Name: MORIONES, Jan Ebenezer B.

Course and Section: BIO20 1 / A3 Program & Year: ECE-2

FASTA SEARCH A.

Date Performed: December 12, 2012 Date Submitted: December 13, 2012 Professor: Suico

STKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGAL FNGINVLQAYNAALLAKILKVSVEEFSPSIAREIYEMYEAVSMQPSLRSE YEYPVFSHVQAGMFSPELRTFTKGDAERWVSTTKKASDSAFWLEVEGNSM TAPTGSKPSFPDGMLILVDPEQAVEPGDFCIARLGGDEFTFKKLIRDSGQ VFLQPLNPQYPMIPCNESCSVVGKVIASQWPEETFG

1. Which protein can be assigned to this sequence? Give the top 3 proteins that are the most similar to the sequence.

Top 3 Proteins are: 1. Repressor protein CI OS=Enterobacteria phage lambda GN=CI PE=1 SV=2 2. Phage lambda repressor protein CI OS=Escherichia coli GN=cI PE=1 SV=1 3. Repressor protein CI OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=BWG_3703 PE=4 SV=1

2.

Open the DB:ID link of each protein (on the second column from the left), and based on the opened link, provide the following information: a. Description of Protein DB:ID : TR:I0ZPI5_ECOLX Protein Name: Repressor protein CI Taxonomic Identifier: 1144303 [NCBI] Taxonomic Lineage: Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia Sequence Length : 237 AA Sequence Status : Complete Protein Existence : Predicted

b. Organism source of the protein : Enterobacteria phage lambda (Bacteriophage lambda)

MORIONES, Jan Ebenezer B. HOMEWORK Bio20-1 / A3

Lys49-Phospholipase A2 Structure Analysis

B.

1.

MRFPELEELKNRRTLKWTRFPEDVLPLWVAESDFGTCPQLKEAMADAVER EVFGYPPDATGLNDALTGFYERRYGFGPNPESVFAIPDVVRGLKLAIEHF TKPGSAIIVPLPAYPPFIELPKVTGRQAIYIDAHEYDLKEIEKAFADGAG SLLFCNPHNPLGTVFSEEYIRELTDIAAKYDARIIVDEIHAPLVYEGTHV VAAGVSENAANTCITITATSKAWNTAGLKCAQIFFSNEADVKAWKNLSDI TRDGVSILGLIAAETVYNEGEEFLDESIQILKDNRDFAAAELEKLGVKVY APDSTYLMWLDFAGTKIEEAPSKILREEGKVMLNDGAAFGGFTTCARLNF ACSRETLEEGLRRIASVL Which protein can be assigned to this sequence? Give the top 3 proteins that are the most similar to the
sequence.

Top 3 Proteins are: 1. Cystathionine beta-Lyase OS=Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) GN=aecD PE=4 SV=1 2 Cystathionine beta-lyase OS=Corynebacterium glutamicum GN=metC PE=4 SV=1 3. PLP-dependent aminotransferase OS=Corynebacterium glutamicum K051 GN=AecD PE=4 SV=1 2. Open the DB:ID link of each protein (on the second column from the left), and based on the opened link, provide the following information: a. Description of Protein DB:ID : TR:H7C6D3_CORGL Protein Name: Cystathionine beta-Lyase (EC 4.4.1.-) (EC 4.4.1.8) Gene Name : aecD cg2536 Taxonomic Identifier: 196627 [NCBI] Taxonomic Lineage: Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium Sequence Length : 368 AA Sequence Status : Complete Protein Existence : Predicted

b. Organism source of the protein : Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG
3730 / NCIMB 10025)

MORIONES, Jan Ebenezer B. HOMEWORK Bio20-1 / A3

Lys49-Phospholipase A2 Structure Analysis

BLAST SEARCH

A.

1. Top 3 Proteins are: 1. Repressor protein CI OS=Enterobacteria phage lambda GN=CI PE=1 SV=2 2. Phage lambda repressor protein CI OS=Escherichia coli GN=cI PE=1 SV=1 3. Repressor protein CI OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=BWG_3703 PE=4 SV=1

2.

A. Description of Protein DB:ID : SR:PRC1_LAMBO Protein Name: Repressor protein CI Gene Name : cI Taxonomic Identifier : 10710[NCBI] Taxonomic Lineage: Viruses dsDNA viruses, no RNA stage Caudovirales Siphoviridae Lambda-like viruses Virus Host : Escherichia coli Sequence Length : 237 AA Sequence Status : Complete Protein Existence : Predicted B. Organism source of the protein : Enterobacteria phage lambda (Bacteriophage lambda)

B.

1. Top 3 Proteins are: 1. Cystathionine beta-Lyase OS=Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) GN=aecD PE=4 SV=1 2 Cystathionine beta-lyase OS=Corynebacterium glutamicum GN=metC PE=4 SV=1 3. PLP-dependent aminotransferase OS=Corynebacterium glutamicum K051 GN=AecD PE=4 SV=1

MORIONES, Jan Ebenezer B. HOMEWORK Bio20-1 / A3

Lys49-Phospholipase A2 Structure Analysis

2.

a. Description of Protein DB:ID : TR:H7C6D3_CORGL Protein Name: Cystathionine beta-Lyase (EC 4.4.1.-) (EC 4.4.1.8) Gene Name : aecD cg2536 Taxonomic Identifier: 196627 [NCBI] Taxonomic Lineage: Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium Sequence Length : 368 AA Sequence Status : Complete Protein Existence : Predicted

b. Organism source of the protein : Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG
3730 / NCIMB 10025)

OVERVIEW

In bioinformatics, BLAST and FASTA is one of the most widely used sequence analysis software program since it is much faster instead of relying on global alignments. BLAST (acronym for Basic Local Alignment Search Tool) is similar to FASTA (short for FAST Alignment). They both perform DNA and protein sequence alignment, compares primary biological sequence information, finds regions of local similarity between sequences and many more. Its just that BLAST is an improvement over FASTA greater speed by pre-indexing the database & more accurate results. As I had done several searches from above, I observed that using FASTA and BLASTA searches were both significantly useful in determining similarities between sequences. Although they differ a liitle, the two software enables people to get genome scale sequences and other biological information more accessible. Some Differences Between FASTA AND BLAST FASTA Slow output of outcomes & results Similar to BLAST Available in only to some formats BLAST Faster output of outcomes & results Similar to FASTA Available in many formats excel, text, etc.

MORIONES, Jan Ebenezer B. HOMEWORK Bio20-1 / A3

Lys49-Phospholipase A2 Structure Analysis