#!/bin/bash
s=">YP_00698.1 hypothetical protein sp [Species 1]
MDMQFGYFTRNPSTKYPATLYPREVSCALYEDDNENTSLIPKSRHYHYTIQPPINYKKLTNVDRYKNFRL
>YP_0098.1 hypothetical protein sp [Species 2]
MDMQFGYFTRNPSTKYPATLYPREVSCALYEDDNENTSLIPKSRHYHYTIQPPINYKKLTNVDRYKNFRL
>YP_009378.1 hypothetical protein sp [Species 3]
MEDNTAEDIIKNHLLNTSNDDDDDADSLKKKKENIDDIVKESKNVNLFFISYIKAYNDLVLFLKQQEIVFINILHLNNLNLSIYNLLQKCYSTKDKYKFLPDNNKNLLQLILTLKKNVKFRLKRLKDK"
sed 's/^>[^[:space:]]\{1,\}/&_CT/' <<< "$s"
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