NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q8T938 UniProt NPD GO	PROF_BRABE	Profilin	0.02	-	cyt	0					126
P18321 UniProt NPD GO	PROF_CLYJA	Profilin	0.02	-	cyt	0					139
P07274 UniProt NPD GO	PROF_YEAST	Profilin	0.02	-	cyt	0		actin cap [IPI] contractile ring (sensu Saccharomyces) [IDA]		1YPR	126
Q9SQI9 UniProt NPD GO	PROF_ARAHY	Profilin (Allergen Ara h 5)	0.02	-	cyt	0					131
P0C0Y3 UniProt NPD GO	PROF_FRAAN	Profilin (Allergen Fra a 4)	0.02	-	cyt	0					131
Q94JN2 UniProt NPD GO	PROF_ANACO	Profilin (Minor food allergen Ana c 1)	0.02	-	cyt	0					131
Q94JN3 UniProt NPD GO	PROF_MUSAC	Profilin (Minor fruit allergen Mus xp 1)	0.02	-	cyt	0					131
P41372 UniProt NPD GO	PROF1_TOBAC	Profilin-1	0.02	-	cyt	0					134
Q42449 UniProt NPD GO	PROF1_ARATH	Profilin-1 (Allergen Ara t 8)	0.02	-	cyt	0				3NUL	131
Q42418 UniProt NPD GO	PROF2_ARATH	Profilin-2	0.02	-	cyt	0					131
Q20025 UniProt NPD GO	PROF2_CAEEL	Profilin-2	0.02	-	cyt	0					131
Q9ST99 UniProt NPD GO	PROF2_TOBAC	Profilin-2	0.02	-	cyt	0					134
Q9STB6 UniProt NPD GO	PROF2_HEVBR	Profilin-2 (Pollen allergen Hev b 8.0102)	0.02	-	cyt	0					131
P26200 UniProt NPD GO	PROF2_DICDI	Profilin-2 (Profilin II)	0.02	-	cyt	1 *					124
Q9ST98 UniProt NPD GO	PROF3_TOBAC	Profilin-3	0.02	-	mit	0					133
P49234 UniProt NPD GO	PROF3_WHEAT	Profilin-3	0.02	-	cyt	0					140
Q8T8M2 UniProt NPD GO	PROF3_DICDI	Profilin-3 (Profilin III)	0.02	-	cyt	0					126
Q8NHR9 UniProt NPD GO	PROF4_HUMAN	Profilin-4 (Profilin IV)	0.02	-	cyt	0					129
Q9D6I3 UniProt NPD GO	PROF4_MOUSE	Profilin-4 (Profilin IV)	0.02	-	cyt	0					129
Q8N4S7 UniProt NPD GO	PAQR4_HUMAN	Progestin and adipoQ receptor family member 4 (Progestin and adipoQ receptor family member IV)	0.02	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				273
P51918 UniProt NPD GO	GON1_HAPBU	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.02	-	exc	0	Secreted protein	extracellular region [NAS]			94
O73812 UniProt NPD GO	GON1_MORSA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.02	-	exc	0	Secreted protein				95
P69109 UniProt NPD GO	GON3_ONCNE	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.02	-	exc	0	Secreted protein				82
P69108 UniProt NPD GO	GON3_SALFO	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.02	-	exc	0	Secreted protein				82
P69107 UniProt NPD GO	GON3_SALSA	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.02	-	exc	0	Secreted protein				82
P07288 UniProt NPD GO	KLK3_HUMAN	Prostate-specific antigen precursor (EC 3.4.21.77) (PSA) (Kallikrein-3) (Semenogelase) (Gamma-semino ...	0.02	-	exc	0	Secreted protein	extracellular region [NAS]	176820	2PSA	261
P15501 UniProt NPD GO	SPBP_MOUSE	Prostatic spermine-binding protein precursor (SBP) (Major prostatic secretory glycoprotein) (P25)	0.02	-	end	0					199
P60808 UniProt NPD GO	PSC1_MOUSE	Prostatic steroid-binding protein C1 chain precursor (Prostatein peptide C1)	0.02	-	exc	0	Secreted protein (By similarity)				111
P02782 UniProt NPD GO	PSC1_RAT	Prostatic steroid-binding protein C1 chain precursor (Prostatein peptide C1)	0.02	-	exc	0	Secreted protein				111
P84755 UniProt NPD GO	IPK2_CENMR	Protease inhibitor 2 (Protease inhibitor-II) (CmPI-II)	0.02	-	nuc	0					50
P25043 UniProt NPD GO	PSB7_YEAST	Proteasome component PUP1 precursor (EC 3.4.25.1) (Macropain subunit PUP1) (Proteinase YSCE subunit ...	0.02	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	261
P40301 UniProt NPD GO	PSA2_DROME	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome 25 kDa subunit) (PROS-Dm25)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				234
Q9V5C6 UniProt NPD GO	PSA3_DROME	Proteasome subunit alpha type 3 (EC 3.4.25.1) (20S proteasome subunit alpha-7)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				253
Q9M4T8 UniProt NPD GO	PSA5_SOYBN	Proteasome subunit alpha type 5 (EC 3.4.25.1) (20S proteasome alpha subunit E) (20S proteasome subun ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
Q2TBX6 UniProt NPD GO	PSB1_BOVIN	Proteasome subunit beta type 1 (EC 3.4.25.1)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				241
O09061 UniProt NPD GO	PSB1_MOUSE	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5) (Multi ...	0.02	-	cyt	0	Cytoplasm. Nucleus				240
P18421 UniProt NPD GO	PSB1_RAT	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5) (Multi ...	0.02	-	cyt	0	Cytoplasm. Nucleus				240
Q9LST6 UniProt NPD GO	PSB2_ORYSA	Proteasome subunit beta type 2 (EC 3.4.25.1) (20S proteasome alpha subunit D) (20S proteasome subuni ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				212
P34065 UniProt NPD GO	PSB5_CHICK	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome chain 1) (Macropain chain 1) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				256
P93395 UniProt NPD GO	PSB6_TOBAC	Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome delta chain) (Tobacco cryptogein- ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				234
Q8LD27 UniProt NPD GO	PSB6_ARATH	Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome subunit beta type 1) (20S proteas ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				233
Q99436 UniProt NPD GO	PSB7_HUMAN	Proteasome subunit beta type 7 precursor (EC 3.4.25.1) (Proteasome subunit Z) (Macropain chain Z) (M ...	0.02	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	604030		277
P70195 UniProt NPD GO	PSB7_MOUSE	Proteasome subunit beta type 7 precursor (EC 3.4.25.1) (Proteasome subunit Z) (Macropain chain Z) (M ...	0.02	-	cyt	0	Cytoplasm. Nucleus				277
Q9JHW0 UniProt NPD GO	PSB7_RAT	Proteasome subunit beta type 7 precursor (EC 3.4.25.1) (Proteasome subunit Z) (Macropain chain Z) (M ...	0.02	-	cyt	0	Cytoplasm. Nucleus				277
O35521 UniProt NPD GO	PSB9_MUSDU	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
O35522 UniProt NPD GO	PSB9_MUSMB	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
O35524 UniProt NPD GO	PSB9_MUSSI	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
P28077 UniProt NPD GO	PSB9_RAT	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
P28076 UniProt NPD GO	PSB9_MOUSE	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
Q925E8 UniProt NPD GO	ADMP_MOUSE	Protein ADMP (Androgen down-regulated protein expressed in mouse prostate)	0.02	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				76

You are viewing entries 85251 to 85300 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.