How To Predict The Potential Promoter In A Gene Of Bacterial?

Question

[User 5570]

hello everyone

i'm a fresh man in this field, so i get a lot of doubts to be solved. recently, i was asked to find the promotor of a gene named pthA, but i didn't know how to use the related profiles download from ncbi. until now, i still had no way out, so i came here for your help.

the following is the related gene sequence from ncbi

AGCACGGTACCCGGCGGTCGCATGACGGGGTTTATGCATTCTTGCATCGCCCGGGCGCAACCGCTATTGT
GCACATGCACCACCGACCGGACCCTGGAGACAGGTGTGGTGCCTCGATAGATCGATAGCTTCACCCGATC
TATCCCTTGCCTGGAGCGGGATACGGCAGAAATGCCCAAAGAGCCTACCGAGTAGTGAATACCGAAAGCG
CTCCAGCGATGGGGCGCTTTCTTTTTATAGGGCAATGGTCTGTTCGGCCAAGCGCCGCCGGTACACAGTC
TCAACCTTGTAGAGCTTCCCGCGCGGGAGTTTATGGATGGTTGTCCCGTCGACGGGGTAGCAGGAGATGA
GGGTCGGCAGGGATTGGTGTAAAAAACAGCCAAAAGTGAGCTAACTCGCTGTCAGCACAGAAATTTTTCA
CAACCTTCTGCCGATCCTCCATGCGGGTCCGTGATCGCCTTCATGTCTGCGCCTCACCCTGGTCGTCGAG
GGTTGCCAGGATCACCCGAAGTTGTGTACTGCCATGCGGCCTCGGAAGCTATGTAGGAACCACAGACCGC
TAGTCTGGAGGCGACCATGTAAAGAGGTATGCCTGATGGATCCCATTCGTTCGCGCACACCAAGTCCTGC
CCGCGAGCTTCTGCCCGGACCCCAACCCGATGGGGTTCAGCCGACTGCAGATCGTGGGGTGTCTCCGCCT
GCCGGCGGCCCCCTGGATGGCTTGCCCGCTCGGCGGACGATGTCCCGGACCCGGCTGCCATCTCCCCCTG
CCCCCTCACCTGCGTTCTCGGCGGGCAGCTTCAGTGACCTGTTACGTCAGTTCGATCCGTCACTTTTTAA
TACATCGCTTTTTGATTCATTGCCTCCCTTCGGCGCTCACCATACAGAGGCTGCCACAGGCGAGTGGGAT
GAGGTGCAATCGGGTCTGCGGGCAGCCGACGCCCCCCCACCCACCATGCGCGTGGCTGTCACTGCCGCGC
GGCCGCCGCGCGCCAAGCCGGCGCCGCGACGACGTGCTGCGCAACCCTCCGACGCTTCGCCGGCCGCGCA
GGTGGATCTACGCACGCTCGGCTACAGCCAGCAGCAACAGGAGAAGATCAAACCGAAGGTTCGTTCGACA
GTGGCGCAGCACCACGAGGCACTGGTCGGCCATGGGTTTACACACGCGCACATCGTTGCGCTCAGCCAAC
ACCCGGCAGCGTTAGGGACCGTCGCTGTCAAGTATCAGGACATGATCGCAGCGTTGCCAGAGGCGACACA
CGAAGCGATCGTTGGCGTCGGCAAACAGTGGTCCGGCGCACGCGCCCTGGAGGCCTTGCTCACGGTGGCG
GGAGAGTTGAGAGGTCCACCGTTACAGTTGGACACAGGCCAACTTCTCAAGATTGCAAAACGTGGCGGCG
TGACCGCAGTGGAGGCAGTGCATGCATGGCGCAATGCACTGACGGGTGCCCCCCTGAACCTGACCCCGGA
GCAGGTGGTGGCCATCGCCAGCAATATTGGTGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCG
GTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCAGCAATGGCGGCAAGCAGG
CGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTGGT
GGCCATCGCCAGCAATATTGGTGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGC
CAGGCCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCAGCAATATTGGTGGCAAGCAGGCGCTGG
AGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGCACAGGTGGTGGCCAT
CGCCAGCAATATTGGCGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCC
CATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCAGCAATGGCGGTGGCAAGCAGGCGCTGGAGACGG
TGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGACCAGGTGGTGGCCATCGCCAG
CCACGATGGCGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGC
CTGACCCCGCAGCAGGTGGTGGCCATCGCCAGCAATGGCGGTGGCAAGCAGGCGCTGGAGACGGTGCAGC
GGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCAGCCACGA
TGGCGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACC
CCGGAGCAGGTGGTGGCCATCGCCAGCAATGGCGGTGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGT
TGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCAGCAATGGCGGTGG
CAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAG
CAGGTGGTGGCCATCGCCAGCAATGGCGGTGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGG
TGCTGTGCCAGGCCCATGGCCTGACCCTGGACCAGGTCGTGGCCATCGCCAGCAATGGCGGTGGCAAGCA
GGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTG
GTGGCCATCGCCAGCAATAGCGGTGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGT
GCCAGGCCCATGGCCTGACCCCGGACCAGGTGGTGGCCATCGCCAGCCACGATGGCGGCAAGCAGGCGCT
GGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTCGTGGCC
ATCGCCAGCCACGATGGCGGCAAGCAGGCGCTGGAGACGGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGG
CCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCCTGCAATGGCGGTGGCAAGCAGGCGCTGGAGAC
GGTGCAGCGGCTGTTGCCGGTGCTGTGCCAGGCCCATGGCCTGACCCCGGAGCAGGTGGTGGCCATCGCC
AGCAATGGCGGCGGCAGGCCGGCGCTGGAGAGCATTGTTGCCCAGTTATCTCGCCCTGATCCGGCGTTGG
CCGCGTTGACCAACGACCACCTCGTCGCCTTGGCCTGCCTCGGCGGACGTCCTGCGCTGGATGCAGTGAA
AAAGGGATTGCCGCACGCGCCGGCCTTGATCAAAAGAACCAATCGCCGTATTCCCGAACGCACATCCCAT
CGCGTTGCCGACCACGCGCAAGTGGTTCGCGTGCTGGGTTTTTTCCAGTGCCACTCCCACCCAGCGCAAG
CATTTGATGACGCCATGACGCAGTTCGGGATGAGCAGGCACGGGTTGTTACAGCTCTTTCGCAGAGTGGG
CGTCACCGAACTCGAAGCCCGCAGTGGAACGCTCCCCCCAGCCTCGCAGCGTTGGGACCGTATCCTCCAG
GCATCAGGGATGAAAAGGGCCAAACCGTCCCCTACTTCAACTCAAACGCCGGACCAGGCGTCTTTGCATG
CATTCGCCGATTCGCTGGAGCGTGACCTTGATGCGCCCAGCCCAACGCACGAGGGAGATCAGAGGCGGGC
AAGCAGCCGTAAACGGTCCCGATCGGATCGTGCTGTCACCGGTCCCTCCGCACAGCAATCGTTCGAGGTG
CGCGCTCCCGAACAGCGCGATGCGCTGCATTTGCCCCTCAGTTGGAGGGTAAAACGCCCGCGTACCAGTA
TCGGGGGCGGCCTCCCGGATCCTGGTACGCCCACGGCTGCCGACCTGGCAGCGTCCAGCACCGTGATGCG
GGAACAAGATGAGGACCCCTTCGCAGGGGCAGCGGATGATTTCCCGGCATTCAACGAAGAGGAGCTCGCA
TGGTTGATGGAGCTATTGCCTCAGTGAGGCTCAGTCGGTGACTACCTGAGCGTCGGCAGGGATTGGTGTA
AGTAACCTTTACTGACAGCGAGTTAGCCCACTTTTGGCTGTTTTTTACACAAATCCCTGCCTCCCCTCAC
CTGGGCACGCAGTCCCTCGGTGCGCATCAATCGATGCACCGATGGCGACTGCAACGTCACCAGATCGGTA
GATCC

[Neilfws]

Please improve this question. It's unclear whether you are interested in software to predict promoters in this sequence or NCBI resources.

[User 5570]

thank you for your help and your advice on my way of putting questions to expert like you,i really mean it ,thank you.

Answer 1

[Neilfws]

Given the lack of information in your question, I used BLAST to search for the sequence that you gave. Top hit: pthA from Xanthomonas citri.

Clicking on that hit took me to the GenBank page for the gene which in this case, is very well-annotated. Here's part of the record. The -35 and -10 positions are related to the gene promoter, in this case.

 LTR             349..410
                 /note="label: IR-L"
 -35_signal      515..521
                 /citation=[1]
                 /citation=[2]
 -10_signal      540..545
                 /citation=[1]
                 /citation=[2]
 RBS             582..587
                 /citation=[1]
                 /citation=[2]
 gene            596..4087

So, no need to predict promoters in this case - it's right there in the annotation.

If it's promoter prediction software that interests you, please improve your question. It's unclear what you mean by "the related profiles download from ncbi."

[User 5570]

thank you for your help i take your advise and have the promoter predicted smoothly!