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
Q5JUK9 UniProt NPD GO	GGED1_HUMAN	Putative G antigen family D member 1 (Prostate-associated gene 3 protein) (PAGE-3)	0.30	+	nuc	0					113
Q9Z2J6 UniProt NPD GO	GPR44_MOUSE	Putative G-protein coupled receptor 44 (Chemoattractant receptor-homologous molecule expressed on Th ...	0.30	-	end	7 *	Membrane; multi-pass membrane protein				382
P34488 UniProt NPD GO	YMJC_CAEEL	Putative G-protein coupled receptor F59B2.13	0.30	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				515
Q9ZPX0 UniProt NPD GO	GAT15_ARATH	Putative GATA transcription factor 15	0.30	-	nuc	0	Nucleus (Probable)				207
Q9D2H2 UniProt NPD GO	KAD7_MOUSE	Putative adenylate kinase 7 (EC 2.7.4.3)	0.30	-	mit	0					614
Q09578 UniProt NPD GO	COL75_CAEEL	Putative cuticle collagen 75	0.30	-	mit	1 *					285
Q09653 UniProt NPD GO	C13AA_CAEEL	Putative cytochrome P450 CYP13A10 (EC 1.14.-.-)	0.30	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				519
Q9SJP6 UniProt NPD GO	FUT10_ARATH	Putative fucosyltransferase 10 (EC 2.4.1.-) (AtFUT10)	0.30	-	end	0	Golgi apparatus (Potential)				514
Q9VFC8 UniProt NPD GO	GYS_DROME	Putative glycogen [starch] synthase (EC 2.4.1.11)	0.30	-	cyt	0					709
Q9VYZ2 UniProt NPD GO	GR10B_DROME	Putative gustatory receptor 10b	0.30	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			373
Q9W2B2 UniProt NPD GO	GR48C_DROME	Putative gustatory receptor 58c	0.30	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			412
Q8IN23 UniProt NPD GO	GR93B_DROME	Putative gustatory receptor 93b	0.30	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			401
Q8IMZ5 UniProt NPD GO	GR94A_DROME	Putative gustatory receptor 94a	0.30	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			404
Q8IMN5 UniProt NPD GO	GR98D_DROME	Putative gustatory receptor 98d	0.30	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			412
Q9W3I5 UniProt NPD GO	OR7A_DROME	Putative odorant receptor 7a	0.30	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			413
P55248 UniProt NPD GO	SH_RAT	Putative protein SH (SH-4)	0.30	-	nuc	0					106
O93918 UniProt NPD GO	PYC_ASPTE	Pyruvate carboxylase (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.30	-	cyt	0	Cytoplasm (By similarity)				1193
Q8X1T3 UniProt NPD GO	PYC_PICAN	Pyruvate carboxylase (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.30	-	nuc	0	Cytoplasm (By similarity)				1175
P11154 UniProt NPD GO	PYC1_YEAST	Pyruvate carboxylase 1 (EC 6.4.1.1) (Pyruvic carboxylase 1) (PCB 1)	0.30	-	cyt	0	Cytoplasm	cytosol [IDA]			1178
Q968X7 UniProt NPD GO	PNO_CRYPV	Pyruvate dehydrogenase [NADP+] (EC 1.2.1.51) (Pyruvate:NADP+ oxidoreductase) (CpPNO)	0.30	+	nuc	0		mitochondrion [ISS]			1934
Q40546 UniProt NPD GO	KPYG_TOBAC	Pyruvate kinase isozyme G, chloroplast precursor (EC 2.7.1.40)	0.30	-	cyt	0	Plastid; chloroplast				562
Q96PM5 UniProt NPD GO	ZN363_HUMAN	RING finger and CHY zinc finger domain-containing protein 1 (Zinc finger protein 363) (CH-rich-inter ...	0.30	-	nuc	0		cytoplasm [IDA]	607680		261
Q5R4N9 UniProt NPD GO	RRN3_PONPY	RNA polymerase I-specific transcription initiation factor RRN3	0.30	-	mit	0	Nucleus (By similarity)				650
P87303 UniProt NPD GO	TFB2_SCHPO	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.30	-	mit	0	Nucleus (By similarity)				447
Q9BWF3 UniProt NPD GO	RBM4_HUMAN	RNA-binding protein 4 (RNA-binding motif protein 4) (RNA-binding motif protein 4a) (Lark homolog) (h ...	0.30	-	nuc	0	Nucleus. Nucleus; nucleolus. Cytoplasm. May undergo continuous nucleocytoplasmic shuttling		602571		364
Q41253 UniProt NPD GO	RAC13_GOSHI	Rac-like GTP-binding protein RAC13	0.30	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				196
Q40220 UniProt NPD GO	RAC2_LOTJA	Rac-like GTP-binding protein RAC2	0.30	+	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				196
Q9QYJ2 UniProt NPD GO	RASA3_RAT	Ras GTPase-activating protein 3 (GAP1(IP4BP)) (Ins P4-binding protein) (R-ras GAP) (Fragment)	0.30	-	nuc	0					124
P22123 UniProt NPD GO	RAPA_DISOM	Ras-related protein O-Krev precursor	0.30	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				184
Q9NX57 UniProt NPD GO	RAB20_HUMAN	Ras-related protein Rab-20	0.30	-	cyt	0	Highly enriched on apical endocytic structures in polarized epithelial cells of kidney proximal tubu ...				234
Q8VHP8 UniProt NPD GO	RB40B_MOUSE	Ras-related protein Rab-40B (SOCS box-containing protein RAR)	0.30	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				278
O14021 UniProt NPD GO	PRW1_SCHPO	RbAp48-related WD40-repeat protein prw1	0.30	-	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			431
P56700 UniProt NPD GO	RGS16_RAT	Regulator of G-protein signaling 16 (RGS16) (Retinally abundant regulator of G-protein signaling) (R ...	0.30	-	nuc	0					199
P97428 UniProt NPD GO	RGS16_MOUSE	Regulator of G-protein signaling 16 (RGS16) (Retinally abundant regulator of G-protein signaling) (R ...	0.30	-	nuc	0		cytoplasm [TAS]			201
O70276 UniProt NPD GO	RPE65_RAT	Retinal pigment epithelium-specific 65 kDa protein	0.30	+	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity). Attached to the membrane by ...				532
O08602 UniProt NPD GO	RAE1A_MOUSE	Retinoic acid early inducible protein 1 alpha precursor (RAE-1alpha)	0.30	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA]			253
Q9QYM5 UniProt NPD GO	RND2_MOUSE	Rho-related GTP-binding protein RhoN (Rho family GTPase 2) (Rnd2) (Rho7)	0.30	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential). Colocalizes with RACGAP1 in Golgi-derived ...				227
P28327 UniProt NPD GO	RK_BOVIN	Rhodopsin kinase precursor (EC 2.7.11.14) (RK) (G protein-coupled receptor kinase 1)	0.30	+	cyt	0	Membrane; lipid-anchor				561
Q93091 UniProt NPD GO	RNAS6_HUMAN	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.30	-	nuc	1 *	Secreted protein	extracellular region [TAS]	601981		150
O46525 UniProt NPD GO	RNAS6_PANTR	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.30	-	nuc	1 *	Secreted protein				150
Q7SID5 UniProt NPD GO	RNS11_NICAL	Ribonuclease S-F11 (EC 3.1.27.1) (Stylar glycoprotein F11) (SF11-RNase)	0.30	-	nuc	0	Secreted protein; extracellular space (By similarity)			1IOO	196
Q6BHB1 UniProt NPD GO	RNY1_DEBHA	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.30	-	nuc	0	Secreted protein (By similarity)				403
P00678 UniProt NPD GO	RNS1A_CAVPO	Ribonuclease pancreatic A (EC 3.1.27.5) (RNase IA)	0.30	-	nuc	0	Secreted protein				124
P00679 UniProt NPD GO	RNS1B_CAVPO	Ribonuclease pancreatic B (EC 3.1.27.5) (RNase IB)	0.30	-	nuc	0	Secreted protein				128
Q8VD93 UniProt NPD GO	RNS1A_RATEX	Ribonuclease pancreatic alpha-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.30	-	exc	0	Secreted protein (By similarity)				149
Q8SQ06 UniProt NPD GO	RNAS1_ATEGE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.30	-	nuc	1 *	Secreted protein (By similarity)				156
Q8SQ13 UniProt NPD GO	RNAS1_GORGO	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.30	-	nuc	1 *	Secreted protein (By similarity)				156
Q8SPN4 UniProt NPD GO	RNAS1_PYGNE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.30	-	nuc	1 *	Secreted protein (By similarity)				156
Q10478 UniProt NPD GO	SAM50_SCHPO	SAM50-like protein SpAC17C9.06	0.30	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				475
Q5R732 UniProt NPD GO	SH2D5_PONPY	SH2 domain-containing protein 5	0.30	-	mit	0					339

You are viewing entries 40701 to 40750 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.