|++.-++||..++.
T Consensus 357 T~~l~et~s~l~y~tr~-~~~~~~~~~~~~~d~~~~~~q~~~~~~~p~~~~~~f~~F~~~~~K~~~~TV~evf~~q---- 431 (501)
T KOG2379|consen 357 TRDLGETVSKLAYLTRG-LLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQ---- 431 (501)
T ss_pred ecChhHHHHHHHHHhHH-HHHHHHHhhccccccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHH----
Confidence 45666666665344444 367777776555 78899999995 889999999999999999986
Q ss_pred CCChhhHhhhcCCCchhhHHHHhhhh
Q 008192 331 QFSPECLLDCLDLSSEHHTLEVANRI 356 (574)
Q Consensus 331 ~Fspe~lL~~ldLssEH~aLe~aNRi 356 (574)
|+.+..+|-| .|.+|++|-
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 4566777777 677777664
No 7
>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=28.88 E-value=58 Score=33.35 Aligned_cols=61 Identities=15% Similarity=0.174 Sum_probs=46.2
Q ss_pred hhhhhhhHHHHHHHHHHhhhhhhccCCCcHHHHhh--cccCCccchhHHHHHHhhcCCCChhh
Q 008192 276 LQQCRDCTNQILKAAMAINSSVLAEMEIPAAYLET--LPKNGKACLGDIIYRYITADQFSPEC 336 (574)
Q Consensus 276 L~~qrd~~nQIlKAAmAINs~vL~EMeVPe~y~es--LPKnGrasLGD~iYr~iT~d~Fspe~ 336 (574)
+-.|-..+.++||.-.+.|..+|..|.+...|.-+ -+..+..+|-|.+=..|....+++++
T Consensus 79 ~~~qP~~a~~~L~~~~~~N~~~L~~i~~s~~~~~~~~~~~~~g~tL~dLv~~g~~~~~~a~~~ 141 (309)
T PF10236_consen 79 LYDQPMYAAKWLKKFLKANEELLKKIKLSKDYKWSKRESTPKGSTLLDLVEQGINDPKYAWDV 141 (309)
T ss_pred eeecHHHHHHHHHHHHHHhHHHHHhccccccccccccccCCCCCCHHHHHHhhcccchhHHHH
Confidence 34677788999999999999999999999998766 33444467777776666666666644
No 8
>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=28.41 E-value=1.7e+02 Score=27.69 Aligned_cols=96 Identities=25% Similarity=0.334 Sum_probs=54.0
Q ss_pred CCcHHHHhhcccCCccchhHHHHHHhhcCCCChhhHhhhcCCCchhhHHHHhhhhHHHHHHHHHhhhcccccCCCCCCCC
Q 008192 302 EIPAAYLETLPKNGKACLGDIIYRYITADQFSPECLLDCLDLSSEHHTLEVANRIEAAVHVWKQKDQRKHLSHSKSRRSS 381 (574)
Q Consensus 302 eVPe~y~esLPKnGrasLGD~iYr~iT~d~Fspe~lL~~ldLssEH~aLe~aNRiEAai~vWrrK~~~k~~~~~~~~ksS 381 (574)
+||+.|.|-||..-. ..|..||.+ ....+.|+++.. . + -.+
T Consensus 1 ~i~~~~k~~iP~ev~-----~~~~~Lt~e--------------eK~~lkev~~~~-----------~-~--------~~~ 41 (154)
T PF05823_consen 1 DIPEEYKELIPSEVV-----EFYKNLTPE--------------EKAELKEVAKNY-----------A-K--------FKN 41 (154)
T ss_dssp -S-HHHHTT--HHHH-----HHHHH--TT--------------THHHHHHHHTT--------------------------
T ss_pred CchHHHHHhCcHHHH-----HHHHcCCHH--------------HHHHHHHHHHHc-----------c-c--------cCC
Confidence 488999988887533 233444443 566666776651 1 1 125
Q ss_pred ccccccccccch-hhHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhcchhhHHHHHHHHHHH
Q 008192 382 WGGKVKGLVADS-EKNHSLAHRAETLLHSLRLRFPGLPQTALDMNKIQYNKDVGQSILESYSRVM 445 (574)
Q Consensus 382 Wg~~Vkd~~~d~-dK~e~laeRAEtlL~~LKqRfPgLpQT~LD~sKIQyNKDVG~aILESYSRVL 445 (574)
| .|++... +|..-|.++++.|...+|.+|=+|...+- +|=+.|....+.-|...+
T Consensus 42 ~----de~i~~LK~ksP~L~~k~~~l~~~~k~ki~~L~peak-----~Fv~~li~~~~~l~~~~~ 97 (154)
T PF05823_consen 42 E----DEMIAALKEKSPSLYEKAEKLRDKLKKKIDKLSPEAK-----AFVKELIAKARSLYAQYS 97 (154)
T ss_dssp -----TTHHHHHHHH-HHHHHHHHHHHHHHHHTTTT--HHHH-----HHHHHHHHHHHHHHHHHH
T ss_pred H----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHHHHHHHhc
Confidence 6 4444444 68899999999999999999999976553 455555555555565543
No 9
>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=23.11 E-value=57 Score=28.13 Aligned_cols=39 Identities=36% Similarity=0.402 Sum_probs=29.5
Q ss_pred cccchhhHHHHHH--------HHHHHHHHHHh-hCCCCCcchhhhhhh
Q 008192 389 LVADSEKNHSLAH--------RAETLLHSLRL-RFPGLPQTALDMNKI 427 (574)
Q Consensus 389 ~~~d~dK~e~lae--------RAEtlL~~LKq-RfPgLpQT~LD~sKI 427 (574)
...+.+|-++.++ .|+.||.+|.+ |=||-.+.++|+=.-
T Consensus 31 ~L~~~~~e~I~a~~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl~AL~~ 78 (88)
T cd08812 31 CLTDEDKEQILAEERNKGNIAAAEELLDRLERCDKPGWFQAFLDALRR 78 (88)
T ss_pred HcCHHHHHHHHHHHhccChHHHHHHHHHHHHHhccCCcHHHHHHHHHH
Confidence 4445556555554 48889999998 999999999997543
No 10
>PF05408 Peptidase_C28: Foot-and-mouth virus L-proteinase; InterPro: IPR008739 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C28 (clan CA).The protein fold of the peptidase unit for members of this family resembles that of papain. The leader peptidase of Foot-and-mouth disease virus cleaves itself from the growing polyprotein and also cleaves the host translation initiation factor 4GI (eIF4G), thus inhibiting 5'-cap dependent translation [].; GO: 0004197 cysteine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 2JQF_R 1QMY_B 1QOL_G 2JQG_R.
Probab=20.38 E-value=20 Score=35.88 Aligned_cols=82 Identities=22% Similarity=0.389 Sum_probs=43.1
Q ss_pred HHHHHHHhhhhhhccCCCcHHHHhhcccCCccchhHHHHHHhh--cC-CC-----ChhhH-hhhcCCCchhhHHHHhhhh
Q 008192 286 ILKAAMAINSSVLAEMEIPAAYLETLPKNGKACLGDIIYRYIT--AD-QF-----SPECL-LDCLDLSSEHHTLEVANRI 356 (574)
Q Consensus 286 IlKAAmAINs~vL~EMeVPe~y~esLPKnGrasLGD~iYr~iT--~d-~F-----spe~l-L~~ldLssEH~aLe~aNRi 356 (574)
++.|.--|+.-.++++.-+..|. +||-++-.|-=-.||+..+ .+ -| +||++ +++++--+|+.-+++..--
T Consensus 12 l~~~~~~~~~l~~~~~~~~~eft-~~PN~~dnCWlNaL~QL~~~~d~~~Fd~~Y~~pe~~t~~~i~~l~e~tG~~l~~Gg 90 (193)
T PF05408_consen 12 LFEAFREIKALFLSRLDGKMEFT-GLPNNHDNCWLNALLQLFRYVDEPFFDWYYDSPENLTRQTIEQLCEQTGLDLHQGG 90 (193)
T ss_dssp --------------------EEE-----SSSTHHHHHHHHHHHHHT-GTTHHHHTSSS-THHHHHHHHHHHH-S-TSSSB
T ss_pred HHHHHHHhhheeeccCCcceEEe-cCCCCCCChHHHHHHHHHHHcCcccchhhcCCcccchHHHHHHHHhhhCceeccCC
Confidence 66677778888888988888877 9999999998777776653 22 22 47777 7887777899889999999
Q ss_pred HHHHHHHHHhhh
Q 008192 357 EAAVHVWKQKDQ 368 (574)
Q Consensus 357 EAai~vWrrK~~ 368 (574)
..|++||+-|-+
T Consensus 91 pP~~vi~~ik~~ 102 (193)
T PF05408_consen 91 PPALVIWKIKHL 102 (193)
T ss_dssp SHHHHHHHTGGG
T ss_pred CcEeeeehhhhh
Confidence 999999998876
No 11
>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=20.13 E-value=47 Score=27.13 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=25.7
Q ss_pred CCCCCcchhhHHHHHHHHhHhHHhhhccccc
Q 008192 112 MSGGGKGVCTALAISNAITNLSATVFGELWR 142 (574)
Q Consensus 112 MSGggKGV~tALAiSNAITNL~AtVFGelwr 142 (574)
+.|-|.|-..-.|.-||..||+..|+|..-.
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 5666777777999999999999999998643
Done!