Protein Families Examples

Updated January 27, 2006. Rob Edwards

Protein Families

General help and description about the protein families is also available. This is a series of working examples, to be extended.

These are some example protein families, mainly chosen because they are small and convenient to look at. They may change over time as the families are updated.

Example 1

This little example shows one protein that is misannotated in PIR and several that are wrong in PFAMs

Example 2

This is a little example from Histidine Biosynthesis

Example

Polymyxin resistance protein PmrJ, predicted deacetylase

A nice small family that you can compare to PFAM. There are two different views. The family centric view shows the whole family. The table that shows the other families that are also represented shows all families that are also related to the proteins in the table.

On the other hand, the protein centric view comes in from a single protein (e.g. if you have clicked a link from the protein page, and only shows you those other families that are related to this particular protein

.
  1. family centric
  2. gene centric

Other examples, not yet explored

These examples are ones that are worth looking at and exploring. The comparisons were done with Family 1 NOT Family 2. The for and against are just as shown in the final tables, so you generally want a result with some "againsts" to look at. Also, the "Red" column is the number of cells that would be colored red (i.e. wrong).

Histidine Biosynthesis compared to PIR

pegFamily 1Family 2ForAgainstRed
  fig|83333.1.peg.1994     fig|PF000056     pir|PIRSF000486     18     -7     1  
  fig|292459.1.peg.2713     fig|PF000056     pir|PIRSF006650     66     0     0  
  fig|272626.1.peg.573     fig|PF003447     pir|PIRSF006650     10     0     0  
  fig|272626.1.peg.574     fig|PF000991     pir|PIRSF001549     19     -7     2  
  fig|243274.1.peg.1033     fig|PF000991     pir|PIRSF027379     0     -17     1  
  fig|83333.1.peg.2001     fig|PF001505     pir|PIRSF001258     108     -147     2  
  fig|83333.1.peg.2001     fig|PF002226     pir|PIRSF001258     111     -155     2  
  fig|272626.1.peg.566     fig|PF001505     pir|PIRSF006833     120     0     0  
  fig|272626.1.peg.567     fig|PF002226     pir|PIRSF029243     112     0     0  
  fig|83333.1.peg.1999     fig|PF002424     pir|PIRSF001484     35     -5     3  
  fig|83333.1.peg.2000     fig|PF001996     pir|PIRSF001454     15     0     0  
  fig|4896.1.peg.2360     fig|PF001996     pir|PIRSF036936     122     -344     3  
  fig|4896.1.peg.2360     fig|PF002743     pir|PIRSF036936     241     -339     2  
  fig|83333.1.peg.1998     fig|PF002743     pir|PIRSF000495     7     -2     1  
  fig|83333.1.peg.1997     fig|PF001687     pir|PIRSF001410     27     -81     2  
  fig|83333.1.peg.1997     fig|PF003299     pir|PIRSF001410     290     -156     2  
  fig|272626.1.peg.571     fig|PF003299     pir|PIRSF001409     115     -3     3  
  fig|83333.1.peg.1996     fig|PF000244     pir|PIRSF000518     316     -5     2  
  fig|272626.1.peg.2026     fig|PF000244     pir|PIRSF006455     327     -3     1  
  fig|272623.1.peg.1241     fig|PF000244     pir|PIRSF005473     374     -5     2  
  fig|272626.1.peg.575     fig|PF001687     pir|PIRSF019058     19     -35     3  
  fig|208964.1.peg.6     fig|PF001687     pir|PIRSF004682     2     -69     3  
  fig|4896.1.peg.210     fig|PF001687     pir|PIRSF017203     38     -37     4  
  fig|196164.1.peg.1995     fig|PF003597     pir|PIRSF004949     8     0     0  
  fig|196164.1.peg.809     fig|PF003597     pir|PIRSF500194     20     0     0  
  fig|83333.1.peg.1995     fig|PF002941     pir|PIRSF000099     11     0     0  

Histidine Biosynthesis compared to PFAM

pegFamily 1Family 2ForAgainstRed
  fig|83333.1.peg.1994     fig|PF000056     pfam|PF08029.1     17     -2     1  
  fig|272626.1.peg.573     fig|PF003447     pfam|PF01634.8     2     0     0  
  fig|272626.1.peg.574     fig|PF000991     pfam|PF00587.14     4     -4     2  
  fig|83333.1.peg.2001     fig|PF001505     pfam|PF01502.8     93     -106     2  
  fig|83333.1.peg.2001     fig|PF001505     pfam|PF01503.7     39     -35     1  
  fig|83333.1.peg.2001     fig|PF002226     pfam|PF01502.8     39     -38     1  
  fig|83333.1.peg.2001     fig|PF002226     pfam|PF01503.7     96     -117     2  
  fig|5141.1.peg.8508     fig|PF001505     pfam|PF00815.9     283     -347     3  
  fig|5141.1.peg.8508     fig|PF002226     pfam|PF00815.9     286     -360     3  
  fig|5141.1.peg.8508     fig|PF002941     pfam|PF00815.9     2     -194     2  
  fig|5141.1.peg.8508     fig|PF002941     pfam|PF01502.8     122     -578     3  
  fig|5141.1.peg.8508     fig|PF002941     pfam|PF01503.7     122     -578     3  
  fig|4896.1.peg.2360     fig|PF001996     pfam|PF00117.15     122     -336     3  
  fig|4896.1.peg.2360     fig|PF002743     pfam|PF00117.15     1     -78     1  
  fig|4896.1.peg.2360     fig|PF002743     pfam|PF00977.10     241     -340     2  
  fig|83333.1.peg.1997     fig|PF001687     pfam|PF00475.8     27     -70     2  
  fig|83333.1.peg.1997     fig|PF003299     pfam|PF00475.8     27     -59     1  
  fig|103690.1.peg.384     fig|PF003299     pfam|PF00702.13     0     -62     2  
  fig|243265.1.peg.1484     fig|PF000244     pfam|PF00815.9     264     -399     3  
  fig|243265.1.peg.1484     fig|PF002941     pfam|PF00155.9     239     -347     2  
  fig|272626.1.peg.575     fig|PF001687     pfam|PF02811.7     0     -35     3  

Leucine Degradation compared to PIR

pegFamily 1Family 2ForAgainstRed
  fig|224308.1.peg.3860     fig|PF002066     pir|PIRSF006468     188     -4     1  
  fig|198094.1.peg.1301     fig|PF002066     pir|PIRSF000523     123     0     0  
  fig|224308.1.peg.2409     fig|PF001207     pir|PIRSF000152     26     -14     1  
  fig|224308.1.peg.2409     fig|PF002751     pir|PIRSF000152     23     -3     1  
  fig|272558.1.peg.213     fig|PF001158     pir|PIRSF000152     31     -147     5  
  fig|224308.1.peg.2408     fig|PF000067     pir|PIRSF000155     37     -2     1  
  fig|224308.1.peg.2408     fig|PF001487     pir|PIRSF000155     41     -29     1  
  fig|258594.1.peg.2850     fig|PF000067     pir|PIRSF036563     149     -110     3  
  fig|258594.1.peg.2850     fig|PF001487     pir|PIRSF036563     195     -236     3  
  fig|258594.1.peg.2850     fig|PF002666     pir|PIRSF036563     137     -279     3  
  fig|224308.1.peg.2407     fig|PF001388     pir|PIRSF000432     31     -1     1  
  fig|211586.1.peg.2120     fig|PF001388     pir|PIRSF000433     132     0     0  
  fig|227882.1.peg.4367     fig|PF001864     pir|PIRSF000432     197     -176     4  
  fig|224308.1.peg.1463     fig|PF003391     pir|PIRSF000210     164     -10     4  
  fig|224914.1.peg.145     fig|PF000100     pir|PIRSF000210     22     0     0  
  fig|257310.1.peg.2524     fig|PF003391     pir|PIRSF000212     769     -263     4  
  fig|119219.1.peg.4104     fig|PF003391     pir|PIRSF000350     840     -288     4  
  fig|224308.1.peg.1830     fig|PF000094     pir|PIRSF000182     518     -427     5  
  fig|224308.1.peg.1830     fig|PF002044     pir|PIRSF000182     183     -27     2  
  fig|224914.1.peg.1924     fig|PF001705     pir|PIRSF001591     102     0     0  
  fig|224308.1.peg.1824     fig|PF003427     pir|PIRSF001593     36     0     0  
  fig|224308.1.peg.1825     fig|PF000095     pir|PIRSF001406     5     -1     0  
  fig|224308.1.peg.1826     fig|PF000193     pir|PIRSF001367     13     -7     3  
  fig|262316.1.peg.2310     fig|PF000193     pir|PIRSF015582     0     -42     1  
  fig|224308.1.peg.1829     fig|PF000104     pir|PIRSF001552     291     -584     3  
  fig|224308.1.peg.1829     fig|PF001188     pir|PIRSF001552     29     -41     3  
  fig|272558.1.peg.1137     fig|PF001188     pir|PIRSF001550     30     -11     2  
  fig|224308.1.peg.3904     fig|PF000160     pir|PIRSF000859     15     -13     1  
  fig|224308.1.peg.3904     fig|PF000359     pir|PIRSF000859     13     -25     1  
  fig|262316.1.peg.3861     fig|PF000359     pir|PIRSF000858     28     -99     2  
  fig|262316.1.peg.3861     fig|PF000530     pir|PIRSF000858     57     -74     2  
  fig|262316.1.peg.3861     fig|PF003527     pir|PIRSF000858     57     -64     2  
  fig|224308.1.peg.3903     fig|PF000530     pir|PIRSF012663     16     -21     1  
  fig|224308.1.peg.3903     fig|PF003527     pir|PIRSF012663     13     -7     1  
  fig|224308.1.peg.1717     fig|PF001265     pir|PIRSF500082     6     0     0  

Leucine Degradation compared to PFAM

pegFamily 1Family 2ForAgainstRed
  fig|224308.1.peg.3860     fig|PF002066     pfam|PF01063.8     3     -1     0  
  fig|224308.1.peg.2409     fig|PF001207     pfam|PF00676.9     16     -11     1  
  fig|224308.1.peg.2409     fig|PF002751     pfam|PF00676.9     16     -3     1  
  fig|272558.1.peg.213     fig|PF001158     pfam|PF00676.9     11     -122     5  
  fig|224308.1.peg.2408     fig|PF000067     pfam|PF02779.12     17     -1     1  
  fig|224308.1.peg.2408     fig|PF000067     pfam|PF02780.9     17     -1     1  
  fig|224308.1.peg.2408     fig|PF001487     pfam|PF02779.12     17     -26     1  
  fig|224308.1.peg.2408     fig|PF001487     pfam|PF02780.9     17     -26     1  
  fig|224914.1.peg.2120     fig|PF000067     pfam|PF00676.9     145     -3     1  
  fig|224914.1.peg.2120     fig|PF001487     pfam|PF00676.9     190     -56     1  
  fig|258594.1.peg.2850     fig|PF000067     pfam|PF00364.11     149     -106     3  
  fig|258594.1.peg.2850     fig|PF001487     pfam|PF00364.11     195     -233     3  
  fig|258594.1.peg.2850     fig|PF002666     pfam|PF00364.11     137     -279     3  
  fig|258594.1.peg.2850     fig|PF002666     pfam|PF02779.12     1     -67     2  
  fig|258594.1.peg.2850     fig|PF002666     pfam|PF02780.9     1     -67     2  
  fig|227377.1.peg.612     fig|PF001864     pfam|PF00198.12     9     -94     1  
  fig|227377.1.peg.612     fig|PF001864     pfam|PF00364.11     11     -98     2  
  fig|227377.1.peg.612     fig|PF001864     pfam|PF02817.6     11     -99     2  
  fig|224308.1.peg.1463     fig|PF003391     pfam|PF00070.16     4     -3     2  
  fig|224308.1.peg.1463     fig|PF003391     pfam|PF07992.2     4     -3     2  
  fig|224308.1.peg.1463     fig|PF003391     pfam|PF02852.11     19     -2     1  
  fig|224914.1.peg.145     fig|PF000100     pfam|PF00070.16     22     0     0  
  fig|224914.1.peg.145     fig|PF000100     pfam|PF07992.2     22     0     0  
  fig|224914.1.peg.145     fig|PF000100     pfam|PF02852.11     22     0     0  
  fig|257310.1.peg.2524     fig|PF003391     pfam|PF00364.11     765     -255     4  
  fig|119219.1.peg.4104     fig|PF003391     pfam|PF00403.14     840     -281     4  
  fig|224308.1.peg.1830     fig|PF000094     pfam|PF00441.13     37     -219     4  
  fig|224308.1.peg.1830     fig|PF000094     pfam|PF02770.8     82     -247     4  
  fig|224308.1.peg.1830     fig|PF000094     pfam|PF02771.6     104     -250     4  
  fig|224308.1.peg.1830     fig|PF002044     pfam|PF00441.13     17     -11     1  
  fig|224308.1.peg.1830     fig|PF002044     pfam|PF02770.8     17     -11     1  
  fig|224308.1.peg.1830     fig|PF002044     pfam|PF02771.6     19     -12     1  
  fig|227882.1.peg.5280     fig|PF003232     pfam|PF02785.8     2     -30     4  
  fig|227882.1.peg.5280     fig|PF003232     pfam|PF00364.11     0     -21     4  
  fig|227882.1.peg.5280     fig|PF003232     pfam|PF00289.11     2     -30     4  
  fig|227882.1.peg.5280     fig|PF003232     pfam|PF02786.6     2     -30     4  
  fig|224308.1.peg.1826     fig|PF000193     pfam|PF00682.8     0     -7     3  
  fig|262316.1.peg.2310     fig|PF000193     pfam|PF03328.4     0     -34     1  
  fig|224308.1.peg.1829     fig|PF000104     pfam|PF00501.15     4     -280     1  
  fig|224308.1.peg.1829     fig|PF001188     pfam|PF00501.15     5     -11     1  
  fig|224308.1.peg.3904     fig|PF000160     pfam|PF01144.12     9     -11     1  
  fig|224308.1.peg.3904     fig|PF000359     pfam|PF01144.12     7     -19     1  
  fig|262316.1.peg.3861     fig|PF000530     pfam|PF01144.12     12     -38     2  
  fig|262316.1.peg.3861     fig|PF003527     pfam|PF01144.12     9     -23     2