Welcome to PerlMonks, randomhero1270! I think you did well on both your question and script...

Given your data set, consider the following:

use strict;
use warnings;

while ( my $protein = <DATA> ) {
    $protein =~ /([^:]+).+\s+([<=>]+)\s+/;
    print "$1 - $2\n";
}

__DATA__
R00005: 00330: C01010 => C00011
R00005: 00791: C01010 => C00011
R00005: 01100: C01010 <=> C00011
R00006: 00770: C00022 => C00900
R00008: 00362: C06033 => C00022
R00008: 00660: C00022 => C06033
R00010: 00500: C01083 => C00031
R00013: 00630: C00048 => C01146
R00013: 01100: C00048 <=> C01146
[download]

Output:

R00005 - =>
R00005 - =>
R00005 - <=>
R00006 - =>
R00008 - =>
R00008 - =>
R00010 - =>
R00013 - =>
R00013 - <=>
[download]

The regex:

/^([^:]+).+\s+([<=>]+)\s+/
 ^   ^    ^      ^
 |   |    |      |
 |   |    |      + - Capture characters from this class enclosed by 1+
+ spaces
 |   |    + - Keep going, matching any character except \n
 |   + - Capture characters that are not :
 + - Start at the beginning
[download]

The () notation creates captures. In this case $1 will contain the captured text, like R00008; $2 will contain the captured characters <, =, or >.

Hope this helps!