Query 008528
Match_columns 562
No_of_seqs 102 out of 124
Neff 2.6
Searched_HMMs 46136
Date Thu Mar 28 13:17:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008528hhsearch_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-192 3E-197 1429.7 25.1 351 118-469 2-364 (365)
2 smart00546 CUE Domain that may 76.6 3 6.6E-05 30.9 3.1 34 405-438 3-36 (43)
3 PF02845 CUE: CUE domain; Int 70.3 5.2 0.00011 29.7 3.0 34 405-438 2-35 (42)
4 PF09539 DUF2385: Protein of u 38.5 3 6.6E-05 37.3 -3.3 30 159-188 10-40 (96)
5 KOG0938 Adaptor complexes medi 28.9 45 0.00098 36.5 2.8 42 159-225 258-299 (446)
6 PF10236 DAP3: Mitochondrial r 26.5 83 0.0018 32.3 4.1 82 287-368 78-165 (309)
7 TIGR02301 conserved hypothetic 25.8 7.2 0.00016 36.4 -3.2 30 159-188 35-65 (121)
8 KOG2379 Endonuclease MUS81 [Re 24.8 1.6E+02 0.0034 33.4 6.0 79 277-367 357-449 (501)
9 PRK09087 hypothetical protein; 23.7 87 0.0019 30.6 3.5 123 316-458 45-200 (226)
10 PF02169 LPP20: LPP20 lipoprot 22.5 28 0.00061 28.4 -0.0 31 137-167 14-44 (92)
11 PF05823 Gp-FAR-1: Nematode fa 20.9 3.2E+02 0.007 25.9 6.5 93 314-444 1-95 (154)
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=1.6e-192 Score=1429.69 Aligned_cols=351 Identities=68% Similarity=1.090 Sum_probs=284.8
Q ss_pred CChHHHHHHHHHhhhhcCCCCCCCCcchhHHHhhhhhhhhhhhhhccccccCCCChhHHhhhhhccceEeeccceeEEee
Q 008528 118 PSDMELMKERFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQRKLEPMPPERKARWRKEINWLLSVTDHIVEFV 197 (562)
Q Consensus 118 ~se~e~MKErFaKLLLGEDmSG~gkGV~tAlAiSNAITNL~AsvFGe~~rLEPl~~ekK~~WrrEmdwLLsv~d~IVElv 197 (562)
++|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCceEEEEeeccccccccCchHHHHHHHHHHHHHHhcCCCCeeeeccCCCCCCC-------CccccccccccC
Q 008528 198 PSQQKSKEGVSMEIMVTRQRNDLHMDIPALRKLDAMLIESLDNFGYQNEFWYPSGKSDDSE-------KNVTRHEDKWWI 270 (562)
Q Consensus 198 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLle~LDsF~d~tEFWYv~~g~~~~~-------~~~~r~eeKWWL 270 (562)
|++|++|||+++||||||||+|||||||||||||+||||+||||+| ||||||++|+.+.. ...+||++||||
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 99999999954422 245799999999
Q ss_pred ccccCCCCCCCHHHHHHHhhhhHHHHHHHHHHHHHhHhhhhcCCCchHHHhhccccCccchhHHHhhhhccCCCChHHHH
Q 008528 271 PTVKVPENGLSEEGRRWIQSQKESVNQVLKAAMAINAQVLSEMEIPESYIESLPKNGRASLGDSIYKSITVEHFDPEQFL 350 (562)
Q Consensus 271 P~pkVP~~GLSe~~RK~L~~qrd~vnQIlKAAmAIN~~vL~EMeiPe~y~esLPKnGrasLGd~iYr~it~d~Fspe~ll 350 (562)
|+|||||+||||++||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+||+|+||||+||
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 008528 351 ATMDLSNEHAVLDLKNRIEASIVIWKRKMHHKDSKSSWGSAVS-----LEKRELFEERAETILLLLKQRFPGISQSTLDI 425 (562)
Q Consensus 351 ~~ldLssEH~~Le~~nRiEAsi~iWrrK~~~k~~kssW~~~v~-----~dKre~l~eRAEtlL~~LK~RfPglpQTsLD~ 425 (562)
+||||||||+|||+||||||||||||||++++++|+|||.+|. .|||++|++||||||+||||||||||||+||+
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 hhhhccchhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccC
Q 008528 426 SKIQYNRDVGQAILESYSRIIESLAHTVMSRIDDVLYADSLAQN 469 (562)
Q Consensus 426 sKIQyNkDVG~aILESYSRVLesLAf~I~sRIdDVL~~D~~~k~ 469 (562)
+|||||||||||||||||||||||||||+||||||||+|+++++
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=76.64 E-value=3 Score=30.88 Aligned_cols=34 Identities=24% Similarity=0.331 Sum_probs=29.2
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhccchhHHHH
Q 008528 405 ETILLLLKQRFPGISQSTLDISKIQYNRDVGQAI 438 (562)
Q Consensus 405 EtlL~~LK~RfPglpQTsLD~sKIQyNkDVG~aI 438 (562)
+..+..|++-||+++...+-..=.++|.||..+|
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 3467789999999999999888888999999876
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=70.33 E-value=5.2 Score=29.67 Aligned_cols=34 Identities=26% Similarity=0.434 Sum_probs=29.3
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhccchhHHHH
Q 008528 405 ETILLLLKQRFPGISQSTLDISKIQYNRDVGQAI 438 (562)
Q Consensus 405 EtlL~~LK~RfPglpQTsLD~sKIQyNkDVG~aI 438 (562)
+..+..|+.-||+++...+...=.++|.||-.+|
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 3567889999999999999999999999998876
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=38.51 E-value=3 Score=37.35 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=26.6
Q ss_pred hhhhccccccCCCCh-hHHhhhhhccceEee
Q 008528 159 ASIFGEQRKLEPMPP-ERKARWRKEINWLLS 188 (562)
Q Consensus 159 AsvFGe~~rLEPl~~-ekK~~WrrEmdwLLs 188 (562)
|-|+|++.-|.+||. +....||.+|.=||-
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
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.85 E-value=45 Score=36.48 Aligned_cols=42 Identities=29% Similarity=0.684 Sum_probs=31.9
Q ss_pred hhhhccccccCCCChhHHhhhhhccceEeeccceeEEeecccccCCCCceEEEEeeccccccccCch
Q 008528 159 ASIFGEQRKLEPMPPERKARWRKEINWLLSVTDHIVEFVPSQQKSKEGVSMEIMVTRQRNDLHMDIP 225 (562)
Q Consensus 159 AsvFGe~~rLEPl~~ekK~~WrrEmdwLLsv~d~IVElvPs~Q~~~dG~~~EvM~~r~RsDl~~NlP 225 (562)
.--|-||-||--.. +.|+++||| ||| .||+|--|-+.+| |||
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 34588998886443 468999998 676 5899999888775 665
No 6
>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=26.54 E-value=83 Score=32.30 Aligned_cols=82 Identities=15% Similarity=0.170 Sum_probs=59.7
Q ss_pred HHhhhhHHHHHHHHHHHHHhHhhhhcCCCchHHHhh--ccccCccchhHHHhhhhccCCCChHH---HHhhcCCcch-hh
Q 008528 287 WIQSQKESVNQVLKAAMAINAQVLSEMEIPESYIES--LPKNGRASLGDSIYKSITVEHFDPEQ---FLATMDLSNE-HA 360 (562)
Q Consensus 287 ~L~~qrd~vnQIlKAAmAIN~~vL~EMeiPe~y~es--LPKnGrasLGd~iYr~it~d~Fspe~---ll~~ldLssE-H~ 360 (562)
.+-.|-..+.++|+.-.+.|..+|..|.+...|.-+ -+.-+..+|-|.+=..+....+++++ |++.|...++ ..
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 455678888999999999999999999999998776 34445578888887777777788754 3445555555 55
Q ss_pred HHHhhhhh
Q 008528 361 VLDLKNRI 368 (562)
Q Consensus 361 ~Le~~nRi 368 (562)
+|=..|-+
T Consensus 158 VL~avD~~ 165 (309)
T PF10236_consen 158 VLVAVDGF 165 (309)
T ss_pred eEEEehhh
Confidence 55444433
No 7
>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=25.81 E-value=7.2 Score=36.38 Aligned_cols=30 Identities=23% Similarity=0.444 Sum_probs=25.6
Q ss_pred hhhhccccccCCCChhHH-hhhhhccceEee
Q 008528 159 ASIFGEQRKLEPMPPERK-ARWRKEINWLLS 188 (562)
Q Consensus 159 AsvFGe~~rLEPl~~ekK-~~WrrEmdwLLs 188 (562)
|.|+|+++-|.+||.... ..||.+|.=|+-
T Consensus 35 AeiLG~lHyLR~LC~~~~~~~WR~~M~~Ll~ 65 (121)
T TIGR02301 35 AEILGSLHYLRNLCGSKGDDYWRSRMQALID 65 (121)
T ss_pred HHHHHHHHHHHHHhCCCcchHHHHHHHHHHH
Confidence 578999999999998665 899999986665
No 8
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=24.76 E-value=1.6e+02 Score=33.44 Aligned_cols=79 Identities=16% Similarity=0.302 Sum_probs=58.1
Q ss_pred CCCCCHHHHHHHhhhhHHHHHHHHHHHHHh-------HhhhhcCCCch-------HHHhhccccCccchhHHHhhhhccC
Q 008528 277 ENGLSEEGRRWIQSQKESVNQVLKAAMAIN-------AQVLSEMEIPE-------SYIESLPKNGRASLGDSIYKSITVE 342 (562)
Q Consensus 277 ~~GLSe~~RK~L~~qrd~vnQIlKAAmAIN-------~~vL~EMeiPe-------~y~esLPKnGrasLGd~iYr~it~d 342 (562)
+.||-++.+|- -.-..-.-||.+-++-=+ .+..-+|++|+ .+.+-++|++.-++||..++.|
T Consensus 357 T~~l~et~s~l-~y~tr~~~~~~~~~~~~~~d~~~~~~q~~~~~~~p~~~~~~f~~F~~~~~K~~~~TV~evf~~qL--- 432 (501)
T KOG2379|consen 357 TRDLGETVSKL-AYLTRGLLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQL--- 432 (501)
T ss_pred ecChhHHHHHH-HHHhHHHHHHHHHhhccccccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHHH---
Confidence 66777777765 333334567777776555 78999999995 7899999999999999999864
Q ss_pred CCChHHHHhhcCCcchhhHHHhhhh
Q 008528 343 HFDPEQFLATMDLSNEHAVLDLKNR 367 (562)
Q Consensus 343 ~Fspe~ll~~ldLssEH~~Le~~nR 367 (562)
+.+-++|-| .|..|++|
T Consensus 433 -------Mqvkg~S~e-rAiAI~d~ 449 (501)
T KOG2379|consen 433 -------MQVKGMSLE-RAIAIADR 449 (501)
T ss_pred -------HhccCccHH-HHHHHHHh
Confidence 556666666 55555554
No 9
>PRK09087 hypothetical protein; Validated
Probab=23.69 E-value=87 Score=30.60 Aligned_cols=123 Identities=15% Similarity=0.225 Sum_probs=69.1
Q ss_pred chHHHhhccccCccchhHHHh-----hhhccCCCChHHHHh---------hcCC--cchhhHHHhhhhhHHH---HHH--
Q 008528 316 PESYIESLPKNGRASLGDSIY-----KSITVEHFDPEQFLA---------TMDL--SNEHAVLDLKNRIEAS---IVI-- 374 (562)
Q Consensus 316 Pe~y~esLPKnGrasLGd~iY-----r~it~d~Fspe~ll~---------~ldL--ssEH~~Le~~nRiEAs---i~i-- 374 (562)
|..|+--=+-+||+.|-..+. .||+.+.|.++.+-. -++. .++....++.|++-.+ +++
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 445666678899999999888 566666666654321 1111 2455555555554322 110
Q ss_pred ------hhhcccCCCCccCcccccc------hhHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhccchhHHHHHHHH
Q 008528 375 ------WKRKMHHKDSKSSWGSAVS------LEKRELFEERAETILLLLKQRFPGISQSTLDISKIQYNRDVGQAILESY 442 (562)
Q Consensus 375 ------WrrK~~~k~~kssW~~~v~------~dKre~l~eRAEtlL~~LK~RfPglpQTsLD~sKIQyNkDVG~aILESY 442 (562)
|.-....=-++..|+.+++ .+++++|..+++. | .|+..+||-.-|++..
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 0000000013446776654 2444444444433 1 3677889999999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 008528 443 SRIIESLAHTVMSRID 458 (562)
Q Consensus 443 SRVLesLAf~I~sRId 458 (562)
.|-+++|-- ++.|++
T Consensus 186 ~r~~~~l~~-~l~~L~ 200 (226)
T PRK09087 186 ERSLFAAQT-IVDRLD 200 (226)
T ss_pred hhhHHHHHH-HHHHHH
Confidence 998888754 345554
No 10
>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=22.53 E-value=28 Score=28.41 Aligned_cols=31 Identities=29% Similarity=0.237 Sum_probs=26.1
Q ss_pred CCCCCCcchhHHHhhhhhhhhhhhhhccccc
Q 008528 137 MSGGGKGVSSALALSNAITNLAASIFGEQRK 167 (562)
Q Consensus 137 mSG~gkGV~tAlAiSNAITNL~AsvFGe~~r 167 (562)
++|-|.|-..-.|.-||..||+..|+|..-.
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 11
>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=20.88 E-value=3.2e+02 Score=25.90 Aligned_cols=93 Identities=19% Similarity=0.299 Sum_probs=51.1
Q ss_pred CCchHHHhhccccCccchhHHHhhhhccCCCChHHHHhhcCCcchhhHHHhhhhhHHHHHHhhhcccCCCCccCcccccc
Q 008528 314 EIPESYIESLPKNGRASLGDSIYKSITVEHFDPEQFLATMDLSNEHAVLDLKNRIEASIVIWKRKMHHKDSKSSWGSAVS 393 (562)
Q Consensus 314 eiPe~y~esLPKnGrasLGd~iYr~it~d~Fspe~ll~~ldLssEH~~Le~~nRiEAsi~iWrrK~~~k~~kssW~~~v~ 393 (562)
+||+.|.+-+|..-.. .|..||. .....+.|+++.- . .-.+|.-++.
T Consensus 1 ~i~~~~k~~iP~ev~~-----~~~~Lt~--------------eeK~~lkev~~~~-------~-------~~~~~de~i~ 47 (154)
T PF05823_consen 1 DIPEEYKELIPSEVVE-----FYKNLTP--------------EEKAELKEVAKNY-------A-------KFKNEDEMIA 47 (154)
T ss_dssp -S-HHHHTT--HHHHH-----HHHH--T--------------TTHHHHHHHHTT---------------------TTHHH
T ss_pred CchHHHHHhCcHHHHH-----HHHcCCH--------------HHHHHHHHHHHHc-------c-------ccCCHHHHHH
Confidence 4888898888875433 3333433 3345556666652 1 1136766655
Q ss_pred --hhHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhccchhHHHHHHHHHH
Q 008528 394 --LEKRELFEERAETILLLLKQRFPGISQSTLDISKIQYNRDVGQAILESYSR 444 (562)
Q Consensus 394 --~dKre~l~eRAEtlL~~LK~RfPglpQTsLD~sKIQyNkDVG~aILESYSR 444 (562)
-.|..-|.++++.+...+|.+|=+|...+- +|=+.|....+.-|..
T Consensus 48 ~LK~ksP~L~~k~~~l~~~~k~ki~~L~peak-----~Fv~~li~~~~~l~~~ 95 (154)
T PF05823_consen 48 ALKEKSPSLYEKAEKLRDKLKKKIDKLSPEAK-----AFVKELIAKARSLYAQ 95 (154)
T ss_dssp HHHHH-HHHHHHHHHHHHHHHHTTTT--HHHH-----HHHHHHHHHHHHHHHH
T ss_pred HHHHhCHHHHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHHHHHHH
Confidence 377789999999999999999999976653 3444444444444554
Done!