PMC:5056897 / 1702-5532 JSONTXT

{"project":"2_test","denotations":[{"id":"27729842-23452293-44840738","span":{"begin":167,"end":168},"obj":"23452293"},{"id":"27729842-25278678-44840739","span":{"begin":361,"end":362},"obj":"25278678"},{"id":"27729842-6145023-44840740","span":{"begin":538,"end":539},"obj":"6145023"},{"id":"27729842-8903587-44840741","span":{"begin":541,"end":542},"obj":"8903587"},{"id":"27729842-9252185-44840742","span":{"begin":544,"end":545},"obj":"9252185"},{"id":"27729842-25052757-44840743","span":{"begin":734,"end":735},"obj":"25052757"},{"id":"27729842-24011239-44840744","span":{"begin":737,"end":738},"obj":"24011239"},{"id":"27729842-24363507-44840745","span":{"begin":1038,"end":1039},"obj":"24363507"},{"id":"27729842-25949992-44840746","span":{"begin":1041,"end":1042},"obj":"25949992"},{"id":"27729842-24833876-44840747","span":{"begin":1044,"end":1046},"obj":"24833876"},{"id":"27729842-25167940-44840748","span":{"begin":1147,"end":1149},"obj":"25167940"},{"id":"27729842-25639461-44840749","span":{"begin":1151,"end":1153},"obj":"25639461"},{"id":"27729842-25743791-44840750","span":{"begin":1155,"end":1157},"obj":"25743791"},{"id":"27729842-11218379-44840751","span":{"begin":1338,"end":1340},"obj":"11218379"},{"id":"27729842-9252185-44840752","span":{"begin":1393,"end":1394},"obj":"9252185"},{"id":"27729842-25894582-44840753","span":{"begin":1954,"end":1956},"obj":"25894582"},{"id":"27729842-25985983-44840754","span":{"begin":1958,"end":1960},"obj":"25985983"},{"id":"27729842-26076386-44840755","span":{"begin":2064,"end":2066},"obj":"26076386"},{"id":"27729842-26303422-44840756","span":{"begin":2068,"end":2070},"obj":"26303422"},{"id":"27729842-24704023-44840757","span":{"begin":3232,"end":3234},"obj":"24704023"},{"id":"27729842-24391926-44840758","span":{"begin":3396,"end":3398},"obj":"24391926"}],"text":"Introduction\nHelicobacter pylori is a Gram-negative bacteria that is associated with several gastric problems in human. It is a slow growing microaerophilic bacteria [1]. Its spiral shape flagellated body helps in locomotion and invasion on the host cells. It belongs to the class of bacteria that are responsible for most common bacterial infections in human [2]. It is adapted to the acidic gastric environment for survival. It is also indigenous to the worldwide human population. It was first isolated by Marshall and Warren in 1984 [3, 4, 5]. Prolonged infection of the organism can be transformed into a chronic infection that causes severe gastric diseases such as duodenal ulcer, gastric ulcer, gastric lymphonema and cancer [6, 7]. Nonchronic infection of the bacteria is usually asymptomatic. There is usually no development of clinical disease observed in the infected person. The prevalence of infection is also guided by the variations in geographical conditions, age, race, and socioeconomic status of the infected persons [8, 9, 10]. A person having bacterial infection at an early age is more prone to develop a chronic infection [11, 12, 13]. H. pylori infection in developing countries is higher in comparison to the developed countries. The reason behind this may be poor hygiene practices in the developing countries [14].\nThe H. pylori genome was first sequenced in 1997 [5]. The genome of H. pylori 26695 strain (NC_000915.1) contains 1,555 coding genes and 65 pseudogenes. The GC content of the genome is 38.9%. The coding genes in the genome encode 1,445 proteins, seven rRNAs, and 36 tRNAs. The genome contains 340 predicted gene products characterized as hypothetical proteins (HPs).\nIn this study, we have analyzed the sequences of all the HPs from H. pylori to assign probable functions. The objective is to identify putative virulence proteins in the proteome that help in pathogenesis. We have used an established protocol [15, 16] for the function prediction of the HPs that comprises leading bioinformatics tools and databases [17, 18, 19]. The analysis goes in a systematic way of predicting physicochemical properties of the proteins using ProtParam. Then, subcellular localization using different programs is carried out to assist the function prediction. Identification of transmembrane helices (TMHs) in the HPs to find out membrane protein is carried out using TMHMM and HMMTOP. We have analyzed the HPs for similarity searching using Basic Local Alignment Search Tool (BLAST). Protein-protein interaction is helpful in assessing the function of novel proteins. We have used Search Tool for the Retrieval of Interacting Genes (STRING) database for predicting protein-protein interaction networks for the HPs. The classification of the HPs is done using CATH, Structural Classification of Proteins (SCOP), Pfam, SVMProt, and Protein Analysis through Evolutionary Relationships (PANTHER) database. Conserved domain discovery and motif search in the HPs are carried out using Conserved Domain Architecture Retrieval Tool (CDART), Simple Modular Architecture Research Tool (SMART), InterProScan, and Motif, respectively. We have made final predictions on the basis of a consensus approach [20, 21, 22]. The putative function predicted by four or more programs for an HP is considered the probable function of that HP with high precision and high confidence [17, 23]. Finally, we have successfully assigned putative functions to 104 HPs out of 340 HPs with high precision. Furthermore, we have classified proteins on the basis of their involvement in the various biological process and predicted molecular functions into diverse functional groups such as enzymes, binding proteins, transporters, and proteins involved in cellular processes and into the proteins exhibiting miscellaneous functions."}