#!/bin/bash
s='1_10090 Mus musculus (house mouse) Gene 1
2_10090 Mus musculus Gene 2
3_10090 (house mouse) Gene 3
4_10090 Gene 4'
sed -E 's/_10090( Mus musculus)?( \(house mouse\))? /_10090 Mus musculus (house mouse) /g' <<< "$s"
IyEvYmluL2Jhc2gKcz0nMV8xMDA5MCBNdXMgbXVzY3VsdXMgKGhvdXNlIG1vdXNlKSBHZW5lIDEKMl8xMDA5MCBNdXMgbXVzY3VsdXMgR2VuZSAyCjNfMTAwOTAgKGhvdXNlIG1vdXNlKSBHZW5lIDMKNF8xMDA5MCBHZW5lIDQnCnNlZCAtRSAncy9fMTAwOTAoIE11cyBtdXNjdWx1cyk/KCBcKGhvdXNlIG1vdXNlXCkpPyAvXzEwMDkwIE11cyBtdXNjdWx1cyAoaG91c2UgbW91c2UpIC9nJyA8PDwgIiRzIg==