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
P32253 UniProt NPD GO	RASC_DICDI	Ras-like protein rasC	0.32	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				189
P97538 UniProt NPD GO	RASM_RAT	Ras-related protein M-Ras (Ras-related protein R-Ras3)	0.32	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				208
O08989 UniProt NPD GO	RASM_MOUSE	Ras-related protein M-Ras (Ras-related protein R-Ras3) (Muscle and microspikes Ras) (X-Ras)	0.32	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			1X1S	208
P52498 UniProt NPD GO	RSR1_CANAL	Ras-related protein RSR1	0.32	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				248
Q8VCD6 UniProt NPD GO	REEP2_MOUSE	Receptor expression-enhancing protein 2	0.32	-	nuc	2 *	Membrane; multi-pass membrane protein (By similarity)				254
O15492 UniProt NPD GO	RGS16_HUMAN	Regulator of G-protein signaling 16 (RGS16) (Retinally abundant regulator of G-protein signaling) (R ...	0.32	-	nuc	0			602514	2BT2	202
Q18312 UniProt NPD GO	RGS3_CAEEL	Regulator of G-protein signaling rgs-3	0.32	-	nuc	0					363
Q01588 UniProt NPD GO	RFA1_XENLA	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (Sin ...	0.32	-	nuc	0	Nucleus				609
Q8JG54 UniProt NPD GO	RGMA_CHICK	Repulsive guidance molecule A precursor	0.32	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				432
O02740 UniProt NPD GO	GUC2F_BOVIN	Retinal guanylyl cyclase 2 precursor (EC 4.6.1.2) (Guanylate cyclase 2F, retinal) (RETGC-2) (Rod out ...	0.32	-	end	2	Membrane; single-pass type I membrane protein				1103
P10404 UniProt NPD GO	ENV1_MOUSE	Retrovirus-related Env polyprotein precursor [Contains: Coat protein GP70] (Fragment)	0.32	-	nuc	0					313
Q03276 UniProt NPD GO	PO11_POPJA	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 (Retrovirus-related Pol ...	0.32	-	cyt	0					245
P11660 UniProt NPD GO	RTL_CHLRE	Reverse transcriptase-like protein	0.32	-	cyt	0					368
Q8BLR7 UniProt NPD GO	RND1_MOUSE	Rho-related GTP-binding protein Rho6 (Rho family GTPase 1) (Rnd1)	0.32	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				232
P02752 UniProt NPD GO	RBP_CHICK	Riboflavin-binding protein precursor (RBP) [Contains: Riboflavin-binding protein, plasma form; Ribof ...	0.32	-	exc	0					238
O46526 UniProt NPD GO	RNAS6_PONPY	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.32	-	nuc	1 *	Secreted protein				150
O80324 UniProt NPD GO	RNS6_PYRPY	Ribonuclease S-6 precursor (EC 3.1.27.1) (S6-RNase)	0.32	-	nuc	1 *					229
Q91VI7 UniProt NPD GO	RINI_MOUSE	Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1)	0.32	-	nuc	0	Cytoplasm (By similarity)				456
P10775 UniProt NPD GO	RINI_PIG	Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1)	0.32	-	nuc	0	Cytoplasm			2BNH	456
P00677 UniProt NPD GO	RNAS1_HYDHY	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.32	-	nuc	0	Secreted protein				128
Q9WUS1 UniProt NPD GO	RNAS1_MYOGL	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.32	-	nuc	0	Secreted protein				156
Q8SQ14 UniProt NPD GO	RNAS1_PANTR	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.32	-	nuc	1 *	Secreted protein (By similarity)				156
P53218 UniProt NPD GO	POP6_YEAST	Ribonucleases P/MRP protein subunit POP6 (EC 3.1.26.5) (RNases P/MRP 18.2 kDa subunit) (RNA-processi ...	0.32	-	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			158
Q5R9G0 UniProt NPD GO	RIR2B_PONPY	Ribonucleoside-diphosphate reductase M2 subunit B (EC 1.17.4.1)	0.32	-	cyt	1	Cytoplasm. Translocates from cytoplasm to nucleus in response to DNA damage (By similarity)				351
Q63531 UniProt NPD GO	KS6A1_RAT	Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase ...	0.32	-	cyt	0					735
P17257 UniProt NPD GO	SEC_HUMAN	SEC protein	0.32	-	mit	0					109
O76054 UniProt NPD GO	S14L2_HUMAN	SEC14-like protein 2 (Alpha-tocopherol-associated protein) (TAP) (hTAP) (Supernatant protein factor) ...	0.32	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic in absence of alpha-tocopherol, and nuclear in presence of alpha-toc ...	cytoplasm [NAS] nucleus [NAS]	607558	1OLM	403
Q8R3V5 UniProt NPD GO	SHLB2_MOUSE	SH3 domain GRB2-like protein B2 (Endophilin B2)	0.32	-	cyt	0	Cytoplasm (By similarity)				395
Q8BHK6 UniProt NPD GO	SLAF7_MOUSE	SLAM family member 7 precursor (Leukocyte cell-surface antigen) (Novel Ly9)	0.32	-	nuc	1	Membrane; single-pass type I membrane protein				333
Q75AQ4 UniProt NPD GO	HSV2_ASHGO	SVP1-like protein 2	0.32	-	mit	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				401
Q9SID1 UniProt NPD GO	STH_ARATH	Salt tolerance-like protein	0.32	-	nuc	0	Nucleus (Potential)				238
Q7TQ48 UniProt NPD GO	SRCA_MOUSE	Sarcalumenin precursor	0.32	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen (By similarity). Associated through calcium wit ...				910
P13666 UniProt NPD GO	SRCA_RABIT	Sarcalumenin precursor	0.32	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. Associated through calcium with the membrane				908
Q9YHX4 UniProt NPD GO	SEM4E_BRARE	Semaphorin-4E precursor (Semaphorin-7) (Semaphorin Z7) (Sema-Z7)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein				766
O62589 UniProt NPD GO	GD_DROME	Serine protease gd precursor (EC 3.4.21.-) (Protein gastrulation defective)	0.32	-	mit	0	Secreted protein				528
P29621 UniProt NPD GO	SPA3C_MOUSE	Serine protease inhibitor A3C precursor (Kallikrein-binding protein) (KBP) (Serpin A3C)	0.32	-	end	0	Secreted protein (By similarity)				417
Q863I2 UniProt NPD GO	OXSR1_PIG	Serine/threonine-protein kinase OSR1 (EC 2.7.11.1) (Oxidative stress-responsive 1 protein)	0.32	-	cyt	0					529
Q06226 UniProt NPD GO	SGK1_RAT	Serine/threonine-protein kinase Sgk1 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 1)	0.32	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Nuclear, upon phosphorylation (By similarity)				430
Q5GIG6 UniProt NPD GO	TNI3K_MOUSE	Serine/threonine-protein kinase TNNI3K (EC 2.7.11.1) (TNNI3-interacting kinase) (Cardiac ankyrin rep ...	0.32	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Expressed at lower levels in the cytoplasm (By s ...				833
Q6CFX5 UniProt NPD GO	PTPA1_YARLI	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.32	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				432
Q8MJ47 UniProt NPD GO	PP1B_CANFA	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
P62207 UniProt NPD GO	PP1B_CHICK	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
P62140 UniProt NPD GO	PP1B_HUMAN	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)		600590	1S70	326
P62141 UniProt NPD GO	PP1B_MOUSE	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
P61292 UniProt NPD GO	PP1B_PIG	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
P62143 UniProt NPD GO	PP1B_RABIT	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
P62142 UniProt NPD GO	PP1B_RAT	Serine/threonine-protein phosphatase PP1-beta catalytic subunit (EC 3.1.3.16) (PP-1B)	0.32	-	mit	0	Cytoplasm (By similarity)				326
Q8MJ46 UniProt NPD GO	PP1G_CANFA	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G) (Protein phos ...	0.32	-	cyt	0	Cytoplasm (By similarity)				323
P48462 UniProt NPD GO	PP1B_DROME	Serine/threonine-protein phosphatase beta isoform (EC 3.1.3.16) (Protein flap wing)	0.32	-	cyt	0					330
O35655 UniProt NPD GO	PPE1_MOUSE	Serine/threonine-protein phosphatase with EF-hands 1 (EC 3.1.3.16) (PPEF-1) (Protein phosphatase wit ...	0.32	-	cyt	0					270

You are viewing entries 38901 to 38950 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.