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I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database.

I have the output:

sp|Q9NZT1|CALL5_HUMAN

However I'm not sure exactly what this is referring to.

  • Is Q9NZT1 q unique identifier?
  • Is CALL5_HUMAN unique too?
  • Should one use both together to get information?

  • How many types of ID are there?

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  • $\begingroup$ Hi and welcome to Bio.SE! I've made a few edits to your question just so that it's clearer what you're getting at. Feel free to roll back those changes :) $\endgroup$ – James Feb 25 '16 at 14:20
  • $\begingroup$ @James thanks, everything is good. i appreciate any comment and help :-) $\endgroup$ – Nik Feb 25 '16 at 14:21
  • $\begingroup$ Glad I could help. I wasn't sure exactly what you were asking when you said "How many types of ID are there?" Did I answer your question, or were you talking more generally "how many databases use different IDs?" $\endgroup$ – James Feb 25 '16 at 14:23
  • $\begingroup$ @James your answer was very good but I appreciate if you make it more general about databases etc. so that I can accept it $\endgroup$ – Nik Feb 25 '16 at 14:26
  • $\begingroup$ If you open the question up to general databases it becomes far too broad to answer in any meaningful way. I would suggest you edit the question to make it clear what you want to know. I've updated my answer with a bit of information relating to some of the most popular databases. $\endgroup$ – James Feb 26 '16 at 2:12
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Common biology ID codes.

  • PDB: 2BIB for example. 4 letter code for a specific structure.

  • Uniprot: Q9NZT1 for example. A six letter combination of numbers and letters for either a TrEMBL or Swissprot record. This record contains information on domains, and Uniprot links out to lots of useful things like interaction databases, redundancy datasets etc.

  • Pfam: X1WG39_DANRE A uniprot ID followed by an identifier. Tightly linked with Uniprot, but with an emphasis on domains.

  • NCBI: NP_000108.1 For example. These IDs link to either a gene, transcript or protein in refseq. In an NCBI record there are two main distinctions in prefix of the ID code: hypothetical/automatic assertions (XM_, XR_, and XP_) and manually curated assertions (NM_, NR_, and NP_). This is followed by a 6 digit number, and sometimes followed by a "." and a number, indicating an splice isoform.


Uniprot IDs

I'm not sure where you got this output so this seems a strange concatenation of Uniprot information.

Q9NZT1 is indeed the unique Uniprot ID. This is specific to uniprot.

CALL5_HUMAN is the "gene name" or "Identifier" and often spans across different databases for that gene. It's a little more back end, but is essentially not unique due to splice isoforms.

There are many IDs in uniprot, and many types. Already below you'll notice some are swiss prot, others are Trembl. These are the main types. Swissprot are manually reviewed, whereas Trembl is an automatically compiled collection.

screenshot showing that there are half a million Swiss-prot IDs and 60 million TrEMBL IDs

There are many many different accession code types with each database using it's own nomenclature that you'll come across. Unfortunately, there are too many to list here comprehensively.

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