Recent Changes

Wednesday, March 22

Friday, April 17

  1. page TLR10 edited TLR10 This Project: This web page originated as an assignment in Emory University's Biology 142…
    TLR10
    This Project:
    This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein.
    (view changes)
  2. page TLR10 edited ... 2e-58 28% ... genome database. The The reciprocal search ... protein function. …
    ...
    2e-58
    28%
    ...
    genome database.
    The

    The
    reciprocal search
    ...
    protein function.
    Orthologs:
    Finding Whale Shark Orthologues
    *PUT CLUSTAL DATA HERE*
    Figure 4. ClustalW comparisons from the first thirteen alignments. Alignment scores indicate the proportion of positive matches to total amino acids.
    ...
    structural similarity.
    Phylogeny:
    *PHYLOGENETIC TREE GOES HERE*
    ...
    independent sequences.
    The phylogenetic tree generated by the ClustalW program depicts an evolutionary flow that should agree with intuition. Arabidopsis, whale shark, and fruit fly genomes are least related to the others, following the elephant shark, zebra fish, and clawed frog whose genomes slowly become more similar to the human genome, and finally the cow, mouse, and human genomes expressed the most orthology.
    Conclusion:
    (view changes)
  3. page TICAM1-TRIF edited ... Phylogeny was determined by the ClustalW program and is presented in Figure 5, which symbolize…
    ...
    Phylogeny was determined by the ClustalW program and is presented in Figure 5, which symbolizes the mathematical significance of the alignment scores from Figure 4. Again it was observed to be the mouse sequence that was most related, but the zebra fish, with what seemed to be a less significant e-value, was more closely related to the human sequence than the rabbit. Finally, the whale shark sequences showed the least significant relation, with g43334.t1 distinguishing itself as the most similar of the five which could suggest that some methods of categorizing sequence similarity exist that aren't being considered within the bounds of the experiment.
    Conclusion:
    ...
    to diverge.
    References:
    1."TIR Domain-containing Adapter Molecule 1." TICAM1. Web. 14 Apr. 2015. <http://www.uniprot.org/uniprot/Q8IUC6>.
    (view changes)
  4. page TICAM1-TRIF edited ... Phylogenetic tree The hit with the lowest E-value for each non-whale shark species search (us…
    ...
    Phylogenetic tree
    The hit with the lowest E-value for each non-whale shark species search (using the human protein as query) along with the top 4 whale shark BLAST hits were used to create a multiple sequence alignment and phylogenetic tree. ClustalW with default settings was used to create the alignment and tree.
    Protein Domains:
    TICAM1/TRIF belongs to the TLR_2 super family. This family is known as the classical TLRs as they perform the basic functions of Toll-like receptors. Proteins belonging to this domain are characterized for binding to molecules of microbial origin.
    {Screen Shot 2015-04-13 at 8.23.24 PM.png}
    Figure 3: NCBI BLASTed protein family: TLR_2 superfamily

    Searching for TICAM1/TRIF in the Whale Shark:
    Species
    Sequence
    e-value
    %ID
    Alignment length
    Human
    ENSP00000248244
    0.0
    100%
    712
    Whale Shark
    Top Hit

    g25712.t1
    5e-05
    34.29%
    35
    Whale Shark
    Second Hit

    g32441.t1
    1e-04
    35.21%
    71
    Whale Shark
    Third Hit

    g410001.t1
    3e-04
    43.59%
    39
    Whale Shark
    Fourth Hit

    g43334.t1
    3e-04
    34.78%
    46
    Whale Shark
    Fifth Hit

    g34803.t1
    3e-04
    24.00%
    225
    Rabbit
    NP001191275.1
    3e-13
    34%
    N/A
    Cow
    XP005208986.1
    0.0
    65%
    559

    Mouse
    NP778154.1
    0.0
    53%
    N/A482
    Zebra Fish
    NP001038224.1
    2e-28
    34%
    N/A114
    Arabidopsis
    NP199897.2
    1.4
    24%
    65
    Elephant Shark
    calMil1_genscan_KI635908.93_1
    1e-16
    31.79%
    173
    Fruit Fly
    N/A*
    N/A*
    N/A*
    N/A*
    Clawed Frog
    XP004911105.1
    2e-33
    36%
    113
    *Denotes that NCBI BLAST returned no significant results

    Table 1:
    ...
    of the rabbit,human, cow, arabidopsis, elephant shark, fruit fly, clawed frog, zebra fish,
    ...
    against the rabbit,cow, mouse, zebra fish, and zebra fishall other species' genomes was
    ...
    the top resultsresult from the rabbit, zebra fish, and mouse genomes wereeach genome respectively was recorded and
    ...
    for othology.
    Reciprocal search:
    Whale Shark Sequence
    Reciprocal Search Result ID

    Protein Domains:
    TICAM1/TRIF belongs to
    Description
    e-value
    Percent Identity
    g25712.t1
    NP891549.1
    TIR domain-containing adapter molecule 1
    5.3
    34%
    g32441.t1
    NP003861.1
    ras GTPase-activating-like protein IQGAP1
    0.030
    40%
    g410001.t1
    XP011527375
    PREDICTED: protein FAM83D isoform X1
    6e-13
    59%
    g43334.t1
    N/A*
    N/A*
    N/A*
    N/A*
    g34803.t1
    NP849195.2
    neuronal PAS domain-containing protein 4
    8e-17
    35%
    *Denotes that NCBI BLAST returned no significant results
    Table 2: Reciprocal search results using top whale shark hits for ENSP00000248244 against human genome database.
    Results from
    the TLR_2 super family. This family is known asreciprocal search show that none of the classical TLRswhale shark hits came back as they performmatches in the basic functions of Toll-like receptors. Proteins belonginghuman genome, which attests to this domain are characterized for binding to moleculesthe dissimilarity of microbial origin.
    {Screen Shot 2015-04-13 at 8.23.24 PM.png}
    Figure 3: NCBI BLASTed protein family: TLR_2 superfamily
    the two genomes. The insignificant results suggest a low chance of being homologous and either orthologous or paralogous.
    Orthologs:
    {11139911_10205666080882792_1762571339_n.jpg}
    Figure
    *CLUSTALW DATA GOES HERE*
    Figure
    4: ClustalW
    ...
    for the 912 tested sequences,
    ...
    human, mouse, rabbit,cow, zebra fish, arabidopsis, elephant shark, clawed frog, and zebra fishfruit fly genomes respectively.
    ...
    percent identity. Table 1 showed the significant results from blast searches of the TICAM1-TRIF (ENSP00000248244) sequence in the whale shark (Top 5 hits displayed), rabbit, mouse, and zebra fish genomes.
    The
    The data found
    ...
    strongly suggests orthologyhomology with an
    ...
    values which could only suggestsuggests a possibility of paraloguesneed for further research in the rabbitcow and zebra
    ...
    change of orthologyhomology to the mouse sequenceand cow sequences while the
    Phylogeny:
    {11125250_10205666079442756_1333775044_n.jpg} *PHYLOGENETIC TREE GOES HERE*
    Figure 5: Phylogenic tree generated with respect to the alignment scores of the ClustalW.
    ...
    of the five.five which could suggest that some methods of categorizing sequence similarity exist that aren't being considered within the bounds of the experiment.
    Conclusion:
    ...
    conclusion that orthologyhomology to the
    ...
    gene sequence. None of the genomes returned results for the same TICAM1/TRIF protein and, with exceptions for only the cow and mouse genomes, this insignificance coupled with low e-values and various other experimental factors, have led to the conclusion that the TICAM1/TRIF gene is novel in our ancestry and likely developed long after our ancestral genomes began to diverge.
    References:
    1."TIR Domain-containing Adapter Molecule 1." TICAM1. Web. 14 Apr. 2015. <http://www.uniprot.org/uniprot/Q8IUC6>.
    (view changes)
  5. page TLR5 edited ... 0.0 56% ... genome database. Results from the reciprocal search prove that unfortunate…
    ...
    0.0
    56%
    ...
    genome database.
    Results from the reciprocal search prove that unfortunately, there is a high chance that the TLR5 gene is NOT orthologous to the whale shark genome. However its similarity to many genes suggests that it is instead a paralogue.
    Orthologs:
    ...
    Figure 4. Phylogenic Tree outlining the relationship betweeen the 5 seperate species, connected by their likelihood of orthology to one another.
    Conclusion:
    ...
    certainly orthologs (their top hits were both significant in e-value and were the TLR5 gene) while the
    References:
    1.Rock, F. L. "A Family of Human Receptors Structurally Related to Drosophila Toll." Proceedings of the National Academy of Sciences (1997): 588-93. Print.
    (view changes)
  6. page TLR10 edited ... The TLR10 human protein sequence (ENSP00000308925) was used as query in a Blast against the pr…
    ...
    The TLR10 human protein sequence (ENSP00000308925) was used as query in a Blast against the predicted whale shark protein database using the whaleshark.georgiaaquarium.org Galaxy server. Top predicted protein hits were then used as queries (using the full predicted sequence not only the aligned sequence) in protein BLASTs against the NCBI human protein database. The whale shark predicted protein database was also searched using the elephant shark predicted TLR10 protein sequence as query.
    Predicted orthologs
    ...
    databases for yeast,the mouse, cow, zebra fish, arabidopsis, elephant shark, fruit fly, and rabbitclawed frog protein databases.
    Phylogenetic tree
    ...
    phylogenetic tree. ClustalW2ClustalW with default
    ...
    and tree.
    Results
    species
    ID
    Alignment Length
    E-value
    Prcnt Identity
    Whale Shark
    ENST00000308973
    317
    3e-34
    31.23
    Rabbit
    NP001076250.1
    775
    4e-101
    31
    Zebra Fish
    NP001124065.1
    773
    2e-126
    34
    Yeast
    CAA60917.1
    195
    0.004
    26
    {http://www.genome.jp/tmp/clustalw/150414100812k2JvN/tree_upgma.png}

    Protein Domains:
    This protein belongs to the LRR family. This family of proteins is known to have protein-to-protein interactions. The proteins belonging to this family also have characteristically distinct functions and cellular locations. Also, they have substrate binding sites.
    TIR10 belongs to the TIR_2 super family. Proteins belonging to this domain are characterized for binding to molecules of microbial origin. This is a family of bacterial toll-like receptors.
    {http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?dhandle=QM3-data_cache-70CE78234084258-5525FE033370A&show_feat=true&mode=std&gwidth=900&output=graph} *PROTEIN DOMAIN GOES HERE*
    Figure 3. NCBI BLASTed protein families: LRR super-family and TIR super-family.
    Searching for TLR10 in the Whale Shark:
    Species
    Sequence ID
    Percent Identity
    e-value
    alignment length
    Homo Sapien
    ENSP00000308925
    100%
    0.0
    811
    Cow
    NP001070386.1
    81%
    0.0
    721
    Mouse
    NP109607.1
    50%
    0.0
    534
    Zebra Fish
    NP001124065.1
    34%
    2e-126
    423
    Arabidopsis
    NP177295.1
    28%
    7e-06
    110
    Elephant Shark
    calMil1_genscan_KI635971.4_1
    32.72%
    3e-112
    764
    Whale Shark
    Top Hit
    g36276.t1
    31.23%
    3e-34
    317
    Whale Shark
    Second
    g48010.t1
    31.17%
    6e-26
    231
    Whale Shark
    Third
    g21305.t1
    34.23%
    9e-24
    149
    Whale Shark
    Fourth
    g47253.t1
    25.34%
    4e-20
    221
    Whale Shark
    Fifth
    g48273.t1
    32.81%
    4e-15
    128
    Fruit Fly
    NP001246845.1
    31%
    3e-28
    115
    Clawed Frog
    XP002938695.1
    44%
    0.0
    503
    Table 1: Table of significant values from NCBI BLASTs, using multiple genomic sequences as databases, against the query sequence (ENSP00000308925)
    The NCBI BLAST results indicated that there is a high chance of orthology with the cow, mouse, clawed frog, zebra fish, and elephant shark, a possibility for homology to the whale shark and fruit fly, and a skeptical homology to arabidopsis. Before definitive conclusions can be made of the whale shark protein sequences, a reciprocal search will have to be conducted to further prove, or disprove, similarity to the human protein sequence.
    Reciprocal search:
    Whale Shark Sequence
    Reciprocal Search Result ID
    Protein Description
    e-value
    Percent Identity
    g36276.t1
    NP84079.3
    leucine-rich repeat transmembrane neuronal protein 3
    0.0
    70%
    g48010.t1
    NP003259.2
    toll-like receptor 5 precursor
    7e-76
    48%
    g21305.t1
    NP057646.1
    toll-like receptor 7 precursor
    5e-86
    48%
    g47253.t1
    NP003255.2
    toll-like receptor 2 precursor
    1e-28
    32%
    g48273.t1
    NP003256.1
    toll-like receptor 3 precursor
    2e-58
    28%
    Table 2: Reciprocal search results using top whale shark hits for ENSP00000540964 against human genome database.
    The reciprocal search hits were within the correct protein domain, but none of the hits directly matched TLR10. Because of this conclusion, it is evident that the whale shark hits are merely similar in sequence to that of the human protein but likely not strongly enough to retain similarity of protein function.
    Orthologs:
    Finding Whale Shark Orthologues
    *PUT CLUSTAL DATA HERE*
    Figure 4. ClustalW comparisons from the first thirteen alignments. Alignment scores indicate the proportion of positive matches to total amino acids.
    The alignment scores of the ClustalW program reinforce the assumption of homology between the human genome, cow, mouse, and clawed frog. Meanwhile, the most significant whale shark score, with reciprocal search results considered as well, likely represents a paralogue because of difference in function but structural similarity.
    Phylogeny:
    *PHYLOGENETIC TREE GOES HERE*
    Figure 5: Phylogenic tree depicting the genetic relationship between the thirteen independent sequences.
    The phylogenetic tree generated by the ClustalW program depicts an evolutionary flow that should agree with intuition. Arabidopsis, whale shark, and fruit fly genomes are least related to the others, following the elephant shark, zebra fish, and clawed frog whose genomes slowly become more similar to the human genome, and finally the cow, mouse, and human genomes expressed the most orthology.

    Conclusion:
    We conclude thatFrom the human protein does not have ainformation gathered from research, it was concluded that homology withinto the TLR10 gene for the whale shark because the proteinsis likely, although probably through paralogues rather than orthologues. The similarity in reciprocal search values to TLR10 suggest that are most similarit is more likely the gene duplicated and continued to eachmutate and diverge from its counterpart. Orthology was found in the cow genome which came back as a direct match while there was some dispute between the mouse results. The other are not closegenomes expressed enough in terms of E-value, allignment length, or percent identity. similarity to suggest paralogues, but enough divergence to reject orthology.
    References:
    "STRING: Functional Protein Association Networks." STRING: Functional Protein Association Networks. STRING 9.05. Web. 31 Mar. 2015.
    (view changes)

Thursday, April 16

  1. page TLR5 edited ... Phylogenetic tree The hit with the lowest E-value for each non-whale shark species search (us…
    ...
    Phylogenetic tree
    The hit with the lowest E-value for each non-whale shark species search (using the human protein as query) along with the top 4 whale shark BLAST hits were used to create a multiple sequence alignment and phylogenetic tree using ClustalW.
    Protein Domains:
    TLR5 belongs to the TLR_2 super family. This family is known as the classical TLRs as they perform the basic functions of Toll-like receptors. Proteins belonging to this domain are characterized for binding to molecules of microbial origin.
    {Screen Shot 2015-04-08 at 12.07.18 AM.png}
    Figure 2: NCBI BLASTed protein family: TLR_2 superfamily

    Searching for TLR5 in the Whale Shark:
    Species
    ID
    Alignment Length
    E-value
    Percent.
    Sequence ID
    Percent
    Identity
    e-value
    alignment length

    Homo Sapien
    ENSP0000044063
    1234
    ENSP 00000540964
    100%

    0.0
    72%858
    Mouse
    NP_058624.2
    1249
    0.0
    NP058624.2
    72%
    Rabbit
    XP_008266592.1
    1214

    0.0
    70%
    Zebrafish
    NP_001124067.1
    535
    6e-176
    704
    Cow
    NP001035591.1
    79%
    0.0
    750
    Zebra Fish
    NP001124067.1

    38%
    6e-176
    478
    Arabidopsis
    NP199445.1
    25%
    5e-10
    213
    Elephant Shark
    calMil1_genscan_KI635879.230_1
    26.05%
    2e-52
    902

    Whale Shark
    g47253.t1
    217
    8e-81
    47.93%
    Top Hit
    g19777.t1
    24.86%
    1e-23
    366
    Whale Shark
    Second
    g29067.t1
    28.57%
    1e-22
    553
    Whale Shark
    Third
    g48010.t1
    23.97%
    3e-22
    242
    Whale Shark
    Fourth
    421305.t1
    23.44%
    2e-20
    273
    Whale Shark
    Fifth
    g45743.t1
    27.32%
    1e-18
    549
    Fruit Fly
    NP524056.3
    28%
    1e-24
    182
    Clawed Frog
    XP002940742.2
    47%
    0.0
    559
    Table 1: Table of significant values from NCBI BLASTs, using multiple genomic sequences as databases, against the query sequence (ENSP00000540964)

    The NCBI BLAST results show that the predicted protein sequence is for TLR5 and that there isindicated a high
    ...
    of homology infor several species including the rabbitmouse, cow, zebra fish, clawed frog and mouse genomes. Meanwhile it appearspotentially even the geneelephant shark (whose genome is much more likelybelieved to be an orthologuehighly similar to that of the zebrafish and whale shark.
    Protein Domains:
    TLR5 belongs
    shark). Results for the whale shark protein sequence BLASTs were too insignificant to make conclusions alone, and so a reciprocal search would have to be conducted.
    Reciprocal search:
    Whale Shark Sequence
    Reciprocal Search Result ID
    Protein Description
    e-value
    Percent Identity
    g19777.t1
    NP821079.3
    leucine-rich transmembrane neuronal protein 3
    4e-166
    72%
    g29067.t1
    XP011520778.1
    insulin-like growth factor-binding protein complex acid labile subunit isoform X1
    2e-59
    34%
    g48010.t1
    NP003255.2
    toll-like receptor 2 precursor
    1e-28
    32%
    g21305.t1
    NP057646
    toll-like receptor 7 precursor
    5e-86
    48%
    g45743.t1
    NP057646.1
    toll-like receptor 7 precursor
    0.0
    56%
    Table 2: Reciprocal search results using top whale shark hits for ENSP00000540964 against human genome database.
    Results from
    the TLR_2 super family. This familyreciprocal search prove that unfortunately, there is known asa high chance that the classical TLRs as they performTLR5 gene is NOT orthologous to the basic functions of Toll-like receptors. Proteins belongingwhale shark genome. However its similarity to this domain are characterized for binding to molecules of microbial origin.
    {Screen Shot 2015-04-08 at 12.07.18 AM.png}
    Figure 2: NCBI BLASTed protein family: TLR_2 superfamily
    many genes suggests that it is instead a paralogue.
    Orthologs:
    Finding Whale Shark Orthologues
    Orthology*PUT CLUSTAL DATA HERE*
    Figure 3. ClustalW comparisons from the first thirteen alignments. Alignment scores indicate the proportion of positive matches to total amino acids.
    Orthology
    was determined by a significant match (throughusing reciprocal searches (for the whale shark sequences) and also alignment length and e-value) and similar function whilescores from the presenceClustalW program. Significant scores, such as those of the actual gene is unlikely. In this case we found the zebrafishMouse and whale shark to be the most likely to be orthologues.
    {Screen Shot 2015-04-08 at 2.16.45 PM.png}
    Figure 3. ClustalW comparisons show
    Cow, suggest orthology. Scores that are higher than average but not definitively significant like those of the highest alignment was between the humanzebra fish and rabbit genome (score of 77.193).clawed frog would require more research (such as reciprocal searches against their databases) to make a more accurate prediction.
    Phylogeny:
    ...
    phylogenetic tree. From this tree, it is evident thatThe phylogenetic tree interestingly depicts a slow transition from distantly related species (fruit fly, arabidopsis, and whale shark) to marine life (whale shark, elephant shark, zebra fish), apmhibians (clawed frog), and finally land-dwelling mammals (mouse, cow, human). This tree mimics the TLR5 protein is more commonly found in the DNAtheoretical assumptions of land dwelling mammals. Interestingly, the rabbit sequence was almost a direct matchspecies' relative similarities. These results helped to the human coded protein sequence for TLR5.
    {Screen Shot 2015-04-08 at 2.15.36 PM.png}
    reassure and reinforce our conclusions.
    *PHYLOGENETIC TREE GOES HERE*

    Figure 4. Phylogenic Tree outlining the relationship betweeen the 5 seperate species, connected by their likelihood of orthology to one another.
    Conclusion:
    In conclusionconclusion, we hypothesizeddetermined that the human gene for TLR-5 proteinwhale shark genome is not homologousdistantly related to the human genome and that TLR5 (ENSP00000540964) is a gene inparalogue, having developed mutations over time from evolution that caused the whale shark since its alignment shows little match. However,genetic similarity once expressed to fade. Analysis of alternative genomes allowed the BLAST comparison showedproduction of a high predicted match,phylogenic tree, which is likely indicative ofdepicts the two genomes' similaritieshypothesized evolutionary change over time, and relation to common ancestry. Further research with other species demonstrated predicted orthologues with similar proteins functions, with the rabbit beingconclusion that the most closely related species for its predicted sequencemouse and cow are certainly orthologs while the mouse beingzebra fish and clawed frog require more information to accurately determine homology (though the most closely related with a known TLR5 sequence. homology of the two species is certain, the degree of which cannot be confirmed).
    References:
    1.Rock, F. L. "A Family of Human Receptors Structurally Related to Drosophila Toll." Proceedings of the National Academy of Sciences (1997): 588-93. Print.
    (view changes)
  2. page TLR5 edited ... TLR5 predicted orthologuess were identified in species other than whale sharks using the NCBI …
    ...
    TLR5 predicted orthologuess were identified in species other than whale sharks using the NCBI Blast server. Protein BLASTs were performed using single species protein databases for mouse, zebra fish, rabbit, whale shark and human protein databases. The human TLR5 protein (ENSP00000540964) was used as query sequence in these searches with default settings.
    Phylogenetic tree
    ...
    tree using ClustalW2.ClustalW.
    Searching for TLR5 in the Whale Shark:
    Species
    (view changes)

More