;; ;; Example PathoLogic format file for T. pallidum ;; ;; ID TP0001 NAME dnaA STARTBASE 4 ENDBASE 1398 FUNCTION chromosomal replication initiator protein DBLINK PID:g3322256 PRODUCT-TYPE P GENE-COMMENT similar to SP:P33768 PID:454039 GB:AE000783 percent identity: 46.67; identified by sequence similarity; putative // ID TP0002 NAME dnaN STARTBASE 1641 ENDBASE 2756 FUNCTION DNA polymerase III, subunit beta DBLINK PID:g3322257 PRODUCT-TYPE P GENE-COMMENT similar to SP:P13455 GB:X14791 PID:45691 percent identity: 30.49; identified by sequence similarity; putative // ID TP0003 NAME recF STARTBASE 2623 ENDBASE 3834 FUNCTION recF protein DBLINK PID:g3322258 PRODUCT-TYPE P GENE-COMMENT similar to PID:1652652 percent identity: 27.27; identified by sequence similarity; putative // ID TP0004 NAME TP0004 STARTBASE 3827 ENDBASE 4264 FUNCTION ORF DBLINK PID:g3322262 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0005 NAME gyrA STARTBASE 4391 ENDBASE 6832 FUNCTION DNA gyrase, subunit A DBLINK PID:g3322255 PRODUCT-TYPE P GENE-COMMENT similar to GB:D26185 SP:P05653 GB:X02369 PID:40019 PID:467397 percent identity: 45.35; identified by sequence similarity; putative // ID TP0006 NAME TP0006 STARTBASE 7014 ENDBASE 7181 FUNCTION Tp75 protein DBLINK PID:g3322259 PRODUCT-TYPE P GENE-COMMENT similar to GB:X61226 PID:48233 percent identity: 100.00; identified by sequence similarity; putative // ID TP0007 NAME TP0007 STARTBASE 7317 ENDBASE 7967 FUNCTION ORF DBLINK PID:g3322260 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0008 NAME TP0008 STARTBASE 7991 ENDBASE 8260 FUNCTION ORF DBLINK PID:g3322261 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0010 NAME TP0010 STARTBASE 10237 ENDBASE 10362 FUNCTION ORF DBLINK PID:g3322269 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0011 NAME tprB STARTBASE 10396 ENDBASE 12378 FUNCTION tpr protein B DBLINK PID:g3322264 PRODUCT-TYPE P GENE-COMMENT similar to GP:2196926 percent identity: 37.13; identified by sequence similarity; putative // ID TP0012 NAME TP0012 STARTBASE 12372 ENDBASE 12548 FUNCTION ORF DBLINK PID:g3322270 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0013 NAME TP0013 STARTBASE 12545 ENDBASE 13210 FUNCTION ORF DBLINK PID:g3322271 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0014 NAME TP0014 STARTBASE 13167 ENDBASE 13775 FUNCTION ORF DBLINK PID:g3322272 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0015 NAME pheT STARTBASE 13966 ENDBASE 15780 FUNCTION phenylalanyl-tRNA synthetase beta subunit DBLINK PID:g3322265 PRODUCT-TYPE P GENE-COMMENT similar to GP:1785608 percent identity: 39.93; identified by sequence similarity; putative // ID TP0016 NAME lon-1 STARTBASE 15743 ENDBASE 18316 FUNCTION ATP-dependent protease LA DBLINK PID:g3322266 PRODUCT-TYPE P GENE-COMMENT similar to GB:L42023 SP:P43865 PID:1007316 PID:1221456 PID:1205562 percent identity: 30.50; identified by sequence similarity; putative // ID TP0017 NAME TP0017 STARTBASE 18404 ENDBASE 19351 FUNCTION ORF DBLINK PID:g3322267 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 36.16; identified by sequence similarity; putative // ID TP0018 NAME TP0018 STARTBASE 19418 ENDBASE 21391 FUNCTION transcription elongation factor DBLINK PID:g3322268 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 33.20; identified by sequence similarity; putative // ID TP0019 NAME greA STARTBASE 21558 ENDBASE 22046 FUNCTION transcription elongation factor DBLINK PID:g3322274 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 36.71; identified by sequence similarity; putative // ID TP0020 NAME TP0020 STARTBASE 22046 ENDBASE 24169 FUNCTION 76K protein DBLINK PID:g3322275 PRODUCT-TYPE P GENE-COMMENT similar to GP:2108236 percent identity: 99.56; identified by sequence similarity; putative // ID tRNA-Ser-1 NAME tRNA-Ser-1 STARTBASE 24338 ENDBASE 24425 FUNCTION Ser GGA PRODUCT-TYPE TRNA // ID tRNA-Ser-2 NAME tRNA-Ser-2 STARTBASE 24482 ENDBASE 24570 FUNCTION Ser CGA PRODUCT-TYPE TRNA // ID tRNA-Arg-1 NAME tRNA-Arg-1 STARTBASE 24628 ENDBASE 24701 FUNCTION Arg GCG PRODUCT-TYPE TRNA // ID tRNA-Ser-3 NAME tRNA-Ser-3 STARTBASE 24733 ENDBASE 24819 FUNCTION Ser GCT PRODUCT-TYPE TRNA // ID tRNA-Ser-4 NAME tRNA-Ser-4 STARTBASE 24860 ENDBASE 24944 FUNCTION Ser TGA PRODUCT-TYPE TRNA // ID TP0021 NAME TP0021 STARTBASE 25107 ENDBASE 25373 FUNCTION ORF DBLINK PID:g3322280 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0022 NAME TP0022 STARTBASE 25328 ENDBASE 27496 FUNCTION ORF DBLINK PID:g3322281 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0023 NAME TP0023 STARTBASE 27557 ENDBASE 28888 FUNCTION sodium- and chloride- dependent transporter DBLINK PID:g3322276 PRODUCT-TYPE P GENE-COMMENT similar to GB:L77117 SP:Q58715 PID:1591959 percent identity: 29.44; identified by sequence similarity; putative // ID TP0024 NAME TP0024 STARTBASE 29068 ENDBASE 29778 FUNCTION ORF DBLINK PID:g3322277 PRODUCT-TYPE P GENE-COMMENT similar to GB:D37799 SP:P39760 PID:520844 PID:1377829 GB:AL009126 percent identity: 30.32; identified by sequence similarity; putative // ID TP0025 NAME TP0025 STARTBASE 29857 ENDBASE 32928 FUNCTION ORF DBLINK PID:g3322278 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 32.52; identified by sequence similarity; putative // ID TP0026 NAME fliG-1 STARTBASE 32957 ENDBASE 33979 FUNCTION flagellar motor switch protein DBLINK PID:g3322279 PRODUCT-TYPE P GENE-COMMENT similar to PID:790528 PID:790935 PID:2105149 percent identity: 28.10; identified by sequence similarity; putative // ID TP0027 NAME TP0027 STARTBASE 34205 ENDBASE 35428 FUNCTION hemolysin, putative DBLINK PID:g3322283 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 25.71; identified by sequence similarity; putative // ID TP0028 NAME TP0028 STARTBASE 35442 ENDBASE 36803 FUNCTION hemolysin, putative DBLINK PID:g3322284 PRODUCT-TYPE P GENE-COMMENT similar to PID:1653594 percent identity: 26.34; identified by sequence similarity; putative // ID TP0029 NAME murA STARTBASE 36911 ENDBASE 38188 FUNCTION UDP-N-acetylglucosamine 1-carboxyvinyltransferase DBLINK PID:g3322285 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 56.21; identified by sequence similarity; putative // ID TP0030 NAME groEL STARTBASE 38307 ENDBASE 39941 FUNCTION heat shock protein DBLINK PID:g3322286 PRODUCT-TYPE P GENE-COMMENT similar to SP:P23033 GB:X54111 PID:297123 percent identity: 99.26; identified by sequence similarity; putative // ID TP0031 NAME TP0031 STARTBASE 40005 ENDBASE 40283 FUNCTION ORF DBLINK PID:g3322292 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0032 NAME TP0032 STARTBASE 40280 ENDBASE 41080 FUNCTION ORF DBLINK PID:g3322287 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 30.36; identified by sequence similarity; putative // ID TP0033 NAME TP0033 STARTBASE 41077 ENDBASE 41688 FUNCTION conserved hypothetical integral membrane protein DBLINK PID:g3322288 PRODUCT-TYPE P GENE-COMMENT similar to PID:1001613 PID:1001643 percent identity: 37.57; identified by sequence similarity; putative // ID TP0034 NAME TP0034 STARTBASE 41789 ENDBASE 42739 FUNCTION ABC transporter, periplasmic binding protein DBLINK PID:g3322289 PRODUCT-TYPE P GENE-COMMENT similar to PID:1117994 percent identity: 31.15; identified by sequence similarity; putative // ID TP0035 NAME TP0035 STARTBASE 42937 ENDBASE 43653 FUNCTION ABC transporter, ATP-binding protein DBLINK PID:g3322290 PRODUCT-TYPE P GENE-COMMENT similar to PID:1652187 percent identity: 38.60; identified by sequence similarity; putative // ID TP0036 NAME TP0036 STARTBASE 43653 ENDBASE 44453 FUNCTION ABC transporter, permease protein DBLINK PID:g3322291 PRODUCT-TYPE P GENE-COMMENT similar to GB:L11577 SP:P42361 percent identity: 26.59; identified by sequence similarity; putative // ID TP0037 NAME TP0037 STARTBASE 44562 ENDBASE 45557 FUNCTION D-specific D-2-hydroxyacid dehydrogenase DBLINK PID:g3322294 PRODUCT-TYPE P GENE-COMMENT similar to GP:1644433 percent identity: 42.48; identified by sequence similarity; putative // ID TP0038 NAME pfoS/R STARTBASE 45654 ENDBASE 46706 FUNCTION regulatory protein DBLINK PID:g3322295 PRODUCT-TYPE P GENE-COMMENT similar to GP:1354775 percent identity: 100.00; identified by sequence similarity; putative // ID TP0039 NAME TP0039 STARTBASE 46755 ENDBASE 46913 FUNCTION ORF DBLINK PID:g3322301 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0040 NAME mcp1 STARTBASE 47591 ENDBASE 49384 FUNCTION methyl-accepting chemotaxis protein DBLINK PID:g3322296 PRODUCT-TYPE P GENE-COMMENT similar to GP:1354776 percent identity: 100.00; identified by sequence similarity; putative // ID TP0041 NAME TP0041 STARTBASE 49386 ENDBASE 49508 FUNCTION ORF DBLINK PID:g3322302 PRODUCT-TYPE P GENE-COMMENT hypothetical protein; identified by GeneMark; putative // ID TP0042 NAME TP0042 STARTBASE 49505 ENDBASE 50437 FUNCTION hypothetical protein DBLINK PID:g3322297 PRODUCT-TYPE P GENE-COMMENT similar to GP:1354777 percent identity: 100.00; identified by sequence similarity; putative // ID TP0043 NAME TP0043 STARTBASE 50418 ENDBASE 52550 FUNCTION soluble lytic transglycosylase, putative DBLINK PID:g3322298 PRODUCT-TYPE P GENE-COMMENT similar to GB:U14003 SP:P03810 GB:M69185 PID:147836 PID:537232 percent identity: 30.81; identified by sequence similarity; putative // ID TP0044 NAME gidA STARTBASE 52590 ENDBASE 54482 FUNCTION glucose inhibited division protein A DBLINK PID:g3322299 PRODUCT-TYPE P GENE-COMMENT similar to PID:1200212 SP:P53362 GB:AE000783 percent identity: 51.39; identified by sequence similarity; putative // ID TP0045 NAME TP0045 STARTBASE 54538 ENDBASE 55437 FUNCTION adenosine deaminase, putative DBLINK PID:g3322300 PRODUCT-TYPE P GENE-COMMENT similar to SP:P53909 PID:1302089 PID:854497 percent identity: 31.76; identified by sequence similarity; putative // ID TP0046 NAME TP0046 STARTBASE 55799 ENDBASE 56500 FUNCTION hypothetical protein DBLINK PID:g3322304 PRODUCT-TYPE P GENE-COMMENT similar to GB:U11881 SP:P45685 PID:517444 percent identity: 100.00; identified by sequence similarity; putative // ID TP0047 NAME TP0047 STARTBASE 56518 ENDBASE 57039 FUNCTION ORF DBLINK PID:g3322305 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 26.47; identified by sequence similarity; putative // ID TP0048 NAME TP0048 STARTBASE 57045 ENDBASE 57476 FUNCTION ORF DBLINK PID:g3322306 PRODUCT-TYPE P GENE-COMMENT similar to PID:1017747 PID:1372995 GB:AE000783 percent identity: 27.08; identified by sequence similarity; putative // ID TP0049 NAME TP0049 STARTBASE 57498 ENDBASE 58526 FUNCTION ORF DBLINK PID:g3322307 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 50.57; identified by sequence similarity; putative // ID TP0050 NAME TP0050 STARTBASE 58819 ENDBASE 59427 FUNCTION ORF DBLINK PID:g3322308 PRODUCT-TYPE P GENE-COMMENT similar to GB:AE000783 percent identity: 41.88; identified by sequence similarity; putative //