User:Bahadur Ali/Sandbox1 Choline Oxidase - Revision history

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 17:15:49 GMT

Methods

←Older revision		Revision as of 17:15, 9 December 2009
Line 4:		Line 4:
	<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>		<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>
	==Methods==		==Methods==
-	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.	+	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.REDIRECT [[blas.JPG]]
-	[[~~Image:Blas~~.JPG]]spank a doodle	+	spank a doodle

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 12:23:37 GMT

Methods

←Older revision		Revision as of 12:23, 9 December 2009
Line 5:		Line 5:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
-	[[Image:Blas.JPG]]	+	[[Image:Blas.JPG]]spank a doodle

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 12:21:23 GMT

Methods

←Older revision		Revision as of 12:21, 9 December 2009
Line 5:		Line 5:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
-	[[Image:~~Bla~~.JPG]]	+	[[Image:Blas.JPG]]

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 12:21:07 GMT

Methods

←Older revision		Revision as of 12:21, 9 December 2009
Line 5:		Line 5:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
-	[[Image:~~Blas~~.JPG]]	+	[[Image:Bla.JPG]]

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 12:06:24 GMT

Methods

←Older revision		Revision as of 12:06, 9 December 2009
Line 5:		Line 5:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
-	[[Image:~~BLAS~~.JPG]]	+	[[Image:Blas.JPG]]

Bahadur Ali at 01:12, 9 December 2009

Bahadur Ali — Wed, 09 Dec 2009 01:12:04 GMT

←Older revision		Revision as of 01:12, 9 December 2009
Line 1:		Line 1:
-	<applet load='2JBV' size='300' frame='true' align='right' caption='Insert caption here' />== Abstract ==	+	<applet load='2JBV' size='300' frame='true' align='right' caption='Insert caption here' />
		+	== Abstract==
	Choline oxidase is the enzyme that catalyzes the reaction between choline and betaine glycine. Betaine glycine is an osmoprotectant and instrumental in helping plants and bacteria survive dry conditions. Studying the choline oxidase may help in the development of controlling populations of beneficial plants or pathogenic bacteria. The data was analyzed using the BLAST and Rasmol programs. The structure of choline oxidase from Arthrobacter globiformis (bacteria) was compared with the structure of the complimentary protein in Mus musculus (mice), carnitine acetyltransferase (Altschul et al., 2005). There are seven amino acids evolutionarily preserved within the vicinity of the flavin group (between amino acids 460 to 483 of each subunit). Of these seven, three are within 9 Å of the flavin group while the other four are farther away. These three are threonine 463, valine 464, and histadine 466. They are colored blue and are connected with the ligand via white monitor lines. The other four conserved residues are colored cyan, but are too far to really interact with the flavin group (colored cpk). Beta sheets are colored yellow to showcase the secondary structure of the entire subunit. Evolutionary preservation of the Thr463, Val464, and His466 may signify an importance in aiding the function of the flavin group as it relates to the activity of the enzyme. Previous studies indicate that His466 is indeed important in the function of choline oxidase (Quaye, Lountos, Fan, Orville, & Gadda, 2008).		Choline oxidase is the enzyme that catalyzes the reaction between choline and betaine glycine. Betaine glycine is an osmoprotectant and instrumental in helping plants and bacteria survive dry conditions. Studying the choline oxidase may help in the development of controlling populations of beneficial plants or pathogenic bacteria. The data was analyzed using the BLAST and Rasmol programs. The structure of choline oxidase from Arthrobacter globiformis (bacteria) was compared with the structure of the complimentary protein in Mus musculus (mice), carnitine acetyltransferase (Altschul et al., 2005). There are seven amino acids evolutionarily preserved within the vicinity of the flavin group (between amino acids 460 to 483 of each subunit). Of these seven, three are within 9 Å of the flavin group while the other four are farther away. These three are threonine 463, valine 464, and histadine 466. They are colored blue and are connected with the ligand via white monitor lines. The other four conserved residues are colored cyan, but are too far to really interact with the flavin group (colored cpk). Beta sheets are colored yellow to showcase the secondary structure of the entire subunit. Evolutionary preservation of the Thr463, Val464, and His466 may signify an importance in aiding the function of the flavin group as it relates to the activity of the enzyme. Previous studies indicate that His466 is indeed important in the function of choline oxidase (Quaye, Lountos, Fan, Orville, & Gadda, 2008).
	<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>		<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 01:09:59 GMT

Methods

←Older revision		Revision as of 01:09, 9 December 2009
Line 3:		Line 3:
	<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>		<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>
	==Methods==		==Methods==
-	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , ~~accession~~ numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.	+	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics) acession numbers]were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
	[[Image:BLAS.JPG]]		[[Image:BLAS.JPG]]

Bahadur Ali: /* Methods */

Bahadur Ali — Wed, 09 Dec 2009 01:06:00 GMT

Methods

←Older revision		Revision as of 01:06, 9 December 2009
Line 4:		Line 4:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
-	[[Image:~~blas~~.~~jpg~~]]	+	[[Image:BLAS.JPG]]

Bahadur Ali at 20:22, 8 December 2009

Bahadur Ali — Tue, 08 Dec 2009 20:22:12 GMT

←Older revision		Revision as of 20:22, 8 December 2009
Line 4:		Line 4:
	==Methods==		==Methods==
	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.		The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.
		+	[[Image:blas.jpg]]

Bahadur Ali at 16:39, 8 December 2009

Bahadur Ali — Tue, 08 Dec 2009 16:39:00 GMT

←Older revision		Revision as of 16:39, 8 December 2009
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	<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>		<scene name='User:Bahadur_Ali/Sandbox1_Choline_Oxidase/Secondary/1'>secondary structure</scene>
	==Methods==		==Methods==
-	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) ~~website~~, accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.	+	The Basic Local Alignment Search Tool([http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&QUERY=&SUBJECTS= BLAST]) was used to find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information ([http://www.ncbi.nlm.nih.gov/guide/proteins/ NCBI]) , accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance. The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. As seen by Figure 3, there are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.