Homework4

Homework4

Q1: Please find the genes for GroEL and GroES that you showed the structures in homework 3.

Ans:

GroEL (>gb|AE000487|AE000487:2515-4161)

ATGGCAGCTAAAGACGTAAAATTCGGTAACGACGCTCGTGTGAAAATGCTGCGCGGCGTAAACGTACTGG

CAGATGCAGTGAAAGTTACCCTCGGTCCAAAAGGCCGTAACGTAGTTCTGGATAAATCTTTCGGTGCACC

GACCATCACCAAAGATGGTGTTTCCGTTGCTCGTGAAATCGAACTGGAAGACAAGTTCGAAAATATGGGT

GCGCAGATGGTGAAAGAAGTTGCCTCTAAAGCAAACGACGCTGCAGGCGACGGTACCACCACTGCAACCG

TACTGGCTCAGGCTATCATCACTGAAGGTCTGAAAGCTGTTGCTGCGGGCATGAACCCGATGGACCTGAA

ACGTGGTATCGACAAAGCGGTTACCGCTGCAGTTGAAGAACTGAAAGCGCTGTCCGTACCATGCTCTGAC

TCTAAAGCGATTGCTCAGGTTGGTACCATCTCCGCTAACTCCGACGAAACCGTAGGTAAACTGATCGCTG

AAGCGATGGACAAAGTCGGTAAAGAAGGCGTTATCACCGTTGAAGACGGTACCGGTCTGCAGGACGAACT

GGACGTGGTTGAAGGTATGCAGTTCGACCGTGGCTACCTGTCTCCTTACTTCATCAACAAGCCGGAAACT

GGCGCAGTAGAACTGGAAAGCCCGTTCATCCTGCTGGCTGACAAGAAAATCTCCAACATCCGCGAAATGC

TGCCGGTTCTGGAAGCTGTTGCCAAAGCAGGCAAACCGCTGCTGATCATCGCTGAAGATGTAGAAGGCGA

AGCGCTGGCAACTCTGGTTGTTAACACCATGCGTGGCATCGTGAAAGTCGCTGCGGTTAAAGCACCGGGC

TTCGGCGATCGTCGTAAAGCTATGCTGCAGGATATCGCAACCCTGACTGGCGGTACCGTGATCTCTGAAG

AGATCGGTATGGAGCTGGAAAAAGCAACCCTGGAAGACCTGGGTCAGGCTAAACGTGTTGTGATCAACAA

AGACACCACCACTATCATCGATGGCGTGGGTGAAGAAGCTGCAATCCAGGGCCGTGTTGCTCAGATCCGT

CAGCAGATTGAAGAAGCAACTTCTGACTACGACCGTGAAAAACTGCAGGAACGCGTAGCGAAACTGGCAG

GCGGCGTTGCAGTTATCAAAGTGGGTGCTGCTACCGAAGTTGAAATGAAAGAGAAAAAAGCACGCGTTGA

AGATGCCCTGCACGCGACCCGTGCTGCGGTAGAAGAAGGCGTGGTTGCTGGTGGTGGTGTTGCGCTGATC

CGCGTAGCGTCTAAACTGGCTGACCTGCGTGGTCAGAACGAAGACCAGAACGTGGGTATCAAAGTTGCAC

TGCGTGCAATGGAAGCTCCGCTGCGTCAGATCGTATTGAACTGCGGCGAAGAACCGTCTGTTGTTGCTAA

CACCGTTAAAGGCGGCGACGGCAACTACGGTTACAACGCAGCAACCGAAGAATACGGCAACATGATCGAC

ATGGGTATCCTGGATCCAACCAAAGTAACTCGTTCTGCTCTGCAGTACGCAGCTTCTGTGGCTGGCCTGA

TGATCACCACCGAATGCATGGTTACCGACCTGCCGAAAAACGATGCAGCTGACTTAGGCGCTGCTGGCGG

TATGGGCGGCATGGGTGGCATGGGCGGCATGATGTAA

GroES (>gb|AE000487|AE000487:2178-2471)

ATGAATATTCGTCCATTGCATGATCGCGTGATCGTCAAGCGTAAAGAAGTTGAAACTAAATCTGCTGGCG

GCATCGTTCTGACCGGCTCTGCAGCGGCTAAATCCACCCGCGGCGAAGTGCTGGCTGTCGGCAATGGCCG

TATCCTTGAAAATGGCGAAGTGAAGCCGCTGGATGTGAAAGTTGGCGACATCGTTATTTTCAACGATGGC

TACGGTGTGAAATCTGAGAAGATCGACAATGAAGAAGTGTTGATCATGTCCGAAAGCGACATTCTGGCAA

TTGTTGAAGCGTAA

Q2: Which organism do these genes come from? How many sequences of DNA and Protein have been known for this organism?

Ans: (1) Escherichia coli

(2) There are 5802 sequences of DNA and 26071 sequences of protein have been known for E. coli.

Q3: How many BLAST hits you can get if you use the gene you found for GroEL as the query sequence to search against non-redundant GenBank + EMBL + DDBJ + PDB sequence database? Please also show 10 sequences that produce significant alignments ( you just need to show their names and ID numbers ).

Ans: (1) There are 369 BLAST hits.

(2)

Names and ID Numbers	Definition
gb\|U14003\|ECOUW93	Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes.
gb\|AE000487\|AE000487	Escherichia coli K-12 MG1655 section 377 of 400 of the complete
emb\|X07850\|ECGROESL	E. coli groE operon.
gb\|U68778\|SMU68778	Stenotrophomonas maltophilia GroEL and GroES genes, complete cds.
gb\|U01039\|U01039	Salmonella typhi TY2 heat shock protein GroEL (groEL) gene,complete cds.
dbj\|AB008148\|AB008148	Klebsiella planticola gene for GroES protein homologue, GroEL protein homologue, partial cds.
dbj\|AB008138\|AB008138	Enterobacter intermedius gene for GroES protein homologue, GroEL protein homologue, partial cds.
dbj\|AB008149\|AB008149	Klebsiella ornithinolytica gene for GroES protein homologue, GroEL protein homologue, partial cds.
dbj\|AB008147\|AB008147	Klebsiella oxytoca gene for GroES protein homologue, GroEL protein homologue, partial cds.
dbj\|AB008142\|AB008142	Enterobacter agglomerans gene for GroES protein homologue, GroEL protein homologue, partial cds.