GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.

Have any questions? Please email us at ecoliwiki@gmail.com

Category:Team Pterodactyl

From GONUTS
Jump to: navigation, search
StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableHELPY:URE23Kpadda1, Team Pterodactyl2012-11-18 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
acceptableHELPY:UREFKpadda1, Team Pterodactyl2012-11-18 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:HMCTKpadda1, Team Pterodactyl2012-11-18 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:AMIEKpadda1, Team Pterodactyl2012-11-18 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
acceptableHELPX:COPA2Kpadda1, Team Pterodactyl2012-11-18 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
requireschangesHELPY:FLIDKpadda1, Team Pterodactyl2012-11-18 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
acceptableHELPY:FLIDKpadda1, Team Pterodactyl2012-11-18 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
acceptableHELPY:FLIDKpadda1, Team Pterodactyl2012-11-18 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:CATAKpadda1, Team Pterodactyl2012-11-18 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
requireschangesHELPY:AMIFKpadda1, Team Pterodactyl2012-11-18 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:HCPAKpadda1, Team Pterodactyl2012-11-18 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
acceptableHELPY:HCPBKpadda1, Team Pterodactyl2012-11-18 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
requireschangesKLEPN:BLAN1Kpadda1, Team Pterodactyl2012-11-18 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
acceptableHAEIF:LIC2BHwang3, Team Pterodactyl2012-11-16 22:38:38 CSTGO:0016757 transferase activity, transferring glycosyl groups (F)PMID:21357723ECO:0000315 mutant phenotype evidence used in manual assertion

Table 3&4. Examination of carbohydrate modification by negative-ion CE-ES-MS. Comparison of lic2B mutant to wildtype reveals structural dissimilarities. Sugar composition analysis indicated that the lic2B mutant LOS was devoid of galactose in its outer core, in contrast to that of the wildtype.

challenge
unacceptableHAEI6:E4QVW6Hwang3, Team Pterodactyl2012-11-16 22:10:24 CSTGO:0006355 regulation of transcription, DNA-dependent (Figure 2: fis is necessary for nutrient upshift activation of the vapBC-1 promoter driving lacZ. )PMID:22427824IMP: Inferred from Mutant Phenotype
challenge
acceptableHAEI8:VAPC1Hwang3, Team Pterodactyl2012-11-16 21:50:32 CSTGO:0004540 ribonuclease activity (F)PMID:17496075ECO:0000314 direct assay evidence used in manual assertion

Figure 7A. Total RNA from E. coli K-12 or H. influenzae strain 86-028NP was used as the substrate in RNase activity assays with increasing amounts of the purified VapC-1 toxin. As shown, RNA bands diminish with increasing VapC-1 concentration.

challenge
acceptableHAEI8:Q4QL75Hwang3, Team Pterodactyl2012-11-16 21:00:58 CSTGO:0015886 heme transport (P)PMID:21441512ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A. Shows that a functional sapC permease is required for normal growth of NTHI because the sapC-deficient mutant was unable to utilize heme as an iron source

challenge
acceptableHAEI8:Q4QL74Hwang3, Team Pterodactyl2012-11-16 20:59:05 CSTGO:0015886 heme transport (P)PMID:21441512ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4A. Shows that a functional sapB permease is required for normal growth of NTHI because the sapB-deficient mutant was unable to utilize heme as an iron source

challenge
requireschangesHAEI8:Q4QL73Hwang3, Team Pterodactyl2012-11-16 20:07:12 CSTGO:0015886 heme transport (P)PMID:21441512ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3A&B. The iron-starved parent strain was unable to grow when subcultured in heme-depleted medium, which indicated that the microorganism was sufficiently starved of all internal iron stores. Parent strain growth was restored, however, when the strain was subcultured in the presence of heme. Although the SapA-deficient strain demonstrated growth comparable to that of the parent in a heme-replete

environment, following iron starvation, the cells were unable to utilize heme for growth.

challenge
requireschangesHAEI8:Q4QNB1Hwang3, Team Pterodactyl2012-11-16 11:20:52 CSTGO:0042710 biofilm formation (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI comF mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNB0Hwang3, Team Pterodactyl2012-11-16 11:19:44 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI comE mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNA9Hwang3, Team Pterodactyl2012-11-16 11:18:57 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI comD mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNA8Hwang3, Team Pterodactyl2012-11-16 11:15:59 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A&B. NTHI comC mutants had significantly reduced biofilm thickness and biomass compared to the wildtype.

challenge
acceptableHAEI8:Q4QNA8Hwang3, Team Pterodactyl2012-11-16 11:15:59 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI comC mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNA6Hwang3, Team Pterodactyl2012-11-16 11:12:20 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI comA mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP6Hwang3, Team Pterodactyl2012-11-16 11:07:27 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A&B. NTHI pilC mutants had significantly reduced biofilm thickness and biomass compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP7Hwang3, Team Pterodactyl2012-11-16 11:04:43 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A&B. NTHI pilD mutants had significantly reduced biofilm thickness and biomass compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP7Hwang3, Team Pterodactyl2012-11-16 11:04:43 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI pilD mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP6Hwang3, Team Pterodactyl2012-11-16 11:02:12 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI pilC mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP5Hwang3, Team Pterodactyl2012-11-16 10:51:01 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A&B. NTHI pilB mutants had significantly reduced biofilm thickness and biomass compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP5Hwang3, Team Pterodactyl2012-11-16 10:51:01 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI pilB mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP4Hwang3, Team Pterodactyl2012-11-16 10:38:27 CSTGO:0052001 Type IV pili-dependent localized adherence to host (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3. NTHI pilA mutants had significant adherence defects on normal human bronchial epithelial cells compared to the wildtype.

challenge
acceptableHAEI8:Q4QNP4Hwang3, Team Pterodactyl2012-11-16 10:38:27 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22328674ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A&B. NTHI pilA mutants had significantly reduced biofilm thickness and biomass compared to the wildtype.

challenge
acceptableORYSJ:I7HHE1Hwang3, Team Pterodactyl2012-11-16 09:40:38 CSTGO:0015693 magnesium ion transport (P)PMID:22732245ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 7A. Al Enhanced Mg uptake in wild type, but not in OsMGT1 knockout lines

challenge
acceptableHAEI8:Q4QL77Hwang3, Team Pterodactyl2012-11-15 23:15:37 CSTGO:1900231 regulation of single-species biofilm formation on inanimate substrate (P)PMID:22919633ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows that the SapF-deficient mutant resulted in a thicker, more robust biofilm tower formation compared to the parent strain.

challenge
acceptableTOXGO:RHBL4Hwang3, Team Pterodactyl2012-11-15 22:21:55 CSTGO:0060352 cell adhesion molecule production (P)PMID:20421941ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 7B. Shedding of MIC2 into the supernatant is decreased in the TgROM4 conditional knockout.

challenge
acceptableTOXGO:RHBL4Hwang3, Team Pterodactyl2012-11-15 22:12:20 CSTGO:0030260 entry into host cell (P)PMID:20421941ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3A. Suppression of TgROM4 results in impaired invasion of host cells

challenge
requireschangesHELPY:FLAAKpadda1, Team Pterodactyl2012-11-04 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
requireschangesHELPY:FLAAKpadda1, Team Pterodactyl2012-11-04 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:FLABKpadda1, Team Pterodactyl2012-11-04 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
acceptableECOLI:FABHKpadda1, Team Pterodactyl2012-11-04 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
requireschangesHELPJ:Q9ZMR6Kpadda1, Team Pterodactyl2012-11-04 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
unacceptableECOLI:FADRKpadda1, Team Pterodactyl2012-10-20 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:FADRKpadda1, Team Pterodactyl2012-10-20 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
requireschangesBACSU:ACPHwang3, Team Pterodactyl2012-10-07 17:57:12 CDTGO:0034305 regulation of asexual sporulation (P)PMID:19850612ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 6 shows that in the absence of ACP, sporulation efficiency was dramatically lower than in the presence of ACP

challenge
acceptableECOLI:FADRKpadda1, Team Pterodactyl2012-10-07 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
acceptableHAEIN:ARCAHwang3, Team Pterodactyl2012-09-23 17:55:50 CDTGO:0006355 regulation of transcription, DNA-dependent (P)PMID:17542927ECO:0000315 mutant phenotype evidence used in manual assertion

Table 1. shows that genes coding for respiratory chain dehydrogenases increased in expression for the arcA mutant

challenge
requireschangesECOLI:ARCBHwang3, Team Pterodactyl2012-09-23 16:07:31 CDTGO:0004673 protein histidine kinase activity (F)PMID:22666479ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A. shows that the formation of ArcB mutants by substituting leucine to valine across the leucine zipper motif adversely affects both kinase and phosphotase activity in the ArcB protein.

challenge
acceptableECOLI:ARCBHwang3, Team Pterodactyl2012-09-23 15:20:36 CDTGO:0046777 protein autophosphorylation (P)PMID:20097862ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1. shows in vitro autophosphorylation reactions of ArcB

challenge


CACAO assessment

  • What do the icons in the status column mean?
cacao icons.jpg

Pages in category "Team Pterodactyl"

The following 2 pages are in this category, out of 2 total.


Jump to pages starting with: H K