( ( ( The ( pH estimate ) ) ( of ( the ( ER lumen ) ) ) ) ( ( is ( based ( on ( ( an ( indirect assay ) ) ( which ( indicates ( that ( ( the pH ) ( is ( ( closer ( to ( pH 7 ) ) ) ( than ( to ( ( the ( binding optimum ) ) ( of ( pH 5.5 ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (NP (DT The) (NN pH) (NN estimate)) (PP (IN of) (NP (DT the) (NNP ER) (NN lumen)))) (VP (VBZ is) (VP (VBN based) (PP (IN on) (NP (NP (DT an) (JJ indirect) (NN assay)) (SBAR (WHNP (WDT which)) (S (VP (VBZ indicates) (SBAR (IN that) (S (NP (DT the) (NN pH)) (VP (VBZ is) (ADJP (ADJP (JJR closer) (S (VP (TO to) (VP (VB pH) (NP (CD 7)))))) (ADVP (IN than) (PP (TO to) (NP (NP (DT the) (VBG binding) (NN optimum)) (PP (IN of) (NP (NNP pH) (CD 5.5))))))))))))))))) (. .)))
The pH estimate of the ER lumen is based on an indirect assay which indicates that the pH is closer to pH 7 than to the binding optimum of pH 5.5.
(ROOT (S (SBAR (IN If) (S (NP (DT a) (NN substance)) (VP (VBZ has) (NP (DT a) (NN ph) (NN value)) (NP (QP (JJR greater) (IN than) (CD 7)))))) (, ,) (NP (DT that)) (VP (VBZ indicates) (SBAR (IN that) (S (NP (PRP it)) (VP (VBZ is) (NP (NN base)))))) (. .)))
If a substance has a ph value greater than 7,that indicates that it is base.