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 DirtyChubi

From GONUTS
Jump to: navigation, search
StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableBPSPP:Q38152Flounlackerkm, Team DirtyChubi2016-05-11 08:10:51 CDTGO:1990077 primosome complex (C)PMID:18157148ECO:0000314 direct assay evidence used in manual assertion

figure 1 shows the hexameric structure of the SPP1 helicase, determined with x-ray crystallography. Helicase binds to and unwinds the DNA prior to replication, and in complex with primase, puts down the DNA primer to initiate replication. Figure 4d shows the binding of primase and helicase into a complex by gel shift, in the presence of primase the helicase complexes with the primase and migrates more slowly and a shorter distacne through the gel than in the absence of primase. Only the full length helicase is able to form a complex with primase. Helicase binds to and unwinds the DNA prior to replication, and in complex with primase, puts down the DNA primer to initiate replication. When mutated the protein does no properly function and complex with primase to activate primase and initiate replication. Table 1 shows the series of deletions and mutations done to assess the helicase and ATPase activity in the presence and absence primase. In the presence of primase, the ATPase activity more than doubles (1 to 2.3) and the helicase activity quadruples (1 to 4.6).

challenge
updatedbyinstructor9BACI:A0A0K9GSD2Flounlackerkm, Team DirtyChubi2016-05-08 16:14:30 CDTGO:0036121 double-stranded DNA-dependent ATP-dependent DNA helicase activity (F)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

blastp e-value of 1.6e-157, query coverage of 98.87, and percent identity of 54.9%

challenge
updatedbyinstructorSTREE:A0A0U0BZQ2Flounlackerkm, Team DirtyChubi2016-05-08 16:09:43 CDTGO:0036121 double-stranded DNA helicase activity (F)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

blastp e-value of 1.4e-144, query coverage of 99.32, with a percent identity of 51.4%

challenge
updatedbyinstructorBPT7:DPOLStrandquistg, Team DirtyChubi2016-04-27 10:45:56 CDTGO:0004529 exodeoxyribonuclease activity (F)PMID:1846298ECO:0000315 mutant phenotype evidence used in manual assertion

Table 3 (specifically k_exo) compares the rates of exonuclease activity between the wild-type enzyme (105 1/s) and mutant enzyme (6.9e-4 1/s), revealing that the wild-type exonuclease rates are dramatically higher than that of the mutant enzyme's exonuclease rates. This shows that this domain of DNA polymerase has exonuclease activity.

challenge
unacceptable9CAUD:A0A024B251Snyderjr2, Team DirtyChubi2016-04-25 10:22:09 CDTGO:0098027 virus tail, sheath (C)GO_REF:00000100ECO:0000255 match to sequence model evidence used in manual assertion

HHpred gives a probability of 99.8 and and an e-value of 4.5E-20

challenge
updatedbyinstructorBPSPP:Q38152Flounlackerkm, Team DirtyChubi2016-04-25 10:13:47 CDTGO:0006268 DNA unwinding involved in DNA replication (P)PMID:18157148ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows the effect of mutated residues on the protein and how the mutations effect the binding ability of the protein to primase using gel electrophoresus. Helicase binds to and unwinds the DNA prior to replication, and in complex with primase, puts down the DNA primer to initiate replication. When mutated the protein does no properly function and complex with primase to activate primase and initiate replication.

Table 1 shows the series of deletions and mutations done to assess the helicase and ATPase activity in the presence and absence primase. DeltaN92 is the first series of deletions performed, deleting amino acids 1 to 92, this mutation decreased the DNA unwinding ability of the protein from 100% to 66% activity. DeltaN112 deleted amino acids 1-112. This deletion caused the DNA unwinding ability of helicase to stop almost completely, with a drop from 100% activity to 3% activity with this deletion. The double point mutation mt1 changed the amino acids I121A and E122A, resulting in a decrease in helicase activity to 7%.

challenge
updatedbyinstructor9CAUD:W8EEZ1Flounlackerkm, Team DirtyChubi2016-04-25 09:42:18 CDTGO:0036121 double-stranded DNA-dependent ATP-dependent DNA helicase activity (F)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

blastp e value of 1.8e-171, with percent identity of 57.6%, and query coverage of 99.54%

challenge
updatedbyinstructor9CAUD:A0A024B0U5Strandquistg, Team DirtyChubi2016-04-24 01:41:58 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

This is a transfer annotation made from a bacillus anthracis gene with a regular annotation previously made on it, see: http://gowiki.tamu.edu/wiki/index.php/BACAN:Q81WA9 Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 6.2e-34. The e-value from blastp is 2e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.

challenge
unacceptable9CAUD:A0A0K2FL53Strandquistg, Team DirtyChubi2016-04-24 01:34:01 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)other:GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

This is a transfer annotation made from a bacillus anthracis gene with a regular annotation previously made on it, see: http://gowiki.tamu.edu/wiki/index.php/BACAN:Q81WA9

Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 6.2e-34. The e-value from blastp is 2e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved.

challenge
updatedbyinstructorBPSPP:Q38152Flounlackerkm, Team DirtyChubi2016-04-11 11:32:59 CDTGO:0036121 double-stranded DNA-dependent ATP-dependent DNA helicase activity (F)PMID:18157148ECO:0000315 mutant phenotype evidence used in manual assertion

Fig 4, Table 1.

challenge
updatedbyinstructor9CAUD:A0A024B2H2Strandquistg, Team DirtyChubi2016-04-11 09:29:30 CDTGO:0051672 catabolism by organism of cell wall peptidoglycan in other organism (P)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 1e-33.

The e-value from blastp is 1e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved. The domain for the peptidoglycan should be annotated separately.

challenge
updatedbyinstructor9CAUD:A0A024B2H2Strandquistg, Team DirtyChubi2016-04-11 09:24:42 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

Fulfilling the minimum requirements for using GO_REF:0000100, the probability from hhpred is 100% and the e-value is 1e-33.

The e-value from blastp is 1e-50. Note that I am annotating the catalytic domain and for this domain the blastp and hhpred criteria are achieved. The domain for the peptidoglycan should be annotated separately.

challenge
updatedbyinstructorBACAN:Q81WA9Strandquistg, Team DirtyChubi2016-04-06 12:23:13 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)PMID:16103125ECO:0000314 direct assay evidence used in manual assertion

PlyL is an endolysin enzyme with 2 separate domains, an N-terminal catalytic domain, and a C-terminal cell wall binding domain. This annotation is for the N-terminal domain of PlyL.

Peptidoglycan from B. subtilis was subjected to both the full-length PlyL and the N-terminal domain only. In supplemental figure 1, (see link: http://www.jbc.org/content/suppl/2005/08/16/M502723200.DC1/Suppdata.pdf) the amount of 2,4-dinitrophenyl-alanine is shown to increase sharply, indicating that PlyL is an N-acetylmuramoyl-L-alanine amidase. Additionally, the figure shows that alanine is increased even more when the N-terminal domain alone is used, compared to the full-length protein.

As additional support that PlyL is an amidase, figure 2 compares the crystal structure of PlyL to other known amidase enzymes.

Figure 4 shows a time course assay where the purified endolysin (PlyL) was able to lyse 4 different bacillus species cultures within 400 seconds.

In 4a, the lysing capabilities of the full-length version of PlyL are shown. In 4b, the lysing capabilities of the N-terminal portion only are shown. The N-terminal domain by itself is more effective at cleaving Bacillus species than the entirety of PlyL.

challenge
updatedbyinstructorBACAN:Q81WA9Strandquistg, Team DirtyChubi2016-04-06 12:23:13 CDTGO:0051672 catabolism by organism of cell wall peptidoglycan in other organism (P)PMID:16103125ECO:0000314 direct assay evidence used in manual assertion

Peptidoglycan from B. subtilis was subjected to both the full-length PlyL and the N-terminal domain only. In supplemental figure 1, (see link: http://www.jbc.org/content/suppl/2005/08/16/M502723200.DC1/Suppdata.pdf) the amount of 2,4-dinitrophenyl-alanine is shown to increase sharply, indicating that PlyL is an N-acetylmuramoyl-L-alanine amidase. Additionally, the figure shows that alanine is increased even more when the N-terminal domain alone is used, compared to the full-length protein.

challenge

What do the icons mean in the status column?

assessment icons.jpg

Pages in category "Team DirtyChubi"

The following 3 pages are in this category, out of 3 total.


Jump to pages starting with: F S