Query 013162
Match_columns 448
No_of_seqs 89 out of 113
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 01:01:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013162hhsearch_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 5E-189 1E-193 1375.0 21.3 335 93-440 2-336 (365)
2 smart00546 CUE Domain that may 81.2 1.9 4.1E-05 31.1 3.1 34 404-437 3-36 (43)
3 PF02845 CUE: CUE domain; Int 75.2 3.8 8.2E-05 29.5 3.2 37 404-440 2-38 (42)
4 PF09539 DUF2385: Protein of u 60.1 1.1 2.4E-05 39.0 -2.6 31 134-164 10-41 (96)
5 PF05823 Gp-FAR-1: Nematode fa 49.2 24 0.00052 32.3 4.0 78 302-422 1-79 (154)
6 TIGR02301 conserved hypothetic 46.1 2.7 5.9E-05 38.0 -2.4 31 134-164 35-66 (121)
7 KOG2379 Endonuclease MUS81 [Re 39.7 68 0.0015 35.2 6.2 81 264-356 356-450 (501)
8 PF10236 DAP3: Mitochondrial r 34.6 45 0.00098 33.2 3.7 82 275-356 78-165 (309)
9 KOG0938 Adaptor complexes medi 31.9 33 0.00072 36.6 2.4 39 137-200 261-299 (446)
10 cd08812 CARD_RIG-I_like Caspas 29.1 43 0.00093 28.0 2.2 38 389-426 31-77 (88)
11 PF02169 LPP20: LPP20 lipoprot 26.6 29 0.00064 27.4 0.8 31 112-142 14-44 (92)
12 PF05408 Peptidase_C28: Foot-a 23.2 17 0.00036 35.5 -1.4 83 286-369 12-103 (193)
13 PF14261 DUF4351: Domain of un 22.6 90 0.002 24.7 2.8 38 401-440 7-49 (59)
14 PF06584 DIRP: DIRP; InterPro 21.7 87 0.0019 27.9 2.8 37 270-313 55-91 (109)
15 PF13671 AAA_33: AAA domain; P 21.6 82 0.0018 26.0 2.5 57 310-366 6-65 (143)
16 COG0323 MutL DNA mismatch repa 21.3 71 0.0015 35.4 2.6 39 159-205 121-161 (638)
17 PF12867 DinB_2: DinB superfam 20.1 1.6E+02 0.0035 23.1 3.8 28 303-330 16-43 (127)
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=4.9e-189 Score=1374.98 Aligned_cols=335 Identities=73% Similarity=1.133 Sum_probs=262.2
Q ss_pred hhHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHhHhHHhhhccccccCCCchhHHhhhhhhcceeeeccceeEEee
Q 013162 93 LSEVEMMKERFAKLLLGEDMSGGGKGVCTALAISNAITNLSATVFGELWRLEPLAPQKKAMWRREMQWLLCVSDSIVELV 172 (448)
Q Consensus 93 ~se~E~MKErFaKLLLGEDMSGggKGV~tALAiSNAITNL~AtVFGelwrLEPL~~ekK~mWrREmdwLLSVsD~IVElv 172 (448)
.+|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
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 ecceecCCCceEEeeccccccccccCchhHHHHHHHHHHHhhccCCCeeEEEeCCcccCCCCCCCCCCCCCCCCCCcccc
Q 013162 173 PSIQQFPGGGTYEVMATRPRSDLYMNLPALKKLDAMLIGMLDGFCETEFWYVDRGIVVGDGGDRDAFSSMVPSGRPSVRH 252 (448)
Q Consensus 173 Ps~Q~~~dG~~~EvM~trpRsDl~~NLPALrKLD~MLle~LDsF~dtEFWYv~~g~~~~~~~~~~~~~~s~s~r~~~~R~ 252 (448)
|++|++|||+++|||+||||+|||||||||||||+||||+||||+|||||||++|+++ +.+ .+++||+..+||
T Consensus 82 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLie~LDsf~dtEFwYv~~g~~~-~~~------~~~~~~~~~~r~ 154 (365)
T PF03759_consen 82 PSKQTFPDGTTMEVMTTRPRSDLYMNLPALRKLDAMLIEILDSFKDTEFWYVDQGIVA-DSD------SSSSFRRSSQRQ 154 (365)
T ss_dssp EEEEE-TTS-EEEEEEEEE-HHHHTHHHHHHHHHHHHHHHHHTTCS-SSEE--TT-------------SHHHHT------
T ss_pred cceeecCCCceEEEEecCccchhhcCcHHHHHHHHHHHHHHHhCCCCeeEEecCCccc-ccc------cCccccCccccc
Confidence 9999999999999999999999999999999999999999999999999999999998 332 267899999999
Q ss_pred CccccccCCCCCCCCCCHHHHHHhhhhhhhHHHHHHHHHHhhhhhhhcCCCcHHHHhhcccCCccchhHHHHHHhhcCCC
Q 013162 253 EEKWWLPCPKVPQNGLSEDVRKKLQQCRDCTNQILKAAMAINSSVLAEMEIPAAYLETLPKNGKACLGDIIYRYITADQF 332 (448)
Q Consensus 253 eeKWWLP~P~VPp~GLSe~~RK~Lq~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~esLPKnGrasLGD~iYr~iT~d~F 332 (448)
++|||||+|||||+||||++||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+||+|+|
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 013162 333 SPECLLDCLDLSSEHHTLEVANRIEAAVHVWKQKDQRKHLSHSKSRRSSWGGKVKGLVADSEKNHSLAHRAETLLHSLRL 412 (448)
Q Consensus 333 spe~lL~~ldLssEH~aLe~anRiEAai~vWrrK~~~k~~~~~~~~ksSWg~~Vkd~~~d~dK~e~laeRAEtlL~~LKq 412 (448)
||||||+||||||||+|||+||||||||||||||+++++ +|+|||++|||++++.|||++|++|||+||+||||
T Consensus 235 spe~ll~~ldlssEH~~le~~NRvEAai~vWrrK~~~k~------~ksSWg~~vkdl~~~~dK~e~l~eRAEtlL~~LK~ 308 (365)
T PF03759_consen 235 SPEQLLDCLDLSSEHKALELANRVEAAIYVWRRKICEKD------SKSSWGSMVKDLMSDGDKRELLAERAETLLLCLKQ 308 (365)
T ss_dssp -HHHHHHTS--SSHHHHHHHHHHHHHHHHHHCH---------------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhcCCC------CccchhhhcccccccchHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999997 89999999999999999999999999999999999
Q ss_pred hCCCCCcchhhhhhhhcccchhhhhhhh
Q 013162 413 RFPGLPQTALDMNKIQYNKVLARSFCIL 440 (448)
Q Consensus 413 RfPgLpQT~LD~sKIQyNkDVG~aILE~ 440 (448)
||||||||+||++||||||||||||||-
T Consensus 309 RfPgl~QT~LD~~KIQyNkDVG~aILES 336 (365)
T PF03759_consen 309 RFPGLPQTSLDISKIQYNKDVGQAILES 336 (365)
T ss_dssp HSTT----HHHHHHHHH---HHHHHHHH
T ss_pred hCCCCCchHHHHHHHHccchhHHHHHHH
Confidence 9999999999999999999999999994
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=81.24 E-value=1.9 Score=31.06 Aligned_cols=34 Identities=21% Similarity=0.306 Sum_probs=30.0
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhcccchhhhh
Q 013162 404 ETLLHSLRLRFPGLPQTALDMNKIQYNKVLARSF 437 (448)
Q Consensus 404 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aI 437 (448)
+..+..|++-||.++...+-..=.++|.||..+|
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 3467889999999999999988888999999976
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=75.21 E-value=3.8 Score=29.49 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=31.2
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhcccchhhhhhhh
Q 013162 404 ETLLHSLRLRFPGLPQTALDMNKIQYNKVLARSFCIL 440 (448)
Q Consensus 404 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aILE~ 440 (448)
+..+..|+.-||+++...+-..=.++|.||-.+|-.|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 4567899999999999999999999999999887443
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=60.12 E-value=1.1 Score=39.00 Aligned_cols=31 Identities=35% Similarity=0.550 Sum_probs=27.3
Q ss_pred HhhhccccccCCCch-hHHhhhhhhcceeeec
Q 013162 134 ATVFGELWRLEPLAP-QKKAMWRREMQWLLCV 164 (448)
Q Consensus 134 AtVFGelwrLEPL~~-ekK~mWrREmdwLLSV 164 (448)
|-|+|+++-|.+|+. +....||.+|.=||-+
T Consensus 10 AeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~~ 41 (96)
T PF09539_consen 10 AEILGALHYLRNLCGGNEDQYWRDRMQALLDA 41 (96)
T ss_pred HHHHHHHHHHHHHhCCCCcchHHHHHHHHHHh
Confidence 679999999999999 8899999999876643
No 5
>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=49.21 E-value=24 Score=32.33 Aligned_cols=78 Identities=27% Similarity=0.316 Sum_probs=44.9
Q ss_pred CCcHHHHhhcccCCccchhHHHHHHhhcCCCChHHHhhhcCCCchhhHHHHhhhhHHHHHHHHhhhhccccCCCCCCcCC
Q 013162 302 EIPAAYLETLPKNGKACLGDIIYRYITADQFSPECLLDCLDLSSEHHTLEVANRIEAAVHVWKQKDQRKHLSHSKSRRSS 381 (448)
Q Consensus 302 eIPe~y~esLPKnGrasLGD~iYr~iT~d~Fspe~lL~~ldLssEH~aLe~anRiEAai~vWrrK~~~k~~~~~~~~ksS 381 (448)
+||+.|.+-+|..-. ++++.|.-.....+.|+++.- .+. .+
T Consensus 1 ~i~~~~k~~iP~ev~-------------------~~~~~Lt~eeK~~lkev~~~~------------~~~--------~~ 41 (154)
T PF05823_consen 1 DIPEEYKELIPSEVV-------------------EFYKNLTPEEKAELKEVAKNY------------AKF--------KN 41 (154)
T ss_dssp -S-HHHHTT--HHHH-------------------HHHHH--TTTHHHHHHHHTT--------------------------
T ss_pred CchHHHHHhCcHHHH-------------------HHHHcCCHHHHHHHHHHHHHc------------ccc--------CC
Confidence 488999988887533 233444444466667777651 111 35
Q ss_pred ccccccccccch-hhHHHHHHHHHHHHHHHHhhCCCCCcchh
Q 013162 382 WGGKVKGLVADS-EKNHSLAHRAETLLHSLRLRFPGLPQTAL 422 (448)
Q Consensus 382 Wg~~Vkd~~~d~-dK~e~laeRAEtlL~~LKqRfPgLpQT~L 422 (448)
+ .|++... .|..-|.++++.+...+|.+|=+|...+-
T Consensus 42 ~----de~i~~LK~ksP~L~~k~~~l~~~~k~ki~~L~peak 79 (154)
T PF05823_consen 42 E----DEMIAALKEKSPSLYEKAEKLRDKLKKKIDKLSPEAK 79 (154)
T ss_dssp -----TTHHHHHHHH-HHHHHHHHHHHHHHHHTTTT--HHHH
T ss_pred H----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHcCCHHHH
Confidence 6 4444444 68899999999999999999999976653
No 6
>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=46.15 E-value=2.7 Score=38.03 Aligned_cols=31 Identities=35% Similarity=0.538 Sum_probs=26.2
Q ss_pred HhhhccccccCCCchhHH-hhhhhhcceeeec
Q 013162 134 ATVFGELWRLEPLAPQKK-AMWRREMQWLLCV 164 (448)
Q Consensus 134 AtVFGelwrLEPL~~ekK-~mWrREmdwLLSV 164 (448)
|.|+|+++-|.+|+.... ..||.+|.=|+-+
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 7
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=39.69 E-value=68 Score=35.24 Aligned_cols=81 Identities=25% Similarity=0.359 Sum_probs=62.4
Q ss_pred CCCCCCHHHHHHhhhhhhhHHHHHHHHHHhh-------hhhhhcCCCcH-------HHHhhcccCCccchhHHHHHHhhc
Q 013162 264 PQNGLSEDVRKKLQQCRDCTNQILKAAMAIN-------SSVLAEMEIPA-------AYLETLPKNGKACLGDIIYRYITA 329 (448)
Q Consensus 264 Pp~GLSe~~RK~Lq~qrd~~nQIlKAAmAIN-------s~vL~EMeIPe-------~y~esLPKnGrasLGD~iYr~iT~ 329 (448)
-..||-+..+|-=.-+|.. -||.+-.+-=+ .+..-+|.+|. ++.+-++|++.-++||..++.
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 RTRDLGETVSKLAYLTRGL-LQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQ--- 431 (501)
T ss_pred EecChhHHHHHHHHHhHHH-HHHHHHhhccccccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHH---
Confidence 3567777777764444544 67777776555 78999999995 889999999999999999996
Q ss_pred CCCChHHHhhhcCCCchhhHHHHhhhh
Q 013162 330 DQFSPECLLDCLDLSSEHHTLEVANRI 356 (448)
Q Consensus 330 d~Fspe~lL~~ldLssEH~aLe~anRi 356 (448)
|+.+-.+|-| .|.+|++|-
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 5677777777 777777764
No 8
>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=34.56 E-value=45 Score=33.18 Aligned_cols=82 Identities=16% Similarity=0.177 Sum_probs=62.7
Q ss_pred HhhhhhhhHHHHHHHHHHhhhhhhhcCCCcHHHHhh--cccCCccchhHHHHHHhhcCCCChHH---HhhhcCCCch-hh
Q 013162 275 KLQQCRDCTNQILKAAMAINSSVLAEMEIPAAYLET--LPKNGKACLGDIIYRYITADQFSPEC---LLDCLDLSSE-HH 348 (448)
Q Consensus 275 ~Lq~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~es--LPKnGrasLGD~iYr~iT~d~Fspe~---lL~~ldLssE-H~ 348 (448)
.+-.|-..+.++||.-.+.|+.+|..|.+...|.-+ -+..+..+|-|.+=..+....+++++ |++.|...++ ..
T Consensus 78 ~~~~qP~~a~~~L~~~~~~N~~~L~~i~~s~~~~~~~~~~~~~g~tL~dLv~~g~~~~~~a~~~~~~l~~EL~~~~~~~P 157 (309)
T PF10236_consen 78 GLYDQPMYAAKWLKKFLKANEELLKKIKLSKDYKWSKRESTPKGSTLLDLVEQGINDPKYAWDVFQALIRELKAQSKRPP 157 (309)
T ss_pred CeeecHHHHHHHHHHHHHHhHHHHHhccccccccccccccCCCCCCHHHHHHhhcccchhHHHHHHHHHHHHHhcccCCc
Confidence 445677888999999999999999999999998776 44445578888888888888888854 4566777777 66
Q ss_pred HHHHhhhh
Q 013162 349 TLEVANRI 356 (448)
Q Consensus 349 aLe~anRi 356 (448)
+|=..|-+
T Consensus 158 VL~avD~~ 165 (309)
T PF10236_consen 158 VLVAVDGF 165 (309)
T ss_pred eEEEehhh
Confidence 65544443
No 9
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.92 E-value=33 Score=36.57 Aligned_cols=39 Identities=38% Similarity=0.775 Sum_probs=31.0
Q ss_pred hccccccCCCchhHHhhhhhhcceeeeccceeEEeeecceecCCCceEEeeccccccccccCch
Q 013162 137 FGELWRLEPLAPQKKAMWRREMQWLLCVSDSIVELVPSIQQFPGGGTYEVMATRPRSDLYMNLP 200 (448)
Q Consensus 137 FGelwrLEPL~~ekK~mWrREmdwLLSVsD~IVElvPs~Q~~~dG~~~EvM~trpRsDl~~NLP 200 (448)
|-||-||--.. +.|+++||| ||| .||.|--|-+.+| |||
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 99999986543 469999999 677 5899999888774 666
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=29.06 E-value=43 Score=27.99 Aligned_cols=38 Identities=37% Similarity=0.434 Sum_probs=28.9
Q ss_pred cccchhhHHHHHH--------HHHHHHHHHHh-hCCCCCcchhhhhh
Q 013162 389 LVADSEKNHSLAH--------RAETLLHSLRL-RFPGLPQTALDMNK 426 (448)
Q Consensus 389 ~~~d~dK~e~lae--------RAEtlL~~LKq-RfPgLpQT~LD~sK 426 (448)
...+.+|-++.++ .|+.||.+|.+ |=||-.+.++|+=.
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 4445555555554 48899999998 99999999998744
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=26.62 E-value=29 Score=27.44 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=25.8
Q ss_pred CCCCCcchhHHHHHHHHHhHhHHhhhccccc
Q 013162 112 MSGGGKGVCTALAISNAITNLSATVFGELWR 142 (448)
Q Consensus 112 MSGggKGV~tALAiSNAITNL~AtVFGelwr 142 (448)
+.|-|.|-..-.|.-||..||+..|+|..-.
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
No 12
>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=23.20 E-value=17 Score=35.48 Aligned_cols=83 Identities=20% Similarity=0.360 Sum_probs=43.8
Q ss_pred HHHHHHHhhhhhhhcCCCcHHHHhhcccCCccchhHHHHHHhh---cC----CC-ChHHH-hhhcCCCchhhHHHHhhhh
Q 013162 286 ILKAAMAINSSVLAEMEIPAAYLETLPKNGKACLGDIIYRYIT---AD----QF-SPECL-LDCLDLSSEHHTLEVANRI 356 (448)
Q Consensus 286 IlKAAmAINs~vL~EMeIPe~y~esLPKnGrasLGD~iYr~iT---~d----~F-spe~l-L~~ldLssEH~aLe~anRi 356 (448)
++.|.--|+.-.++++.-+..|. +||-++-.|-=-.||+..+ .- .| +||++ +++++--+|+--+++..--
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 66777778888999999888887 9999999887777776553 22 22 58888 8888888898889999999
Q ss_pred HHHHHHHHhhhhc
Q 013162 357 EAAVHVWKQKDQR 369 (448)
Q Consensus 357 EAai~vWrrK~~~ 369 (448)
..|++||+-|-+-
T Consensus 91 pP~~vi~~ik~~l 103 (193)
T PF05408_consen 91 PPALVIWKIKHLL 103 (193)
T ss_dssp SHHHHHHHTGGGS
T ss_pred CcEeeeehhhhhh
Confidence 9999999988763
No 13
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=22.63 E-value=90 Score=24.68 Aligned_cols=38 Identities=32% Similarity=0.346 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhCCCCCcchhhhhhhhcc-----cchhhhhhhh
Q 013162 401 HRAETLLHSLRLRFPGLPQTALDMNKIQYN-----KVLARSFCIL 440 (448)
Q Consensus 401 eRAEtlL~~LKqRfPgLpQT~LD~sKIQyN-----kDVG~aILE~ 440 (448)
..+.-++..|++||..+|...- .||+== .+.|-+||..
T Consensus 7 g~~~lllRlL~rrFG~lp~~~~--~~I~~l~~eqLE~l~e~ildf 49 (59)
T PF14261_consen 7 GEARLLLRLLTRRFGELPPEIQ--ERIQQLSLEQLEALAEAILDF 49 (59)
T ss_pred HHHHHHHHHHHHHcCCCCHHHH--HHHHcCCHHHHHHHHHHHhCC
Confidence 5577799999999999998743 444421 2445555543
No 14
>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=21.67 E-value=87 Score=27.90 Aligned_cols=37 Identities=27% Similarity=0.462 Sum_probs=25.2
Q ss_pred HHHHHHhhhhhhhHHHHHHHHHHhhhhhhhcCCCcHHHHhhccc
Q 013162 270 EDVRKKLQQCRDCTNQILKAAMAINSSVLAEMEIPAAYLETLPK 313 (448)
Q Consensus 270 e~~RK~Lq~qrd~~nQIlKAAmAINs~vL~EMeIPe~y~esLPK 313 (448)
+++|.+|.++|+.+.|+-+ .-+.+-+....+++.||+
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 233333445556666654
No 15
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=21.64 E-value=82 Score=26.00 Aligned_cols=57 Identities=19% Similarity=0.168 Sum_probs=40.3
Q ss_pred hcccCCccchhHHHHHHhhcCCCChHHHhhhcCC---CchhhHHHHhhhhHHHHHHHHhh
Q 013162 310 TLPKNGKACLGDIIYRYITADQFSPECLLDCLDL---SSEHHTLEVANRIEAAVHVWKQK 366 (448)
Q Consensus 310 sLPKnGrasLGD~iYr~iT~d~Fspe~lL~~ldL---ssEH~aLe~anRiEAai~vWrrK 366 (448)
-+|-+||+++.+.|.+.+..-.++.|.+...+.- .+.+...+..+++...+..+-++
T Consensus 6 G~pgsGKSt~a~~l~~~~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (143)
T PF13671_consen 6 GPPGSGKSTLAKRLAKRLGAVVISQDEIRRRLAGEDPPSPSDYIEAEERAYQILNAAIRK 65 (143)
T ss_dssp ESTTSSHHHHHHHHHHHSTEEEEEHHHHHHHHCCSSSGCCCCCHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHCCCEEEeHHHHHHHHcccccccchhHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999889999998877654 23233344555555555444433
No 16
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=21.33 E-value=71 Score=35.43 Aligned_cols=39 Identities=33% Similarity=0.474 Sum_probs=28.0
Q ss_pred ceeeeccceeEE--eeecceecCCCceEEeeccccccccccCchhHHHH
Q 013162 159 QWLLCVSDSIVE--LVPSIQQFPGGGTYEVMATRPRSDLYMNLPALKKL 205 (448)
Q Consensus 159 dwLLSVsD~IVE--lvPs~Q~~~dG~~~EvM~trpRsDl~~NLPALrKL 205 (448)
.|-+.+....++ .-|.. .|-||++|| .||+-|+||-||.
T Consensus 121 ~~~~~~~g~~~~~~~~p~a--~~~GTtVeV------~dLF~NtPaRrKf 161 (638)
T COG0323 121 GTQIYAEGGGMEVTVKPAA--HPVGTTVEV------RDLFYNTPARRKF 161 (638)
T ss_pred eEEEEecCCcccccccCCC--CCCCCEEEe------hHhhccChHHHHh
Confidence 455666666555 33443 456999999 6999999998774
No 17
>PF12867 DinB_2: DinB superfamily; InterPro: IPR024775 DinB from Bacillus subtilis and related Gram-positive bacteria is a DNA-damage-induced gene and the corresponding protein contains a four helix bundle. This fold is shared by diverse proteins []. This entry represents a DinB-like structural domain found in uncharacterised proteins and putative metal-dependent hydrolases.; PDB: 2YQY_B 2RD9_D 2QNL_A 2HKV_A 1RXQ_B 3CEX_B 2P1A_B.
Probab=20.12 E-value=1.6e+02 Score=23.09 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=23.0
Q ss_pred CcHHHHhhcccCCccchhHHHHHHhhcC
Q 013162 303 IPAAYLETLPKNGKACLGDIIYRYITAD 330 (448)
Q Consensus 303 IPe~y~esLPKnGrasLGD~iYr~iT~d 330 (448)
+|+..+.--|..|+-|+|..++..+..+
T Consensus 16 l~~~~~~~~p~~~~~si~~~~~Hl~~~~ 43 (127)
T PF12867_consen 16 LPEEQLNWKPAPGKWSIGEILGHLADWE 43 (127)
T ss_dssp S-HHHHTSBSSTTSSBHHHHHHHHHHHH
T ss_pred CCHHHHhcCCCCCCCCHHHHHHHHHHHH
Confidence 7899999999999999999998876543
Done!