A list of P450s in C. elegans

 

March 24, 2004

 

D. Nelson

 

My count is 76 full length intact P450s

and 8 pseudogenes

CYP25A6P, CYP31A1P, CYP31A4P, CYP31A5P, CYP33C10P, CYP33C12P, CYP33E3P, CYP35D2P

 

This list was sent from Daniel Lawson at Wormpep as a compilation of P450s and a cross-reference

to my CYP names.  The list has been used for the basis of a reannotation and revision of the

C. elegans P450s.  All CEXXXX numbers were blast searched against the C. elegans P450s in the

P450 blast server.  Any differences were examined and the sequences were revised as needed.  This

list has those sequences that match 100% between my set and WormPep marked with 100%.

pseudogenes and genes without a current Wormpep ID could not be compared this way. 

Sequences with a WormPep ID but not a 100% mark next to them did not match completely. 

I feel after looking at these genes that my assemblies are better than WormPep. 

Though Wormpep had many genes that were better than my earlier assemblies, if I agreed,

then I changed my sequence, so only the non-agreeing sequences are left without the 100%.

Some annotations are given, but the evidence for these is under the evidence for revisions link.

 

http://www.pir.uniprot.org/cgi-bin/textSearch

 

This link will take you to UNIPROT where you can search for the WormPep ID numbers or the UNIPROT IDs.

I hope the 23 genes that do not agree can be resolved soon leaving a 100% agreement.

I hope that Wormpep IDs will also be issued for all pseudogenes.  Daniel Lawson is going over

this data and should be able to reach a consensus about these genes.

 

The CYP29A1 gene is fused in WormPep.  I don't agree with this.

The CYP13B1 gene has three isoforms in WormPep, none of them match CYP13B2.

I think the true sequence is a hybrid of isoform a and isoform c.

daf-9 = CYP22A1 has two isoforms.  Isoform a has EST support.

 

The official C. elegans nomenclature for P450s is a root ccp- followed by numbers and letters.

I am trying to get this changed to cyp- but cyp- is used for 17 cyclophilin genes.  Negotiations are

underway to switch those to another root like ppi- for peptidyl prolyl isomerase.

 

 

Clone name      wormpepID              UNIPROT ID Genbank Acc#  CYP name

========================================================================================

B0213.10         CE16781   100%         TR:O44655 AAC47935.1 "(CYP34A5)"

B0213.11         CE35205   100%         TR:O44656 AAC47936.2 "(CYP34A6)"

B0213.12         CE16783   100%         TR:O44657 AAC47937.1 "(CYP34A7)"

B0213.14         CE16784                TR:O44658 AAC47938.1 "(CYP34A8)"

  some extra sequence, some missing sequence

B0213.15         CE30582   100%         TR:O44659 AAC47939.2 "(CYP34A9)"

B0213.16         CE16786   100%         TR:O61204 AAC47940.1 "(CYP34A10)"

B0304.3          CE27050   100%         TR:Q27465 AAK31395.1 "(CYP23A1)"

B0331.1          CE15551   100%         TR:O45219 CAB11775.1 "(CYP29A4)"

C01F6.3          n/a               ccp-31A1                  "(CYP31A1P) pseudogene"

C03G6.14         CE07888                TR:O02627 AAB52314.1 "(CYP35A1)"

C03G6.15         CE35217   100%         TR:O02628 AAB52315.2 "(CYP35A2)"

C06B3.3          CE27662   100%         TR:O02651 CAB03393.2 "(CYP35C1)"

C12D5.7          CE06809   100%         TR:Q27470 AAA98571.1 "(CYP33A1)"

C25E10.2         CE35248   100%         TR:Q27471 AAA92310.2 "(CYP33B1)"

C26F1.2          CE32809                TR:Q27472 AAB37074.3 "(CYP32A1)"

C34B7.3          CE08567   100%         SW:P90771 CAB05702.1 "(CYP36A1)"

C36A4.1          CE03070                TR:Q27477 CAA91268.1 "(CYP25A1)"

  middle exon wrong

C36A4.2          CE03071                TR:Q27476 CAA91267.1 "(CYP25A2)"

  some extra seq in middle

C36A4.3          n/a                                         "(CYP25A3)"

C36A4.6          CE03074   100%         TR:Q27479 CAA91272.1 "(CYP25A4)"

C41G6.1          CE15699                TR:O17655 CAB02827.1 "(CYP34A3)"

  frameshifted might be a pseudogene or seq error

C44C10.2         CE05409                TR:Q27480 CAA93636.1 "(CYP29A1)"

  artifactual gene fusion.  Fix this

C45H4.2          CE08736                TR:O44704 AAC25869.1 "(CYP33C1)"

C45H4.17         CE25818   100%         TR:O44706 AAC25881.2 "(CYP33C2)"

C49C8.4          CE31452   100%         TR:Q27482 AAB03125.2 "(CYP33E1)"

C49G7.8          CE08866   100%         TR:O16220 AAK18902.1 "(CYP35A4)"

C50H11.15        CE08931   100%         TR:O16482 AAG24002.1 "(CYP33C9)"

E03E2.1          CE29747   100%         TR:O17329 AAB71246.2 "(CYP43A1)"

F01D5.9          CE35449   100%         TN:CAB04044 CAB04044.2 "(CYP37A1)"

F02C12.5a        CE09177                TR:O17624 CAA91023.1 "(CYP13B1)"

  this isoform leaves out an important exon found in isoform c

F02C12.5b        CE09178                TR:O17624 CAA91024.1 "(CYP13B1)"

  this isoform has a short N-term compared to CYP13B2

  The best gene model would have isoform a N-term and isoform c C-term.

F08F3.7          CE09262 100% ccp-14A5  TR:Q27531 AAB04873.1 "(CYP14A5)"

F14F7.2          CE15822  100%          TR:O17806 CAB04112.1 "(CYP13A11)"

F14F7.3          CE15823  100%          TR:O17807 CAB04113.1 "(CYP13A12)"

F14H3.13  n/a                                                "(CYP35D2P) pseudogene"

F14H3.10         CE15834    100%        TR:O45364 CAB05484.1 "(CYP35D1)"

F23A7.3          CE09577                TR:Q93556 CAB02977.1 "

(fusion protein with CYP29A1 top half is not a P450)"

F28G4.1          CE15919    100%        TR:O17851 CAB07604.1 "(CYP37B1)"

F41B5.2          CE10218                TR:O16673 AAG24100.1 "(CYP33C7)"

  C-term wrong

F41B5.3          CE27379    100%        TR:O16671 AAG24101.2 "(CYP33C5)"

F41B5.4          CE10222    100%        TR:O16670 AAG24106.1 "(CYP33C3)"

F41B5.5          n/a                                         "(CYP33C10P) pseudogene"

F41B5.7          CE10228                TR:O16672 AAG24104.1 "(CYP33C6)"

  C-term wrong

F42A6.4          CE17056                TR:O44485 AAB92049.1 "(CYP25A5)"

  contains 1 stop codon possible pseudogene or seq error

F42A9.4          n/a                                         "(CYP33E3P) pseudogene"

F42A9.5          CE07227    100%        TR:Q27499 AAB03160.1 "(CYP33E2)"

F44C8.1          CE10378    100%        TR:O16362 AAB65888.1 "(CYP33C4)"

H02I12.8         CE32901                TR:O45605 CAB07222.2 "(CYP31A2)"

  add MWNSFIYNL

K05D4.4          CE16230    100%        TR:O45659 CAB07250.1 "(CYP33D1)"

K06B9.1          n/a                                         "(CYP25A6P) pseudogene"

K06G5.2          CE34202                TR:Q9XUT8 CAB04582.2 "(CYP13B2)"

  N-term is wrong too short see CYP13B1

K07C6.2          CE17173    100%        TR:O44652 AAB94245.1 "(CYP35B3)"

K07C6.3          CE17174    100%        TR:O44651 AAB94246.1 "(CYP35B2)"

K07C6.4          CE17175                TR:O44650 AAB94247.1 "(CYP35B1)"

  extra seq needs to be removed

K07C6.5          CE17176    100%        TR:O44649 AAB94248.1 "(CYP35A5)"

K09A11.2         CE03473    100%        TR:Q27506 CAA90616.1 "(CYP14A1)"

K09A11.3         CE03474    100%        TR:Q27505 CAA90615.1 "(CYP14A2)"

K09A11.4         CE03475    100%        TR:Q27507 CAA90617.1 "(CYP14A3)"

K09D9.2          CE21056    100%        TR:Q9N5I1 AAF39921.1 "(CYP35A3)"

R04D3.1          CE06222    100%        TR:Q27508 CAA94168.1 "(CYP14A4)"

R08F11.3         CE12584    100%        TR:O02641 AAB54245.1 "(CYP33C8)"

T09H2.1          CE18231    100%        TR:O61935 AAC17779.1 "(CYP34A4)"

T10B9.1          CE01654    100%        SW:Q27513 CAA88603.1 "(CYP13A4)"

T10B9.2          CE01656    100%        SW:Q27514 CAA88604.1 "(CYP13A5)"

T10B9.3          CE01657    100%        SW:Q27515 CAA88605.1 "(CYP13A6)"

T10B9.4          CE13541    100%        SW:Q27516 CAB09134.1 "(CYP13A8)"

T10B9.5          CE01658    100%        SW:Q27517 CAA88606.1 "(CYP13A3)"

T10B9.6          n/a                                         "(CYP13A9P) pseudogene"

T10B9.7          CE01659    100%        SW:Q27518 CAA88607.1 "(CYP13A2)"

T10B9.8          CE01660    100%        SW:Q27520 CAA88610.1 "(CYP13A1)"

T10B9.10         CE01655 100% ccp-13A7  SW:Q27519 CAA88609.1 "(CYP13A7)"

T10H4.10         CE16395    100%        TR:O62378 CAB03340.1 "(CYP34A1)"

T10H4.11         CE16396    100%        TR:O62377 CAB03339.1 "(CYP34A2)"

T13C5.1a         CE27206    100% daf-9  TR:Q27523 AAK39293.1 "(CYP22A1)"

T13C5.1b         CE30451      daf-9     TR:Q8WRT7 AAM15602.1 "(CYP22A1)"

  odd unsupported N-term in this isoform of CYP22A1

T19B10.1         CE06455    100%        TR:Q21424 CAA98548.1 "(CYP29A2)"

Y17D7A.4         CE16589                TN:CAB04001 CAA16294.2 "(CYP33D3)"

  some extra sequence present

Y17G9B.3         CE24183                TR:Q9N574 AAF60444.1 "(CYP31A3)"

  some extra sequence present

Y17G9B.x   n/a                                               "(CYP31A4P) pseudogene"

  downstream of 31A3

Y38C9B.1         CE35365    100%        TR:Q9N525 AAF60505.2 "(CYP29A3)"

Y62E10A.15       CE28717                TR:Q9U1X2 CAB60602.2 "(CYP31A5P) pseudogene"

  add some sequence

ZK1320.4         CE30715                SW:Q09653 CAA87042.2 "(CYP13A10)"

  delete some sequence

ZK177.5          CE25682    100% ccp-44 SW:Q09660 AAG00050.1 "(CYP44A1)

mitochondrial"

Y49C4A.9         CE22218    100%        TR:Q965T7 AAK72319.1 "(CYP33C11)"

Y80D3A.5         CE23108                TR:Q9U1R5 CAB60436.1 "(CYP42A1)"

  C-term is wrong

Y5H2B.6          CE21315                TR:Q9N4Q4 AAF59628.1 "(CYP33C12P)"

  missing C-term

Y5H2B.5          CE26222                TR:Q9N4Q5 AAF59629.2 "(CYP32B1)"

  add some sequence

==========================================================================