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
Q9US03 UniProt NPD GO	KLP2_SCHPO	Kinesin-like protein 2	0.78	-	nuc	0	Cytoplasm. Nucleus. During interphase. When in the nucleus, it associates with chromatin	cytoplasm [IDA] kinetochore [TAS] nucleus [IDA]			817
Q9D2Z8 UniProt NPD GO	KIF12_MOUSE	Kinesin-like protein KIF12	0.78	-	nuc	0					642
P53671 UniProt NPD GO	LIMK2_HUMAN	LIM domain kinase 2 (EC 2.7.11.1) (LIMK-2)	0.78	-	cyt	0	Cytoplasm. Nucleus. Isoform LIMK2a is distributed in the cytoplasm and the nucleus, and isoform LIMK ...	cytoplasm [TAS] nucleus [TAS]	601988	1X6A	638
Q9NQ69 UniProt NPD GO	LHX9_HUMAN	LIM/homeobox protein Lhx9	0.78	-	nuc	0	Nucleus (Probable)		606066		388
Q26457 UniProt NPD GO	LA_AEDAL	La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.78	+	nuc	0	Nucleus. Cytoplasm. Primarily nuclear, but significant amounts are present in the cytoplasm				383
Q9H069 UniProt NPD GO	LRC48_HUMAN	Leucine-rich repeat-containing protein 48	0.78	-	nuc	0					523
Q5E9X4 UniProt NPD GO	LRC59_BOVIN	Leucine-rich repeat-containing protein 59	0.78	+	nuc	0	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				306
P50851 UniProt NPD GO	LRBA_HUMAN	Lipopolysaccharide-responsive and beige-like anchor protein (CDC4-like protein) (Beige-like protein) ...	0.78	-	end	0			606453	1T77	2863
P32048 UniProt NPD GO	SYKM_YEAST	Lysyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.78	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			576
P48968 UniProt NPD GO	MPIP3_MESAU	M-phase inducer phosphatase 3 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25C)	0.78	+	nuc	0	Nucleus				420
Q9ATE5 UniProt NPD GO	FBP24_PETHY	MADS-box protein FBP24 (Floral-binding protein 24)	0.78	-	nuc	0	Nucleus (By similarity)				268
Q9XJ66 UniProt NPD GO	MAD22_ORYSA	MADS-box transcription factor 22 (OsMADS22)	0.78	-	nuc	0	Nucleus (Probable)				228
Q6EU39 UniProt NPD GO	MADS6_ORYSA	MADS-box transcription factor 6 (OsMADS6)	0.78	-	nuc	0	Nucleus (Probable)				250
Q66L33 UniProt NPD GO	R13LA_XENLA	MAK16-like protein RBM13 A (RNA-binding motif protein 13-like A)	0.78	+	nuc	0	Nucleus; nucleolus (By similarity)				301
Q9BUB5 UniProt NPD GO	MKNK1_HUMAN	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.78	+	nuc	0	Isoform 2: Cytoplasm. Isoform 3: Cytoplasm. Nucleus		606724		465
Q66JF3 UniProt NPD GO	MKNK1_XENTR	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.78	+	nuc	0					417
Q8VHF0 UniProt NPD GO	MARK3_RAT	MAP/microtubule affinity-regulating kinase 3 (EC 2.7.11.1)	0.78	-	nuc	0					797
Q01926 UniProt NPD GO	MRS2_YEAST	Magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.78	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			470
Q9HDS5 UniProt NPD GO	MTAL2_KLULA	Mating-type protein ALPHA2 (MATalpha2 protein)	0.78	+	nuc	0	Nucleus (By similarity)				223
Q3LFX6 UniProt NPD GO	MATK_AERJP	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				517
Q9GF51 UniProt NPD GO	MATK_ARAHA	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				504
Q5J2X6 UniProt NPD GO	MATK_BETVU	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				505
Q7YKY5 UniProt NPD GO	MATK_CHACO	Maturase K (Intron maturase)	0.78	-	cyt	0	Plastid; chloroplast				516
Q7I9M7 UniProt NPD GO	MATK_COLHT	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				508
O47164 UniProt NPD GO	MATK_LEIBU	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				507
O47169 UniProt NPD GO	MATK_LOIPR	Maturase K (Intron maturase)	0.78	-	nuc	0	Plastid; chloroplast				507
Q5GA98 UniProt NPD GO	MATK_MIMGU	Maturase K (Intron maturase)	0.78	-	pox	0	Plastid; chloroplast				512
Q9MUY9 UniProt NPD GO	MATK_POAPR	Maturase K (Intron maturase)	0.78	-	cyt	0	Plastid; chloroplast				511
Q8WJP5 UniProt NPD GO	MATK_POTAN	Maturase K (Intron maturase)	0.78	-	cyt	0	Plastid; chloroplast				500
Q507T3 UniProt NPD GO	MATK_RANRE	Maturase K (Intron maturase)	0.78	-	cyt	0	Plastid; chloroplast				507
Q9TKP9 UniProt NPD GO	MATK_ROBPS	Maturase K (Intron maturase)	0.78	-	mit	0	Plastid; chloroplast				507
Q9HCI5 UniProt NPD GO	MAGE1_HUMAN	Melanoma-associated antigen E1 (MAGE-E1 antigen) (Hepatocellular carcinoma-associated protein 1)	0.78	+	nuc	0		dendrite [ISS] nucleus [ISS] perinuclear region [ISS] plasma membrane [ISS] postsynaptic membrane [ISS]			957
P13819 UniProt NPD GO	MSP1_PLAFF	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA)	0.78	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1701
P19598 UniProt NPD GO	MSP1_PLAF3	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (P190)	0.78	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1682
P08569 UniProt NPD GO	MSP1_PLAFM	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (P190)	0.78	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1701
Q9URY2 UniProt NPD GO	ALP7_SCHPO	Microtubule protein alp7 (Altered polarity protein 7)	0.78	-	nuc	0	Nucleus. Cytoplasm. Nuclear and associated with microtubules	spindle pole body [IDA]			474
Q2KID9 UniProt NPD GO	RT05_BOVIN	Mitochondrial 28S ribosomal protein S5 (S5mt) (MRP-S5)	0.78	+	mit	0	Mitochondrion (By similarity)				430
P26867 UniProt NPD GO	RT07_MARPO	Mitochondrial ribosomal protein S7	0.78	-	nuc	0	Mitochondrion				230
O08648 UniProt NPD GO	M3K4_MOUSE	Mitogen-activated protein kinase kinase kinase 4 (EC 2.7.11.25) (MAPK/ERK kinase kinase 4) (MEK kina ...	0.78	-	nuc	0	Cytoplasm; perinuclear region. Localized in perinuclear vesicular-like structures, probably Golgi-as ...				1597
P46150 UniProt NPD GO	MOEH_DROME	Moesin/ezrin/radixin homolog 1 (Ezrin-moesin-radixin 1) (Protein D17) (Protein moesin) (dMoesin)	0.78	-	nuc	0	Cell membrane; cell-cell junction; adherens junction; peripheral membrane protein	adherens junction [IDA] cytoplasm [NAS] plasma membrane [IDA] subapical complex [TAS]			578
O88940 UniProt NPD GO	MUSC_MOUSE	Musculin (Myogenic repressor)	0.78	-	nuc	0	Nucleus				201
P06876 UniProt NPD GO	MYB_MOUSE	Myb proto-oncogene protein (C-myb)	0.78	+	nuc	0	Nucleus	nucleus [IDA]		2AGH	636
P34127 UniProt NPD GO	MYBH_DICDI	Myb-like protein (Fragment)	0.78	-	nuc	0	Nucleus (Probable)				451
P59044 UniProt NPD GO	NALP6_HUMAN	NACHT, LRR and PYD-containing protein 6 (PYRIN-containing APAF1-like protein 5)	0.78	-	nuc	0	Cytoplasm		609650		892
P70211 UniProt NPD GO	DCC_MOUSE	Netrin receptor DCC precursor (Tumor suppressor protein DCC)	0.78	-	end	2 *	Membrane; single-pass type I membrane protein	axon [IDA]			1447
O35274 UniProt NPD GO	NEB2_RAT	Neurabin-2 (Neurabin-II) (Spinophilin) (Protein phosphatase 1 regulatory subunit 9B) (Neural tissue- ...	0.78	-	nuc	0	Cytoplasm. Nucleus (By similarity). Enriched at synapse and cadherin-based cell-cell adhesion sites. ...				817
Q6ZS30 UniProt NPD GO	NBEAL_HUMAN	Neurobeachin-like 1 (Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 17 protein)	0.78	-	nuc	0			609816		1314
Q91616 UniProt NPD GO	NDF1_XENLA	Neurogenic differentiation factor 1 (NeuroD1)	0.78	-	nuc	0	Nucleus (Potential)				352
P46530 UniProt NPD GO	NOTC1_BRARE	Neurogenic locus notch homolog protein 1 precursor	0.78	+	exc	1	Membrane; single-pass type I membrane protein				2437
O42606 UniProt NPD GO	NGN1_BRARE	Neurogenin 1 (Neurogenic differentiation factor 3) (NeuroD3) (Neurogenin-related protein 1)	0.78	+	nuc	0	Nucleus (Probable)				208

You are viewing entries 9901 to 9950 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.