This web page was produced as an assignment for Genetics 677, an undergraduate course at UW‐Madison.
BLM Gene Motifs
Using MOTIF Program, I was able to find 12 DNA motifs for the full-length BLM gene. See below for summary of the 12 DNA motifs.
Motif: EGF_1
Prosite ID: EGF_1 (PS00022) Description: EGF-like domain signature 1. Pattern: C-x-C-x(2)-{V}-x(2)-G-{C}-x-C. Motif:INTEGRIN_BETA Prosite ID:INTEGRIN_BETA (PS00243) Description: Integrins beta chain cysteine-rich domain signature. Pattern:C-x-[GNQ]-x(1,3)-G-x-C-x-C-x(2)-C-x-C. Motif:CTCK_1 Prosite ID:CTCK_1 (PS01185) Description:C-terminal cystine knot signature. Pattern:C-C-x(13)-C-x(2)-[GN]-x(12)-C-x-C-x(2,4)-C. Motif:ANAPHYLATOXIN_1 Prosite ID:ANAPHYLATOXIN_1 (PS01177) Description:Anaphylatoxin domain signature. Pattern:[CSH]-C-x(2)-[GAP]-x(7,8)-[GASTDEQR]-C-[GASTDEQL]-x(3,9)- [GASTDEQN]-x(2)-[CE]-x(6,7)-C-C. Motif:4FE4S_FERREDOXIN Prosite ID:4FE4S_FERREDOXIN (PS00198) Description:4Fe-4S ferredoxins, iron-sulfur binding region signature. Pattern:C-x-{P}-C-{C}-x-C-{CP}-x-{C}-C-[PEG]. Motif:THIOLASE_3 Prosite ID:THIOLASE_3 (PS00099) Description:Thiolases active site. Pattern:[AG]-[LIVMA]-[STAGCLIVM]-[STAG]-[LIVMA]-C-{Q}-[AG] -x-[AG]-x-[AG]-x-[SAG]. |
Motif:TUBULIN
Prosite ID:TUBULIN (PS00227) Description:Tubulin subunits alpha, beta, and gamma signature. Pattern:[SAG]-G-G-T-G-[SA]-G. Motif:HYDROPHOBIN Prosite ID:HYDROPHOBIN (PS00956) Description:Fungal hydrophobins signature. Pattern:[GN]-[DNQPSA]-x-C-[GSTANK]-[GSTADNQ]-[STNQI]-[PTIV]-x-C-C-[DENQKPST]. Motif:VWFC_1 Prosite ID:VWFC_1 (PS01208) Description:VWFC domain signature. Pattern:C-x(2,3)-C-{CG}-C-x(6,14)-C-x(3,4)-C-x(2,10)-C-x(9,16)-C-C-x(2,4)-C. Motif:2FE2S_FER_1 Prosite ID:2FE2S_FER_1 (PS00197) Description:2Fe-2S ferredoxins, iron-sulfur binding region signature. Pattern:C-{C}-{C}-[GA]-{C}-C-[GAST]-{CPDEKRHFYW}-C. Motif:DEFENSIN Prosite ID:DEFENSIN (PS00269) Description:Mammalian defensins signature. Pattern:C-x-C-x(3,5)-C-x(7)-G-x-C-x(9)-C-C. |
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I inputed all the gene sequenes of BLM gene homologs into MEME database and 3 motifs were returned. In the figure shown below, the top is motif one, the middle motif 2, and the bottom motif 3.
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Also, I repeated the previous step, but with BLM protein sequences of all homologs this time. MEME database found 3 motifs, too. Instead of showing each motif, I decided to include the following figure to show that BLM gene motif is indeed well conserved across species that shared homologous BLM gene/protein.