Query 047173
Match_columns 557
No_of_seqs 94 out of 117
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 08:26:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047173.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047173hhsearch_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 2E-195 5E-200 1447.2 23.5 352 97-449 2-364 (365)
2 smart00546 CUE Domain that may 77.1 3 6.4E-05 30.8 3.1 34 385-418 3-36 (43)
3 PF02845 CUE: CUE domain; Int 71.2 5.1 0.00011 29.6 3.1 34 385-418 2-35 (42)
4 PF09539 DUF2385: Protein of u 37.7 3.2 6.9E-05 37.1 -3.3 30 138-167 10-40 (96)
5 PF05823 Gp-FAR-1: Nematode fa 31.6 1.5E+02 0.0032 28.0 6.4 95 294-426 1-97 (154)
6 KOG0938 Adaptor complexes medi 28.3 47 0.001 36.3 2.8 42 138-204 258-299 (446)
7 PF10236 DAP3: Mitochondrial r 27.7 79 0.0017 32.3 4.2 80 267-346 78-163 (309)
8 TIGR02301 conserved hypothetic 25.3 7.5 0.00016 36.2 -3.2 30 138-167 35-65 (121)
9 KOG0527 HMG-box transcription 24.0 40 0.00086 35.8 1.4 47 350-398 68-130 (331)
10 KOG2379 Endonuclease MUS81 [Re 23.5 1.8E+02 0.004 32.9 6.2 80 257-348 357-450 (501)
11 PRK09087 hypothetical protein; 23.3 56 0.0012 31.8 2.1 123 296-438 45-200 (226)
12 PF02169 LPP20: LPP20 lipoprot 23.2 26 0.00057 28.5 -0.1 31 116-146 14-44 (92)
13 PF05408 Peptidase_C28: Foot-a 22.0 25 0.00055 35.1 -0.5 83 278-361 12-103 (193)
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=2.3e-195 Score=1447.22 Aligned_cols=352 Identities=69% Similarity=1.088 Sum_probs=287.4
Q ss_pred hhhHHHHHHHHHhhhhcCCCCCCCCcchhHHHhhhhhhhhHHhhhhcccccCCCCHHHHHHhhhccceEeeccCeeEEee
Q 047173 97 QQDMEQMKERFAKLLLGEDMSGGGKGVSSALALSNAITNLAASVFSEQARLEPMSAETKARWRKEIDWLLSVTDHIVEFV 176 (557)
Q Consensus 97 ~se~E~MKErFaKLLLGEDMSG~gKGV~tALAiSNAITNL~AsvFGelwrLEPl~~ekK~~WrrEmdwLLsv~D~IVElv 176 (557)
++|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCeEEEEeeccccccccCchHHHhhhHHHHHHHHccCCCCeeeeeecCC------CCCCCCCCccccccccc
Q 047173 177 PSQQKSKDGTNMEIMVTRQRTDLHMNIPALRKLDAMLVECLENFKDQSEFYYVSKDA------PDSEKGNTKRSDEKWWL 250 (557)
Q Consensus 177 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLle~LDsF~d~tEFWYv~~g~------~~~~~~~~~r~eeKWWL 250 (557)
|++|++|||+++||||||||+|||||||||||||+||||+||||+| ||||||++|+ ..+++...+||++||||
T Consensus 82 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLie~LDsf~d-tEFwYv~~g~~~~~~~~~~~~~~~~r~~~KWWL 160 (365)
T PF03759_consen 82 PSKQTFPDGTTMEVMTTRPRSDLYMNLPALRKLDAMLIEILDSFKD-TEFWYVDQGIVADSDSSSSFRRSSQRQEEKWWL 160 (365)
T ss_dssp EEEEE-TTS-EEEEEEEEE-HHHHTHHHHHHHHHHHHHHHHHTTCS--SSEE--TT------SHHHHT------CCCTTS
T ss_pred cceeecCCCceEEEEecCccchhhcCcHHHHHHHHHHHHHHHhCCC-CeeEEecCCcccccccCccccCcccccCCcccC
Confidence 9999999999999999999999999999999999999999999998 9999999993 23467789999999999
Q ss_pred cCCCCCCCCCCHHHHHHHhHhHHHHHHHHHHHHHHhHhhhhccCchhhHHhhccccCccchhHHHHHhhcccCCChhHHh
Q 047173 251 PTPKVPPNGLSDMARKFLQYQKDCVNQVLKAAMAINAQVLSEMEIPENYIETLPKNGRASLGDAIYRSITVEYFNPDQFL 330 (557)
Q Consensus 251 P~p~VPp~GLSe~~RK~Lq~qrd~vnQIlKAAmAIN~~vL~EMeIPe~y~esLPKnGrasLGD~iYr~iT~d~Fspe~lL 330 (557)
|+|||||+||||.+||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+||+|+|||||||
T Consensus 161 P~p~VP~~GLse~~rK~L~~~rd~~~QilKAAmaIN~~vL~EMeiP~~y~esLPKnGrasLGd~iYr~it~~~Fspe~ll 240 (365)
T PF03759_consen 161 PVPRVPPNGLSEESRKWLQHQRDCVNQILKAAMAINSQVLAEMEIPESYLESLPKNGRASLGDSIYRYITSEQFSPEQLL 240 (365)
T ss_dssp --EE--TT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---HHHHHCS-SSHHHHHHHHHHHHCTSSS--HHHHH
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcccccHHHHHHHHhccCcCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCcchhhHHhhhhhhHHHHHHHhhcccCCCCcCCCccccc-----hhhHHHHHHHHHHHHHHHHhhCCCCCCchhhh
Q 047173 331 STMDLSSEHKILDLKNRIEASIVIWRRKMNQKDGKSAWGSAVS-----LEKREQFEERAETILLILKQWYPGIPQSSLDI 405 (557)
Q Consensus 331 ~~ldLssEH~~Le~~nRiEAsi~iWrrK~~~k~~kssW~~~v~-----~dKre~l~eRAEtlL~~LKqRfPglpQT~LD~ 405 (557)
+||||||||+|||+||||||||||||||++++++|+|||.+|. .|||++|++|||+||+||||||||||||+||+
T Consensus 241 ~~ldlssEH~~le~~NRvEAai~vWrrK~~~k~~ksSWg~~vkdl~~~~dK~e~l~eRAEtlL~~LK~RfPgl~QT~LD~ 320 (365)
T PF03759_consen 241 DCLDLSSEHKALELANRVEAAIYVWRRKICEKDSKSSWGSMVKDLMSDGDKRELLAERAETLLLCLKQRFPGLPQTSLDI 320 (365)
T ss_dssp HTS--SSHHHHHHHHHHHHHHHHHHCH---------------------HHHHHHHHHHHHHHHHHHHHHSTT----HHHH
T ss_pred HhcccccHHHHHHHHHHHHHHHHHHHHHhcCCCCccchhhhcccccccchHHHHHHHHHHHHHHHHHHhCCCCCchHHHH
Confidence 9999999999999999999999999999999999999976554 89999999999999999999999999999999
Q ss_pred hhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCC
Q 047173 406 SKIQFNKDIGQAVLESYSRILESLAFTVLSRIEDVLYADFATQN 449 (557)
Q Consensus 406 sKIQyNkDVG~aILESYSRVLEsLAf~I~sRIdDVL~~D~l~~~ 449 (557)
+|||||||||||||||||||||||||||+||||||||+|+++++
T Consensus 321 ~KIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~~~~~ 364 (365)
T PF03759_consen 321 SKIQYNKDVGQAILESYSRVLESLAFNILSRIDDVLYADDLTKN 364 (365)
T ss_dssp HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Confidence 99999999999999999999999999999999999999999875
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=77.06 E-value=3 Score=30.85 Aligned_cols=34 Identities=15% Similarity=0.270 Sum_probs=29.1
Q ss_pred HHHHHHHHhhCCCCCCchhhhhhhhhcchhHHHH
Q 047173 385 ETILLILKQWYPGIPQSSLDISKIQFNKDIGQAV 418 (557)
Q Consensus 385 EtlL~~LKqRfPglpQT~LD~sKIQyNkDVG~aI 418 (557)
+..+..|++-||.++...+-..=.++|.||..+|
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 3467789999999999999888888999998876
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=71.23 E-value=5.1 Score=29.63 Aligned_cols=34 Identities=18% Similarity=0.369 Sum_probs=29.2
Q ss_pred HHHHHHHHhhCCCCCCchhhhhhhhhcchhHHHH
Q 047173 385 ETILLILKQWYPGIPQSSLDISKIQFNKDIGQAV 418 (557)
Q Consensus 385 EtlL~~LKqRfPglpQT~LD~sKIQyNkDVG~aI 418 (557)
+..+..|+.-||+++...+-..=.++|.||-.+|
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 3567899999999999999999999999998876
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=37.75 E-value=3.2 Score=37.15 Aligned_cols=30 Identities=20% Similarity=0.426 Sum_probs=26.7
Q ss_pred HhhhhcccccCCCCH-HHHHHhhhccceEee
Q 047173 138 ASVFSEQARLEPMSA-ETKARWRKEIDWLLS 167 (557)
Q Consensus 138 AsvFGelwrLEPl~~-ekK~~WrrEmdwLLs 167 (557)
|-|+|+++-|.+|+. +.-..||.+|.=||.
T Consensus 10 AeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~ 40 (96)
T PF09539_consen 10 AEILGALHYLRNLCGGNEDQYWRDRMQALLD 40 (96)
T ss_pred HHHHHHHHHHHHHhCCCCcchHHHHHHHHHH
Confidence 679999999999999 889999999976664
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=31.59 E-value=1.5e+02 Score=28.03 Aligned_cols=95 Identities=18% Similarity=0.261 Sum_probs=52.9
Q ss_pred CchhhHHhhccccCccchhHHHHHhhcccCCChhHHhhhcCCcchhhHHhhhhhhHHHHHHHhhcccCCCCcCCCccccc
Q 047173 294 EIPENYIETLPKNGRASLGDAIYRSITVEYFNPDQFLSTMDLSSEHKILDLKNRIEASIVIWRRKMNQKDGKSAWGSAVS 373 (557)
Q Consensus 294 eIPe~y~esLPKnGrasLGD~iYr~iT~d~Fspe~lL~~ldLssEH~~Le~~nRiEAsi~iWrrK~~~k~~kssW~~~v~ 373 (557)
+||+.|.+-+|..-.. .|. .|.-.....+.|+++.. . .-++|.-++.
T Consensus 1 ~i~~~~k~~iP~ev~~-----~~~--------------~Lt~eeK~~lkev~~~~-------~-------~~~~~de~i~ 47 (154)
T PF05823_consen 1 DIPEEYKELIPSEVVE-----FYK--------------NLTPEEKAELKEVAKNY-------A-------KFKNEDEMIA 47 (154)
T ss_dssp -S-HHHHTT--HHHHH-----HHH--------------H--TTTHHHHHHHHTT---------------------TTHHH
T ss_pred CchHHHHHhCcHHHHH-----HHH--------------cCCHHHHHHHHHHHHHc-------c-------ccCCHHHHHH
Confidence 4889999888875442 233 33333445666666651 1 1135665544
Q ss_pred --hhhHHHHHHHHHHHHHHHHhhCCCCCCchhhhhhhhhcchhHHHHHHHHHHHH
Q 047173 374 --LEKREQFEERAETILLILKQWYPGIPQSSLDISKIQFNKDIGQAVLESYSRIL 426 (557)
Q Consensus 374 --~dKre~l~eRAEtlL~~LKqRfPglpQT~LD~sKIQyNkDVG~aILESYSRVL 426 (557)
-+|..-|.++++.+...+|.+|=+|...+ -+|=+.|....+.-|...+
T Consensus 48 ~LK~ksP~L~~k~~~l~~~~k~ki~~L~pea-----k~Fv~~li~~~~~l~~~~~ 97 (154)
T PF05823_consen 48 ALKEKSPSLYEKAEKLRDKLKKKIDKLSPEA-----KAFVKELIAKARSLYAQYS 97 (154)
T ss_dssp HHHHH-HHHHHHHHHHHHHHHHTTTT--HHH-----HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhCHHHHHHHHHHHHHHHHHHHcCCHHH-----HHHHHHHHHHHHHHHHHhc
Confidence 37889999999999999999999986554 3455555555555555533
No 6
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.32 E-value=47 Score=36.32 Aligned_cols=42 Identities=36% Similarity=0.771 Sum_probs=31.4
Q ss_pred HhhhhcccccCCCCHHHHHHhhhccceEeeccCeeEEeecccccCCCCCeEEEEeeccccccccCch
Q 047173 138 ASVFSEQARLEPMSAETKARWRKEIDWLLSVTDHIVEFVPSQQKSKDGTNMEIMVTRQRTDLHMNIP 204 (557)
Q Consensus 138 AsvFGelwrLEPl~~ekK~~WrrEmdwLLsv~D~IVElvPs~Q~~~dG~~~EvM~~r~RsDl~~NlP 204 (557)
.--|-||-||--.. +.|+++||| ||| .||.|--|-+.+| |||
T Consensus 258 Dc~FHqCV~L~kFn-----------------~eh~IsFvP-----PDG-e~ELMkYr~~enI--nlP 299 (446)
T KOG0938|consen 258 DCTFHQCVRLDKFN-----------------SEHIISFVP-----PDG-EFELMKYRVTENI--NLP 299 (446)
T ss_pred ccchheeecccccc-----------------ccceEEEeC-----CCC-ceEeEeeeeccCc--ccc
Confidence 34588888886443 469999999 676 5899988877764 666
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=27.68 E-value=79 Score=32.32 Aligned_cols=80 Identities=18% Similarity=0.190 Sum_probs=57.3
Q ss_pred HHhHhHHHHHHHHHHHHHHhHhhhhccCchhhHHhh--ccccCccchhHHHHHhhcccCCChhHH---hhhcCCcch-hh
Q 047173 267 FLQYQKDCVNQVLKAAMAINAQVLSEMEIPENYIET--LPKNGRASLGDAIYRSITVEYFNPDQF---LSTMDLSSE-HK 340 (557)
Q Consensus 267 ~Lq~qrd~vnQIlKAAmAIN~~vL~EMeIPe~y~es--LPKnGrasLGD~iYr~iT~d~Fspe~l---L~~ldLssE-H~ 340 (557)
.+-.|-..+.++|+.-.+.|+.+|..|.+...|.-+ -+.-+..+|-|.+=..+....++++++ ++.|...++ ..
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 345677888899999999999999999999998766 344445788888887788888887553 444555555 44
Q ss_pred HHhhhh
Q 047173 341 ILDLKN 346 (557)
Q Consensus 341 ~Le~~n 346 (557)
+|=..|
T Consensus 158 VL~avD 163 (309)
T PF10236_consen 158 VLVAVD 163 (309)
T ss_pred eEEEeh
Confidence 443333
No 8
>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=25.27 E-value=7.5 Score=36.19 Aligned_cols=30 Identities=17% Similarity=0.386 Sum_probs=25.7
Q ss_pred HhhhhcccccCCCCHHHH-HHhhhccceEee
Q 047173 138 ASVFSEQARLEPMSAETK-ARWRKEIDWLLS 167 (557)
Q Consensus 138 AsvFGelwrLEPl~~ekK-~~WrrEmdwLLs 167 (557)
|.|+|+++-|.+|+.... ..||.+|.=|+-
T Consensus 35 AeiLG~lHyLR~LC~~~~~~~WR~~M~~Ll~ 65 (121)
T TIGR02301 35 AEILGSLHYLRNLCGSKGDDYWRSRMQALID 65 (121)
T ss_pred HHHHHHHHHHHHHhCCCcchHHHHHHHHHHH
Confidence 579999999999998655 899999987665
No 9
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=24.03 E-value=40 Score=35.78 Aligned_cols=47 Identities=28% Similarity=0.566 Sum_probs=36.0
Q ss_pred HHHHHHh----hcccCCC------------CcCCCccccchhhHHHHHHHHHHHHHHHHhhCCCC
Q 047173 350 ASIVIWR----RKMNQKD------------GKSAWGSAVSLEKREQFEERAETILLILKQWYPGI 398 (557)
Q Consensus 350 Asi~iWr----rK~~~k~------------~kssW~~~v~~dKre~l~eRAEtlL~~LKqRfPgl 398 (557)
-|+.||. |||.... |+ .|....+.|||= |.+.||.|..+=++.||+-
T Consensus 68 NAFMVWSq~~RRkma~qnP~mHNSEISK~LG~-~WK~Lse~EKrP-Fi~EAeRLR~~HmkehPdY 130 (331)
T KOG0527|consen 68 NAFMVWSQGQRRKLAKQNPKMHNSEISKRLGA-EWKLLSEEEKRP-FVDEAERLRAQHMKEYPDY 130 (331)
T ss_pred chhhhhhHHHHHHHHHhCcchhhHHHHHHHHH-HHhhcCHhhhcc-HHHHHHHHHHHHHHhCCCc
Confidence 4788994 5664422 32 499999999997 5567999999999999985
No 10
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=23.51 E-value=1.8e+02 Score=32.86 Aligned_cols=80 Identities=19% Similarity=0.365 Sum_probs=59.7
Q ss_pred CCCCCHHHHHHHhHhHHHHHHHHHHHHHHh-------HhhhhccCchh-------hHHhhccccCccchhHHHHHhhccc
Q 047173 257 PNGLSDMARKFLQYQKDCVNQVLKAAMAIN-------AQVLSEMEIPE-------NYIETLPKNGRASLGDAIYRSITVE 322 (557)
Q Consensus 257 p~GLSe~~RK~Lq~qrd~vnQIlKAAmAIN-------~~vL~EMeIPe-------~y~esLPKnGrasLGD~iYr~iT~d 322 (557)
..||-+..+|- -.-..-.-||.+-.+-=+ .+..-+|.+|. ++.+-++|++.-++||..|+.
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 TRDLGETVSKL-AYLTRGLLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQ---- 431 (501)
T ss_pred ecChhHHHHHH-HHHhHHHHHHHHHhhccccccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHH----
Confidence 56777777664 444445567777776555 78999999995 789999999999999999986
Q ss_pred CCChhHHhhhcCCcchhhHHhhhhhh
Q 047173 323 YFNPDQFLSTMDLSSEHKILDLKNRI 348 (557)
Q Consensus 323 ~Fspe~lL~~ldLssEH~~Le~~nRi 348 (557)
|+.+-.+|-| .|..|++|-
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 4556667666 666666653
No 11
>PRK09087 hypothetical protein; Validated
Probab=23.33 E-value=56 Score=31.80 Aligned_cols=123 Identities=12% Similarity=0.170 Sum_probs=67.3
Q ss_pred hhhHHhhccccCccchhHHHH-----HhhcccCCChhHHhh---------hcCC--cchhhHHhhhhhhHHH---HHH--
Q 047173 296 PENYIETLPKNGRASLGDAIY-----RSITVEYFNPDQFLS---------TMDL--SSEHKILDLKNRIEAS---IVI-- 354 (557)
Q Consensus 296 Pe~y~esLPKnGrasLGD~iY-----r~iT~d~Fspe~lL~---------~ldL--ssEH~~Le~~nRiEAs---i~i-- 354 (557)
|..|+--=+-+||+.|-..+. +||+.+.|.++.+-. -++. .++....++.|++-.+ +++
T Consensus 45 ~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~iDDi~~~~~~~~~lf~l~n~~~~~g~~ilits 124 (226)
T PRK09087 45 PVVVLAGPVGSGKTHLASIWREKSDALLIHPNEIGSDAANAAAEGPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMTS 124 (226)
T ss_pred CeEEEECCCCCCHHHHHHHHHHhcCCEEecHHHcchHHHHhhhcCeEEEECCCCCCCCHHHHHHHHHHHHhCCCeEEEEC
Confidence 445777778899999999988 566666666654221 1111 2344444444443221 100
Q ss_pred ------HhhcccCCCCcCCCccccc------hhhHHHHHHHHHHHHHHHHhhCCCCCCchhhhhhhhhcchhHHHHHHHH
Q 047173 355 ------WRRKMNQKDGKSAWGSAVS------LEKREQFEERAETILLILKQWYPGIPQSSLDISKIQFNKDIGQAVLESY 422 (557)
Q Consensus 355 ------WrrK~~~k~~kssW~~~v~------~dKre~l~eRAEtlL~~LKqRfPglpQT~LD~sKIQyNkDVG~aILESY 422 (557)
|.-....=-++-.|+.+++ .++.++|..+++. | .|...+||-.-|++..
T Consensus 125 ~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~-------~------------~~~l~~ev~~~La~~~ 185 (226)
T PRK09087 125 RLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFAD-------R------------QLYVDPHVVYYLVSRM 185 (226)
T ss_pred CCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHH-------c------------CCCCCHHHHHHHHHHh
Confidence 0000000002334665543 3444444444433 1 3677889999999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 047173 423 SRILESLAFTVLSRIE 438 (557)
Q Consensus 423 SRVLEsLAf~I~sRId 438 (557)
.|-+++|-- ++.|++
T Consensus 186 ~r~~~~l~~-~l~~L~ 200 (226)
T PRK09087 186 ERSLFAAQT-IVDRLD 200 (226)
T ss_pred hhhHHHHHH-HHHHHH
Confidence 998888754 446665
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=23.20 E-value=26 Score=28.47 Aligned_cols=31 Identities=26% Similarity=0.266 Sum_probs=26.1
Q ss_pred CCCCCCcchhHHHhhhhhhhhHHhhhhcccc
Q 047173 116 MSGGGKGVSSALALSNAITNLAASVFSEQAR 146 (557)
Q Consensus 116 MSG~gKGV~tALAiSNAITNL~AsvFGelwr 146 (557)
++|-|.|-..-.|.-||..||+..|+|..-.
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 5677777777999999999999999998643
No 13
>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=21.98 E-value=25 Score=35.11 Aligned_cols=83 Identities=24% Similarity=0.374 Sum_probs=43.4
Q ss_pred HHHHHHHHhHhhhhccCchhhHHhhccccCccchhHHHHHhhc---ccCC-----ChhHH-hhhcCCcchhhHHhhhhhh
Q 047173 278 VLKAAMAINAQVLSEMEIPENYIETLPKNGRASLGDAIYRSIT---VEYF-----NPDQF-LSTMDLSSEHKILDLKNRI 348 (557)
Q Consensus 278 IlKAAmAIN~~vL~EMeIPe~y~esLPKnGrasLGD~iYr~iT---~d~F-----spe~l-L~~ldLssEH~~Le~~nRi 348 (557)
++.|.--|+.-+++++.-+..|. +||-++-.|-=-+||...+ .--| +||++ +++++--+|+--+++..--
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 67777888999999999999887 9999999887777766543 2222 48888 7888888888889999999
Q ss_pred HHHHHHHhhcccC
Q 047173 349 EASIVIWRRKMNQ 361 (557)
Q Consensus 349 EAsi~iWrrK~~~ 361 (557)
..|++||+=|-+-
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 9999999987653
Done!