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
P51333 UniProt NPD GO	DNAB_PORPU	Probable replicative DNA helicase (EC 3.6.1.-) [Contains: Ppu dnaB intein]	0.78	-	nuc	0	Plastid; chloroplast				568
P19593 UniProt NPD GO	RDPO_SCEOB	Probable reverse transcriptase (EC 2.7.7.49)	0.78	-	nuc	0	Plastid; chloroplast				608
P28708 UniProt NPD GO	KKL6_YEAST	Probable serine/threonine-protein kinase YKL116C (EC 2.7.11.1)	0.78	+	nuc	0		cytoplasm [IDA]			518
Q9GT24 UniProt NPD GO	ZYG1_CAEEL	Probable serine/threonine-protein kinase zyg-1 (EC 2.7.11.1) (Zygote defective protein 1)	0.78	-	nuc	0	Centrosome. Component of the centrosome. Present at centrioles only immediately before their duplica ...	centrosome [IDA]			706
Q09511 UniProt NPD GO	RSP4_CAEEL	Probable splicing factor, arginine/serine-rich 4 (RNA-binding protein srp-2) (CeSC35)	0.78	+	nuc	0	Nucleus	nucleus [IDA]			196
P25611 UniProt NPD GO	YCZ6_YEAST	Probable transcriptional regulatory protein YCR106W	0.78	+	nuc	0	Nucleus (Probable)	nucleus [IC]			832
P34442 UniProt NPD GO	PTP4_CAEEL	Probable tyrosine-protein phosphatase F54C8.4 (EC 3.1.3.48)	0.78	+	nuc	0					359
Q9H939 UniProt NPD GO	PPIP2_HUMAN	Proline-serine-threonine phosphatase-interacting protein 2	0.78	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				333
Q99M15 UniProt NPD GO	PPIP2_MOUSE	Proline-serine-threonine phosphatase-interacting protein 2 (Macrophage actin-associated tyrosine-pho ...	0.78	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoskeleton [IDA] cytosol [IDA] membrane fraction [IDA]			333
Q64171 UniProt NPD GO	RELX_MESAU	Prorelaxin precursor [Contains: Relaxin B chain; Relaxin A chain]	0.78	-	exc	0	Secreted protein				177
P01348 UniProt NPD GO	RELX_PIG	Prorelaxin precursor [Contains: Relaxin B chain; Relaxin A chain]	0.78	-	exc	0	Secreted protein			4RLX	182
Q6S5H5 UniProt NPD GO	POT14_HUMAN	Prostate, ovary, testis-expressed protein on chromosome 14	0.78	-	end	1			608916		594
P69014 UniProt NPD GO	PRT1_ONCKE	Protamine (Salmine-AI)	0.78	+	nuc	0	Nucleus				32
P02328 UniProt NPD GO	PRTIA_ONCMY	Protamine IA (Iridine IA)	0.78	+	nuc	0	Nucleus				33
P02333 UniProt NPD GO	PRT4_ONCMY	Protamine PTP4	0.78	+	nuc	0	Nucleus				30
P08147 UniProt NPD GO	PRT17_ONCMY	Protamine TP17	0.78	+	nuc	0	Nucleus				32
P02332 UniProt NPD GO	PRT1B_ONCMY	Protamine-1B	0.78	+	nuc	0	Nucleus				30
P35314 UniProt NPD GO	PRM2_HYLLA	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.78	+	nuc	0	Nucleus				102
P61253 UniProt NPD GO	PRM2_MACFU	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.78	+	nuc	0	Nucleus (By similarity)				103
P35298 UniProt NPD GO	PRM2_MACNE	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.78	+	nuc	0	Nucleus				103
P19757 UniProt NPD GO	PRM2_PIG	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.78	+	nuc	0	Nucleus				92
P69015 UniProt NPD GO	PRT2B_ONCMY	Protamine-2B (Salmine-AI)	0.78	+	nuc	0	Nucleus				32
P69012 UniProt NPD GO	PRTY1_CLUHA	Protamine-YI (Clupeine-YI)	0.78	+	nuc	0	Nucleus				31
P69013 UniProt NPD GO	PRTY1_CLUPA	Protamine-YI (Clupeine-YI)	0.78	+	nuc	0	Nucleus				31
P69008 UniProt NPD GO	PRTY2_CLUHA	Protamine-YII (Clupeine-YII)	0.78	+	nuc	0	Nucleus				30
P69009 UniProt NPD GO	PRTY2_CLUPA	Protamine-YII (Clupeine-YII)	0.78	+	nuc	0	Nucleus				30
Q38914 UniProt NPD GO	ANT_ARATH	Protein AINTEGUMENTA (Complementing a protein kinase C mutant protein 1) (Protein Dragon) (Protein o ...	0.78	-	nuc	0	Nucleus (Probable)				555
Q6ZU80 UniProt NPD GO	CN145_HUMAN	Protein C14orf145	0.78	-	nuc	0					623
Q8N9Y4 UniProt NPD GO	CN152_HUMAN	Protein C14orf152	0.78	-	nuc	0					354
Q96IY1 UniProt NPD GO	CA048_HUMAN	Protein C1orf48	0.78	-	nuc	0	Nucleus. Associated with the kinetochore		609174		281
Q8N3R3 UniProt NPD GO	CC023_HUMAN	Protein C3orf23	0.78	-	nuc	0					496
Q5RC87 UniProt NPD GO	CI078_PONPY	Protein C9orf78 homolog	0.78	-	nuc	0					289
Q9LS42 UniProt NPD GO	CASP_ARATH	Protein CASP	0.78	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein				689
Q8K2F3 UniProt NPD GO	DEPP_MOUSE	Protein DEPP (Fat-specific expressed gene protein)	0.78	-	nuc	0					205
Q8CGC4 UniProt NPD GO	FA61B_MOUSE	Protein FAM61B	0.78	-	nuc	0					385
Q566L7 UniProt NPD GO	FA61B_XENTR	Protein FAM61B homolog	0.78	-	nuc	0					382
Q04233 UniProt NPD GO	GIS4_YEAST	Protein GIS4	0.78	-	nuc	0	Cytoplasm	cytoplasm [IDA]			774
Q15397 UniProt NPD GO	K0020_HUMAN	Protein KIAA0020 (HBV X-transactivated gene 5 protein) (Minor histocompatibility antigen HA-8) (HLA- ...	0.78	+	nuc	0	Nucleus; nucleolus	endoplasmic reticulum [IDA]	609960		648
O15027 UniProt NPD GO	K0310_HUMAN	Protein KIAA0310	0.78	-	nuc	0					2179
P35728 UniProt NPD GO	MPE1_YEAST	Protein MPE1	0.78	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			441
P38339 UniProt NPD GO	RGD1_YEAST	Protein RGD1	0.78	-	nuc	0		actin cortical patch [IDA] bud [IDA]			666
P53266 UniProt NPD GO	SHY1_YEAST	Protein SHY1	0.78	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [IDA] mitochondrial inner membrane [IDA]			389
Q5XIB1 UniProt NPD GO	TSSC4_RAT	Protein TSSC4	0.78	-	nuc	0					317
Q99222 UniProt NPD GO	YHS9_YEAST	Protein YOR129C	0.78	-	nuc	0	Cytoplasm; perinuclear region. Cytoplasm. Localized in the region of the nucleus and in the vicinity ...	cytoplasm [IDA] outer plaque of spindle pole body [IPI]			893
Q8BH05 UniProt NPD GO	ZN750_MOUSE	Protein ZNF750	0.78	-	nuc	0					703
Q8MSG8 UniProt NPD GO	APTX_DROME	Protein aprataxin-like	0.78	-	nuc	0	Nucleus (Potential)				662
Q9VQU9 UniProt NPD GO	BOWEL_DROME	Protein bowel (Brother of odd with entrails limited)	0.78	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			744
Q5U4U4 UniProt NPD GO	DONS_XENLA	Protein downstream neighbor of son homolog	0.78	-	nuc	0	Nucleus (By similarity)				579
O88907 UniProt NPD GO	PIAS1_MOUSE	Protein inhibitor of activated STAT protein 1 (DEAD/H box-binding protein 1)	0.78	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Interaction with CSRP2 may induce a partial r ...				651
O75925 UniProt NPD GO	PIAS1_HUMAN	Protein inhibitor of activated STAT protein 1 (Gu-binding protein) (GBP) (RNA helicase II-binding pr ...	0.78	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Interaction with CSRP2 may induce a partial redistribution al ...	nucleus [TAS]	603566	1V66	651

You are viewing entries 10001 to 10050 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.