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

User:Jason Snow58

From GONUTS
Jump to: navigation, search

CACAO Spring 2020

No annotations for this user (yet.)
See the documentation at Special:CACAO for more information.

My Annotations

Annotations challenged by Jason Snow58

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history

0 annotations fixed by Jason Snow58

CACAO Fall 2019

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptable9CAUD:A0A219YHF32019-09-10 16:15:21 CDTGO:0016798 hydrolase activity, acting on glycosyl bonds (F)PMID:28676686ECO:0005801 enzymatic activity assay evidence used in manual assertion

Figure 3B shows K5-4 purified ORF38 depolymerization activity on bacterial lawn. Figure 3C shows degradation of purified capsule when treated with purified K5-4 ORF38.

UniProtKB: Uncharacterized protein (k54_38).

Organism: Klebsiella phage K5-4

challenge
requireschangesBPT1:SPANU2019-09-17 15:25:02 CDTGO:0045918 negative regulation of cytolysis (P)PMID:30135120ECO:0007699 cell growth assay evidence used in manual assertion

Fig. 4D shows GTG-to-GTC mutations in downstream alternative starts Val 63 and Val 65 cause early onset of lysis.

Isoform gp11a (Q6XQ97-2) V63M

Isoform gp11a' (Q6XQ97-3) V65M

Organism: Escherichia phage T1 (Bacteriophage T1)

challenge
flaggedBPT1:SPANU2019-09-24 16:10:15 CDTGO:0044659 cytolysis by virus of host cell (P)PMID:30135120ECO:0007699 cell growth assay evidence used in manual assertion

Fig 3B. shows PRE plasmids containing the gp11 U-spanin complement MC4100 λRzamRz1am lysogens to rescue the wt lysis phenotype.

Organism: Escherichia phage T1 (Bacteriophage T1)

challenge
acceptableBPM:K7QK872019-10-22 22:58:26 CDTGO:0031224 intrinsic component of membrane (C)PMID:28894177ECO:0006042 cell fractionation evidence used in manual assertion

Supp. Fig. 3 shows presence of LysM in membrane fractions.

UniProtKB - K7QK87 (K7QK87_BPM)

Organism - Enterobacteria phage M (Escherichia levivirus M)

challenge
acceptable9CAUD:A0A494RGB72019-10-23 00:59:14 CDTGO:0044659 cytolysis by virus of host cell (P)PMID:30404215ECO:0001565 cell-based assay evidence

Fig. 7A measures effect of concentration on the the lytic activity of gp41

Fig. 7B measures effect of pH on the lytic activity of gp41

Submitted name in UniProt: N-acetylmuramoyl-L-alanine amidase

UniProtKB - A0A494RGB7 (A0A494RGB7_9CAUD) Organism - Bacillus phage vB_BthS_BMBphi

challenge
acceptableI33A0:M12019-11-12 15:23:35 CSTGO:0071426 ribonucleoprotein complex export from nucleus (P)PMID:10644350ECO:0005804 immunofluorescence evidence used in manual assertion

Fig. 4 shows that infected CHO cells stably expressing M1 are able to export NP to the cytoplasm while infected CHO cells not expressing M1 cannot.

Organism: Influenza A virus (strain A/Wilson-Smith/1933 H1N1) (Influenza A virus (strain A/WS/1933 H1N1))

UniProtKB: P05777 (M1_I33A0) UniProt submitted name: Matrix protein 1

challenge
acceptableI33A0:M12019-11-12 15:42:34 CSTGO:0042025 host cell nucleus (C)PMID:10644350ECO:0005804 immunofluorescence evidence used in manual assertion

Fig. 4 Shows M1 is required for NP export from the host nucleus.

Organism: Influenza A virus (strain A/Wilson-Smith/1933 H1N1) (Influenza A virus (strain A/WS/1933 H1N1))

UniProtKB:P05777 (M1_I33A0) UniProt submitted name: Matrix protein 1

challenge
acceptableI33A0:M12019-11-12 16:20:05 CSTGO:0031224 intrinsic component of membrane (C)PMID:10954572ECO:0007104 co-fractionation evidence used in manual assertion

Fig. 1 shows presence of M1 in cell membrane fraction as analyzed by SDS-PAGE.

Organism: Influenza A virus (strain A/Wilson-Smith/1933 H1N1) (Influenza A virus (strain A/WS/1933 H1N1))

UniProtKB: P05777 (M1_I33A0) UniProt submitted name: Matrix protein 1

challenge
requireschanges9CAUD:A0A1L7DQ032019-11-19 09:23:12 CSTGO:0016787 hydrolase activity (F)PMID:30305030ECO:0000255 match to sequence model evidence used in manual assertion

CwlQ (orf8) shows strong identity to other known hydrolases.

UniProtKB: A0A1L7DQ03 (A0A1L7DQ03_9CAUD) Organism: Vibrio phage Vp670 UniProt submitted name: Endolysin

challenge
acceptable9CAUD:A0A1L7DPV82019-11-19 09:43:08 CSTGO:0019835 cytolysis (P)PMID:30305030ECO:0001165 colony counting evidence used in manual assertion

Fig. 6 shows that recombinantly expressed HolA reduced the survival rate of both E. coli and V. alginolyticus.

UniProtKB: A0A1L7DPV8 (A0A1L7DPV8_9CAUD)

Organism: Vibrio phage Vp670 UniProt submitted name: Holin

challenge
requireschanges9CAUD:A0A1L7DPV82019-11-19 09:51:15 CSTGO:0033644 host cell membrane (C)PMID:30305030ECO:0005649 machine learning prediction of motif instance evidence used in manual assertion

Fig. 5 shows prediction of transmembrane domain at C-terminus by TMHMM and shows a hydrophilic C-terminus by a hydrophilicity analysis.

UniProtKB: A0A1L7DPV8 (A0A1L7DPV8_9CAUD)

Organism: Vibrio phage Vp670 UniProt submitted name: Holin

challenge
acceptableSYNE7:CCMM2019-11-21 19:04:05 CSTGO:0031470 carboxysome (C)PMID:31048338ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion

Fig. 2 and Supp. Fig. 6 show YFP-tagged CcmM is localized in the carboxysomes.

UniProtKB: Q03513 (CCMM_SYNE7)

Organism: Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) UniProt submitted name: Carbon dioxide concentrating mechanism protein CcmM

challenge
acceptableSYNE7:CCMK2019-11-21 19:11:43 CSTGO:0031470 carboxysome (C)PMID:31048338ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion

Fig. 2 and Supp. Fig. 6 show YFP-tagged CcmK4 localized in the carboxysomes.

UniProtKB: Q03511 (CCMK_SYNE7)

Organism: Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) UniProt submitted name: Carbon dioxide-concentrating mechanism protein CcmK

challenge
acceptableSYNE7:CCML2019-11-21 19:15:18 CSTGO:0031470 carboxysome (C)PMID:31048338ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion

Supp. Fig. 6 show YFP-tagged CcmL localized in the carboxysomes.

UniProtKB: Q03512 (CCML_SYNE7)

Organism: Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) UniProt submitted name:Carbon dioxide concentrating mechanism protein CcmL

challenge
acceptableBPP1:ENLYS2019-11-22 22:13:52 CSTGO:0033644 host cell membrane (C)PMID:15090650ECO:0006042 cell fractionation evidence used in manual assertion

Fig. 3 shows presence of Lyz in membrane fraction.

UniProtKB: Q37875 (ENLYS_BPP1)

Organism: Escherichia phage P1 (Bacteriophage P1) UniProt submitted name: SAR-endolysin

challenge
unacceptableBPP1:ENLYS2019-11-22 22:23:43 CSTGO:0033646 host intracellular part (C)PMID:15090650ECO:0006042 cell fractionation evidence used in manual assertion

Fig. 3 shows presence of Lyz in soluble fraction.

UniProtKB: Q37875 (ENLYS_BPP1)

Organism: Escherichia phage P1 (Bacteriophage P1) UniProt submitted name: SAR-endolysin

challenge
acceptableBPP1:ENLYS2019-11-22 22:31:11 CSTGO:0042597 periplasmic space (C)PMID:15090650ECO:0006042 cell fractionation evidence used in manual assertion

Fig. 3B shows presence of Lyz in periplasmic fractions.

UniProtKB: Q37875 (ENLYS_BPP1)

Organism: Escherichia phage P1 (Bacteriophage P1) UniProt submitted name: SAR-endolysin

challenge
acceptableBPP1:ENLYS2019-11-22 22:44:47 CSTGO:0019835 cytolysis (P)PMID:15090650ECO:0007699 cell growth assay evidence used in manual assertion

Fig. 1A shows culture clearing after induction of recombinant Lys in XL1-Blue cells.

UniProtKB: Q37875 (ENLYS_BPP1)

Organism: Escherichia phage P1 (Bacteriophage P1) UniProt submitted name: SAR-endolysin

challenge
acceptableBPPRD:P52019-11-23 16:44:24 CSTGO:0060187 cell pole (C)PMID:24291253ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion

Fig. 3 shows eYFP-P5 protein fusions localize at cell poles.

UniProtKB: P22536 (P5_BPPRD)

Organism: Enterobacteria phage PRD1 (Bacteriophage PRD1) UniProt submitted name: Spike protein P5

challenge
acceptableBPPRD:VP312019-11-23 16:51:43 CSTGO:0060187 cell pole (C)PMID:24291253ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion

Fig. 3 shows that eYFP-P31 protein fusion localizes at the cell pole.

UniProtKB: P27384 (VP31_BPPRD)

Organism: Enterobacteria phage PRD1 (Bacteriophage PRD1) UniProt submitted name: Penton protein P31

challenge
acceptableBPKMV:ENLYS2019-11-23 17:09:02 CSTGO:0044659 cytolysis by virus of host cell (P)PMID:21687532ECO:0007699 cell growth assay evidence used in manual assertion

Fig. 2A shows that induced recombinant KMV45 causes lysis of culture.

UniProtKB: Q7Y2C0 (ENLYS_BPKMV)

Organism: Pseudomonas phage phiKMV UniProt submitted name: SAR-endolysin

challenge

acceptable:16
unacceptable:1
requires_changes:3
flagged:1

Annotations challenged by Jason Snow58

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
requireschangesKFaye0721,
Team-age Mutant Ninja Turtles
ECOLI:MURJGO:0031224 - obsolete intrinsic component of membrane (C)PMID:28894177ECO:0006005 fractionation evidence used in manual assertionchallengeC: 1

0 annotations fixed by Jason Snow58

What do the icons mean in the status column?

assessment icons.jpg