1. Blank library.
- Start with blank library
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2. Upload my own file containing FASTA formatted protein sequences.
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3. PSI-BLAST output, PDB names, and accession numbers.
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Example:
ref|NP_395419.1| (NC_003134) hypothetical protein YPMT1.73 [Yers... 163 3e-40
emb|CAA73744.1| (Y13308) endonuclease [Yersinia enterocolitica] 148 1e-35
ref|NP_052524.1| (NC_002122) nuclease [Plasmid ColIb-P9] >gi|451... 146 6e-35
dbj|BAA77997.1| (AB027308) EDTA-resistant nuclease [Plasmid R64]... 145 6e-35
ref|NP_221168.1| (NC_000963) unknown [Rickettsia prowazekii] >gi... 134 1e-31
ref|NP_052444.1| (NC_002120) putative endonuclease Nuc [Yersinia... 134 2e-31
1d09_D
CAA85678.1
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Start with PSI-BLAST, PDB, and accession numbers
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4. Select and combine pre-existing libraries.
- Start with pre-existing libraries
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5. Run PSI-BLAST on a FASTA formatted protein sequence.
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Example:
>Protein_name
MRFKLSVIIFVLVSASALATPSFNVGFSPSHTALENVLSVVNNAQSSLDVEAYTFTSK
QISTAIVSAQKRGVNVRVVADAKANRLNYSAIHYLAQQHVPVRLNNNYSIHHNKVMIA
DGDTIQTGSMNYTTNGDTHNAENVLVIRGAPEIAGKYQVEFNRLWA
- Start with protein sequence
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