Search Topic Text   All Text Title Only Gene Set Overlap Query   Proteomics: Protein-protein Interactions (PPI) Proteome Chips Proteome Chips: Mismatch Binding 1 A:C mismatch binding 20 G:T mismatch binding 20 Abasic site:G binding 20 Abasic site:A binding 20 Abasic site:C binding 19 Abasic site:T binding 20 YbaZ-binding Proteins 20 Protein Complexes Blue Native 2D PAGE (Lasserre) Blue Native 2D PAGE (Stenberg) Doodle Cross-linked Peptides Mass Spectrometry APEX Protein levels 449 Cisplatin Targets 29 [Pt(dien)(H2O)]2+ Targets 8 Cysteine Sulfenic Acid 23 Cross-linked Peptides Cytoplasmic Viscosity Virtual Cytoplasm 2D PAGE Blue Native 2D PAGE (Lasserre) Blue Native 2D PAGE (Stenberg) SubProteomes Periplasmic Proteome Extracellular Proteome 63 Structural Genomics Projects Structure2Function Project 111 Genetics: Essential Genes 290 Keio Collection Glycogen Content Mutants 65 Glycogen Excess Mutants 35 Glycogen Deficient Mutants 30 Biofilm Defective Mutants 110 Keio Mutant Validations 2 Minimal Genome Reduced Genome Minimal Gene Sets Common Core 2097 CommonCore-5 2150 HT1006 1006 Non-Core971 Non-Core 971 Core Pseudogenes 20 Synthetic Biology Gene Expression Protein Translation tRNA 86 mRNA Codons Codon Usage Start Codons Stop Codons The Ribosome rRNA 22 Ribosomal Proteins 54 Small Ribosomal Proteins 21 Large Ribosomal proteins 33 Translation Factors 9 Initiation Factors 3 Elongation Factors 2 Release Factors 4 Mistranslation Translational Regulation Translation Frameshifting RNA Transcription RNA Polymerase Holenzyme 11 RNAP Core Enzyme 4 RNAP Sigma Factors 7 RNA Expression Microarrays Transcriptional Regulation Transcription Factors TFBS AraC Transcriptional Activator Family 28 5'UTR Attenuators Riboswitches lysC 5' UTR 1 thiM 5' UTR 1 moaA 5' UTR 1 thiB 5' UTR 1 Ribosome Binding Sites Transcription Start Points flhDC 5'UTR Long 5' UTRs gadE 5' UTR 1 Short 5' UTRs tauA 5' UTR 1 Regulatory Modeling cAMP Input Functions 19 Operon Known Operons Predicted Operons Predicted yeaVWX 3 Predicted yihO-U 7 Regulon Sigma 54 Regulons bEBP 13 cAMP Input Functions 19 Predicted Regulons McCue 2002 219 Nitrogen regulated (Ntr) response Transcription Initiation Promoters Curved Promoters 225 Stalled RNAP-Promoter Complexes 2 7 Stalled Complexes 7 34 Active Assayable Promoters 34 118 Screened Promoters Transcription Elongation Transcription Termination 1 Rho-independent Termination Rho-dependent Termination Chromosome Metabolism 1 DNA Replication DNA Polymerases 14 DNA Repair Proteome Chips: Mismatch Binding 1 A:C mismatch binding 20 G:T mismatch binding 20 Abasic site:G binding 20 Abasic site:A binding 20 Abasic site:C binding 19 Abasic site:T binding 20 YbaZ-binding Proteins 20 DNA Polymerases 14 DNA Recombination DNA Restriction and Modification Intergenes RNA Intergenes Intergenic Repeat Families REP Elements 4 IRU Repeats BOXC Repeats RSA Repeats TERM Repeats SIB Repeats TRIP Repeats PAIR Repeats CRISPR Repeats 10 LDR Repeats TLR Repeats 20 JUMP Repeats PDR-A Repeats PDR-E Repeats PDR-Z Repeats RNPB Repeats 5'UTR Attenuators Riboswitches lysC 5' UTR 1 thiM 5' UTR 1 moaA 5' UTR 1 thiB 5' UTR 1 Ribosome Binding Sites Transcription Start Points flhDC 5'UTR Long 5' UTRs gadE 5' UTR 1 Short 5' UTRs tauA 5' UTR 1 Transcription Termination 1 Rho-independent Termination Rho-dependent Termination DNA Intergenes Promoters Curved Promoters 225 TFBS Replication Intergenes 1 KOPS 1 Chi Sites oriC 1 Ter and pTer Sites 14 DatA 2 Dif 3 MigS 2 Regions of Extreme Structure 20 Pseudogenes 175 RNA gene-derived Pseudogenes 5 Reconstructed Pseudogenes 84 Frameshifted Pseudogenes 31 In-frame Stop Pseudogenes 30 Deletion Pseudogenes 95 5' Deletion Pseudogenes 59 3' Deletion Pseudogenes 36 Internal Deletion Pseudogenes 5 Interrupted Pseudogenes 15 Functional Pseudogenes Y-pseudogenes 116 Horizontal Gene Transfer 911 IS Elements 17 IS1 2 IS2 2 IS3 2 IS4 1 IS5 1 IS30 1 IS600 1 IS911 2 IS186 1 ISX' and ISZ' 2 IS150 2 Prophages 224 CP4-6 35 DLP12 32 e14 23 Rac 29 Qin/Kim 37 CPS-53/KpLE1 18 Eut/CPZ-55 9 CP4-57 26 CP4-44 14 PR-X 2 Genetic Transfer Transduction Conjugation Transformation HT1006 1006 HT Pseudogenes 28 EcoFam Orthologs YjhY 1 YpfM 1 YbfG 1 YbbD 1 YfdP 1 Paralogs MscS Mechanosensitive Channels 6 Major Facilitator Permeases 84 Rhs Element Repeat-encoded Proteins 9 FimD Usher Family Paralogs 11 FimA Paralogs 25 AAA+ ATPases 120 bEBP 13 ABC transporter ATPases 75 AraC Transcriptional Activator Family 28 Rhodanese domain proteins 8 L,D-transpeptidases 5 Nucleobase permeases 10 ABC transporter ATPases 75 Outer membrane factor (OMF) proteins 4 Periplasmic binding proteins 47 Periplasmic binding proteins, OppA family 9 Periplasmic binding proteins, HisJ family 10 Periplasmic binding proteins, BtuF family 4 Periplasmic binding proteins, MalE family 11 Periplasmic binding proteins, RbsB family 8 Periplasmic binding proteins, ProX family 3 Periplasmic binding proteins, ProX family 3 ABC transporter permeases, major family 50 DNA Biotechnology Polymerase Chain Reaction DNA Restriction and Modification Recombineering Molecular Cloning DNA Hybridization DNA Sequencing Whole Genome Resequencing DNA Protection Assays Gel Mobility Shift Assay Expression Systems Cell-free Expression DNA Purification GFP Reporters DNA Repeats Intergenic Repeat Families REP Elements 4 IRU Repeats BOXC Repeats RSA Repeats TERM Repeats SIB Repeats TRIP Repeats PAIR Repeats CRISPR Repeats 10 LDR Repeats TLR Repeats 20 JUMP Repeats PDR-A Repeats PDR-E Repeats PDR-Z Repeats RNPB Repeats Microsatellites (SSRs) 3 Annotation Science Experimental Verification Verification of Activity Verification of Start and Stop Verified Set Verification of Expression Verified Set Verification of Mutation and Phenotype Verification of Protein Localization Verified Set Predictive Annotation Comparative Genomics and Homology Analysis Functional Predictions using Homology Gene or Feature Interval Predictions using Homology Minimal Gene Sets Common Core 2097 CommonCore-5 2150 HT1006 1006 Non-Core971 Non-Core 971 Core Pseudogenes 20 Phylogenetic Profiles PanColi PanColi strains Intrinsic Sequence Analysis Functional Predictions using Intrinsic Properties Gene or Feature Interval Predictions using Intrinsic Properties Text Mining Systematic nomenclature Y-genes 1523 Y-pseudogenes 116 Prophage gene mnemonics Common Core 2097 CommonCore-5 2150 HT1006 1006 Non-Core971 Non-Core 971 Core Pseudogenes 20 Biochemistry: Peptidases and their homologs 136 Aspartic Peptidases 7 A08 Family Peptidases 1 A24 Family Peptidases 2 A26 Family Peptidases 1 A31 Family Peptidases 3 Cysteine Peptidases 20 C26 Family Peptidases 6 C40 Family Peptidases 4 C44 Family Peptidases 5 C48 Family Peptidases 1 C56 Family Peptidases 4 Metallo Peptidases 54 M01 Family Peptidases 1 M03 Family Peptidases 2 M14 Family Peptidases 1 M15 Family Peptidases 2 M16 Family Peptidases 3 M17 Family Peptidases 2 M20 Family Peptidases 8 M22 Family Peptidases 3 M23 Family Peptidases 4 M24 Family Peptidases 4 M28 Family Peptidases 2 M38 Family Peptidases 12 M41 Family Peptidases 1 M42 Family Peptidases 3 M48 Family Peptidases 4 M50 Family Peptidases 1 M74 Family Peptidases 1 Serine Peptidases 45 S01 Family Peptidases 4 S09 Family Peptidases 9 S11 Family Peptidases 4 S12 Family Peptidases 3 S13 Family Peptidases 1 S14 Family Peptidases 1 S16 Family Peptidases 4 S24 Family Peptidases 3 S26 Family Peptidases 1 S33 Family Peptidases 9 S41 Family Peptidases 1 S49 Family Peptidases 2 S51 Family Peptidases 1 S54 Family Peptidases 1 S66 Family Peptidases 1 Threonine Peptidases 3 T01 Family Peptidases 1 T02 Family Peptidases 1 T03 Family Peptidases 1 Colony formation and morphology Unknown Peptidases 7 U32 Family Peptidases 4 U49 Family Peptidases 1 U62 Family Peptidases 2 Protein Modifications Oxidized Proteins 58 Oxidized Proteins, Nitrogen 34 Oxidized Proteins, Carbon 36 Oxidized Proteins, Phosphate 9 Protein Phosphorylation Chaperones GroESL chaperonin GroESL substrates Kerner GroESL substrates Kerner Class I GroESL substrates Kerner Class II GroESL substrates Kerner Class III GroESL substrates DnaJK-GrpE chaperone system Clp Protease/Chaperones Structural Biology Protein Structure Kinetically Stable Proteins 45 X-ray Crystal Structures Structural Genomics Projects Structure2Function Project 111 NMR Structures Protein Dynamics Intrinsically Disordered Proteins Predicted IDPs Experimental IDPs 3 Protein Folding BBL Fast Folding 1 Protein unfolding Heat-stable Proteins 17 Nucleic Acid Structure RNA Structure DNA Structure Regions of Extreme Structure 20 Membranes Membrane Proteome Inner Membrane Proteome 807 IMemProt-C IN(Exp) 395 IMemProt-C OUT(Exp) 119 IMemProt-C IN(Pred) 85 IMemProt-C OUT(Pred) 14 IMemProt Pred 124 IMem_Loc_2DMS 78 LipoProteome 120 Verified Lipoproteins 82 Predicted Lipoproteins 38 Outer Membrane Proteome FimD Usher Family Paralogs 11 Mem_Loc_2DMS 28 MemProtExpress 120 MemProtEx-Minus 26 MemProtEx-Plus 91 MemProtEx-Both 33 MemProtEx-VivoOnly 18 MemProtEx-VitroOnly 40 MemProtEx-VivoStrong 15 MemProtEx-VitroStrong 35 MemProtEx-VivoWeak 36 MemProtEx-VitroWeak 38 Multicomponent Transport Systems Major Facilitator Permeases 84 PTS Sugar Transport Multidrug Resistance (MDR) Efflux Pumps 28 ABC (ATP-Binding Cassette) systems ABC transporter permeases 58 ABC transporter permeases, major family 50 ABC transporter permeases, FecCD family 6 ABC transporter ATPases 75 Membrane fusion proteins 15 Outer membrane factor (OMF) proteins 4 Periplasmic binding proteins 47 Periplasmic binding proteins, OppA family 9 Periplasmic binding proteins, HisJ family 10 Periplasmic binding proteins, BtuF family 4 Periplasmic binding proteins, MalE family 11 Periplasmic binding proteins, RbsB family 8 Periplasmic binding proteins, ProX family 3 Individual ABC transporter systems ABC importers ThiBPQ thiamine ABC transporter 3 FhuABCD iron-ferrichrome ABC transport system 4 MetNIQ L,D-methionine ABC transpotrer 3 TauABC taurine ABC transporter 3 Defective ABC importers AfuB'C defective ferric ABC transporter 2 ABC exporters MdlAB multidrug ABC exporter 2 ABC transporter permease-ATPases 3 Model Membranes Inner Membrane Inner Membrane Proteome 807 IMemProt-C IN(Exp) 395 IMemProt-C OUT(Exp) 119 IMemProt-C IN(Pred) 85 IMemProt-C OUT(Pred) 14 IMemProt Pred 124 IMem_Loc_2DMS 78 Outer Membrane Outer Membrane Proteome FimD Usher Family Paralogs 11 Murein biosynthesis and degradation Penicillin Binding Proteins 11 Murein hydrolases 21 Murein synthases 6 L,D-transpeptidases 5 Thiol Redox System 10 SecY Translocon 12 Microbiology: Biofilms Biofilm Competitive Fitness 190 Biofilm-Important Genes 114 Planktonic-Important Genes 76 Biofilm Defective Mutants 110 Bacterial Growth Stress Responses Stringent response and growth rate control 3 Growth Media Cell division Mouse Gut Colonization Cyclic-di-GMP Signaling 2 Diguanylate cyclase 19 Cyclic-di-GMP phosphodiesterase 17 Dual GGDEF/EAL domain proteins 7 Cell Surface Chemotaxis Motility and Flagella L-forms Optical Tweezers Cell Shape Cell Adhesion Autotransporters 14 Cell Fusion Microinformatics Whole Cell Modeling E. coli Websites RNA: RNA Products 173 sRNA 61 rRNA 22 tRNA 86 mRNA Codons Codon Usage Start Codons Stop Codons RNA gene-derived Pseudogenes 5 Proteins of RNA Metabolism Ribosomal Proteins 54 Small Ribosomal Proteins 21 Large Ribosomal proteins 33 Ribonucleases Exoribonucleases RNA degradosome 4 Endoribonucleases RNA Modification RNA Methyltransferases Pseudouridine Synthases 11 RNA Chaperones RNA Helicases RNA Polymerase Holenzyme 11 RNAP Core Enzyme 4 RNAP Sigma Factors 7 RNA Biotechnology RNA End Mapping RACE Primer Extension RNA Protection Assays Transcription Start Points flhDC 5'UTR Northern Blots :