These pulses are normally called soybeans in American English and soya beans (two words) in British English.

"Meal" means flour here. The beans are ground to extract the oil and what is left is the meal or flour.

http://en.wikipedia.org/wiki/Soybean_meal

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Note added at 1 hr (2014-09-03 08:01:10 GMT)
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I didn't realise that you wanted an explanation of the allowance clause. As I understand it, the meaning is as follows.

"Allowance" means price adjustment.
The protein content of the soybean meal is agreed in the contract as 46.50% (basis).
If the meal contains this much protein, the buyer will pay the seller the price agreed in the contract.
The minimum is 45.5%. If the content is lower than that, presumably the meal will be rejected and the buyer will pay nothing.
If the content is above the minimum but below the basis, there will be an allowance: essentially a discount. The buyer will pay a reduced price.
The size of the reduction depends on how far the content falls short of the basis. If it is considerably below (less than 46%), the allowance or reduction will be 2:1, which means that for each 1% that the content falls below the basis the price will be reduced by 2%.
If the shortfall in protein content is minor (content between 46% and the basis of 46.5%) the allowance (price reduction) will be 1:1: a reduction in price of 1% for each 1% deficit in protein content.
If these situations arise, the deficit in protein content, and therefore the allowance, will actually be a fraction of a percent. So it says "fractions in proportion": a tenth of 1% deficit in protein content will give rise to an allowance of a tenth of 1% on the price, and so on.

"Non-reciprocal" means that these allowances only work in the buyer's favour, not the seller's. In other words, the buyer has an allowance (proportional price reduction) if the meal contains less protein than the basis figure, but the seller does not enjoy an corresponding allowance (a price increase) if the content is above the basis figure.

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Note added at 1 hr (2014-09-03 08:16:24 GMT)
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By the way, I suspect that in your text "From 45.90% to 45.99%" should read "From 45.50% to 45.99%". Otherwise there is no provision for meal containing more than the minimum but less than 45.90%.

Let's take a concrete example.

Suppose the agreed price is 500 dollars per metric ton and that the protein content of the meal turns out to be 45.90%.
The content is 0.6% below the basis of 46.50%
So the price will be reduced by 0.6%. In this band, the allowance is 2:1, so the price will be reduced by 1.2%. 1.2% of 500 is 6. So the buyer will pay 494 dollars per metric ton instead of 500 for the meal.

Suppose the content is 46.20%. This is 0.3% below basis. In this band the allowance is 1:1. So the allowance (price reduction) will be 0.3%. 0.3% of 500 is 1.5. So the buyer will pay 498.5 dollars per metric ton.


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Note added at 2 hrs (2014-09-03 08:24:34 GMT)
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Sorry; in my latest note I meant to delete "So the price will be reduced by 0.6%" at the beginning of the last paragraph in my first example. Pardon the confusion (it's confusing enough already!).

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Note added at 2 hrs (2014-09-03 08:39:49 GMT)
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Just to confirm the meaning of non-reciprocal versus reciprocal allowances, the following may be helpful. It is the European Quality Terms for Feedingstuffs Contracts from the Grain and Feed Trade Association. It uses the term "without reciprocal allowances" instead of "non-reciprocal allowances", but the meaning is the same.

If you look at Section 2, you find explanations of various scenarios. For example:

"2.1(A) Oil & Protein combined without reciprocal allowances:
For any deficiency of oil and protein combined as warranted in Clause 1.1 (A) there shall be allowances to Buyers at the following rates [...]".

No mention here of allowances in the Seller's favour. But see here:

"2.1(B) Oil & Protein combined with reciprocal allowances:
For any deficiency of oil and protein combined as warranted in Clause 1.1 (B) there shall be an allowance to Buyers as per the scale provided in Clause 2.1 (A). For any excess of oil and protein combined Buyers shall pay to Sellers a premium on a 1:1 basis and fractions in proportion."
http://www.gtradesystem.com/Commodities_Files/GAFTA 93.pdf

So if the content is above the basis, with a reciprocal allowance, the Buyer pays the Seller a premium above the agreed price. But this does not happen if the allowance is non-reciprocal.


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Note added at 5 hrs (2014-09-03 11:57:46 GMT)
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According to the example you've given in the discussion, I have misunderstood the way they calculate the percentages. But I'm sure that the meanings of "non-reciprocal" and "allowance" are as I've said here.