GeneNo,STM_GeneID,ECO_GeneID,GeneName,STM_sValues,ECO_sValues,FunctionalCategory_GO,TPM,PPI,PPI_TPM10,PPI_TPM50,PPI_TPM100,DEV_GC,DEV_FOP,STM_Length,ECO_Length,Disorder_reg_STM ,Disorder_reg_ECO,Dosage,Divergence,COG_Category,COG_MainCategory,HU2009_ModuleID,HTorCore,KeioEssential ,Function,,,
1,STM0160,b0119,yacL,-0.002062499,-0.008600576,Unknown,76.41240999,37,35,33,32,0.001324433,0.05785124,363,363,0,0,Sensitive,0.15,S,POORLY.CHARACTERIZED,131,NA,N,UPF0231 family protein,,,
2,STM0172,b0127,yadG,-0.132936423,-0.0315291,Operational,48.55616434,39,39,39,38,0.001613473,0.01618123,927,927,2,2,Insensitive,0.048701299,V,CELLULAR.PROCESSES.SIGNALING,196,HT,N,Putative ABC transporter ATPase,,,
3,STM0226,b0179,lpxD,0.009209151,0.009593918,Operational,379.7172028,32,32,30,26,0.008257553,0.040935673,1026,1026,3,3,NA,0.04398827,M,CELLULAR.PROCESSES.SIGNALING,2,Core,Y,"ÊLipid A synthesis, UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase is involved in the third step of lipid A biosynthesis",,,
4,STM0264,b0215,dnaQ,-0.019588228,-0.042937877,Informational,63.49560268,14,14,12,7,0.010246834,0.020491803,732,732,1,1,Sensitive,0.065843621,L,INFORMATION.STORAGE.PROCESSING,201,Core,N,"DNA polymerase III epsilon subunit; streptomycin, azaserine resistant; 3' to 5' proofreading, lexA regulon; The epsilon subunit of DNA polymerase III catalyzes the 3' to 5' proofreading exonuclease activity of the holoenzyme ",,,
5,STM0425,b0423,thiI,-0.151824614,-0.212389915,Informational,114.6698084,1,1,1,1,0.002430213,0.01242236,1449,1449,2,2,Sensitive,0.03526971,H,METABOLISM,175,HT,N,"tRNA s(4)U8 sulfurtransferase, activated by IscS; ThiS-thiocarboxylate (ThiS-COSH) synthesis; mutant is near-UV resistant;ThiI is a bifunctional enzyme that is required both for the synthesis of the thiazole moiety of thiamine and for the conversion of uridine to 4-thiouridine at position 8 in tRNA ",,,
6,STM0451,b0440,hupB,-0.082107198,-0.03702847,Informational,2558.926293,29,26,20,16,0.0054544,0,273,273,1,1,Insensitive,0.011111111,L,INFORMATION.STORAGE.PROCESSING,61,Core,N,"Histone-like protein HU-beta, HU-1",,,
7,STM0614,b0607,uspG,-0.006809993,-0.007160274,Operational,185.5502808,13,13,12,9,0.022139101,0.027972028,429,429,0,1,Sensitive,0.105633803,T,CELLULAR.PROCESSES.SIGNALING,164,HT,N,"Stress protein, induced in stationary phase; native GroEL substrate; heat shock; mutant sensitive to CCCP; dimeric; UspG belongs to the class II (UspF/G) subfamily of universal stress proteins [Kvint03]. UspG possesses intrinsic autophosphorylation and autoadenylation activity; the C-terminal domain of UspG is important for these activities and required for dimerization [Weber06b]. UspG binds to GroEL",,,
8,STM0629,b0623,cspE,-0.009228028,0.005886998,Informational,7758.413457,31,31,31,30,0.002076281,0.071428571,210,210,2,2,Insensitive,0.014492754,K,INFORMATION.STORAGE.PROCESSING,106,Core,N,"Transcription antitermination protein; constitutively-expressed cold shock family protein; negative regulator of cspA transcription; binds and melts RNA; binds ssDNA; dimeric; CspE belongs to the cold shock family of proteins and was shown to be involved in a variety of cellular processes both in vitro and by studying mutants and overexpressing strains. CspE is involved in resistance to camphor-induced chromosome decondensation [Hu96, Sand03], and a model of how its ssDNA binding activity might affect chromosome condensation has been proposed ",,,
9,STM0648,b0642,leuS,-0.275755814,-0.306440165,Informational,220.0128757,8,8,8,7,0.024596702,0.042973287,2583,2583,5,5,Sensitive,0.045348837,J,INFORMATION.STORAGE.PROCESSING,42,Core,Y,"Leucine--tRNA ligase; Leucyl-tRNA synthetase (LeuRS) is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. LeuRS belongs to the Class IB aminoacyl tRNA synthetases; apart from sequence motifs within the active site, the different enzymes show little similarity in their primary amino acid sequences ",,,
10,STM0703,b0695,kdpD,-0.034105963,-0.023971333,Operational,9.112611133,1,1,1,0,0.013249749,0.005586592,2685,2685,6,8,Insensitive,0.104026846,T,CELLULAR.PROCESSES.SIGNALING,79,Core,N,"Sensor kinase for the kdp operon; two-component system; has autokinase activity and KdpE-directed phosphotransferase and phosphatase activities; responds to ionic strength, ATP and potassium; dimeric;KdpD is the sensor member of the KdpDE two-component system which responds to changes in internal and/or external potassium ion (K+) concentration and regulates transcription of the kdpFABC operon encoding a K+ transporting ATPase.",,,
11,STM0801,b0780,ybhK,0.008960322,-0.03490118,Operational,27.13711449,3,3,3,3,0.030267532,0.072607261,909,909,4,4,NA,0.082781457,S,POORLY.CHARACTERIZED,36,Core,N,"ÊPutative CofD superfamily transferase, function unknown; dimeric",,,
12,STM0806,b0785,moaE,-0.006240632,-0.020081563,Operational,30.23357143,2,2,0,0,0.043192228,0.033112583,453,453,0,0,Sensitive,0.086666667,H,METABOLISM,245,HT,N,"Molybdopterin (MPT) synthase, large subunit; chlorate resistance; dimer of dimers with MoaD",,,
13,STM0831,b0812,dps,-0.009631172,-0.006475211,Operational,442.5892641,19,18,12,9,0.006966054,0.017857143,504,504,0,0,Insensitive,0.047904192,P,METABOLISM,45,Core,N,Stress-induced Fe-binding and storage protein; forms biocrystals with DNA; copper homeostatsis; Dps is a highly abundant protein in stationary-phase E. coli and is required for the normal starvation response ,,,
14,STM0943,b0880,cspD,-0.024273825,-0.13406004,Informational,91.13610066,28,28,28,27,0.035717133,0.006126126,222,225,2,2,Sensitive,0.067567568,K,INFORMATION.STORAGE.PROCESSING,106,Core,N," Inhibitor of DNA replication; cold shock protein homolog, not cold shock inducible; stationary phase and starvation inducible; lethal when overproduced; persistance gene",,,
15,STM0945,b0882,clpA,-0.049583022,-0.022430218,Informational,165.892123,32,32,31,29,0.016041238,0.036890646,2277,2277,4,4,Insensitive,0.027704485,O,CELLULAR.PROCESSES.SIGNALING,41,Core,N, ATPase subunit of ClpAP ATP-dependent protease; protease Ti; molecular chaperone,,,
16,STM0961,b0891,lolA,-0.432620713,-0.014270714,Operational,97.0307363,1,1,1,1,0.004907227,0.017479675,615,612,2,2,Insensitive,0.06372549,M,CELLULAR.PROCESSES.SIGNALING,14,Core,Y,Periplasmic protein responsible for sorting and transporting lipoproteins to outer membrane,,,
17,STM1061,b0948,rlmL,0.000351731,-0.005059507,Informational,79.0587234,22,22,21,18,0.008060726,0.011379801,2109,2109,8,6,NA,0.07977208,L,INFORMATION.STORAGE.PROCESSING,315,Core,N,Fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase; SAM-dependent,,,
18,STM1112,b1000,cbpA,-0.006781963,-0.024568562,Informational,66.89909543,24,24,23,21,0.006002388,0.104234528,921,921,1,3,Sensitive,0.117647059,O,CELLULAR.PROCESSES.SIGNALING,297,Core,N,"DnaK co-chaperone, binds curved DNA",,,
19,STM1185,b1084,rne,-0.158607026,-0.223641863,Informational,187.729445,36,36,35,33,0.027947103,0.062771112,3204,3186,8,12,Sensitive,0.168372093,J,INFORMATION.STORAGE.PROCESSING,88,Core,Y,RNase E; component of RNA degradosome; mRNA turnover; 5S and 16S RNA maturation,,,
20,STM1196,b1094,acpP,-0.077888853,-0.066966665,Operational,10743.33998,23,23,20,18,0.002198348,0,237,237,1,1,Insensitive,0,IQ,METABOLISM,111,Core,Y,Acyl carrier protein ACP,,,
21,STM1298,b1763,topB,-0.451928537,-0.594282582,Informational,65.1801464,17,17,16,12,0.012111616,0.021717243,1950,1962,5,5,Sensitive,0.059724349,L,INFORMATION.STORAGE.PROCESSING,169,Core,N,Topoisomerase III; mutR phenotype is decreased deletion formation between short repeats,,,
22,STM1334,b1718,infC,0.001252319,0.002655141,Informational,3656.568398,38,37,36,33,0.010155996,0.005524862,543,543,0,0,NA,0.005555556,J,INFORMATION.STORAGE.PROCESSING,1,Core,Y,Translation initiation factor IF-3; unusual AUU start codon,,,
23,STM1366,b1686,ydiI,-0.000821081,-0.00670275,Operational,56.13263008,26,26,25,24,0.052346869,0.02189781,411,411,2,2,NA,0.110294118,Q,METABOLISM,316,Core,N,"DHNA-CoA thioesterase, menaquinone biosynthesis; 1,4-dihydroxy-2-naphthoyl-CoA hydrolase",,,
24,STM1696,b1290,sapF,-0.001814773,-0.015143039,Operational,35.58472535,2,2,2,2,0.031612316,0.011152416,807,807,1,1,Sensitive,0.02238806,V,CELLULAR.PROCESSES.SIGNALING,6,Core,N,Antimicrobial peptide ABC transporter ATPase,,,
26,STM1946,b1913,uvrC,-0.605552377,-0.597446173,Informational,115.1282464,22,22,21,20,0.01664861,0.008183306,1833,1833,3,5,Insensitive,0.045901639,L,INFORMATION.STORAGE.PROCESSING,252,Core,NA,Excision nuclease subunit C; repair of UV damage to DNA; multicopy causes mucoidy,,,
27,STM2388,b2341,fadJ,-0.131262209,-0.02219078,Operational,4.158686467,6,3,3,2,0.0172045,0.045452592,2148,2145,5,7,Insensitive,0.13986014,I,METABOLISM,27,Core,N,"Multifunctional anaerobic fatty acid oxidation complex FadIJ; has 3-hydroxyacyl-CoA dehydrogenase and medium-long-chain-length enoyl-CoA hydratase activities; probable beta-hydroxybutyryl-CoA epimerase and dodecenoyl-CoA-delta-isomerase,enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase",,,
28,STM2543,b2530,iscS,-0.026930937,-0.061979352,Operational,166.8407878,7,7,5,4,0.016076457,0.064197531,1215,1215,3,3,Sensitive,0.027227723,E,METABOLISM,20,Core,NA,"(iscS)Cysteine desulfurase, PLP-dependent; used in synthesis of Fe-S clusters and 4-thiouridine; ThiI transpersulfidase; TusA transpersulfidase; YnjE transpersulfidase; MoaD transpersulfidase; pyridoxal phosphate cofactor linked to Lys206",,,
29,STM2643,b2576,srmB,-0.341742843,-0.038216982,Informational,77.44099004,34,33,31,27,0.004084528,0.026966292,1335,1335,6,6,Insensitive,0.06981982,LKJ,INFORMATION.STORAGE.PROCESSING,395,Core,N,"ATP-dependent RNA helicase, 50S ribosomal subunit biogenesis; suppresses 50S ribosome assembly defect of rplX(ts); required for effiicient ribosomal 50S subunit assembly; stabilizes exposed mRNA, possibly by protecting or destabilizing secondary structure",,,
30,STM3143,b2990,hybG,-0.002828354,-0.014404384,Operational,89.70392887,12,11,7,7,0.006104418,0.048192771,249,249,0,1,Sensitive,0.06097561,O,CELLULAR.PROCESSES.SIGNALING,15,Core,N,Hydrogenase 2 accessory protein; chaperone-like function,,,
31,STM3159,b3006,exbB,-0.002441982,-0.003016963,Operational,368.5232384,16,15,14,12,0.026571281,0.012244898,735,735,0,1,NA,0.102459016,U,CELLULAR.PROCESSES.SIGNALING,7,Core,N,Uptake of enterochelin; resistance or sensitivity to colicins; similarity with TolQ,,,
32,STM3215,b3071,yqjI,-0.050911372,-0.014837148,Informational,30.034373,15,14,14,14,0.000506173,0.030626781,648,624,3,3,Insensitive,0.314814815,K,INFORMATION.STORAGE.PROCESSING,363,HT,N,"Transcriptional repressor for yqjH, nickel- or iron-inducible; autorepressor",,,
33,STM3282,b3164,pnp,0.000369879,-0.039171627,Informational,770.9833768,40,38,37,36,0.022003763,0.008426966,2136,2136,5,6,NA,0.029535865,J,INFORMATION.STORAGE.PROCESSING,1,Core,NA,Polynucleotide phosphorylase; exoribonuclease; PNPase component of RNA degradosome; cold shock protein required for growth at low temperatures,,,
35,STM3514,b3417,malP,-0.102790824,-0.134122085,Operational,30.5701684,28,28,25,21,0.03071126,0.020050125,2394,2394,6,7,Sensitive,0.089084065,G,METABOLISM,129,Core,NA,Maltodextrin phosphorylase,,,
36,STM3656,b3560,glyQ,-0.011166132,-0.410623168,Informational,244.4948139,9,9,9,7,0.002674574,0.059210526,912,912,4,4,Sensitive,0.00660066,J,INFORMATION.STORAGE.PROCESSING,185,Core,Y,"Glycine--tRNA ligase, alpha-subunit",,,
37,STM3682,b3590,selB,-0.080215696,-0.109388948,Informational,35.88980728,30,30,29,27,0.007662398,0.039021755,1851,1845,4,5,Sensitive,0.150974026,J,INFORMATION.STORAGE.PROCESSING,10,Core,N,Elongation factor promoting selenocysteine incorporation; specific for selenocysteyl tRNA,,,
38,STM3689,b3602,yibL,-0.016225029,-0.016024084,Informational,78.81540631,25,25,24,23,0.001354706,0.05785124,363,363,0,1,Sensitive,0.1,-,NA,182,NA,NA,"Ribosome-associated DUF2810 family protein, function unknown",,,
39,STM3808,b3686,ibpB,-0.009915929,-0.000452021,Operational,7.576301664,8,8,3,3,0.029110424,0.118881119,429,429,4,3,Insensitive,0.112676056,O,CELLULAR.PROCESSES.SIGNALING,64,NA,N,"Chaperone, heat-inducible protein of HSP20 family",,,
40,STM3854,b3725,pstB,-0.053549153,-0.049369835,Operational,26.22136409,20,19,17,14,0.000675169,0.027131783,774,774,4,4,Insensitive,0.015564202,P,METABOLISM,105,Core,N,Phosphate ABC transporter ATPase,,,
41,STM4170,b4000,hupA,-0.027435225,-0.044590528,Informational,1720.314127,40,40,34,29,0.005561349,0.010989011,273,273,0,0,Sensitive,0.011111111,L,INFORMATION.STORAGE.PROCESSING,477,Core,N,"Histone-like protein HU-alpha, HU-2",,,
43,STM4237,b4043,lexA,-0.101565598,-0.074247987,Informational,348.2136033,16,16,14,10,0.032049315,0.004926108,609,609,0,0,Insensitive,0.02970297,KT,CELLULAR.PROCESSES.SIGNALING,278,Core,Y,Global regulator (repressor) for SOS regulon; dimeric,,,
44,STM4361,b4172,hfq,0.002853197,0.003355261,Informational,1171.243782,27,27,24,20,0.011285103,0.029126214,309,309,2,3,NA,0.058823529,R,POORLY.CHARACTERIZED,3,Core,N,Global regulator of sRNA function; host factor for RNA phage Q beta replication; HF-I; DNA- and RNA-binding protein; RNA chaperone; binds ATP and RNAP,,,
46,STM4394,b4203,rplI,-0.005908822,-0.000375235,Informational,4963.791145,31,30,27,23,0.012214831,0.013333333,450,450,1,1,Insensitive,0.046979866,J,INFORMATION.STORAGE.PROCESSING,47,Core,N,50S ribosomal subunit protein L9,,,
47,STM4458,b4243,ridA,-0.009172903,-0.00369391,Operational,3069.722299,12,10,9,9,0.016869123,0.031007752,387,387,2,2,Insensitive,0.0625,J,INFORMATION.STORAGE.PROCESSING,160,Core,N,"(ridA)Enamine/imine deaminase, reaction intermediate detoxification",,,
48,STM4558,b4373,rimI,-0.007755418,-0.003560464,Informational,70.27514844,14,14,12,11,0.026845638,0.026845638,447,447,1,1,Insensitive,0.135135135,R,POORLY.CHARACTERIZED,333,Core,N,Ribosomal protein S18 N-acetyltransferase; modification of 30S ribosomal subunit protein S18; acetylation of N-terminal alanine,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,
STM_sValues = Selection Coefficients of S. Typhimurium genes,,,,,,,,,,,,,,,,,,,,,,,,,,,,
ECO_sValues =  = Selection Coefficients of E. coli genes,,,,,,,,,,,,,,,,,,,,,,,,,,,,
TPM = Transcript per million,,,,,,,,,,,,,,,,,,,,,,,,,,,,
PPI = number of protein protein interactions,,,,,,,,,,,,,,,,,,,,,,,,,,,,
PPI_TPM10 = number of protein protein interactions after eliminating genes below 10TPM,,,,,,,,,,,,,,,,,,,,,,,,,,,,
All_50_GI = number of protein protein interactions after eliminating genes below 50TPM,,,,,,,,,,,,,,,,,,,,,,,,,,,,
All_100_GI = number of protein protein interactions after eliminating genes below 100TPM,,,,,,,,,,,,,,,,,,,,,,,,,,,,
DEV_GC = Deviation in the %GC between orthologs,,,,,,,,,,,,,,,,,,,,,,,,,,,,
DEV_FOP = Deviation in the FOP between orthologs,,,,,,,,,,,,,,,,,,,,,,,,,,,,
STM_Length = Length of the S. Typhimurium genes in nucleotides,,,,,,,,,,,,,,,,,,,,,,,,,,,,
ECO_Length = Length of the E. coli genes in nucleotides,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"Disorder_reg_STM  = Number of the disordered regions in protein sequences of the S. Typhimurium genes, obtained from Globplot database (globplot.embl.de).",,,,,,,,,,,,,,,,,,,,,,,,,,,,
"Disorder_reg_ECO  = Number of the disordered regions in protein sequences of the E. coli genes, obtained from Globplot database (globplot.embl.de).",,,,,,,,,,,,,,,,,,,,,,,,,,,,
HU2009_ModuleID = The module ID of PPI obtained from Hu at al 2009.,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"HTorCore = obtained from EcoGene (ecogene.org) for horizontally transferred or core (HT/Core), ",,,,,,,,,,,,,,,,,,,,,,,,,,,,
KeioEssential = whether the gene is identified as essential or not from Keio collection.,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"Function = information is taken from McClelland, 2001, DOI: 10.1038/35101614",,,,,,,,,,,,,,,,,,,,,,,,,,,,