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
P28737 UniProt NPD GO	MSP1_YEAST	Protein MSP1 (TAT-binding homolog 4)	0.45	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane [IDA]			362
Q923Z3 UniProt NPD GO	MTO1_MOUSE	Protein MTO1 homolog, mitochondrial precursor	0.45	-	mit	0	Mitochondrion				669
Q5BDB9 UniProt NPD GO	OS9_EMENI	Protein OS-9 homolog precursor	0.45	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				509
Q52KW8 UniProt NPD GO	RCC2_XENLA	Protein RCC2 homolog	0.45	-	cyt	0	Nucleus; nucleolus (By similarity)				513
Q9WTZ0 UniProt NPD GO	UXT_MOUSE	Protein UXT (Ubiquitously expressed transcript protein)	0.45	-	nuc	0					157
Q12044 UniProt NPD GO	WSP1_YEAST	Protein WSP1 (Weak suppressor of PAT1 ts protein 1)	0.45	-	nuc	0	Cytoplasm	cytoplasm [IDA]			265
P31292 UniProt NPD GO	WNT10_XENLA	Protein Wnt-10 (XWnt-10) (Fragment)	0.45	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				128
P28131 UniProt NPD GO	WN10A_PLEJO	Protein Wnt-10a (Fragment)	0.45	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				119
P28465 UniProt NPD GO	WNT2_DROME	Protein Wnt-2 precursor (dWnt-2)	0.45	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				352
O46098 UniProt NPD GO	BCN92_DROME	Protein bcn92	0.45	-	nuc	0					92
P34704 UniProt NPD GO	HER1_CAEEL	Protein her-1 precursor (Hermaphrodization of XO animals protein 1)	0.45	-	exc	0	Secreted protein			1SZH	175
O46236 UniProt NPD GO	HUNB_DROCR	Protein hunchback (Fragments)	0.45	-	nuc	0	Nucleus (By similarity)				190
O46242 UniProt NPD GO	HUNB_DROIK	Protein hunchback (Fragments)	0.45	-	nuc	0	Nucleus (By similarity)				193
Q8NE28 UniProt NPD GO	CI096_HUMAN	Protein kinase-like protein C9orf96	0.45	-	mit	0					680
Q09329 UniProt NPD GO	MLO2_SCHPO	Protein mlo2	0.45	-	nuc	0					329
Q6DIQ3 UniProt NPD GO	PP1R7_XENTR	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.45	-	nuc	0	Nucleus (By similarity)				346
Q6BZG3 UniProt NPD GO	PPME1_DEBHA	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.45	-	nuc	0					390
Q9Y570 UniProt NPD GO	PPME1_HUMAN	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.45	-	mit	0					385
Q5R4F9 UniProt NPD GO	PPME1_PONPY	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.45	-	mit	0					385
Q6V4S5 UniProt NPD GO	SDK2_MOUSE	Protein sidekick-2 precursor	0.45	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				2176
Q6FWT0 UniProt NPD GO	SEC22_CANGA	Protein transport protein SEC22	0.45	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				215
Q9Z183 UniProt NPD GO	PADI4_MOUSE	Protein-arginine deiminase type-4 (EC 3.5.3.15) (Protein-arginine deiminase type IV) (Peptidylargini ...	0.45	-	cyt	0	Cytoplasmic granule (By similarity)				666
P16369 UniProt NPD GO	CUPP_DROPS	Pupal cuticle protein precursor	0.45	-	exc	0					192
O74523 UniProt NPD GO	ATIF_SCHPO	Putative ATPase inhibitor, mitochondrial precursor	0.45	-	mit	0	Mitochondrion (By similarity)				90
Q26696 UniProt NPD GO	HE64_TRYBB	Putative DEAD-box RNA helicase HEL64 (EC 3.6.1.-)	0.45	-	cyt	0	Nucleus (Potential)				568
O78442 UniProt NPD GO	RPOZ_GUITH	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.45	-	nuc	0	Plastid; chloroplast				76
O64836 UniProt NPD GO	LBD10_ARATH	Putative LOB domain-containing protein 10	0.45	-	nuc	0					311
Q9M9L8 UniProt NPD GO	LONH3_ARATH	Putative Lon protease homolog 3, mitochondrial precursor (EC 3.4.21.-)	0.45	+	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			924
Q9FIW5 UniProt NPD GO	NAC94_ARATH	Putative NAC domain-containing protein 94 (ANAC094)	0.45	-	nuc	0	Nucleus (Potential)				337
Q9M0R6 UniProt NPD GO	ATL4B_ARATH	Putative RING-H2 finger protein ATL4B precursor	0.45	-	cyt	1 *					302
Q9LMG8 UniProt NPD GO	SNP30_ARATH	Putative SNAP25 homologous protein SNAP30 (AtSNAP30) (Synaptosomal-associated protein SNAP25-like 3) ...	0.45	-	nuc	0					263
P93286 UniProt NPD GO	CCMF_ARATH	Putative cytochrome c biogenesis ccmF-like mitochondrial protein	0.45	-	end	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				442
Q8IMQ6 UniProt NPD GO	GR97A_DROME	Putative gustatory receptor 97a	0.45	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			423
Q5H8A6 UniProt NPD GO	CASTO_LOTJA	Putative ion channel CASTOR, chloroplast precursor	0.45	-	end	4	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				853
P57792 UniProt NPD GO	ALA12_ARATH	Putative phospholipid-transporting ATPase 12 (EC 3.6.3.1) (Aminophospholipid flippase 12)	0.45	+	end	10	Membrane; multi-pass membrane protein				1184
Q9LNQ4 UniProt NPD GO	ALA4_ARATH	Putative phospholipid-transporting ATPase 4 (EC 3.6.3.1) (Aminophospholipid flippase 4)	0.45	-	end	10	Membrane; multi-pass membrane protein				1216
Q09298 UniProt NPD GO	YQO9_CAEEL	Putative serine/threonine-protein kinase EEED8.9 (EC 2.7.11.1)	0.45	-	mit	0					641
P38705 UniProt NPD GO	YHH1_YEAST	Putative seryl-tRNA synthetase YHR011W (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.45	-	mit	0		cytoplasm [IDA] mitochondrion [IGI]			446
Q06201 UniProt NPD GO	YL445_YEAST	Putative transcriptional activator YLR445W	0.45	-	nuc	0					188
Q25322 UniProt NPD GO	OAR2_LOCMI	Putative tyramine receptor 2 (Tyr-Loc2)	0.45	+	end	7	Membrane; multi-pass membrane protein				484
Q11112 UniProt NPD GO	YX05_CAEEL	Putative tyrosine-protein kinase C03B1.5 in chromosome X (EC 2.7.10.2)	0.45	-	cyt	0					328
Q40545 UniProt NPD GO	KPYA_TOBAC	Pyruvate kinase isozyme A, chloroplast precursor (EC 2.7.1.40)	0.45	-	mit	0	Plastid; chloroplast				593
Q62739 UniProt NPD GO	RAB3I_RAT	RAB3A-interacting protein (Rabin-3) (SSX2-interacting protein)	0.45	-	nuc	0	Cytoplasm; cytosol. Nucleus. Predominantly cytosolic but a small proportion colocalizes with SSX2 in ...	cytosol [IDA] nucleus [ISS]			460
Q9BV68 UniProt NPD GO	RN126_HUMAN	RING finger protein 126	0.45	-	nuc	0					326
Q91YL2 UniProt NPD GO	RN126_MOUSE	RING finger protein 126	0.45	-	nuc	0					313
Q9JI90 UniProt NPD GO	RNF14_MOUSE	RING finger protein 14 (Androgen receptor-associated protein 54) (Triad2 protein)	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			485
Q3SWY0 UniProt NPD GO	RN183_BOVIN	RING finger protein 183	0.45	-	nuc	1	Membrane; single-pass membrane protein (Potential)				188
Q7ZW16 UniProt NPD GO	RNF41_BRARE	RING finger protein 41	0.45	-	cyt	0					318
Q6DEW6 UniProt NPD GO	REXO4_XENTR	RNA exonuclease 4 (EC 3.1.-.-) (Exonuclease XPMC2) (Prevents mitotic catastrophe 2 protein)	0.45	-	nuc	0	Nucleus				414
Q6BZX4 UniProt NPD GO	TFB2_YARLI	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.45	-	mit	0	Nucleus (By similarity)				467

You are viewing entries 28551 to 28600 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.