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

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

GenomepegFamily 1Family 2ForAgainstRed
Escherichia coli K12fig|83333.1.peg.1994fig|PF000056pir|PIRSF00048618-71
Symbiobacterium thermophilum IAM 14863fig|292459.1.peg.2713fig|PF000056pir|PIRSF0066506600
Listeria innocua Clip11262fig|272626.1.peg.573fig|PF003447pir|PIRSF0066501000
Listeria innocua Clip11262fig|272626.1.peg.574fig|PF000991pir|PIRSF00154919-72
Thermotoga maritima MSB8fig|243274.1.peg.1033fig|PF000991pir|PIRSF0273790-171
Escherichia coli K12fig|83333.1.peg.2001fig|PF001505pir|PIRSF001258108-1472
Escherichia coli K12fig|83333.1.peg.2001fig|PF002226pir|PIRSF001258111-1552
Listeria innocua Clip11262fig|272626.1.peg.566fig|PF001505pir|PIRSF00683312000
Listeria innocua Clip11262fig|272626.1.peg.567fig|PF002226pir|PIRSF02924311200
Escherichia coli K12fig|83333.1.peg.1999fig|PF002424pir|PIRSF00148435-53
Escherichia coli K12fig|83333.1.peg.2000fig|PF001996pir|PIRSF0014541500
Schizosaccharomyces pombefig|4896.1.peg.2360fig|PF001996pir|PIRSF036936122-3443
Schizosaccharomyces pombefig|4896.1.peg.2360fig|PF002743pir|PIRSF036936241-3392
Escherichia coli K12fig|83333.1.peg.1998fig|PF002743pir|PIRSF0004957-21
Escherichia coli K12fig|83333.1.peg.1997fig|PF001687pir|PIRSF00141027-812
Escherichia coli K12fig|83333.1.peg.1997fig|PF003299pir|PIRSF001410290-1562
Listeria innocua Clip11262fig|272626.1.peg.571fig|PF003299pir|PIRSF001409115-33
Escherichia coli K12fig|83333.1.peg.1996fig|PF000244pir|PIRSF000518316-52
Listeria innocua Clip11262fig|272626.1.peg.2026fig|PF000244pir|PIRSF006455327-31
Lactococcus lactis subsp. lactis Il1403fig|272623.1.peg.1241fig|PF000244pir|PIRSF005473374-52
Listeria innocua Clip11262fig|272626.1.peg.575fig|PF001687pir|PIRSF01905819-353
Pseudomonas aeruginosa PAO1fig|208964.1.peg.6fig|PF001687pir|PIRSF0046822-693
Schizosaccharomyces pombefig|4896.1.peg.210fig|PF001687pir|PIRSF01720338-374
Corynebacterium efficiens YS-314fig|196164.1.peg.1995fig|PF003597pir|PIRSF004949800
Corynebacterium efficiens YS-314fig|196164.1.peg.809fig|PF003597pir|PIRSF5001942000
Escherichia coli K12fig|83333.1.peg.1995fig|PF002941pir|PIRSF0000991100

Histidine Biosynthesis compared to PFAM

GenomepegFamily 1Family 2ForAgainstRed
Escherichia coli K12fig|83333.1.peg.1994fig|PF000056pfam|PF08029.117-21
Listeria innocua Clip11262fig|272626.1.peg.573fig|PF003447pfam|PF01634.8200
Listeria innocua Clip11262fig|272626.1.peg.574fig|PF000991pfam|PF00587.144-42
Escherichia coli K12fig|83333.1.peg.2001fig|PF001505pfam|PF01502.893-1062
Escherichia coli K12fig|83333.1.peg.2001fig|PF001505pfam|PF01503.739-351
Escherichia coli K12fig|83333.1.peg.2001fig|PF002226pfam|PF01502.839-381
Escherichia coli K12fig|83333.1.peg.2001fig|PF002226pfam|PF01503.796-1172
Neurospora crassafig|5141.1.peg.8508fig|PF001505pfam|PF00815.9283-3473
Neurospora crassafig|5141.1.peg.8508fig|PF002226pfam|PF00815.9286-3603
Neurospora crassafig|5141.1.peg.8508fig|PF002941pfam|PF00815.92-1942
Neurospora crassafig|5141.1.peg.8508fig|PF002941pfam|PF01502.8122-5783
Neurospora crassafig|5141.1.peg.8508fig|PF002941pfam|PF01503.7122-5783
Schizosaccharomyces pombefig|4896.1.peg.2360fig|PF001996pfam|PF00117.15122-3363
Schizosaccharomyces pombefig|4896.1.peg.2360fig|PF002743pfam|PF00117.151-781
Schizosaccharomyces pombefig|4896.1.peg.2360fig|PF002743pfam|PF00977.10241-3402
Escherichia coli K12fig|83333.1.peg.1997fig|PF001687pfam|PF00475.827-702
Escherichia coli K12fig|83333.1.peg.1997fig|PF003299pfam|PF00475.827-591
Nostoc sp. PCC 7120fig|103690.1.peg.384fig|PF003299pfam|PF00702.130-622
Photorhabdus luminescens subsp. laumondii TTO1fig|243265.1.peg.1484fig|PF000244pfam|PF00815.9264-3993
Photorhabdus luminescens subsp. laumondii TTO1fig|243265.1.peg.1484fig|PF002941pfam|PF00155.9239-3472
Listeria innocua Clip11262fig|272626.1.peg.575fig|PF001687pfam|PF02811.70-353

Leucine Degradation compared to PIR

GenomepegFamily 1Family 2ForAgainstRed
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3860fig|PF002066pir|PIRSF006468188-41
Bacillus anthracis str. Amesfig|198094.1.peg.1301fig|PF002066pir|PIRSF00052312300
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2409fig|PF001207pir|PIRSF00015226-141
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2409fig|PF002751pir|PIRSF00015223-31
Bacillus halodurans C-125fig|272558.1.peg.213fig|PF001158pir|PIRSF00015231-1475
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF000067pir|PIRSF00015537-21
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF001487pir|PIRSF00015541-291
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF000067pir|PIRSF036563149-1103
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF001487pir|PIRSF036563195-2363
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF002666pir|PIRSF036563137-2793
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2407fig|PF001388pir|PIRSF00043231-11
Shewanella oneidensis MR-1fig|211586.1.peg.2120fig|PF001388pir|PIRSF00043313200
Streptomyces avermitilis MA-4680fig|227882.1.peg.4367fig|PF001864pir|PIRSF000432197-1764
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1463fig|PF003391pir|PIRSF000210164-104
Brucella melitensis 16Mfig|224914.1.peg.145fig|PF000100pir|PIRSF0002102200
Bordetella bronchiseptica RB50fig|257310.1.peg.2524fig|PF003391pir|PIRSF000212769-2634
Ralstonia metallidurans CH34fig|119219.1.peg.4104fig|PF003391pir|PIRSF000350840-2884
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF000094pir|PIRSF000182518-4275
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF002044pir|PIRSF000182183-272
Brucella melitensis 16Mfig|224914.1.peg.1924fig|PF001705pir|PIRSF00159110200
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1824fig|PF003427pir|PIRSF0015933600
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1825fig|PF000095pir|PIRSF0014065-10
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1826fig|PF000193pir|PIRSF00136713-73
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.2310fig|PF000193pir|PIRSF0155820-421
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1829fig|PF000104pir|PIRSF001552291-5843
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1829fig|PF001188pir|PIRSF00155229-413
Bacillus halodurans C-125fig|272558.1.peg.1137fig|PF001188pir|PIRSF00155030-112
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3904fig|PF000160pir|PIRSF00085915-131
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3904fig|PF000359pir|PIRSF00085913-251
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.3861fig|PF000359pir|PIRSF00085828-992
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.3861fig|PF000530pir|PIRSF00085857-742
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.3861fig|PF003527pir|PIRSF00085857-642
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3903fig|PF000530pir|PIRSF01266316-211
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3903fig|PF003527pir|PIRSF01266313-71
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1717fig|PF001265pir|PIRSF500082600

Leucine Degradation compared to PFAM

GenomepegFamily 1Family 2ForAgainstRed
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3860fig|PF002066pfam|PF01063.83-10
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2409fig|PF001207pfam|PF00676.916-111
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2409fig|PF002751pfam|PF00676.916-31
Bacillus halodurans C-125fig|272558.1.peg.213fig|PF001158pfam|PF00676.911-1225
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF000067pfam|PF02779.1217-11
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF000067pfam|PF02780.917-11
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF001487pfam|PF02779.1217-261
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.2408fig|PF001487pfam|PF02780.917-261
Brucella melitensis 16Mfig|224914.1.peg.2120fig|PF000067pfam|PF00676.9145-31
Brucella melitensis 16Mfig|224914.1.peg.2120fig|PF001487pfam|PF00676.9190-561
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF000067pfam|PF00364.11149-1063
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF001487pfam|PF00364.11195-2333
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF002666pfam|PF00364.11137-2793
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF002666pfam|PF02779.121-672
Rhodopseudomonas palustris CGA009fig|258594.1.peg.2850fig|PF002666pfam|PF02780.91-672
Coxiella burnetii RSA 493fig|227377.1.peg.612fig|PF001864pfam|PF00198.129-941
Coxiella burnetii RSA 493fig|227377.1.peg.612fig|PF001864pfam|PF00364.1111-982
Coxiella burnetii RSA 493fig|227377.1.peg.612fig|PF001864pfam|PF02817.611-992
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1463fig|PF003391pfam|PF00070.164-32
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1463fig|PF003391pfam|PF07992.24-32
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1463fig|PF003391pfam|PF02852.1119-21
Brucella melitensis 16Mfig|224914.1.peg.145fig|PF000100pfam|PF00070.162200
Brucella melitensis 16Mfig|224914.1.peg.145fig|PF000100pfam|PF07992.22200
Brucella melitensis 16Mfig|224914.1.peg.145fig|PF000100pfam|PF02852.112200
Bordetella bronchiseptica RB50fig|257310.1.peg.2524fig|PF003391pfam|PF00364.11765-2554
Ralstonia metallidurans CH34fig|119219.1.peg.4104fig|PF003391pfam|PF00403.14840-2814
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF000094pfam|PF00441.1337-2194
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF000094pfam|PF02770.882-2474
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF000094pfam|PF02771.6104-2504
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF002044pfam|PF00441.1317-111
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF002044pfam|PF02770.817-111
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1830fig|PF002044pfam|PF02771.619-121
Streptomyces avermitilis MA-4680fig|227882.1.peg.5280fig|PF003232pfam|PF02785.82-304
Streptomyces avermitilis MA-4680fig|227882.1.peg.5280fig|PF003232pfam|PF00364.110-214
Streptomyces avermitilis MA-4680fig|227882.1.peg.5280fig|PF003232pfam|PF00289.112-304
Streptomyces avermitilis MA-4680fig|227882.1.peg.5280fig|PF003232pfam|PF02786.62-304
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1826fig|PF000193pfam|PF00682.80-73
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.2310fig|PF000193pfam|PF03328.40-341
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1829fig|PF000104pfam|PF00501.154-2801
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.1829fig|PF001188pfam|PF00501.155-111
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3904fig|PF000160pfam|PF01144.129-111
Bacillus subtilis subsp. subtilis str. 168fig|224308.1.peg.3904fig|PF000359pfam|PF01144.127-191
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.3861fig|PF000530pfam|PF01144.1212-382
Mycobacterium avium subsp. paratuberculosis str. k10fig|262316.1.peg.3861fig|PF003527pfam|PF01144.129-232