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Category:Team Atlantis

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableBPA51:Q37916Vishwanathk, Team Atlantis2016-05-06 05:42:49 CDTGO:0098027 virus tail, sheath (C)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

The blast data shows a 98% coverage and a 42% identity to a tail sheath protein precursor in Eyuki. Also, the e-value is 7e-142.

challenge
unacceptable9CAUD:A0A0K2D0H8Vishwanathk, Team Atlantis2016-05-06 05:22:54 CDTGO:0008233 peptidase activity (F)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

The blast data shows that there is a 95% coverage and a 58% identity to a prohead protease gene in Moonbeam. Also, the e-value is 3e-102.

challenge
unacceptable9CAUD:A0A0K2D000Vishwanathk, Team Atlantis2016-05-06 01:26:55 CDTGO:0004146 dihydrofolate reductase activity (F)other:GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

The blast data for this sequence from Eyuki matches the diydrofolate reductase gene on TsarBomba. This data shows an e-value of 7e-41, an identity match of 46%, and a coverage of 98%.

challenge
acceptableBPT4:END7Vishwanathk, Team Atlantis2016-05-02 20:50:37 CDTGO:0004519 endonuclease activity (F)PMID:2269300ECO:0000314 direct assay evidence used in manual assertion

The enzyme endonuclease VII cleaves the DNA into smaller pieces. This article presents a figure (3a and 3b) that shows the enzyme activity of endonuclease VIIcl (cl = clone, Y-axis) versus the sedimentation centrifugation fraction (including inset with fraction for molecular masses of each marker protein used). The activity of the endnuclease VIIcl enzyme is shown to be in between the appropriate masses of each protein (monomer and aggregated forms) used in the sedimentation experiment.

challenge
unacceptableECOLX:M8QE87Gardneret2, Team Atlantis2016-04-28 11:31:07 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableSHIFL:A0A0F6E7R1Gardneret2, Team Atlantis2016-04-28 11:31:03 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:E3XLA9Gardneret2, Team Atlantis2016-04-28 11:30:58 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:A0A073W4B8Gardneret2, Team Atlantis2016-04-28 11:30:06 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableSHIFL:I6HB10Gardneret2, Team Atlantis2016-04-28 11:27:50 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:M2PXW9Gardneret2, Team Atlantis2016-04-28 11:26:53 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:H9UN41Gardneret2, Team Atlantis2016-04-28 11:25:58 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableSHIBS:Q326I5Gardneret2, Team Atlantis2016-04-28 11:24:35 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:A0A062YH18Gardneret2, Team Atlantis2016-04-27 23:28:49 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:A0A070UWT2Gardneret2, Team Atlantis2016-04-27 22:28:59 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:H4JXW8Gardneret2, Team Atlantis2016-04-27 22:25:28 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:V6G243Gardneret2, Team Atlantis2016-04-27 22:24:09 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:A0A070U7Z1Gardneret2, Team Atlantis2016-04-27 16:53:42 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOSE:B6HZ29Gardneret2, Team Atlantis2016-04-27 16:51:55 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECO1A:C8UGR7Gardneret2, Team Atlantis2016-04-27 11:47:14 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableECOLX:A0A029N4F6Gardneret2, Team Atlantis2016-04-27 11:45:27 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:K3K3U9Gardneret2, Team Atlantis2016-04-27 10:50:26 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECO45:B7MAH1Gardneret2, Team Atlantis2016-04-27 10:49:24 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results show 100% sequence match with an e-value of 1.1E-114

challenge
unacceptableECOLX:A0A026S6B3Gardneret2, Team Atlantis2016-04-27 10:47:52 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableECOLX:D6J5R1Gardneret2, Team Atlantis2016-04-27 10:47:04 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptableSHIDY:F3V116Gardneret2, Team Atlantis2016-04-27 10:46:18 CDTGO:0004146 dihydrofolate reductase activity (Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.)GO_REF:0000002ISA: Inferred from Sequence Alignment PMID:26147643

UniProtKB:P0ABQ4

challenge
unacceptableBPT4:PORTLYachuwbg, Team Atlantis2016-04-27 10:34:45 CDTGO:0046718 viral entry into host cell (P)PMID:24126213ECO:0000314 direct assay evidence used in manual assertion

This protein aids in head assembly, genome packaging, and genome injection. The most common function is of a portal protein that aids in infection by forming a channel, connecting the phage to the membrane of the host bacteria. See Figure 5 for complete outline and analysis of function.

challenge
updatedbyinstructor9CAUD:Q8H9R7Yachuwbg, Team Atlantis2016-04-27 09:53:59 CDTGO:0043493 viral terminase complex (C)PMID:23011306ECO:0000314 direct assay evidence used in manual assertion

The terminase function in this phage requires both of the proteins p01 and p03. The p01 protein in this phage corresponds to the small subunit of terminase, while p03 corresponds to the large subunit of terminase. Although p03 can function without p01, p01 cannot function without p03. However, the endonucleolytic activity of p03 functions more effectively with the presence of p01. Thus exhibiting a cos-dependent endonucleolytic activity. See Figure 3

challenge
updatedbyinstructor9CAUD:Q8H9R7Yachuwbg, Team Atlantis2016-04-27 09:39:39 CDTGO:0016887 ATPase activity (F)PMID:23011306ECO:0000314 direct assay evidence used in manual assertion

ATPase Activity has been found to be largely associated with the large subunit in terminase in this phage. This has been found through sequence analysis, as well as experimentally. The ATPase activity from p03 gel filtration columns were analyzed and it was found that there is a direct, positive correlation between the amount of product made and the presence of p03. The ATPase product greatly increases with the addition of p01 (the small subunit of terminase) as well. See Figure 6.

challenge
unacceptableBPSP1:B6V2P5Puthuveetilnp, Team Atlantis2016-04-27 09:38:50 CDTGO:0098026 virus tail, tube (In Figure 3, a protein gel was run on Bacillus phage SP01 tails. Two proteins were identified (look at the T section of the gel), T3 and T6. T6 is identified as a core protein and is said to be a very abundant small protein in tails. This implies that T6 is a tail core protein, which is otherwise known as a tail tube.)PMID:6827651IDA: Inferred from Direct Assay
challenge
updatedbyinstructor9CAUD:K0ILM7Yachuwbg, Team Atlantis2016-04-25 10:13:30 CDTGO:0043493 viral terminase complex (C)GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

On Blastp, this protein matched up with the terminase, large subunit protein of Pseudomonas phage PaP3 with a 100% coverage match, and an 81% identity match. The e-value came back as 0.0 (the e-values get rounded when they're too small).

challenge
unacceptable9CAUD:J9PVF5Yachuwbg, Team Atlantis2016-04-25 10:02:39 CDTGO:0016301 kinase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

On Blast, this protein matches the Dephospho-CoA Kinase protein from Bacillus phage Spock with a 100% coverage, 82% identity, and an e-value of 3e-113. On HHpred, the probability of this gene being Dephospho-CoA Kinase is 99.8%, and the e-value is 1.1e-18. Also, in the article, Table 2 shows functional grouping of proteins, which includes the dephospho-CoA kinase, however not much more information is provided in the article.

challenge
unacceptable9CAUD:G9J213Puthuveetilnp, Team Atlantis2016-04-23 23:55:27 CDTGO:0098026 virus tail, tube (The blast results of gene BCP78_0213 with SP01 10.1 gave these results: query cover of 97%, E-value of 7e-43, and identity of 46%.)other:GO_REF:0000100ISA: Inferred from Sequence Alignment UniProtKB:B6V2P5

UniProtKB:G9J213

challenge
unacceptable9CAUD:A0A076G711Puthuveetilnp, Team Atlantis2016-04-23 23:55:06 CDTGO:0098026 virus tail, tube (Blastp results for gp_186 for Bobb and gene 10.1 for SPO1 are a query cover of 97%, E-value of 2e-41, and identity of 44%.)other:GO_REF:0000100ISA: Inferred from Sequence Alignment UniProtKB:A0A076G711

UniProtKB:B6V2P5

challenge
unacceptable9CAUD:S5YD00Puthuveetilnp, Team Atlantis2016-04-23 23:54:58 CDTGO:0098026 virus tail, tube (C)other:GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results for gene 85 for Troll and gene 10.1 for SPO1 have a query cover of 97%, E-value of 6e-41, and identity of 44%.

challenge
unacceptable9CAUD:A0A0K2D034Puthuveetilnp, Team Atlantis2016-04-23 23:54:22 CDTGO:0098026 virus tail, tube (C)other:GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results shows that this gene TsarBomba_87 and SPO1 10.1 has a query cover of 97%, E-value of 7e-43, and identity of 46%.

challenge
updatedbyinstructor9CAUD:W0XAC1Yachuwbg, Team Atlantis2016-04-20 09:41:26 CDTGO:0043493 viral terminase complex (C)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

The Blastp results for this gene showed a 97% identity, 100% coverage, and an e-value of 0.0 (Blast automatically rounds down when the e-value is very small) match to the large subunit of terminase gene in phage PaP3. HHpred showed a 99.9% probability and an e-value of 3e-23 for the large subunit in terminase function.

challenge
updatedbyinstructor9CAUD:A0A0F6SJ84Yachuwbg, Team Atlantis2016-04-20 09:40:53 CDTGO:0043493 viral terminase complex (C)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

When run through Blastp, this gene matched with the orf3 gene from the phage PaP3 (terminase large subunit) with a 100% coverage, 97% identity, and an e-value of 0.0 (when the e-value gets too low, Blast automatically rounds to 0.0). On HHpred, there is a 99.9% probability that the gene is the large subunit of terminase, and an e-value of 1.5e-23.

challenge
updatedbyinstructor9CAUD:A0A0B5A471Yachuwbg, Team Atlantis2016-04-20 09:40:18 CDTGO:0043493 viral terminase complex (C)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

The Blastp results for gene PhiCHU_71, when compared with phage PaP3, showed 100% coverage, 99.8% identity, and an e-value of 0.0 (the e-value gets rounded when it is close enough to 0) in favor of the large subunit of terminase. When run through HHpred, it gave a 99.9% probability with an e-vaule of 1.5e-23 for the large subunit of terminase protein.

challenge
unacceptable9CAUD:K4F7V6Yachuwbg, Team Atlantis2016-04-20 09:39:35 CDTGO:0098009 virus terminase, large subunit (For gene GAP52_005, the Blastp results, when compared with phage PaP3, showed 93% coverage, 42% identity, and an e-value of 4e-110 in favor of the large subunit of terminase. When run through HHpred, it gave a 99.9% probability with an e-vaule of 2.9e-23 for the large subunit of a terminase protein.)GO_REF:0000100ISS: Inferred from Sequence Similarity UniProtKB:K4F7V6

UniProtKB:Q8H9R7

challenge
unacceptable9CAUD:J9PLX2Yachuwbg, Team Atlantis2016-04-20 09:38:48 CDTGO:0016301 kinase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

On Blast, this gene from Bastille matched with the Adenylate Kinase gene from Bacillus phage Evoli with a 100% coverage, 89% identity, and an e-value of 1e-123. Also, HHpred says that there is a 99.9% probability that Adenylate Kinase is the gene's function. The e-value from HHpred is 1.7e-20.

challenge
unacceptable9CAUD:A0A0K2FLF8Yachuwbg, Team Atlantis2016-04-20 09:35:51 CDTGO:0016301 kinase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

On Blast, the protein matches the Dephospho-CoA Kinase protein in Bacillus phage Spock with an 81% coverage, 39% identity, and an e-value of 8e-33. On HHpred, the probability of this gene being Dephospho-CoA Kinase is 99.8%, and the e-value is 4.4e-18.

challenge
unacceptableECOLX:E9XQS5Gardneret2, Team Atlantis2016-04-20 09:24:01 CDTGO:0004146 dihydrofolate reductase activity (F)GO_REF:0000002ECO:0000247 sequence alignment evidence used in manual assertion

Blastp results showed 100.0% sequence similarity, with an E-value of 1.1E-114.

challenge
unacceptable9CAUD:Q8H9R7Yachuwbg, Team Atlantis2016-04-19 09:05:36 CDTGO:0098009 virus terminase, large subunit (C)PMID:23011306ECO:0000314 direct assay evidence used in manual assertion

The Orf3 Gene has a terminase function. Terminase typically has two subunits, the smaller is responsible for binding the viral DNA, while the larger subunit is responsible primarily for DNA cleavage and translocation. This particular gene makes the protein p03, which is the larger subunit in the terminase process (Figure 1). When unassembled from p01, p03 can typically perform the binding function by itself, however, when performing endonucleolytic activity, efficiency was tested, and was found to perform higher when both p01 and p03 were present (Figure 4).

challenge
unacceptableBPSP1:B6V2P5Puthuveetilnp, Team Atlantis2016-04-18 06:14:39 CDTGO:0098026 virus tail, tube (In this paper, specifically in the section about tail assembly proteins, the authors discuss the potential function of gene 10.1. They speculate it might be a tail tube protein because the length of gene 10.1 corresponds to a gene that codes for a tail tube protein. Additionally, figure 5 shows how the authors analyzed other homologs to show how 10.01 was a tail tube protein.)PMID:19285085IGC: Inferred from Genomic Context UniProtKB:B6V2P4
challenge
unacceptableBPSP1:RP34Puthuveetilnp, Team Atlantis2016-04-11 10:34:48 CDTGO:0016987 sigma factor activity (F)PMID:6441846ECO:0000314 direct assay evidence used in manual assertion

Refer to Figure 2 which shows how the function of gene 34 on Bacillus SPO1 was determined. A vector plasmid was used to help identify function. A solution of isolated RNA polymerases were inserted into lane 5 in the gel causing an aggregation of proteins at specific locations.

challenge
unacceptableBPT4:RIR1Gardneret2, Team Atlantis2016-04-11 10:25:45 CDTGO:0055114 oxidation-reduction process (P)PMID:9309223ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows allosteric substrate specificity site is occupied by the effector molecule dTTP.

challenge
unacceptable9CAUD:A0A0K2FL49Puthuveetilnp, Team Atlantis2016-04-11 10:13:54 CDTGO:0016987 sigma factor activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

On Blastp, gp34 for Bacillus phage SPO1 had a query cover of 43%, E-value of 1e-09, and an identity of 45% when blasted against Gene 182 in Eyuki. HHpred results were the similar for Bacillus phage SPO1 and Gene 182 in Eyuki. Phage SPO1 results were: probability of 99.9% and E-value of 1.4E-26. Gene 182 in Eyuki results were: probability of 99.9% and E-value of 6.3E-24. Both were matched to protein 1OR7, a RNA Polymerase Sigma-E factor.

challenge
unacceptable9CAUD:S5Y0G8Yachuwbg, Team Atlantis2016-04-11 09:59:26 CDTGO:0016301 kinase activity (F)GO_REF:0000100ECO:0000250 sequence similarity evidence used in manual assertion

On Blast, the gene matched the Dephospho-CoA Kinase on Bacillus phage Riley with 100% coverage, 99% identity, and an e-value of 2e-141. On HHpred, there is a 99.8% probability that this gene is, in fact, Dephospho-CoA Kinase. The e-value on HHpred is 1.1e-17.

challenge
unacceptable9CAUD:J9PW75Vishwanathk, Team Atlantis2016-04-11 04:57:47 CDTGO:0004527 exonuclease activity (F)other:GO_REF:0000100ECO:0000247 sequence alignment evidence used in manual assertion

On Blast, the gene matches the putative exonuclease 2 protein and has 97% coverage and 60% identity to the sequence that was processed from Eyuki. This sequence also has an E-value of 1e-160.

challenge
unacceptableECOLX:A0A080F3Q6Gardneret2, Team Atlantis2016-04-11 04:17:59 CDTGO:0000166 nucleotide binding (Blastp results showed 100.0% sequence similarity with Enterobacteria phage T4.)GO_REF:0000037ISA: Inferred from Sequence Alignment UniProtKB:P32282
challenge

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Pages in category "Team Atlantis"

The following 4 pages are in this category, out of 4 total.


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