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
Q5T6V5 UniProt NPD GO	CI064_HUMAN	Protein C9orf64	0.01	-	cyt	0					341
Q9D2P4 UniProt NPD GO	CI074_MOUSE	Protein C9orf74 homolog	0.01	-	cyt	0				1XO3	101
O88668 UniProt NPD GO	CREG1_MOUSE	Protein CREG1 precursor (Cellular repressor of E1A-stimulated genes 1)	0.01	-	exc	0	Secreted protein (By similarity)	transcription factor complex [IDA]			220
Q66KY3 UniProt NPD GO	CUTA_XENLA	Protein CutA homolog precursor	0.01	-	mit	1 *					151
P54186 UniProt NPD GO	D1_ONCVO	Protein D1 (Fragment)	0.01	-	cyt	0					152
P54188 UniProt NPD GO	D3_ONCVO	Protein D3 (Fragment)	0.01	-	cyt	0					134
P89113 UniProt NPD GO	DDR2_YEAST	Protein DDR2 precursor	0.01	-	exc	0		cytoplasm [IDA] vacuole (sensu Fungi) [IDA]			61
Q99LX0 UniProt NPD GO	PARK7_MOUSE	Protein DJ-1	0.01	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with mitochondria in some cells, part ...				189
Q99497 UniProt NPD GO	PARK7_HUMAN	Protein DJ-1 (Oncogene DJ1)	0.01	-	cyt	0	Nucleus. Cytoplasm. Associated with mitochondria in some cells, particularly after oxidative stress. ...	cytoplasm [IDA] nucleus [IDA]	168600	1UCF	189
Q8VEC4 UniProt NPD GO	FA26B_MOUSE	Protein FAM26B	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				323
Q5RJQ8 UniProt NPD GO	FA26B_RAT	Protein FAM26B	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				323
Q7TNV1 UniProt NPD GO	FA57B_MOUSE	Protein FAM57B	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				225
Q05827 UniProt NPD GO	HOR7_YEAST	Protein HOR7 precursor (Protein A0.5)	0.01	-	exc	0		cell wall (sensu Fungi) [TAS] endoplasmic reticulum [IDA] membrane fraction [IDA] plasma membrane [IDA]			59
Q92441 UniProt NPD GO	MET17_KLULA	Protein MET17 [Includes: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) (OAH sulfhydrylase) (Homocys ...	0.01	-	cyt	0	Cytoplasm (By similarity)				443
O95424 UniProt NPD GO	MYLE_HUMAN	Protein MYLE (Dexamethasone-induced protein)	0.01	-	mit	1 *					95
Q5TZ51 UniProt NPD GO	MPV17_BRARE	Protein Mpv17	0.01	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				177
Q16617 UniProt NPD GO	NKG7_HUMAN	Protein NKG7 (Natural killer cell protein 7) (G-CSF-induced gene 1 protein) (Protein GIG-1)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	606008		165
Q9BS92 UniProt NPD GO	NPS3B_HUMAN	Protein NipSnap3B (SNAP1)	0.01	-	mit	0			608872		247
Q96495 UniProt NPD GO	ORM1_SACMO	Protein ORM1	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				148
Q75EG5 UniProt NPD GO	PNS1_ASHGO	Protein PNS1	0.01	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				553
Q5AB93 UniProt NPD GO	PNS1_CANAL	Protein PNS1	0.01	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				518
Q6BIV4 UniProt NPD GO	PNS1_DEBHA	Protein PNS1	0.01	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				513
Q12412 UniProt NPD GO	PNS1_YEAST	Protein PNS1 (pH nine sensitive protein 1)	0.01	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				539
P83365 UniProt NPD GO	PL3_LUPLU	Protein PR-L3 (Fragment)	0.01	-		0					20
Q7LZT1 UniProt NPD GO	S10A1_MISFO	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.01	-	nuc	0	Cytoplasm (By similarity)				95
P10462 UniProt NPD GO	S10A2_BOVIN	Protein S100-A2 (S100 calcium-binding protein A2) (Protein S-100L)	0.01	-	cyt	0					97
Q98953 UniProt NPD GO	S10A6_CHICK	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin)	0.01	-	cyt	0		nuclear envelope [ISS]			92
O77691 UniProt NPD GO	S10A6_HORSE	Protein S100-A6 (S100 calcium-binding protein A6) (Calcyclin)	0.01	-	cyt	0		nuclear envelope [ISS]			92
P50115 UniProt NPD GO	S10A8_RAT	Protein S100-A8 (S100 calcium-binding protein A8) (Calgranulin-A) (Migration inhibitory factor-relat ...	0.01	-	cyt	0					88
P02633 UniProt NPD GO	S100G_BOVIN	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.01	-	nuc	0				4ICB	78
Q04902 UniProt NPD GO	SNO4_YEAST	Protein SNO4	0.01	-	cyt	0					237
P84580 UniProt NPD GO	SP1_POPEU	Protein SP1 (Fragment)	0.01	-		0					16
P39931 UniProt NPD GO	SS120_YEAST	Protein SSP120 precursor	0.01	-	mit	0		cytoplasm [IDA]			234
P54003 UniProt NPD GO	SUR7_YEAST	Protein SUR7	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cell cortex [IDA] lipid raft [IDA] mitochondrion [IDA] spore wall (sensu Fungi) [IDA]			302
Q5KND6 UniProt NPD GO	SYM1_CRYNE	Protein SYM1	0.01	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				190
Q8N2H4 UniProt NPD GO	SYS1_HUMAN	Protein SYS1 homolog	0.01	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				156
Q78S06 UniProt NPD GO	SYS1_MOUSE	Protein SYS1 homolog	0.01	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				156
Q6UWH6 UniProt NPD GO	TX261_HUMAN	Protein TEX261	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				196
Q5RFE0 UniProt NPD GO	TX261_PONPY	Protein TEX261	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				196
Q5BJW3 UniProt NPD GO	TX261_RAT	Protein TEX261	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				196
Q62302 UniProt NPD GO	TX261_MOUSE	Protein TEX261 (Testis-expressed protein 261) (Testis-expressed sequence 261 protein)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				196
Q06793 UniProt NPD GO	USP1_PUCGR	Protein USP1 precursor	0.01	-	exc	0	Secreted protein (Probable)				113
P28116 UniProt NPD GO	WNT4_EUMSK	Protein Wnt-4 (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				119
P28135 UniProt NPD GO	WNT4_PLEJO	Protein Wnt-4 (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				119
Q6NYF1 UniProt NPD GO	YIPF4_BRARE	Protein YIPF4 (YIP1 family member 4)	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				237
Q5ZJD7 UniProt NPD GO	YIPF4_CHICK	Protein YIPF4 (YIP1 family member 4)	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				249
Q9BSR8 UniProt NPD GO	YIPF4_HUMAN	Protein YIPF4 (YIP1 family member 4)	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				244
Q8C407 UniProt NPD GO	YIPF4_MOUSE	Protein YIPF4 (YIP1 family member 4)	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				246
Q5M7T4 UniProt NPD GO	YIPF4_RAT	Protein YIPF4 (YIP1 family member 4)	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				246
Q6FMU3 UniProt NPD GO	YOP1_CANGA	Protein YOP1	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				177

You are viewing entries 90901 to 90950 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.