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Relating destabilizing regions to known functional sites in proteins.

(2007) BMC Bioinformatics 8

PubMed: 17470296 | PubMedCentral: PMC1890302 | DOI: 10.1186/1471-2105-8-141

d N IR e Sens. f PPV g Exp N IR h P-value Small 1e1a 13 38 7 53.8 18.4 1.6 0.00023 1e3f 32 18 8 25.0 44.4 1.2 5.9e-06 1gu7 62 53 10 16.1 18.9 4.5 0.00999 1gud 24 36 14 58.3 38.9 3.0 1.5e-08 1gus 24 73... 0 0.0 0.0 4.4 1.0 1gus i 84 73 41 48.8 56.2 15.2 6.2e-14 1gxy 24 18 7 29.2 38.9 1.9 0.00100 1hf8 8 46 0 0.0 0.0 0.7 1.0 1hhq 102 126 30 29.4 23.8 14.3 1.2e-05 1is5 88 16 16 18.2 100.0 2.6 8.2e-14 1jcf 34 46 12 35.3 26.1 4.7 0.00061 1odl 150 190 60 40.0 31.6 20.3 3.3e-18 1ofn 30 46 13 43.3 28.3 3.4 2.9e-06 1tm2 19 26 6 31.6 23.1 1.6 0.00232 1usg 30 56 14 46.7 25.0 2.4 5.6e-09 1usl 36 28 15 41.7 53.6 3.2 5.5e-09 1w1h 10 7 6 60.0 85.7 0.5 9.6e-08 1w2i 16 24 0 0.0 0.0 2.1 1.0 1w37 48 101 16 33.3 15.8 4.1 6.5e-07 1y2t 108 66 0 0.0 0.0 12.6 1.0 Polysaccharide 1nof 12 43 7 58.3 16.3 1.4 7.3e-05 1o88 15 34 12 80.0 35.3 1.4 3.2e-11 1ob0 41 24 8 19.5 33.3 2.0 0.00037 1ogb 32 53 4 12.5 7.5 1.7 0.08496 1qhz 14 29 10 71.4 34.5 1.3 1e-08 1qjv 10 45 4 40.0 8.9 1.3 0.03039 1uuq 16 35 10 62.5 28.6 1.4 3.1e-08 1w0n 8 10 0 0.0 0.0 0.7 1.0 1w6z 20 14 6 30.0 42.9 2.2 0.00887 Peptide 1c7k 9 7 0 0.0 0.0 0.5 1.0 1e5t 18 33 4 22.2 12.1 0.8 0.00748 1ea7 7 41 0 0.0 0.0 0.9 1.0 1gt9 21 28 4 19.0 14.3 1.6 0.07134 1kl4 68 22 12 17.6 54.5 3.1 5.6e-06 1oes 16 27 5 31.2 18.5 1.5 0.01154 Protein 1e3f 60 18 0 0.0 0.0 2.3 1.0 1e6l 10 6 3 30.0 50.0 0.5 0.00632 1e6l 15 6 0 0.0 0.0 0.7 1.0 1f2x 24 4 0 0.0 0.0 0.4 1.0 1gcp 21 10 2 9.5 20.0 3.1 0.89027 1gqv 36 8 6 16.7 75.0 2.1 0.00465 1obq 44 19 11 25.0 57.9 2.3 9.6e-07 1uns 19 4 0 0.0 0.0 0.9 1.0 1uns 20 4 4 20.0 100.0 0.9 0.00852 1uol 18 7 2 11.1 28.6 0.7 0.12811 1uq4 42 5 4 9.5 80.0 0.8 0.00254 Nucleic acid 1o7i 5 4 0 0.0 0.0 0.2 1.0 1okb 30 24 12 40.0 50.0 3.2 3.7e-06 1uol 19 7 0 0.0 0.0 0.7 1.0 1gqv 9 8 0 0.0 0.0 0.5 1.0 1uq4 17 5 0 0.0 0.0 0.3 1.0 Lipid 1obq 42 19 7 16.7 36.8 2.2 0.00305 1qmd 14 37 4 28.6 10.8 1.4 0.04088 Metal 1e6l 7 6 0 0.0 0.0 0.3 1.0 1qmd 6 37 1 16.7 2.7 0.6 0.47097 Peptide-Protein 1mix 26 21 6 23.1 28.6 2.6 0.03234 Small-Metal 1h1y 38 33 17 44.7 51.5 2.9 8.6e-12 2poo 16 25 10 62.5 40.0 1.1 2.8e-09 1oid 19 60 14 73.7 23.3 2.2 1.2e-10 Polysaccharide-Metal 1gkb 76 88 48 63.2 54.5 7.0 1.4e-36 Lipid-Metal 1umv 34 19 0 0.0 0.0 2.6 1.0 Protein-Metal 1o6v 49 40 12 24.5 30.0 4.2 0.00032 Small 34.4 (21.4) j 32.3 (25.5) k Polysaccharide 43.7 (27.3) 26.2 (17.4) Peptide 18.3 (14.0) 16.6 (16.7) Protein 13.0 (10.9) 36.2 (33.9) Nucleic acid 8.0 (17.9) 10.0 (22.4) Lipid 15.1 (14.4) 15.9 (18.9) Metal 35.7 (29.4) 25.3 (22.6) a No destabilizing regions were detected in 11 entries of the dataset (1utx, 1gv2, 1eao, 1e7l, 1vyi, 1w9s, 1upq, 1w53, 1tgr, 1r29, 1sif) and these entries are not listed in this table.

Pdb id a Holo-pdb ids b N res c F res d ASA e F ASA f Cleft g Small 1e1a 13 4.2 272 2.1 T 1e3f 1bm7 , 1e4h , 1e5a , 1eta , 1tha 8 6.9 193 1.0 T 1gu7 1guf , 1n9g 31 8.5 1158 3.7 T 1gud 1rpj 24 8.3 976 7.4 T 1gus 1gug , 1gun , 1guo 4 6.0 119 0.9 F 1gus h 1gug , 1gun , 1guo 14 20.9 110 0.8 F 1gxy 1og1 , 1og3 , 1og4 24 10.8 947 8.7 T 1hf8 1hfa , 1hg2 , 1hg5 4 1.5 329 1.4 F 1hhq 1hiy , 1b4s , 1b99 , 1bux 17 11.3 1006 2.8 T 1is5 1is3 , 1is4 , 1is6 22 16.4 663 3.0 T 1jcf 1jcg 34 10.1 820 5.6 F 1odl 1odi , 1odj 25 10.7 339 0.8 T 1ofn 1oi6 15 7.4 669 4.0 T 1tm2 1tjy 19 6.1 437 3.2 T 1upq 1upr 12 11.2 783 11.9 T 1usg 1usk , 1usi 15 4.3 268 1.0 T 1usl 2bes , 2bet 18 11.5 505 3.9 T 1w1h 1w1d , 1w1g 10 6.6 560 6.2 T 1w2i 1w2i 8 8.9 450 5.0 F 1w37 1w3i , 1w3n , 1w3t 12 4.1 107 0.3 T 1y2t 1y2x , 1y2w 27 19.0 1191 5.6 F Polysaccharide 1nof 12 3.1 471 3.2 T 1o88 15 4.2 472 3.5 T 1ob0 1e3z 41 8.5 1572 8.9 T 1ogb 1e6n , 1e6r , 1h0g , 1h0i , 1ogg 16 3.2 565 1.5 T 1qhz 1qi2 , 8a3h , 4a3h , 1e5j , 1qi0 14 4.6 590 5.2 T 1qjv 10 2.9 265 1.8 T 1uuq 1uz4 16 3.9 256 1.7 T 1w0n 1ux7 8 6.7 642 11.2 T 1w6z 1sf7 , 1sfb , 1sfg 20 15.5 891 13.6 T 1w9s 1w9t , 1w9w 12 9.0 376 5.9 F Peptide 1c7k 9 6.8 275 4.2 T 1e5t 1e8m , 1e8n , 1o6g , 1qfs , 1uop 18 2.5 485 1.7 T 1ea7 7 2.3 97 0.9 T 1gt9 1gtj , 1gtl 21 5.9 450 3.4 F 1kl4 1hqq , 1kl3 , 1kl5 , 1rsu 17 14.2 854 4.2 T 1oes 1g1f , 1g1g , 1g1h , 1ptt , 1ptu 16 5.7 885 6.6 T 1r29 1r2b 29 23.8 1760 13.8 F Protein 1e3f 1qab , 1rlb 15 13.0 971 5.0 F 1e6l 1bdj 10 7.9 775 11.7 F 1e6l 1a0o , 1eay , 1ffg , 1ffs , 1ffw 15 11.8 1212 18.4 T 1eao 1e50 , 1h9d 26 22.8 1819 28.2 F 1f2x 12 9.5 604 5.2 F 1gcp 1gcq 21 31.3 1405 33.2 F 1gqv 2bex 36 26.7 2246 28.9 F 1obq 1gka 22 12.2 1023 6.1 T 1sif 1cmx , 1fxt , 1nbf , 1otr , 1q5w , 1s1q , 1uzx 14 19.7 937 21.7 T 1tgr 1h59 15 28.8 1236 29.5 T 1uns 1jck 19 8.1 1620 13.5 F 1uns 1jwm 20 8.5 1386 11.6 F 1uol 1gzh , 1kzy 18 9.2 1301 13.1 F 1uq4 2aai 42 16.0 2796 21.6 F 1w53 12 14.3 770 8.8 T Nucleic acid 1e7l 8 5.1 352 2.0 T 1eao 1h9d , 1hjb 18 15.8 1375 21.3 F 1gqv 1hi3 , 1hi4 , 1hi5 9 6.7 245 3.2 T 1gv2 1h88 , 1h89 , 1mse 30 29.1 2289 30.2 T 1o7i 5 4.3 497 7.4 F 1okb 1emh , 1emj , 1q3f , 1ssp , 2ssp , 4skn 30 13.5 1539 15.0 T 1uol 1tsr , 1tup 19 9.7 1229 12.4 F 1uq4 1apg , 1br5 17 6.5 364 2.8 T 1utx 10 15.2 691 9.0 F 1vyi 10 9.0 1009 15.0 F Lipid 1obq 1h91 , 1i4u , 1s2p , 1s44 21 11.6 350 2.1 T 1qmd 14 3.8 465 2.9 F Metal 1e6l 1chn , 1ymv 7 5.5 350 5.3 T 1qmd 1kho 6 1.6 67 0.4 T Peptide-Protein 1mix 1mk7 , 1mk9 26 12.6 1526 11.9 F Small-Metal 1h1y 19 8.6 365 2.2 T 1h6l 2poo , 1h6l 16 4.5 627 4.4 T 1oid 1ho5 , 1hp1 , 1hpu 19 3.6 872 3.9 F Polysaccharide-Metal 1gkb 1bxh , 1cjp , 1c57 , 1ces , 1dq1 , 1gkb , 3cna , 3enr 19 8.0 586 1.8 F Lipid-Metal 1umv 1pob , 1umv , 1c1j 17 13.9 492 3.8 T Protein-Metal 1o6v 1o6s 49 10.6 2224 11.3 F Properties of known binding sites of the dataset proteins.

Pdb id a N Reg b N res c F res d ASA e F ASA f Cleft g 1c7k 1 7 5.3 196 3.0 F 1e1a 1 9 2.9 331 2.5 T 1 10 3.2 290 2.2 F 1 19 6.1 256 1.9 F 1e3f 1 18 3.9 170 0.9 T 1e5t 1 18 2.5 450 1.6 T 1 11 1.5 405 1.4 T 1 4 0.6 143 0.5 T 1e6l 1 6 4.7 410 6.2 T 1ea7 1 4 1.3 207 1.9 T 1 17 5.5 495 4.5 F 1 7 2.3 546 4.9 F 1 9 2.9 82 0.7 F 1 4 1.3 196 1.8 T 1f2x 1 4 1.6 230 2.0 F 1gcp 1 10 14.9 644 15.2 F 1gkb 4 22 9.3 152 2.0 F 1gqv 1 8 5.9 573 7.4 F 1gt9 1 8 2.2 309 2.3 F 1 10 2.8 114 0.9 F 1 10 2.8 534 4.0 F 1gu7 2 6 1.6 434 2.8 T 2 11 3.0 465 3.0 T 1gud 1 6 2.1 422 3.2 F 1 20 6.9 571 4.4 T 1 4 1.4 289 2.2 T 1 6 2.1 234 1.8 F 1gus 4 13 12.9 262 7.6 T 1gxy 1 12 5.4 107 1.0 T 1 6 2.7 386 3.5 T 1h1y 1 12 2.7 546 3.3 T 2 9 4.1 179 2.2 T 1h6l 1 21 5.9 493 3.5 F 1 4 1.1 195 1.4 T 1hf8 2 5 1.9 425 3.6 F 2 18 6.8 816 6.8 T 1hhq 6 7 4.7 114 1.8 F 6 13 8.7 748 12.6 T 1is5 4 4 3.0 185 3.2 T 1jcf 1 14 4.2 553 3.8 T 1 5 1.5 256 1.7 F 1 19 5.7 316 2.2 F 1 8 2.4 662 4.5 T 1kl4 4 5 4.2 429 8.4 T 1mix 1 11 5.3 705 5.5 T 1 6 2.9 408 3.2 F 1 4 1.9 304 2.4 T 1nof 1 25 6.5 587 4.0 F 1 6 1.6 255 1.7 F 1 6 1.6 415 2.8 F 1 6 1.6 144 1.0 F 1o6v 1 11 2.4 376 1.9 F 1 11 2.4 679 3.5 F 1 13 2.8 608 3.1 F 1 5 1.1 315 1.6 F 1o7i 1 4 3.5 346 5.1 T 1o88 1 7 2.0 198 1.5 T 1 5 1.4 296 2.2 F 1 7 2.0 313 2.3 F 1 4 1.1 211 1.6 F 1 4 1.1 248 1.8 F 1 7 2.0 190 1.4 T 1ob0 1 6 1.2 314 1.8 F 1 7 1.5 226 1.3 T 1 4 0.8 138 0.8 F 1 7 1.5 93 0.5 T 1obq 1 4 1.1 217 1.3 T 1 15 4.2 318 1.9 T 1odl 3 10 2.1 547 3.6 F 6 12 5.1 276 3.6 T 3 23 4.9 54 0.3 T 1oes 1 6 2.1 97 0.7 F 1 5 1.8 105 0.8 T 1 7 2.5 377 2.8 T 1 9 3.2 423 3.1 F 1ofn 2 11 5.4 395 4.8 T 2 9 4.4 324 3.8 T 1ogb 1 11 1.1 455 1.2 F 1 15 1.5 149 0.4 F 2 14 2.8 765 4.0 F 2 4 0.8 236 1.2 F 1oid 1 4 0.8 291 1.3 F 1 17 3.3 438 2.0 F 1 14 2.7 641 2.9 F 1 20 3.8 504 2.3 T 1 5 1.0 325 1.5 F 1okb 1 4 1.8 300 2.9 F 1 14 6.3 704 6.9 T 1 6 2.7 329 3.2 T 1qhz 1 24 7.9 328 2.9 T 1 5 1.7 170 1.5 F 1qjv 1 5 1.5 359 2.4 T 1 33 9.6 1164 7.9 F 1 7 2.0 165 1.1 T 1qmd 1 6 1.6 129 0.8 T 1 4 1.1 319 2.0 T 1 6 1.6 417 2.6 F 1 21 5.7 828 5.2 T 1tm2 1 4 1.3 330 2.4 F 1 22 7.0 663 4.9 T 1umv 2 5 4.1 233 3.6 T 1uns 1 4 1.7 246 2.1 T 1 7 3.0 262 2.2 F 1uol 1 7 3.6 368 3.7 F 1uq4 1 5 1.9 251 1.9 T 1usg 1 30 4.3 715 2.7 T 2 13 3.8 340 2.6 T 1usl 2 8 5.1 304 4.8 F 1uuq 1 13 3.2 50 0.3 F 1 5 1.2 53 0.3 T 1 6 1.5 182 1.2 F 1 11 2.7 356 2.3 F 1w0n 1 10 8.3 455 7.9 F 1w1h 1 7 4.6 431 4.8 T 1w2i 2 13 14.4 750 16.6 T 1w37 8 7 4.8 131 2.4 F 8 8 5.5 83 1.6 F 1w6z 1 14 10.9 592 9.0 F 1y2t 1 8 1.4 274 1.3 T 2 8 2.8 1 0.0 F 4 10 7.0 415 7.6 T a Pdb identifier of structure used for energy calculations.

Publication Year: 2007


Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches.

(2008) BMC Genomics 9

PubMed: 18423054 | PubMedCentral: PMC2387172 | DOI: 10.1186/1471-2164-9-181

Table 5 43 Putative extracellular proteins (EX) derived from the 2 out of 3 predictions with significant DBSubloc or/and GTD prediction Lai Locus Copen Locus Protein annotation SWISS-PROT a PDB Code b... LA1027 LIC12632 Sphingomyelinase C precursor (Sph1)/hemolysin - 1bix LA1029 LIC12631 Sphingomyelinase C precursor (Sph2)/hemolysin - 1bix LA4004 LIC13198 Sphingomyelinase C precursor hemolysin (Sph3)/sph- like - 1bix LA3540 LIC10657 Sphingomyelinase C precursor; hemolysin - 1bix LA3050 LIC11040 Hemolytic protein-like protein/hemolysin (sph4) - 1aq0 LA3466 LIC10715 Thermolysin P43133 1hyt LA3454 LIC10723 Flagellar hook-associated protein(fliD) Q9KWW7 1osp LA3097 LIC11003 Treponemal membrane protein B precursor-like protein/LipL71 P19649 1l8w LA1530 LIC12234 LRR containing protein Q9RBS2 1d0b LA1324 LIC12401 LRR containing protein/cytoplasmic membrane protein - 1ogq LA1354 LIC12375 LRR containing protein/cytoplasmic membrane protein Q9RBS2 1ogq LA2452 LIC11504 LRR containing protein/cytoplasmic membrane protein Q9RBS2 1ogq LA2862 LIC11180 LRR containing protein/cytoplasmic membrane protein Q9RBS2 1ogq LA2966 LIC11097 LRR containing protein/cytoplasmic membrane protein Q9RBS2 1ogq LA3324 LIC10831 LRR containing protein/conserved hypothetical protein Q9RBS2 1ogq LA3321 LIC10830 LRR containing protein/putative lipoprotein Q9RBS2 1ogq LA3322 LIC10830 LRR containing protein/putative lipoprotein Q9RBS2 1ogq LA0701 LIC12901 LRR containing protein/molybdate metabolism regulator Q9RBS2 1ogq LA2377 LIC11568 Peptidase, M23/M37/membrane associated peptidase P24204 1acc LA0505 LIC13050 Probable glycosyl hydrolase/conserved hypothetical protein - 1f00 LA3725 LIC10502 Probable phenazine biosynthesis family protein/CM protein - 1air LA3730 LIC10498 Putative lipoprotein P15921 1rmg LA1368 LIC12364 Putative outer membrane protein/CagA P47460 - LA1759 LIC12050 Putative outer membrane protein/conserved hypothetical protein Q52657 1czf LA2443 LIC11507 Putative outer membrane protein/conserved hypothetical protein Q9RBS2 1ogq LA2447 LIC11505 Putative outer membrane protein/conserved hypothetical protein Q9RBS2 1jl5 LA2450 LIC11505 Putative outer membrane protein/conserved hypothetical protein Q9RBS2 1ogq LA1915 LIC11990 TPR-repeat-containing proteins/cytoplasmic membrane protein P80544 1qqe LA0043 LIC10038 TPR-repeat-containing proteins/conserved hypothetical protein Q9KQ40 1qqe LA2773 LIC11246 Conserved hypothetical protein Q06852 1l8w LA3233 LIC10902 Conserved hypothetical protein O83497 1qcx LB001 LIC20001 Conserved hypothetical protein - 1eut LA1499 LIC12259 Conserved hypothetical protein/cytoplasmic membrane protein P35825 1dab LA1766 LIC12047 Conserved hypothetical protein/cytoplasmic membrane protein Q07833 1czf LA3333 LIC10825 Conserved hypothetical protein/cytoplasmic membrane protein Q07833 1acc LA2208 LIC11720 Conserved hypothetical protein/hypothetical protein - 1e15 LA3276 c LIC10868 Conserved hypothetical protein/hypothetical protein P15345 1dab LA0022 LIC10021 Conserved hypothetical protein/putative lipoprotein - 1dab LA3210 LIC10920 Conserved hypothetical protein/putative lipoprotein - 1rmg LA3726 LIC10501 Conserved hypothetical protein/putative lipoprotein Q9PJY2 1acc LB216 LIC20172 Conserved hypothetical protein/putative lipoprotein - 1wxr LB225 LIC20176 Conserved hypothetical protein/putative lipoprotein - 1wxr LA4135 d LIC13296 hypothetical protein/putative lipoprotein - 1koe Note LRR: Leucine rich repeat a: Swiss-Prot ID derived from DBsubloc database b: PDB code derived from GTD prediction c: Pfam: PF06739: SBBP (Seven Beta Blade Propeller domain) d: pfam07588: DUF1554 Table 6 56 Putative extracellular proteins (EX) derived from the 1 out of 3 predictions with significant DBSubloc or/and GTD prediction Lai Locus Copen locus Protein annotation SWISS-PROT a PDB code b LB258 LIC20197 Cysteine protease - 1deu LA0975 LIC12680 Fimh-like protein - 1a6c LA0858 LIC12930 Fimh-like protein/hypothetical protein - 1dab LA0492 LIC13060 LipL36 protein - 1acc LA3469 LIC10713 Iron-reglulated protein A/LruB/putative lipoprotein - 1rmg LA3075 LIC10464 Surface protein Lk90-like protein/Ig-like repeat domain P35828 1dab LA3778 LIC10464 Surface protein Lk90-like protein/Ig-like repeat domain Q52657 1dbg LA0378 LIC10325 TPR-repeat-containing proteins/hemolysin Q98KC1 1a17 LA3138 LIC10973 Transmembrane outer membrane protein L1 - 1acc LA1353 LIC12375 LRR containing protein Q9RBS2 1jl5 LB196 LIC20154 LRR containing protein/lipoprotein - 1d0b LA0416 e LIC10365 Putative lipoprotein (LpL effector) - 1gq8 LA0962 d LIC12690 Putative lipoprotein - 1eut / 1koe LA1569 c LIC12208 Putative lipoprotein P15345 1acc LA2823 e LIC11207 Putative lipoprotein - 1gq8 LA3064 e LIC11030 Putative lipoprotein - 1czf LA3848 c LIC13075 Putative lipoprotein - 1qjv LA3867 LIC13086 Putative lipoprotein - 1cwv LA1159 LIC12525 Putative outer membrane protein/putative lipoprotein - 1cs6 LA1905 LIC11996 Putative outer rmembrane protein/hypothetical protein - 1kit LA1939 LIC11966 Putative outer membrane protein/hypothetical protein - 1fio LA2273 LIC11665 Putative outer membrane protein/hypothetical protein 1air LA0563 d LIC13006 Hypothetical protein/putative lipoprotein (LenC) - 1koe LA0695 d LIC12906 Hypothetical protein/putative lipoprotein (LenA/LfhA/Lsa24) - 1koe LA1433 d LIC12315 Hypothetical protein/putative lipoprotein (LenD) - 1koe LA3103 d LIC10997 Hypothetical protein (LenB) - 1koe LA4073 d LIC13248 Hypothetical protein/putative lipoprotein (LenF) - 1koe LA4324 d LIC13467 Hypothetical protein/conserved hypothetical protein (LenE) - 1koe LA3370 LIC10793 Conserved hypothetical protein/surface antigen (Lp24) - 1loq LA0965 LIC12676 Conserved hypothetical protein P25156 1d0b LA1066 LIC12601 Conserved hypothetical protein - 1dbg LA1498 LIC12260 Conserved hypothetical protein - 1ogq LA2811 LIC11217 Conserved hypothetical protein P25146 1ogq LA3734 LIC10495 Conserved hypothetical protein/CM protein - 1dab LA3834 c LIC13066 Conserved hypothetical protein P15345 1acc LA4227 LIC13381 Conserved hypothetical protein - 1sli LA0663 LIC12930 Conserved hypothetical protein/hypothetical protein - 1acc LA0423 c LIC10371 Conserved hypothetical protein/putative lipoprotein P15345 1qjv LA1567 c LIC12209 Conserved hypothetical protein/putative lipoprotein P15345 1czf LA1568 c LIC12209 Conserved hypothetical protein/putative lipoprotein P15345 1czf / 1dbg LA1691 c LIC12099 Conserved hypothetical protein/putative lipoprotein - 1acc LA3340 e LIC10821 Conserved hypothetical protein/putative lipoprotein - 1ee6 LA3394 e LIC10774 Conserved hypothetical protein/putative lipoprotein - 1gq8 LA3501 LIC10686 Conserved hypothetical protein/putative lipoprotein - 1air LA0283 c LIC10239 Hypothetical protein - 1air LA0426 c LIC10373 Hypothetical protein P56964 1acc LA0996 d LIC12668 Hypothetical protein - 1koe LA1764 LIC12048 Hypothetical protein - 1qlg LA1869 LIC12023 Hypothetical protein - 1k14 LA2272 LIC11664 Hypothetical protein 1dab LA3240 LIC10898 Hypothetical protein 1rmg LA0074 LIC10067 Hypothetical protein/conserved hypothetical protein - 1dbg LA1065 LIC12602 Hypothetical protein/conserved hypothetical protein - 1dab LA1762 LIC12048 Hypothetical protein/conserved hypothetical protein - 1qcx LA3649 LIC10561 Hypothetical protein/conserved hypothetical protein - 1qcx LA3881 LIC13101 Hypothetical protein/OM with integrin like repeat domains P35825 1dab Note LRR: Leucine-rich repeat, a: Swiss-Prot ID derived from DBsubloc database, b: PDB code derived from GTD prediction, c: pfam06739: SBBP (seven bladed beta propeller) repeat d: pfam07588: DUF1554, e: pfam07602: DUF1565 Table 7 23 Putative outer membrane proteins (OM) derived the 2 out of 3 predictions with significant DBSubloc or/and GTD prediction Lai locus LIC locus Protein annotation SWISS-PROT a PDB code b LA3471 LIC10711 Iron-reglulated protein A/cytoplasmic membrane protein P12608 1i5p LA1161 LIC12524 Long-chain fatty acid transport protein/fatty acid transport protein - 1kmo LA1100 LIC12575 Outer membrane efflux protein/cytoplasmic membrane protein - 1ek9 LA1445 LIC12307 Outer membrane efflux protein/OM- TolC superfamily P50468 1ek9 LA3685 LIC10537 Outer membrane protein/PG- associated periplasmic protein P38369 1r1m LA0056 LIC10050 Outer membrane protein OmpA family/PG-associated CM protein Q05146 1r1m LA2318 LIC11623 Predicted outer membrane protein/outer membrane protein - 1a0t LA1968 LIC11935 Putative outer membrane protein/conserved hypothetical protein - 1a0t LA2444 LIC11506 Putative outer membrane protein/outer membrane protein - 1fep LB110 LIC20087 Putative outer membrane protein/outer membrane protein - 1uyn LA2242 LIC11694 TonB-dependent outer membrane receptor P46359 1fep LA3242 LIC10896 TonB-dependent outer membrane receptor P37409 1kmo LA0465 LIC10405 TPR-repeat-containing proteins/conserved hypothetical P58937 - LA3675 LIC10544 Hypothetical protein/outer membrane protein - 1a0t LA2063 LIC11851 Conserved hypothetical protein/cytoplasmic membrane protein - 1by5 LA3102 LIC10998 Conserved hypothetical protein P76115 1nqe LA3675 LIC10544 Hypothetical protein/outer membrane protein - 1a0t LA2168 - Hypothetical protein P43153 1a0t LA3809 LIC10439 Hypothetical protein - 1a0t LA1501 LIC12258 Hypothetical protein - 2mpr LA3552 LIC10647 Hypothetical protein/conserved hypothetical protein - 1kmo LA2818 LIC11211 Hypothetical protein/conserved hypothetical protein - 2mpr LA4059 LIC13238 Hypothetical protein/conserved hypothetical protein - 1by5 LB279 LIC20214 Hypothetical protein/conserved hypothetical protein - 1kmo Note a: Swiss-Prot ID derived from DBsubloc database, b: PDB code derived from GTD prediction Table 8 25 Putative outer membrane proteins (OM) derived from the 1 out of 3 predictions with significant DBSubloc and/or GTD prediction Lai locus Copen Locus Protein annotation SWISS-PROT a PDB Code b LA0616 LIC12966 LipL41/Outer membrane lipoprotein lipL41 - 1a17 LA2295 LIC11643 LipL45 protein P02977 1l8w LA0957 LIC12693 Outer membrane efflux protein/conserved hypothetical protein P24145 1ek9 LA0581 LIC12990 Outer membrane efflux protein/conserved hypothetical protein Q9ZHD2 1ek9 LA3733 LIC10496 Outer membrane efflux protein/conserved hypothetical protein - 1ek9 LA0301 LIC10258 Outer membrane protein OmpA family/hypothetical protein Q926C3 1r1m LA0222 LIC10191 Outer membrane protein OmpA family/PG-associated CM protein P22263 1r1m LA1192 LIC12499 Putative outer membrane protein - 1fep LA1404 LIC12337 Putative outer membrane protein - 2mpr LA1931 LIC11975 Putative outer membrane protein/outer membrane protein - 2mpr LA1987 LIC11918 Putative outer membrane protein/conserved hypothetical protein - 1osp LB199 LIC20157 Putative outer membrane protein/conserved hypothetical protein - 1fep LA1030 LIC12630 TPR-repeat-containing proteins/hypothetical protein P58937 1a17 LA0568 LIC13002 Conserved hypothetical protein - 1kmo LA1510 LIC12252 Conserved hypothetical protein - 2mpr LA0835 LIC12791 Hypothetical protein/conserved hypothetical protein - 1fnf LA2746 LIC11268 Hypothetical protein/conserved hypothetical protein - 2mpr LA2940 LIC11121 Hypothetical protein/conserved hypothetical protein - 2mpr LA2976 LIC11086 Hypothetical protein/conserved hypothetical protein - 2mpr LA3870 LIC13089 Hypothetical protein/conserved hypothetical protein - 2mpr LA4272 LIC13418 Hypothetical protein/conserved hypothetical protein - 2mpr LA4335 LIC13477 Hypothetical protein/conserved hypothetical protein - 1kmo LA0706 LIC12898 Unknown protein P38370 1fep LA1507 LIC12254 Unknown protein/outer membrane protein - 1a0t LA3853 LIC13078 Unknown protein/conserved hypothetical protein - 1bxw Note a: Swiss-Prot ID derived from DBsubloc database, b: PDB code derived from GTD prediction Table 9 Protein subcellular localizations of L. interrogans predicted by PSORTb, PA, ProtCompB and the combination prediction Localization Subcellular localization prediction PSORTb PA ProtCompB Combination prediction Cytoplasm (CP) 1125 921 2013 2690 Cytoplasmic membrane (CM) 606 715 1726* 813 Outer membrane (OM) 112 28 63 Periplasmic (PP) 30 86 478 75 Extracellular (EX) 29 326 510 114 Unknown 2825 2652 - 972 * Note that in ProtCompB prediction in this version, CM and OM were predicted as membrane proteins.

Publication Year: 2008