Blastx the sequence below against SwissProt. It has an orf that's 493 amino acids long, but the best hsp it turns up (from a protein that is completely identical to the orf) is 453 a.a. long. The same is true when you do tblastn the other way. However, when you first translate the orf (for instance here) and Blastp against SwissProt, you get an hsp covering the whole orf. What's going on here? Does Blast have a maximum length it stores translations at? Hopefully someday I'll have time to investigate this further, or maybe some knowledgeable stranger will pass by this blog and let me know. (edit: This seems to be a freak occurrence with this particular sequence. I have since noticed other Blastx searches to find longer hsps than this one. There is a truncated version of this protein in the NCBI Protein database so maybe that has something to do with it)
GCTGAAAAAAAGTGTAACGTCTCTAGCGGGACGGAGGTAGTATTTATTAAGTTCTGGCGT GAGAAATAGGAATAAATCTGGACCACCGATCTTAGTTAGATCTATGGTTGATATTTATTT AAGCATAGTTACAAGATACAATATGCATGATTTTATTTAAGCATTGATTTTACATTAAAA AGCACAATCGTATAATAAGCATAATATAATGCGTATTTAAGCATGACTTTGTATAGTTTT AAACATTATTCAAATTTTCTCACGTGAAGATTTATTTACACACGAACCCTTCCCTTCCGT GTGTATATGTATATAAATATTTAATCAAGATTGACGTGGAGTAGCAAGCACAAGCAAAGG AGACTTCTTATGGACTACAAATCCAGGAGCTTCAGTCATGTCCAAATCCTCCGCTCTATC TCCATTACCCAATCTGAAATCGAACTCGTTTACCAGCTTGGATAGTGCAAGCTCGTATAA AGCCATCGCAAACGTGGATCCGGGGCACCCTCTTCGACCCGACCCGAACGGAAGCATCTC AAAATGCAACCCTTTATAGTCTATGCTCGTCTCGAGGAACCTTTCTGGACGAAATTCTTC GGGATTTTCCCACAACGAGGGGTCTCTCGATATGGCCCAGTTGTTGACCAACACGACCGT GCCACGTGGGATGTCGTAGCCGAGCATATTGGCGTCTTGAGTCAATTCTCGAGGGAGCAG AATTGCGAAAGGTGGATGTAGGCGTAGAATCTCCTTGGATACTGCTTTCAGATATGGCAT CTTGTCCACGTCATCCTCGGTAATCCCACCTTTGTTTCTAGAAACTTCTCGCACCTCGTT CTGCAAAGTTTTTAGGGTACGCGGGTTTTTTATGAGCTCCGCCATCGTCCACTCTAGAGC CGCGAAAGTCGTATCGGTTCCGGCAGAAACCATGTCGAAGATTAGAGCTTTGATTACGTC ATCCTCGACGGGGTCAGTATCTTTACTCTCTCTCTGAAACTGAAGCAATGTGTCTACGAA ATTCGTTTCATCATCACCCACCTTCTTCCTTCTATATTTTCGAAGAATACCCTCCATTGA TCCATCCAACTTTGTACCGACTTTTTCCACTTCTGCATCGACGCCATTTATCCGGTTGAT CCAAGACAGCCATGGAACGTAATCCCCCACGTTGAAACTTCCCAAGAGCTTGATAACCTT GATCAGAATCCGATTAAAATCATCTCCGCCGTCGCCCTTCCTCCCTAACACCGCCCTGTG AATTACGCCGTTCGTCAGCGCCATGAACATCTCGCTCAAGTTCACGACCGTCGTCGGCTT CGATCGCCTGATCTTCTCAATCATAGCCGACGTTTCCTCTTCTCGAATCCCGCCGAACGA CTGGACCCTCTTAGCGCTGAGCAGCTGCAGCATGCACATGCTCCGCGCGTTGCGCCAGTG CTCGCCGTAGGGGGCGAAGGCCACGCCCTTGCCGCTGTACATCAGCCTGTCGAAGATGCT CAGCCTCGGCCTGCTCGCGAAGATCACGTCTTGGTTCTTCATGATCTCACGCGCCGCCGC CGCTGAGGAGGCCACTAGGACAGGAGCGCTGCCGAAATGGAGTAGCATCACCTCGCCGTA GCGCTTGGATAAGGAGGTGAAGGAGCGGTGGGAGAGGGCTCCGATCAGGTGGAAATGGCC GATCACCGGAAGCCTTAATGGAGACGGCGGCGGCCTCTTTCTTGAGGAAAGACTGGACTT TCGTTTATGGAAAAGGACCGCCAGTAAGATTAAAGAGACAGAGAAAAATACTAGAAGAGC GGCCATTTTCTCTTCAGTTGAATATAATGATGGACAAGTTCTTGGAGAAGG
