Add transport rxn GPR

[feiranl]

Main improvements in this PR:

• Addressing issue feat: add gene annotation for transport reactions #171:
• This PR is mainly for adding GPR rules to transport rxns according to different databases, mainly TCDB annotation. All information are stored in the file of TransRxnGeneAnnotation.tsv
• addTransNewGPR.m is the function that we used to adding new GPRs to rxns.
• Reaction confidence scores were also updated with addConfidenceScores.m (leading to changes in some unexpected rxns due to old PRs not updating them).

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected devel as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[BenjaSanchez]

@feiranl the changes look good. My only comment is that if you are adding gene rules, then the corresponding reactions should now have a reaction confidence score = 2 (if they don't have pmid) or = 3 (if they have pmid). For updating the model with this you could try running addConfidenceScores.m, but make sure that no undesired changes occur (i.e. only these rxns change).

• Compatibility: no unexpected errors when the model goes through an I/O cycle.
• Documentation: The corresponding scripts are well documented.
• Reproducibility: All changes introduced to the model can be reproduced with the corresponding scripts.
• Style: Compliant style in the model/functions/data.

[feiranl]

Okay, will change the confidence score today.

[feiranl]

I used this function, and found also confidence score of other rxns will also change.

[BenjaSanchez]

@feiranl everything looks good now! after your latest commit using addConfidenceScores.m I see that some rxn confidence scores not from this PR are also getting modified, such as r_0475 or r_1667. However, those changes are correct and likely to have been forgotten in previous PRs (e.g. #124), so for simplicity we can integrate them here as well (I included this observation in the PR description above).

@feiranl @hongzhonglu note that this PR will be merged after the next release, to separate it from #174

[feiranl]

I include this note in last commit, confidence scores for those rxns which don't belong to this PR were also changed :
Note: r_0475, r_1667, r_1729, r_1805, r_2025, r_2064, r_4403 ,r_4435, r_4484, r_4598, r_4599 rxn confidence scores were also changed since they have gRrules.