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
P46198 UniProt NPD GO	IF2M_BOVIN	Translation initiation factor IF-2, mitochondrial precursor (IF-2Mt) (IF-2(Mt))	0.32	-	mit	0	Mitochondrion				727
Q8CHW4 UniProt NPD GO	EI2BE_MOUSE	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.32	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			717
Q15035 UniProt NPD GO	TRAM2_HUMAN	Translocation-associated membrane protein 2	0.32	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				370
Q9D7L8 UniProt NPD GO	TMIGD_MOUSE	Transmembrane and immunoglobulin domain-containing protein precursor	0.32	-	end	1	Membrane; single-pass type I membrane protein (Potential)				261
Q5BK83 UniProt NPD GO	T106A_RAT	Transmembrane protein 106A	0.32	-	nuc	1	Membrane; single-pass membrane protein (Potential)				261
Q8QZV2 UniProt NPD GO	TMM46_MOUSE	Transmembrane protein 46 homolog precursor	0.32	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				295
Q6UWI4 UniProt NPD GO	TMM46_HUMAN	Transmembrane protein 46 precursor	0.32	-	exc	2 *	Membrane; single-pass type I membrane protein (Probable)				295
Q865W2 UniProt NPD GO	TRI50_PIG	Tripartite motif-containing protein 50	0.32	-	cyt	0					486
Q2KIQ5 UniProt NPD GO	T23O_BOVIN	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.32	-	cyt	0					406
P33632 UniProt NPD GO	TBB3_ANEPH	Tubulin beta-3 chain (Beta-3 tubulin) (Fragment)	0.32	-	cyt	0					239
Q39582 UniProt NPD GO	TBG_CHLRE	Tubulin gamma chain (Gamma tubulin)	0.32	-	cyt	0					468
Q8NHH1 UniProt NPD GO	TTL11_HUMAN	Tubulin--tyrosine ligase-like protein 11	0.32	-	nuc	0					538
P80585 UniProt NPD GO	TBCA_CHICK	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A)	0.32	-	nuc	0					107
Q5QJ74 UniProt NPD GO	TBCEL_HUMAN	Tubulin-specific chaperone cofactor E-like protein (Leucine-rich repeat-containing protein 35)	0.32	-	nuc	0					424
P63308 UniProt NPD GO	TNFL6_MACFA	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.32	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				280
P63307 UniProt NPD GO	TNFL6_MACMU	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.32	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				280
P63306 UniProt NPD GO	TNFL6_MACNE	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.32	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				280
P22934 UniProt NPD GO	TNR1A_RAT	Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (TNFR-I) (p55 ...	0.32	-	exc	2 *	Membrane; single-pass type I membrane protein				461
P43489 UniProt NPD GO	TNR4_HUMAN	Tumor necrosis factor receptor superfamily member 4 precursor (OX40L receptor) (ACT35 antigen) (TAX ...	0.32	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600315	1D0A	277
P97525 UniProt NPD GO	TNR8_RAT	Tumor necrosis factor receptor superfamily member 8 precursor (CD30L receptor) (Lymphocyte activatio ...	0.32	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				493
Q6PCT3 UniProt NPD GO	TPD54_RAT	Tumor protein D54 (Tumor protein D52-like 2)	0.32	-	nuc	0		cytoplasm [ISS] perinuclear region [ISS]			220
Q8WTW4 UniProt NPD GO	TUSC4_HUMAN	Tumor suppressor candidate 4 (NPR2-like) (Gene 21 protein) (G21 protein)	0.32	-	cyt	0			607072		380
P53356 UniProt NPD GO	HTK16_HYDAT	Tyrosine-protein kinase HTK16 (EC 2.7.10.2)	0.32	-	mit	0					757
Q8BUM3 UniProt NPD GO	PTN7_MOUSE	Tyrosine-protein phosphatase non-receptor type 7 (EC 3.1.3.48)	0.32	-	nuc	0	Cytoplasm (By similarity)				359
P35236 UniProt NPD GO	PTN7_HUMAN	Tyrosine-protein phosphatase non-receptor type 7 (EC 3.1.3.48) (Protein-tyrosine phosphatase LC-PTP) ...	0.32	-	mit	0	Cytoplasm	cytoplasm [TAS]	176889	1ZC0	360
Q6FV04 UniProt NPD GO	RU2A_CANGA	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.32	-	cyt	0	Nucleus (By similarity)				266
Q6BT60 UniProt NPD GO	RU2A_DEBHA	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.32	-	nuc	0	Nucleus (By similarity)				238
Q9USX8 UniProt NPD GO	RU2A_SCHPO	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.32	-	nuc	0	Nucleus				239
P53905 UniProt NPD GO	LSM7_YEAST	U6 snRNA-associated Sm-like protein LSm7	0.32	-	nuc	0	Nucleus. Cytoplasm	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			107
O93448 UniProt NPD GO	UTS1_ONCMY	UI precursor [Contains: Urophysin; Urotensin-1 (Urotensin I)]	0.32	-	nuc	0	Secreted protein				165
Q5PR01 UniProt NPD GO	CT149_RAT	UPF0362 protein C20orf149 homolog	0.32	-	nuc	0					115
P32628 UniProt NPD GO	RAD23_YEAST	UV excision repair protein RAD23	0.32	-	nuc	0	Nucleus (Probable)	mitochondrion [IDA] nucleotide-excision repair factor 2 complex [IDA] proteasome complex (sensu Eukaryota) [IMP] repairosome [IDA]		1X3Z	398
Q9VVG6 UniProt NPD GO	COQ4_DROME	Ubiquinone biosynthesis protein COQ4 homolog	0.32	-	mit	0		mitochondrial inner membrane [ISS]			268
Q8LAM0 UniProt NPD GO	UBP4_ARATH	Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) (Ubiquitin thioesterase 4) (Ubiquitin-specific ...	0.32	+	cyt	0	Nucleus				365
Q640W6 UniProt NPD GO	UBTD1_XENLA	Ubiquitin domain-containing protein 1	0.32	-	nuc	0					234
Q9CQX0 UniProt NPD GO	OTUB2_MOUSE	Ubiquitin thioesterase protein OTUB2 (EC 3.4.-.-) (Otubain 2) (OTU domain-containing ubiquitin aldeh ...	0.32	-	cyt	0					234
Q6BYG4 UniProt NPD GO	UBC6_DEBHA	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC6) (Ubiquitin carrier p ...	0.32	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane (By similarity)				242
Q8K2Z8 UniProt NPD GO	UB2Q2_MOUSE	Ubiquitin-conjugating enzyme E2 Q2 (EC 6.3.2.19) (Ubiquitin-protein ligase Q2) (Ubiquitin carrier pr ...	0.32	-	nuc	0	Cytoplasm (By similarity)				378
P42746 UniProt NPD GO	UBC3_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 3 (EC 6.3.2.19) (Ubiquitin-protein ligase 3) (Ubiquitin carri ...	0.32	-	nuc	0					150
P38226 UniProt NPD GO	YB42_YEAST	Uncharacterized acyltransferase YBR042C (EC 2.3.-.-)	0.32	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	lipid particle [IDA]			397
Q9D0A3 UniProt NPD GO	CO038_MOUSE	Uncharacterized protein C15orf38 homolog	0.32	-	mit	0					226
Q8NCQ2 UniProt NPD GO	CS034_HUMAN	Uncharacterized protein C19orf34	0.32	-	nuc	0					242
Q9DA57 UniProt NPD GO	CT165_MOUSE	Uncharacterized protein C20orf165 homolog	0.32	-	nuc	0					226
Q9NUS5 UniProt NPD GO	CT029_HUMAN	Uncharacterized protein C20orf29	0.32	-	mit	0					200
Q5ZJH7 UniProt NPD GO	CB024_CHICK	Uncharacterized protein C2orf24 homolog	0.32	-	nuc	1					439
Q5FWS4 UniProt NPD GO	CF188_RAT	Uncharacterized protein C6orf188 homolog	0.32	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				309
Q8BTE0 UniProt NPD GO	CF057_MOUSE	Uncharacterized protein C6orf57 homolog precursor	0.32	-	mit	0	Secreted protein (Potential)				104
P53144 UniProt NPD GO	YGK1_YEAST	Uncharacterized protein YGL101W	0.32	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			215
P53063 UniProt NPD GO	YGZ6_YEAST	Uncharacterized protein YGL246C	0.32	-	cyt	0		nucleus [IDA]			387
Q3E826 UniProt NPD GO	YK068_YEAST	Uncharacterized protein YKL068W-A	0.32	-	nuc	0					78

You are viewing entries 39001 to 39050 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.