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
O13644 UniProt NPD GO	SED5_SCHPO	Integral membrane protein sed5	0.65	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				309
Q61739 UniProt NPD GO	ITA6_MOUSE	Integrin alpha-6 precursor (VLA-6) (CD49f antigen) [Contains: Integrin alpha-6 heavy chain; Integrin ...	0.65	-	end	1	Membrane; single-pass type I membrane protein	basolateral plasma membrane [IDA] integrin complex [IDA] plasma membrane [IDA]			1091
P27594 UniProt NPD GO	MX1_PIG	Interferon-induced GTP-binding protein Mx1	0.65	-	cyt	0	Cytoplasm				663
P09922 UniProt NPD GO	MX1_MOUSE	Interferon-induced GTP-binding protein Mx1 (Influenza resistance protein)	0.65	+	nuc	0	Nucleus	nucleus [IDA]			631
Q60462 UniProt NPD GO	IFIT2_CRIGR	Interferon-induced protein with tetratricopeptide repeats 2 (IFIT-2) (Interferon-induced 54 kDa prot ...	0.65	-	nuc	0					468
Q12906 UniProt NPD GO	ILF3_HUMAN	Interleukin enhancer-binding factor 3 (Nuclear factor of activated T-cells 90 kDa) (NF-AT-90) (Doubl ...	0.65	-	nuc	0	Nucleus; nucleolus	nucleus [IDA]	603182		894
O62678 UniProt NPD GO	IL16_AOTTR	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.65	-	nuc	0	Secreted protein (By similarity)				632
O62677 UniProt NPD GO	IL16_SAISC	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.65	-	nuc	0	Secreted protein (By similarity)				627
P26954 UniProt NPD GO	IL3B2_MOUSE	Interleukin-3 receptor class 2 beta chain precursor (Interleukin-3 receptor class II beta chain) (Co ...	0.65	-	nuc	1	Membrane; single-pass type I membrane protein				878
Q921I2 UniProt NPD GO	KLDC4_MOUSE	Kelch domain-containing protein 4	0.65	+	nuc	0					584
Q8IVT5 UniProt NPD GO	KSR1_HUMAN	Kinase suppressor of ras-1 (Kinase suppressor of ras)	0.65	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). In unstimulated ce ...	intracellular [NAS]	601132		921
Q9H0B6 UniProt NPD GO	KLC2_HUMAN	Kinesin light chain 2 (KLC 2)	0.65	-	nuc	0		cytosol [ISS] kinesin complex [ISS]			622
O35231 UniProt NPD GO	KIFC3_MOUSE	Kinesin-like protein KIFC3	0.65	-	nuc	0		Golgi apparatus [IDA] kinesin complex [IDA]			687
P50748 UniProt NPD GO	KNTC1_HUMAN	Kinetochore-associated protein 1 (Rough deal homolog) (hRod) (HsROD) (Rod)	0.65	-	nuc	0	Cytoplasm. Nucleus. Dynamic pattern of localization during the cell cycle. At interphase, uniformly ...	kinetochore microtubule [IDA] nucleus [NAS] spindle pole [IDA]	607363		2209
P10074 UniProt NPD GO	HKR3_HUMAN	Krueppel-related zinc finger protein 3 (Protein HKR3)	0.65	-	nuc	0	Nucleus		165270		688
Q8I7C3 UniProt NPD GO	LASP1_DROME	LIM and SH3 domain protein Lasp	0.65	-	nuc	0					657
P22079 UniProt NPD GO	PERL_HUMAN	Lactoperoxidase precursor (EC 1.11.1.7) (LPO) (Salivary peroxidase) (SPO)	0.65	-	mit	0	Secreted protein; extracellular space		170990		712
P23913 UniProt NPD GO	LBR_CHICK	Lamin-B receptor	0.65	+	end	8	Nucleus; nuclear inner membrane; multi-pass membrane protein				637
Q61087 UniProt NPD GO	LAMB3_MOUSE	Laminin beta-3 chain precursor (Laminin 5 beta 3) (Kalinin B1 chain)	0.65	-	exc	0	Secreted protein; extracellular space				1168
Q00918 UniProt NPD GO	LTBP1_RAT	Latent-transforming growth factor beta-binding protein 1 precursor (LTBP-1) (Transforming growth fac ...	0.65	-	nuc	0	Secreted protein				1712
Q8CG19 UniProt NPD GO	LTB1L_MOUSE	Latent-transforming growth factor beta-binding protein, isoform 1L precursor (LTBP-1) (Transforming ...	0.65	-	nuc	0	Secreted protein (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			1713
Q9H9A6 UniProt NPD GO	LRC40_HUMAN	Leucine-rich repeat-containing protein 40	0.65	-	nuc	0					602
P48732 UniProt NPD GO	DET1_ARATH	Light-mediated development protein DET1 (DEETIOLATED1 protein)	0.65	-	nuc	0	Nucleus				541
Q9VCI3 UniProt NPD GO	LSD1_DROME	Lipid storage droplets surface-binding protein 1	0.65	-	nuc	0	Cytoplasm. Cytoplasmic and in lipid storage droplets of adipocytes of first instar larvae. Colocaliz ...	lipid particle [IDA]			431
Q95JB4 UniProt NPD GO	LEAP2_PIG	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)	0.65	-	exc	0	Secreted protein				77
Q801G1 UniProt NPD GO	ARHA_XENLA	Low density lipoprotein receptor adapter protein 1-A (Autosomal recessive hypercholesterolemia prote ...	0.65	-	nuc	0	Cytoplasm (By similarity)				309
P98157 UniProt NPD GO	LRP1_CHICK	Low-density lipoprotein receptor-related protein 1 precursor (LRP) (Alpha-2-macroglobulin receptor) ...	0.65	-	exc	1	Membrane; single-pass type I membrane protein			1LPX	4543
Q8RVL4 UniProt NPD GO	DEF21_ANTMA	MADS-box protein defh21 (DEFICIENS homolog 21)	0.65	-	nuc	0	Nucleus (By similarity)				247
P28750 UniProt NPD GO	EXU_DROME	Maternal protein exuperantia	0.65	-	nuc	0		cytoplasm [IDA]			532
Q8SE90 UniProt NPD GO	MATK_ACEPS	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				517
Q5J300 UniProt NPD GO	MATK_AMAGR	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				505
Q5GIR6 UniProt NPD GO	MATK_BACCT	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				503
O98636 UniProt NPD GO	MATK_BARLO	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				505
Q6EIJ3 UniProt NPD GO	MATK_BOMBU	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				504
O98634 UniProt NPD GO	MATK_BRASC	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				500
Q9GHE1 UniProt NPD GO	MATK_DISSE	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				516
O98639 UniProt NPD GO	MATK_EURFE	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				507
Q7YJZ1 UniProt NPD GO	MATK_HARGR	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				506
Q5GF62 UniProt NPD GO	MATK_IRISE	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				526
Q95EF3 UniProt NPD GO	MATK_KOKDR	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				504
Q9TKB9 UniProt NPD GO	MATK_KUNCA	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				505
Q9TMB2 UniProt NPD GO	MATK_MEDVI	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				516
Q95ED9 UniProt NPD GO	MATK_OPUQU	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				509
Q9MUZ5 UniProt NPD GO	MATK_PHAAD	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				511
Q85X50 UniProt NPD GO	MATK_PINKO	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				515
Q8HQR0 UniProt NPD GO	MATK_PINPR	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				513
Q6BDH3 UniProt NPD GO	MATK_PINPU	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				515
Q6BDH1 UniProt NPD GO	MATK_PINSI	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				515
Q8WJP2 UniProt NPD GO	MATK_PRULA	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				500
Q6ENX8 UniProt NPD GO	MATK_SACOF	Maturase K (Intron maturase)	0.65	-	nuc	0	Plastid; chloroplast				513

You are viewing entries 16401 to 16450 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.