Sequence alignment between 3j9v(N) and UniProt seq P39111 (VATF_YEAST):

P39111 (VATF_YEAST): V-type proton ATPase subunit F from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
                 10        20        30        40        50        60        70        80        90       100       110        
         ---------+---------+---------+---------+---------+---------+---------+---------+---------+---------+---------+--------
UniProt: MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE
PDB seq: -AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLF--
          --------+---------+---------+---------+---------+---------+---------+---------+---------+---------+---------+------  
                 10        20        30        40        50        60        70        80        90       100       110