POTbaseMS
Current version is 0.8
I.) Description
The scaffold of the POTbase is a OrthoMCL-based clustering of 21 plant proteomes resulting in 64,820 ORTHO clusters (Sebastian Proost, MPI-MP manuscript in preparation). By BLAST (cutoff E-value < E-5), the protein sequences of Nicotiana sylvestris and Nicotinana tomentosiformis were assigend to 16,020 of the 64,829 reference ORTHO clusters .
The resulting "POTs" ("Putative Orthologs of Tobacco") were numbered according to the following nomenclature:
- POT#: protein was assigned to a reference cluster
- POR#: protein was assigned to a reference orphan
- UNA#: protein was not assigned to any reference protein
- PCP#: 98 chloroplast encoded proteins (N. tabacum)
- PMT#: 156 mitochondrial encoded proteins (N. tabacum)
II.) Curation
1. POT Splittings
PPR protein family
ORTHOs of the scaffold network that contain members of the PPR family were split into subORTHOs (Proost et al., manuscript in preparation). Nicotiana sequences were assigned to the corresponding POTs.
Other protein families
POT000967 (containing glyceraldehyde-3-phosphate dehydrogenases A & B)
was subsplit into POT000967a and -b (GAPDH-A and -B, respectively):
gi|697150722|ref|XP_009629570.1| POT000967b
gi|697153656|ref|XP_009631078.1| POT000967a
gi|697173886|ref|XP_009595874.1| POT000967b
gi|698457909|ref|XP_009780936.1| POT000967b
gi|698478327|ref|XP_009786329.1| POT000967b
gi|698510587|ref|XP_009800449.1| POT000967a
POT000278 (containing chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases)
was subsplit into POT000278a, -b and -c (c: probably pseudo)
gi|697105321|ref|XP_009606469.1 POT000278a
gi|697124150|ref|XP_009616068.1 POT000278a
gi|697140501|ref|XP_009624354.1 POT000278b
gi|697156339|ref|XP_009586920.1 POT000278a
gi|697168461|ref|XP_009593112.1 POT000278b
gi|697176947|ref|XP_009597424.1 POT000278a
gi|698428456|ref|XP_009789769.1 POT000278a
gi|698455273|ref|XP_009780356.1 POT000278a
gi|698481129|ref|XP_009787576.1 POT000278a
gi|698491156|ref|XP_009792011.1 POT000278a
gi|698508009|ref|XP_009799303.1 POT000278c
gi|698542277|ref|XP_009766349.1 POT000278b
POT000723 (erroneous transcript fusion in scaffold)
gi|697104297|ref|XP_009605957.1 POT000723a
gi|697104299|ref|XP_009605958.1 POT000723b
gi|697111057|ref|XP_009609407.1 POT000723a
gi|697111059|ref|XP_009609408.1 POT000723b
gi|698435708|ref|XP_009800885.1 POT000723a
gi|698435720|ref|XP_009800901.1 POT000723b
gi|698498451|ref|XP_009795130.1 POT000723a
gi|698588092|ref|XP_009779361.1 POT000723b
gi|698588096|ref|XP_009779362.1 POT000723b
POT000366 (ftsH protease subunits and erroneous transcript fusion in scaffold)
gi|697101290|ref|XP_009595359.1 POT000366c
gi|697106040|ref|XP_009606853.1 POT000366a
gi|697122036|ref|XP_009615004.1 POT000366b
gi|697129561|ref|XP_009618840.1 POT000366a
gi|697186967|ref|XP_009602523.1 POT000366z
gi|698459837|ref|XP_009781388.1 POT000366z
gi|698496042|ref|XP_009794094.1 POT000366b
gi|698547278|ref|XP_009767982.1 POT000366a
gi|698548064|ref|XP_009768214.1 POT000366c
gi|698548067|ref|XP_009768215.1 POT000366c
gi|698581750|ref|XP_009777632.1 POT000366a
POT000109 (clp protease subunits)
gi|697118272|ref|XP_009613059.1 POT000109d
gi|697123347|ref|XP_009615664.1 POT000109c
gi|697149867|ref|XP_009629142.1 POT000109a
gi|697149869|ref|XP_009629143.1 POT000109a
gi|697149871|ref|XP_009629144.1 POT000109a
gi|697149873|ref|XP_009629145.1 POT000109a
gi|697161117|ref|XP_009589338.1 POT000109b
gi|697167642|ref|XP_009592686.1 POT000109c
gi|697167644|ref|XP_009592687.1 POT000109c
gi|697176624|ref|XP_009597265.1 POT000109d
gi|697189681|ref|XP_009603901.1 POT000109e
gi|698426192|ref|XP_009786473.1 POT000109e
gi|698483248|ref|XP_009788495.1 POT000109d
gi|698491653|ref|XP_009792235.1 POT000109a
gi|698491655|ref|XP_009792236.1 POT000109a
gi|698492154|ref|XP_009792440.1 POT000109d
gi|698505347|ref|XP_009798134.1 POT000109c
gi|698508933|ref|XP_009799705.1 POT000109b
gi|698538470|ref|XP_009765150.1 POT000109c
gi|698538473|ref|XP_009765151.1 POT000109c
gi|698538476|ref|XP_009765152.1 POT000109c
gi|698552141|ref|XP_009769540.1 POT000109c
2. Removal of non-assigned proteins from N. tomentosiformis
All UNAs from N. tomentosiformis were removed from POTbaseMS.
3. Removal of redundant entries
the following entries were omitted from POTbaseMS, because they are redundant with chloroplast or mitochondrial encoded proteins:
gi|697098262|ref|XP_009625853.1
gi|697128022|ref|XP_009618060.1
gi|697129483|ref|XP_009618804.1
gi|697143893|ref|XP_009626068.1
gi|697172234|ref|XP_009595052.1
gi|697172236|ref|XP_009595053.1
gi|697172449|ref|XP_009595162.1
gi|697172478|ref|XP_009595174.1
gi|697174559|ref|XP_009596209.1
gi|697186402|ref|XP_009602239.1
gi|698451580|ref|XP_009777945.1
gi|698517853|ref|XP_009803808.1
gi|698525526|ref|XP_009759578.1
gi|698558526|ref|XP_009771313.1
gi|698576553|ref|XP_009776241.1
gi|698585443|ref|XP_009778651.1
gi|698585446|ref|XP_009778652.1
gi|126165910|ref|YP_358662.2
gi|126165911|ref|YP_358680.2
gi|126165917|ref|YP_398849.2
gi|126165918|ref|YP_398867.2
gi|200003946|ref|YP_398850.2
gi|697112343|ref|XP_009610049.1
gi|697150573|ref|XP_009629495.1
gi|698479552|ref|XP_009786858.1
gi|698532107|ref|XP_009762881.1
gi|698575260|ref|XP_009775887.1
gi|78102510|ref|YP_358651.1
gi|78102511|ref|YP_358652.1
gi|78102512|ref|YP_358653.1
gi|78102513|ref|YP_358654.1
gi|78102514|ref|YP_358655.1
gi|78102515|ref|YP_358656.1
gi|78102516|ref|YP_358657.1
gi|78102517|ref|YP_358658.1
gi|78102518|ref|YP_358659.1
gi|78102519|ref|YP_358660.1
gi|78102520|ref|YP_358661.1
gi|78102522|ref|YP_358663.1
gi|78102523|ref|YP_358664.1
gi|78102524|ref|YP_358665.1
gi|78102525|ref|YP_358666.1
gi|78102526|ref|YP_358667.1
gi|78102527|ref|YP_358668.1
gi|78102528|ref|YP_358669.1
gi|78102529|ref|YP_358670.1
gi|78102530|ref|YP_358671.1
gi|78102531|ref|YP_358672.1
gi|78102532|ref|YP_358673.1
gi|78102533|ref|YP_358674.1
gi|78102534|ref|YP_358675.1
gi|78102535|ref|YP_358676.1
gi|78102536|ref|YP_358677.1
gi|78102537|ref|YP_358678.1
gi|78102538|ref|YP_358679.1
gi|78102540|ref|YP_358681.1
gi|78102541|ref|YP_358682.1
gi|78102542|ref|YP_358683.1
gi|78102543|ref|YP_358684.1
gi|78102544|ref|YP_358685.1
gi|78102545|ref|YP_358686.1
gi|78102546|ref|YP_358687.1
gi|78102547|ref|YP_358688.1
gi|78102548|ref|YP_358689.1
gi|78102549|ref|YP_358690.1
gi|78102550|ref|YP_358691.1
gi|78102551|ref|YP_358692.1
gi|78102552|ref|YP_358693.1
gi|78102553|ref|YP_358694.1
gi|78102554|ref|YP_358695.1
gi|78102555|ref|YP_358696.1
gi|78102556|ref|YP_358697.1
gi|78102557|ref|YP_358698.1
gi|78102558|ref|YP_358699.1
gi|78102559|ref|YP_358700.1
gi|78102560|ref|YP_358701.1
gi|78102561|ref|YP_358702.1
gi|78102562|ref|YP_358650.1
gi|78102563|ref|YP_358703.1
gi|78102564|ref|YP_358704.1
gi|78102565|ref|YP_358705.1
gi|78102566|ref|YP_358706.1
gi|78102567|ref|YP_358707.1
gi|78102568|ref|YP_358708.1
gi|78102569|ref|YP_358709.1
gi|78102570|ref|YP_358710.1
gi|78102571|ref|YP_358711.1
gi|78102572|ref|YP_358712.1
gi|78102573|ref|YP_358713.1
gi|78102574|ref|YP_358714.1
gi|78102575|ref|YP_358715.1
gi|78102577|ref|YP_358717.1
gi|78102578|ref|YP_358718.1
gi|78102579|ref|YP_358719.1
gi|78102580|ref|YP_358720.1
gi|78102581|ref|YP_358721.1
gi|78102582|ref|YP_358722.1
gi|78102586|ref|YP_358726.1
gi|78102587|ref|YP_358727.1
gi|78102588|ref|YP_358728.1
gi|78102589|ref|YP_358649.1
gi|78102590|ref|YP_358729.1
gi|78102591|ref|YP_358730.1
gi|78102593|ref|YP_358732.1
gi|78102594|ref|YP_358733.1
gi|78102595|ref|YP_358734.1
gi|78102596|ref|YP_358735.1
gi|78102597|ref|YP_358736.1
gi|78102598|ref|YP_358737.1
gi|78102599|ref|YP_358738.1
gi|78102600|ref|YP_358739.1
gi|78102601|ref|YP_358740.1
gi|78102602|ref|YP_358741.1
gi|78102603|ref|YP_358742.1
gi|78102604|ref|YP_358743.1
gi|78102605|ref|YP_358744.1
gi|78102606|ref|YP_358745.1
gi|78102607|ref|YP_358746.1
gi|78102609|ref|YP_358748.1
gi|78102610|ref|YP_358749.1
gi|78102611|ref|YP_358750.1
gi|78102612|ref|YP_358751.1
gi|78102613|ref|YP_358752.1
gi|78102617|ref|YP_358756.1
gi|78102618|ref|YP_358757.1
gi|78102619|ref|YP_358758.1
gi|81301541|ref|YP_398838.1
gi|81301542|ref|YP_398839.1
gi|81301543|ref|YP_398840.1
gi|81301544|ref|YP_398841.1
gi|81301545|ref|YP_398842.1
gi|81301546|ref|YP_398843.1
gi|81301547|ref|YP_398844.1
gi|81301548|ref|YP_398845.1
gi|81301549|ref|YP_398846.1
gi|81301550|ref|YP_398847.1
gi|81301551|ref|YP_398848.1
gi|81301554|ref|YP_398851.1
gi|81301555|ref|YP_398852.1
gi|81301556|ref|YP_398853.1
gi|81301557|ref|YP_398854.1
gi|81301558|ref|YP_398855.1
gi|81301559|ref|YP_398856.1
gi|81301560|ref|YP_398857.1
gi|81301561|ref|YP_398858.1
gi|81301562|ref|YP_398859.1
gi|81301563|ref|YP_398860.1
gi|81301564|ref|YP_398861.1
gi|81301565|ref|YP_398862.1
gi|81301566|ref|YP_398863.1
gi|81301567|ref|YP_398864.1
gi|81301568|ref|YP_398865.1
gi|81301569|ref|YP_398866.1
gi|81301571|ref|YP_398868.1
gi|81301572|ref|YP_398869.1
gi|81301573|ref|YP_398870.1
gi|81301574|ref|YP_398871.1
gi|81301575|ref|YP_398872.1
gi|81301576|ref|YP_398873.1
gi|81301577|ref|YP_398874.1
gi|81301578|ref|YP_398875.1
gi|81301579|ref|YP_398876.1
gi|81301580|ref|YP_398877.1
gi|81301581|ref|YP_398878.1
gi|81301582|ref|YP_398879.1
gi|81301583|ref|YP_398880.1
gi|81301584|ref|YP_398881.1
gi|81301585|ref|YP_398882.1
gi|81301586|ref|YP_398883.1
gi|81301587|ref|YP_398884.1
gi|81301588|ref|YP_398885.1
gi|81301589|ref|YP_398886.1
gi|81301590|ref|YP_398887.1
gi|81301591|ref|YP_398888.1
gi|81301592|ref|YP_398837.1
gi|81301593|ref|YP_398889.1
gi|81301594|ref|YP_398890.1
gi|81301595|ref|YP_398891.1
gi|81301596|ref|YP_398892.1
gi|81301597|ref|YP_398893.1
gi|81301598|ref|YP_398894.1
gi|81301599|ref|YP_398895.1
gi|81301600|ref|YP_398896.1
gi|81301601|ref|YP_398897.1
gi|81301602|ref|YP_398898.1
gi|81301603|ref|YP_398899.1
gi|81301604|ref|YP_398900.1
gi|81301605|ref|YP_398901.1
gi|81301607|ref|YP_398903.1
gi|81301608|ref|YP_398904.1
gi|81301609|ref|YP_398905.1
gi|81301610|ref|YP_398906.1
gi|81301611|ref|YP_398907.1
gi|81301612|ref|YP_398908.1
gi|81301616|ref|YP_398912.1
gi|81301617|ref|YP_398913.1
gi|81301618|ref|YP_398914.1
gi|81301619|ref|YP_398836.1
gi|81301620|ref|YP_398915.1
gi|81301621|ref|YP_398916.1
gi|81301622|ref|YP_398917.1
gi|81301623|ref|YP_398918.1
gi|81301624|ref|YP_398919.1
gi|81301625|ref|YP_398920.1
gi|81301626|ref|YP_398921.1
gi|81301627|ref|YP_398922.1
gi|81301628|ref|YP_398923.1
gi|81301629|ref|YP_398924.1
gi|81301630|ref|YP_398925.1
gi|81301631|ref|YP_398926.1
gi|81301632|ref|YP_398927.1
gi|81301633|ref|YP_398928.1
gi|81301634|ref|YP_398929.1
gi|81301635|ref|YP_398930.1
gi|81301636|ref|YP_398931.1
gi|81301637|ref|YP_398932.1
gi|81301638|ref|YP_398933.1
gi|81301639|ref|YP_398934.1
gi|81301640|ref|YP_398935.1
gi|81301641|ref|YP_398936.1
gi|81301642|ref|YP_398937.1
gi|81301643|ref|YP_398938.1
gi|81301647|ref|YP_398942.1
gi|81301648|ref|YP_398943.1
gi|81301649|ref|YP_398944.1