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
P61371 UniProt NPD GO	ISL1_HUMAN	Insulin gene enhancer protein ISL-1 (Islet-1)	0.76	+	nuc	0	Nucleus		600366		349
P61373 UniProt NPD GO	ISL1_MESAU	Insulin gene enhancer protein ISL-1 (Islet-1)	0.76	+	nuc	0	Nucleus				349
P61372 UniProt NPD GO	ISL1_MOUSE	Insulin gene enhancer protein ISL-1 (Islet-1)	0.76	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			349
P61374 UniProt NPD GO	ISL1_RAT	Insulin gene enhancer protein ISL-1 (Islet-1)	0.76	+	nuc	0	Nucleus				349
P53405 UniProt NPD GO	ISL1_BRARE	Insulin gene enhancer protein isl-1 (Islet-1)	0.76	+	nuc	0	Nucleus	nucleus [IDA]			349
Q28516 UniProt NPD GO	INSR_MACMU	Insulin receptor (EC 2.7.10.1) (IR) [Contains: Insulin receptor alpha subunit; Insulin receptor subu ...	0.76	+	nuc	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			210
Q9QY05 UniProt NPD GO	INSL6_MOUSE	Insulin-like peptide INSL6 precursor (Insulin-like peptide 6) [Contains: Insulin-like peptide INSL6 ...	0.76	-	exc	0	Secreted protein (By similarity)				191
Q01590 UniProt NPD GO	SED5_YEAST	Integral membrane protein SED5	0.76	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	Golgi cis-face [IDA]		1MQS	340
Q5ZLS8 UniProt NPD GO	INT10_CHICK	Integrator complex subunit 10	0.76	-	cyt	0	Nucleus (By similarity)				710
Q5ZKU4 UniProt NPD GO	INT2_CHICK	Integrator complex subunit 2 (Int2)	0.76	-	cyt	0	Nucleus; nuclear membrane; single-pass membrane protein (By similarity)				1192
P23570 UniProt NPD GO	IRF1_RAT	Interferon regulatory factor 1 (IRF-1)	0.76	+	nuc	0	Nucleus				328
P19525 UniProt NPD GO	E2AK2_HUMAN	Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1) (Interferon-inducible ...	0.76	-	nuc	0			176871	2A1A	551
O02365 UniProt NPD GO	IFA2_CAEEL	Intermediate filament protein ifa-2 (Intermediate filament protein A2) (IF-A2) (Cel IF A2)	0.76	-	nuc	0	Cell membrane; cell-cell junction; hemidesmosome. Colocalizes with myoactin				581
Q86DC6 UniProt NPD GO	IFD1_CAEEL	Intermediate filament protein ifd-1 (Intermediate filament protein D1) (IF-D1) (Cel IF D1)	0.76	+	nuc	0	Cytoplasm (Probable)				575
P81067 UniProt NPD GO	IRX3_MOUSE	Iroquois-class homeodomain protein IRX-3 (Iroquois homeobox protein 3) (Homeodomain protein IRXB1)	0.76	-	nuc	0	Nucleus (Probable)				507
Q5ZIX8 UniProt NPD GO	JHD2A_CHICK	JmjC domain-containing histone demethylation protein 2A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.76	+	nuc	0	Nucleus (By similarity)				1325
Q9WV86 UniProt NPD GO	KTNA1_MOUSE	Katanin p60 ATPase-containing subunit A1 (EC 3.6.4.3) (Katanin p60 subunit A1) (p60 katanin) (Lipotr ...	0.76	-	nuc	0	Cytoplasm (By similarity). Predominantly. Centrosome (By similarity). Also localized to the interpha ...	axon [IDA] centrosome [IDA] lipid particle [IDA] nucleus [IDA] plasma membrane [IDA]			491
Q10173 UniProt NPD GO	NUF2_SCHPO	Kinetochore protein nuf2	0.76	-	nuc	0	Nucleus. Associated with kinetochores	Ndc80 complex [TAS]			441
Q6TNJ1 UniProt NPD GO	KRIT1_BOVIN	Krev interaction trapped protein 1 (Krev interaction trapped 1) (Cerebral cavernous malformations 1 ...	0.76	+	nuc	0	Membrane; peripheral membrane protein (Probable)				736
Q9EPF4 UniProt NPD GO	KLF11_MOUSE	Krueppel-like factor 11 (Transforming growth factor-beta-inducible early growth response protein 2) ...	0.76	-	nuc	0	Nucleus (By similarity)				511
Q13887 UniProt NPD GO	KLF5_HUMAN	Krueppel-like factor 5 (Intestinal-enriched krueppel-like factor) (Colon krueppel-like factor) (Tran ...	0.76	-	nuc	0	Nucleus		602903		457
Q9Z0Z7 UniProt NPD GO	KLF5_MOUSE	Krueppel-like factor 5 (Intestinal-enriched krueppel-like factor) (Transcription factor BTEB2) (Basi ...	0.76	-	nuc	0	Nucleus				446
P56584 UniProt NPD GO	SID1_USTMA	L-ornithine 5-monooxygenase (EC 1.13.12.-) (L-ornithine N5-oxygenase)	0.76	-	nuc	0					570
Q61033 UniProt NPD GO	LAP2A_MOUSE	Lamina-associated polypeptide 2 isoforms alpha/zeta (Thymopoietin isoforms alpha/zeta) (TP alpha/zet ...	0.76	+	nuc	0	Nucleus (By similarity). Expressed diffusely throughout the nucleus (By similarity)	nuclear envelope [IDA]			692
Q5KLL9 UniProt NPD GO	LCMT1_CRYNE	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.76	-	nuc	0					398
Q52KR2 UniProt NPD GO	LRIG2_MOUSE	Leucine-rich repeats and immunoglobulin-like domains protein 2 precursor	0.76	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Cytoplasm (By similarity)				1054
O94898 UniProt NPD GO	LRIG2_HUMAN	Leucine-rich repeats and immunoglobulin-like domains protein 2 precursor (LIG-2)	0.76	-	end	1	Cell membrane; single-pass type I membrane protein. Cytoplasm		608869		1065
Q95JC3 UniProt NPD GO	LEAP2_BOVIN	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)	0.76	-	exc	0	Secreted protein				77
Q7KQZ4 UniProt NPD GO	LOLA3_DROME	Longitudinals lacking protein, isoforms A/B/C/L	0.76	-	nuc	0	Nucleus	nucleus [IDA]			787
Q7GCP2 UniProt NPD GO	MADS5_ORYSA	MADS-box transcription factor 5 (OsMADS5) (FDRMADS2)	0.76	-	nuc	0	Nucleus (Probable)				225
Q94KB1 UniProt NPD GO	MLO14_ARATH	MLO-like protein 14 (AtMlo14)	0.76	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				554
O00339 UniProt NPD GO	MATN2_HUMAN	Matrilin-2 precursor	0.76	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [NAS]	602108		956
Q5GAA9 UniProt NPD GO	MATK_ARTFM	Maturase K (Intron maturase)	0.76	-	nuc	0	Plastid; chloroplast				506
Q5I6K6 UniProt NPD GO	MATK_BARAL	Maturase K (Intron maturase)	0.76	-	pox	0	Plastid				510
Q7YKQ5 UniProt NPD GO	MATK_CAMRA	Maturase K (Intron maturase)	0.76	-	pox	0	Plastid; chloroplast				511
Q8M9L8 UniProt NPD GO	MATK_IMPCA	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				504
Q9GF36 UniProt NPD GO	MATK_LEPCM	Maturase K (Intron maturase)	0.76	-	mit	0	Plastid; chloroplast				504
Q6E4Q8 UniProt NPD GO	MATK_PROJU	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				499
O78254 UniProt NPD GO	MATK_ROSGI	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				503
Q5GIQ5 UniProt NPD GO	MATK_SYZCU	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				518
Q5GIQ4 UniProt NPD GO	MATK_SYZSA	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				505
Q5YJX5 UniProt NPD GO	MATK_VATMA	Maturase K (Intron maturase)	0.76	-	cyt	0	Plastid; chloroplast				509
P23179 UniProt NPD GO	SPO11_YEAST	Meiosis-specific protein SPO11 (Sporulation-specific protein 11)	0.76	+	nuc	0	Nucleus	nuclear chromosome [IPI]			398
P53102 UniProt NPD GO	MND1_YEAST	Meiotic nuclear division protein 1	0.76	+	nuc	0	Nucleus	condensed nuclear chromosome [IDA]			219
P32841 UniProt NPD GO	RE114_YEAST	Meiotic recombination protein REC114	0.76	-	nuc	0		nucleus [IC]			428
Q22236 UniProt NPD GO	SPO11_CAEEL	Meiotic recombination protein spo-11	0.76	-	cyt	0	Nucleus (By similarity)				425
O15481 UniProt NPD GO	MAGB4_HUMAN	Melanoma-associated antigen B4 (MAGE-B4 antigen)	0.76	-	nuc	0			300153		346
P04934 UniProt NPD GO	MSP1_PLAFC	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (P195)	0.76	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1726
P46752 UniProt NPD GO	RT14_PROWI	Mitochondrial ribosomal protein S14	0.76	-	nuc	0	Mitochondrion				99
Q80Y86 UniProt NPD GO	MK15_MOUSE	Mitogen-activated protein kinase 15 (EC 2.7.11.24) (Extracellular signal-regulated kinase 7)	0.76	-	nuc	0		extracellular region [ISS] intracellular [ISS] nucleus [ISS]			549

You are viewing entries 10901 to 10950 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.