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User:Kpadda1

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My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableECOLI:FADR2012-10-07 16:13:33 CDTGO:0019217 regulation of fatty acid metabolic process (P)PMID:11566998ECO:0000316 genetic interaction evidence used in manual assertion

Table 3: fabA mutants compromised in catalytic efficiency are synthetically lethal with null fadR mutations. fabB mutants compromised in catalytic efficiency are also synthetically lethal with null fadR mutations.

challenge
unacceptableECOLI:FADR2012-10-20 22:26:38 CDTGO:0045723 positive regulation of fatty acid biosynthetic process (P)PMID:11566998ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1: fadR null mutants were shown to be significantly more susceptible than wild-type strains to cerulenin, a specific 3-ketoacyl-ACP synthase inhibitor. The fatty acid biosynthetic genes fabB and fabF both code for 3-ketoacyl-ACP synthases, but FabB (synthase I) is sevenfold more sensitive than FabF (synthase II) to cerulenin in vitro.

challenge
acceptableECOLI:FADR2012-10-20 22:25:24 CDTGO:0045723 positive regulation of fatty acid biosynthetic process (P)PMID:11566998ECO:0000315 mutant phenotype evidence used in manual assertion

Results under heading "Decreased expression of fabB in fadR strains": The promoter of the fatty acid biosynthetic gene fabB was transcriptionally fused with a promoterless CAT gene. CAT confers resistance to chloramphenicol. A strain with the transcriptional fusion and a fadR null mutation tolerated significantly lower levels of chloramphenicol than the strain with the transcriptional fusion and a functional fadR gene.

challenge
requireschangesHELPJ:Q9ZMR62012-11-04 13:36:24 CSTGO:0006351 transcription, DNA-dependent (P)PMID:16672598ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2: pH-responsive transcription of the amidase genes amiE and amiF are mediated mainly by the ArsRS two-component system. ArsS-deficient mutant strains, in which the response regulator ArsR cannot be phosphorylated to affect gene expression (no ArsR~P), showed significantly decreased transcription of amiE and amiF in neutral pH conditions and acidic pH (5.0) conditions compared to wild-type strains.

challenge
acceptableECOLI:FABH2012-11-04 13:55:07 CSTGO:0006631 fatty acid metabolic process (P)PMID:1551888ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: The level of FabH expression is correlated to the overall fatty acid membrane composition.

challenge
requireschangesHELPY:FLAB2012-11-04 15:13:02 CSTGO:0009420 bacterial-type flagellum filament (C)PMID:8501031ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 6: Western blot of flagella shows disappearance of weak band in flaB mutant strains.

challenge
requireschangesHELPY:FLAA2012-11-04 15:20:35 CSTGO:0009420 bacterial-type flagellum filament (C)PMID:8501031ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 6: Western blot of flagella showed the disappearance of the 53-kDa FlaA band in the N6 flaA mutant.

challenge
requireschangesHELPY:FLAA2012-11-04 15:20:36 CSTGO:0071978 bacterial-type flagellar swarming motility (P)PMID:8501031ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 7: Bacterial colonies of flaA mutants were completely nonmotile across a solid surface.

challenge
requireschangesKLEPN:BLAN12012-11-18 13:47:15 CSTGO:0046677 response to antibiotic (P)PMID:19770275ECO:0000314 direct assay evidence used in manual assertion

Table 1: bla(NDM-1) from K. pneumoniae was inserted into E. coli strains, conferring resistance to several antibiotics.

challenge
acceptableHELPY:HCPB2012-11-18 14:05:25 CSTGO:0008800 beta-lactamase activity (F)PMID:11777911ECO:0000314 direct assay evidence used in manual assertion

Table 1: Purified HcpB hydrolyzes several antibiotics by opening of the beta-lactam ring, which was monitored by absorption variation.

challenge
acceptableHELPY:HCPA2012-11-18 14:11:16 CSTGO:0008800 beta-lactamase activity (F)PMID:10748053ECO:0000314 direct assay evidence used in manual assertion

Table 2: Purified HcpA demonstrates the ability to hydrolyze several beta-lactam antibiotics.

challenge
requireschangesHELPY:AMIF2012-11-18 14:53:17 CSTGO:0006807 nitrogen compound metabolic process (P)PMID:11359566ECO:0000315 mutant phenotype evidence used in manual assertion

Table 3: An amiF-deficient mutant strain showed decreased formamidase activity, which was measured by the rate of formation of ammonia. The residual formamidase activity was accounted for by the urease genes ureA and ureB. A mutant strain that was deficient in ureA, ureB, and amiF showed no formamidase acitivty.

challenge
acceptableHELPY:CATA2012-11-18 15:26:34 CSTGO:0042744 hydrogen peroxide catabolic process (P)PMID:8955320ECO:0000315 mutant phenotype evidence used in manual assertion

Under Results, section "Construction and characterization of catalase-deficient H. pylori mutant strains by transposon shuttle mutagenesis": The insertional inactivation of the chromosomal katA gene completely abolished catalase activity, which was measured by the disappearance of hydrogen peroxide. The wild-type strain (which contained katA but lacked known catalases) produced a high level of specific catalase activity (4,422 U/mg), but the katA mutant revealed only background activity (5 U/mg).

challenge
acceptableHELPY:FLID2012-11-18 16:24:03 CSTGO:0071978 bacterial-type flagellar swarming motility (P)PMID:10559162ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5: Motility testing of H. pylori wild-type and isogenic fliD mutant strains revealed that the wild-type strain formed colonies with the large diffuse spreading halo typical of motile bacteria, while the fliD mutant strain showed no apparent motility (produced small and and sharply delineated colonies).

challenge
acceptableHELPY:FLID2012-11-18 16:29:20 CSTGO:0009288 bacterial-type flagellum (C)PMID:10559162ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3: In wild-type cells, full length sheathed flagella are observed. Within the wild-type flagellar sheath, filaments are elongated to the tips of the flagella and terminal bulbs are observed. In the fliD mutant, truncated flagella are observed and terminal bulbs are not apparent. Filament elongation is not observed in the fliD mutant.

challenge
requireschangesHELPY:FLID2012-11-18 16:37:48 CSTGO:0007155 cell adhesion (P)PMID:10559162ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: No H. pylori cells could be recovered from the gastric tissue of the mice inoculated orally with the fliD mutant strain. The researchers recovered 2.23 x 10^5 cells per gram of gastric tissue from the mice inoculated orally with wild-type H. pylori.

challenge
acceptableHELPX:COPA22012-11-18 16:55:02 CSTGO:0006825 copper ion transport (P)PMID:9440521ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: The copA mutant was susceptible to the same concentrations of the divalent cations of Ni, Zn, Co, and Mg as the wild-type strain but had a

different susceptibility to divalent cation of Cu. The wild-type strain had a divalent cation Cu MIC of 50 mM, whereas the mutant had a divalent cation Cu MIC of 7.5 mM, suggesting that the ATPase can function as a copper ion export pump.

challenge
acceptableHELPY:AMIE2012-11-18 17:12:36 CSTGO:0006807 nitrogen compound metabolic process (P)PMID:9364923ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: No amidase activity was detected on propionamide, acrylamide, acetamide, or isobutyramide in the amiE mutant. Amidase activity was measured by the rate of release of ammonia.

challenge
acceptableHELPY:HMCT2012-11-18 17:31:59 CSTGO:0030001 metal ion transport (P)PMID:10417643ECO:0000315 mutant phenotype evidence used in manual assertion

Table 1: Growth of all four cadA mutants was at least 10- fold more sensitive to cadmium and zinc compared with the parental strain. This phenotype could be reversed by the H. pylori CadA expression vector pY178, as demonstrated for H. pylori 439-3[py178] and 13-9[pY178]. Additionally, strains harbouring plasmid pY178 grew in 10-fold to 20-fold higher concentrations of cobalt than the control strains. The increase in cobalt resistance corresponds to the elevated CadA protein content of strains carrying pY178. This evidence suggests that CadA is involved in the transport of these metal ions.

challenge
acceptableHELPY:UREF2012-11-18 17:55:27 CSTGO:0006807 nitrogen compound metabolic process (P)PMID:1313413ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: The ureF mutant showed no urease activity, which was measured by the rate of release of urea.

challenge
acceptableHELPY:URE232012-11-18 17:59:48 CSTGO:0043419 urea catabolic process (P)PMID:1313413ECO:0000315 mutant phenotype evidence used in manual assertion

Table 2: The ureA mutant showed no urease activity, which was measured by the rate of release of urea.

challenge

acceptable:13
unacceptable:1
requires_changes:7
flagged:0

Annotations challenged by Kpadda1

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
requireschangesKelsi.Carlson,
Team Shenanigans
MOUSE:ARBK1GO:0022415 - viral reproductive process (P)PMID:23029581ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
requireschangesColin.taylor,
Team Gene Wilder
HUMAN:SOX2GO:0045289 - luciferin monooxygenase activity (F)PMID:22265740ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
requireschangesColin.taylor,
Team Gene Wilder
MOUSE:SESN2GO:0010255 - glucose mediated signaling pathway (P)PMID:22958918ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
requireschangesPaige.stump,
Team Team
ECOLI:PBP2GO:0009252 - peptidoglycan biosynthetic process (P)PMID:2681889ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
requireschangesCourtney.kast,
Team Team
DROME:SYMMGO:0044429 - obsolete mitochondrial part (C)PMID:22448145ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
acceptableAshley.Carlisle,
Team Shenanigans
RABIT:G1TRT1GO:0035556 - intracellular signal transduction (P)PMID:12885773ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
requireschangesAshley.Carlisle,
Team Shenanigans
9VIRU:Q3HM11GO:0010941 - regulation of cell death (P)PMID:23071821ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
acceptableKatelin.Aisenbrey,
Team Gene Wilder
HUMAN:PA2G5GO:0070374 - positive regulation of ERK1 and ERK2 cascade (P)PMID:22837859ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
acceptableKatelin.Aisenbrey,
Team Gene Wilder
HUMAN:PA2G5GO:0010518 - positive regulation of phospholipase activity (P)PMID:22837859ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorRomero.alan,
Team BTHO PubMed!
DROME:PSNGO:0006915 - apoptotic process (P)PMID:10491396ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2
updatedbyinstructorRomero.alan,
Team BTHO PubMed!
DROME:Q9Y1T2GO:0007399 - nervous system development (P)PMID:10491393ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorRomero.alan,
Team BTHO PubMed!
DROME:Q9Y1T2GO:0009968 - negative regulation of signal transduction (P)PMID:10491393ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2

0 annotations fixed by Kpadda1