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PDB ID Mentions in PubMed Central

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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


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4407003

Model Generation The template chosen for model generation was PME of Daucous carota (PDB ID: 1GQ8) on the basis of maximum similarity.

Publication Year: 2015