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
Q9Y5H9 UniProt NPD GO	PCDA2_HUMAN	Protocadherin alpha 2 precursor (PCDH-alpha2)	0.34	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606308		948
Q5DRF0 UniProt NPD GO	PCDA2_PANTR	Protocadherin alpha 2 precursor (PCDH-alpha2)	0.34	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				948
Q9Y5E3 UniProt NPD GO	PCDB6_HUMAN	Protocadherin beta 6 precursor (PCDH-beta6)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606332		794
Q5DRC8 UniProt NPD GO	PCDB6_PANTR	Protocadherin beta 6 precursor (PCDH-beta6)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				794
Q9Y5G5 UniProt NPD GO	PCDG8_HUMAN	Protocadherin gamma A8 precursor (PCDH-gamma-A8)	0.34	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606295		932
Q6CTW6 UniProt NPD GO	COX10_KLULA	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.34	-	cyt	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				452
Q11011 UniProt NPD GO	PSA_MOUSE	Puromycin-sensitive aminopeptidase (EC 3.4.11.-) (PSA)	0.34	-	mit	0	Cytoplasm. Nucleus				920
P16425 UniProt NPD GO	Y2R2_DROME	Putative 115 kDa protein in type-1 retrotransposable element R1DM (Putative 115 kDa protein in type ...	0.34	-	end	0					1021
Q09181 UniProt NPD GO	DHH1_SCHPO	Putative ATP-dependent RNA helicase ste13 (EC 3.6.1.-)	0.34	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				485
Q9FFK0 UniProt NPD GO	WOX7_ARATH	Putative WUSCHEL-related homeobox 7	0.34	-	nuc	0	Nucleus (By similarity)				122
Q8IMN6 UniProt NPD GO	GR98C_DROME	Putative gustatory receptor 98c	0.34	+	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			408
P82718 UniProt NPD GO	LCR3_ARATH	Putative low-molecular-weight cysteine-rich protein LCR3 precursor	0.34	-	exc	1 *					78
P40152 UniProt NPD GO	YNV7_YEAST	Putative metallophosphoesterase YNL217W precursor (EC 3.1.-.-)	0.34	-	mit	1 *	Vacuole	vacuole (sensu Fungi) [IDA]			326
P49404 UniProt NPD GO	RM03_CAEEL	Putative mitochondrial 39S ribosomal protein L3	0.34	-	mit	0	Mitochondrion (By similarity)				403
Q9XWV5 UniProt NPD GO	RT10_CAEEL	Putative mitochondrial ribosomal protein S10	0.34	-	mit	0	Mitochondrion (By similarity)				156
Q99288 UniProt NPD GO	YD051_YEAST	Putative phosphoglycerate mutase YDR051C (EC 5.4.2.1) (Phosphoglyceromutase YDR051C)	0.34	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			334
Q2TUM3 UniProt NPD GO	KCNRG_MOUSE	Putative potassium channel regulatory protein (Potassium channel regulator) (Protein CLLD4)	0.34	-	cyt	0					264
Q9UET6 UniProt NPD GO	RRMJ1_HUMAN	Putative ribosomal RNA methyltransferase 1 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase)	0.34	-	nuc	0			300501		329
P52714 UniProt NPD GO	YXD2_CAEEL	Putative serine carboxypeptidase C08H9.1 (EC 3.4.16.-)	0.34	-	cyt	0					505
Q6ZR72 UniProt NPD GO	CU125_HUMAN	Putative uncharacterized protein C21orf125	0.34	-	nuc	0					161
P39711 UniProt NPD GO	YAG4_YEAST	Putative uncharacterized protein YAL064W	0.34	-	mit	0					108
Q12478 UniProt NPD GO	YL156_YEAST	Putative uncharacterized protein YLR156W/YLR157W-D/YLR159W/YLR161W	0.34	-	nuc	0					114
Q9STM4 UniProt NPD GO	ZFNL6_ARATH	Putative zinc finger CCCH domain-containing protein ZFN-like 6	0.34	-	nuc	0	Nucleus (By similarity)				448
Q32NN2 UniProt NPD GO	QKIA_XENLA	Quaking protein A (Xqua)	0.34	+	nuc	0	Nucleus. Cytoplasm			2BL5	341
Q9CR50 UniProt NPD GO	ZN363_MOUSE	RING finger and CHY zinc finger domain-containing protein 1 (Zinc finger protein 363) (CH-rich-inter ...	0.34	-	nuc	0					261
Q8N8N0 UniProt NPD GO	RN152_HUMAN	RING finger protein 152	0.34	-	cyt	1					203
Q3KPU8 UniProt NPD GO	RN166_XENLA	RING finger protein 166	0.34	-	mit	0					241
Q8W571 UniProt NPD GO	ATL4O_ARATH	RING-H2 finger protein ATL4O precursor	0.34	-	nuc	2 *					322
Q08273 UniProt NPD GO	RBX1_YEAST	RING-box protein HRT1 (RING-box protein 1) (E3 ubiquitin ligase complex SCF subunit HRT1) (High leve ...	0.34	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nuclear ubiquitin ligase complex [TAS] nucleus [IDA] SCF ubiquitin ligase complex [IDA]			121
P06140 UniProt NPD GO	HA1B_RABIT	RLA class I histocompatibility antigen, alpha chain 19-1 precursor	0.34	-	end	1	Membrane; single-pass type I membrane protein				361
Q03264 UniProt NPD GO	NGL2_YEAST	RNA exonuclease NGL2 (EC 3.1.-.-) (Carbon catabolite repressor protein 4 homolog)	0.34	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)	intracellular [IDA]			515
Q9US45 UniProt NPD GO	MED6_SCHPO	RNA polymerase II mediator complex subunit 6 (RNA polymerase II mediator complex protein pmc5)	0.34	-	nuc	0	Nucleus (Potential)	mediator complex [IDA]			216
Q6CVX9 UniProt NPD GO	TFB4_KLULA	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.34	-	nuc	0	Nucleus (By similarity)				337
Q9CQK7 UniProt NPD GO	RWDD1_MOUSE	RWD domain-containing protein 1 (IH1)	0.34	-	cyt	0					243
O82480 UniProt NPD GO	RAC7_ARATH	Rac-like GTP-binding protein ARAC7 (GTPase protein ROP9)	0.34	+	cyt	0	Membrane; lipid-anchor				209
Q6BPN7 UniProt NPD GO	ERFD_DEBHA	Ras modification protein ERF4	0.34	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				253
P97379 UniProt NPD GO	G3BP2_MOUSE	Ras-GTPase-activating protein-binding protein 2 (GAP SH3-domain-binding protein 2) (G3BP-2)	0.34	-	nuc	0					482
Q4KMI4 UniProt NPD GO	REEP2_BRARE	Receptor expression-enhancing protein 2	0.34	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				268
Q95JK0 UniProt NPD GO	RTP1_MACFA	Receptor-transporting protein 1	0.34	-	nuc	1	Cell membrane; single-pass type III membrane protein (By similarity). Effective cell surface express ...				263
Q96DX8 UniProt NPD GO	RTP4_HUMAN	Receptor-transporting protein 4 (28 kDa interferon-responsive protein)	0.34	-	nuc	0	Membrane; single-pass type III membrane protein (Potential)		609350		246
Q03956 UniProt NPD GO	RAV2_YEAST	Regulator of V-ATPase in vacuolar membrane protein 2	0.34	-	nuc	0	Cytoplasm (Probable). May be membrane-associated and localize to early endosomes via its interaction ...	RAVE complex [IPI]			351
Q8VEE4 UniProt NPD GO	RFA1_MOUSE	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (p70 ...	0.34	-	cyt	0	Nucleus (By similarity)	condensed chromosome [IDA] nucleus [IDA]			623
Q6PGU2 UniProt NPD GO	MAF1_BRARE	Repressor of RNA polymerase III transcription MAF1 homolog	0.34	-	nuc	0	Nucleus (By similarity)				247
Q8CI96 UniProt NPD GO	RSNL2_MOUSE	Restin-like protein 2	0.34	-	nuc	0				1WHK	704
Q66HD5 UniProt NPD GO	RSNL2_RAT	Restin-like protein 2	0.34	-	nuc	0					599
Q5R9F4 UniProt NPD GO	RND3_PONPY	Rho-related GTP-binding protein RhoE (Rho family GTPase 3) (Rnd3)	0.34	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				244
P67929 UniProt NPD GO	RNAS1_CAMBA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.34	-	nuc	0	Secreted protein				124
Q9WUV5 UniProt NPD GO	RNAS1_PERLE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.34	-	exc	0	Secreted protein				148
P11157 UniProt NPD GO	RIR2_MOUSE	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.34	-	cyt	0	Cytoplasm			1XSM	390
O15909 UniProt NPD GO	RIR1_TRYBB	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase R1 subunit) ...	0.34	-	nuc	0					838

You are viewing entries 37051 to 37100 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.