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
P46601 UniProt NPD GO	HAT2_ARATH	Homeobox-leucine zipper protein HAT2 (HD-ZIP protein 2)	0.74	+	nuc	0	Nucleus (Potential)				283
P42859 UniProt NPD GO	HD_MOUSE	Huntingtin (Huntington disease protein homolog) (HD protein)	0.74	+	end	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasmic membrane-bound vesicle [IDA] inclusion body [IDA]			3119
Q96JB3 UniProt NPD GO	HIC2_HUMAN	Hypermethylated in cancer 2 protein (Hic-2) (Hic-3) (HIC1-related gene on chromosome 22) (Zinc finge ...	0.74	-	nuc	0	Nucleus	nucleus [IEP]	607712		615
P34562 UniProt NPD GO	YNP9_CAEEL	Hypothetical GRIP and coiled-coil domain-containing protein T05G5.9 in chromosome III	0.74	+	nuc	0					660
Q09230 UniProt NPD GO	YQ15_CAEEL	Hypothetical protein C05C10.5	0.74	-	nuc	0					212
Q10302 UniProt NPD GO	YD49_SCHPO	Hypothetical protein C22H10.09 in chromosome I	0.74	-	mit	0					646
O43006 UniProt NPD GO	YBO7_SCHPO	Hypothetical protein C2G2.07c in chromosome II	0.74	-	nuc	0					225
P34366 UniProt NPD GO	YLJ1_CAEEL	Hypothetical protein C50C3.1	0.74	-	nuc	0					469
O94662 UniProt NPD GO	YBW4_SCHPO	Hypothetical protein C651.04 in chromosome II	0.74	-	nuc	0					237
O14211 UniProt NPD GO	YDT6_SCHPO	Hypothetical protein C6B12.06c in chromosome I	0.74	-	nuc	0					117
P78813 UniProt NPD GO	YCTB_SCHPO	Hypothetical protein C794.11c in chromosome III	0.74	-	nuc	0					476
Q10042 UniProt NPD GO	YRC3_CAEEL	Hypothetical protein K01A12.3	0.74	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				417
Q9HDV3 UniProt NPD GO	YOE7_SCHPO	Hypothetical protein P19A11.07c in chromosome II	0.74	-	nuc	0					676
O14076 UniProt NPD GO	YEAB_SCHPO	Hypothetical protein UNK4.11c in chromosome I	0.74	+	nuc	0					188
P34643 UniProt NPD GO	YOQ5_CAEEL	Hypothetical protein ZK512.5	0.74	-	mit	0					1232
Q6TNU3 UniProt NPD GO	INT10_BRARE	Integrator complex subunit 10	0.74	-	cyt	0	Nucleus (By similarity)				715
Q01514 UniProt NPD GO	GBP1_MOUSE	Interferon-induced guanylate-binding protein 1 (GTP-binding protein 1) (Guanine nucleotide-binding p ...	0.74	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				589
Q96J02 UniProt NPD GO	ITCH_HUMAN	Itchy homolog E3 ubiquitin protein ligase (EC 6.3.2.-) (Itch) (Atrophin-1-interacting protein 4) (AI ...	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		606409		903
O74746 UniProt NPD GO	SPF31_SCHPO	J domain-containing protein spf31	0.74	+	nuc	0					209
Q4P5U1 UniProt NPD GO	JHD1_USTMA	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.74	-	nuc	0	Nucleus (By similarity)				669
Q07866 UniProt NPD GO	KLC1_HUMAN	Kinesin light chain 1 (KLC 1)	0.74	-	nuc	0		cytosol [ISS] kinesin complex [ISS]	600025		569
Q9V877 UniProt NPD GO	SUB_DROME	Kinesin-like protein subito (Protein double or nothing)	0.74	-	nuc	0	Cytoplasm. Microtubule-associated	microtubule associated complex [IDA] spindle pole [IMP]			628
P23678 UniProt NPD GO	UN104_CAEEL	Kinesin-like protein unc-104 (Uncoordinated protein 104)	0.74	-	nuc	0		axon [IDA] dendrite [IDA]			1584
P13054 UniProt NPD GO	KNRL_DROME	Knirps-related protein	0.74	-	nuc	0	Nucleus				647
Q6S5J6 UniProt NPD GO	KRIT1_MOUSE	Krev interaction trapped protein 1 (Krev interaction trapped 1) (Cerebral cavernous malformations 1 ...	0.74	+	nuc	0	Membrane; peripheral membrane protein (Probable)				736
Q12802 UniProt NPD GO	LBC_HUMAN	LBC oncogene (P47) (Lymphoid blast crisis oncogene)	0.74	-	cyt	0		membrane fraction [TAS]	604686		424
P84551 UniProt NPD GO	LBXCO_RAT	Ladybird homeobox corepressor 1	0.74	-	nuc	0	Nucleus (By similarity)				964
P15215 UniProt NPD GO	LAMC1_DROME	Laminin gamma-1 chain precursor (Laminin B2 chain)	0.74	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basal lamina [IDA]			1639
Q9BRK4 UniProt NPD GO	LZTS2_HUMAN	Leucine zipper putative tumor suppressor 2 (Protein LAPSER1)	0.74	-	nuc	0					669
P30303 UniProt NPD GO	MPIP_EMENI	M-phase inducer phosphatase (EC 3.1.3.48)	0.74	-	nuc	0					556
P23748 UniProt NPD GO	MPIP_YEAST	M-phase inducer phosphatase (EC 3.1.3.48) (Mitosis initiation protein MIH1) (Mitotic inducer homolog ...	0.74	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			554
Q9XGJ4 UniProt NPD GO	GGM13_GNEGN	MADS-box protein GGM13	0.74	-	nuc	0	Nucleus (By similarity)				237
Q9H8J5 UniProt NPD GO	MANS1_HUMAN	MANSC domain-containing protein 1 precursor	0.74	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				431
Q9NS73 UniProt NPD GO	MBIP1_HUMAN	MAP3K12-binding inhibitory protein 1 (MAPK upstream kinase-binding inhibitory protein) (MUK-binding ...	0.74	-	nuc	0	Nucleus. Cytoplasm. Shows a cytoplasmic localization when co-expressed with MAP3K12		609431		344
Q9BQA5 UniProt NPD GO	MIZF_HUMAN	MBD2-interacting zinc finger protein (Methyl-CpG-binding protein 2-interacting zinc finger protein)	0.74	-	nuc	0	Nucleus		607099		517
Q8JZQ0 UniProt NPD GO	CSF1_RAT	Macrophage colony-stimulating factor 1 precursor (CSF-1) (MCSF)	0.74	+	exc	1	Cell membrane; single-pass membrane protein (By similarity). Processed form: Secreted protein; extra ...	integral to plasma membrane [TAS]			566
Q64449 UniProt NPD GO	MRC2_MOUSE	Macrophage mannose receptor 2 precursor (Lectin lambda) (CD280 antigen)	0.74	-	nuc	1	Membrane; single-pass type I membrane protein				1479
Q9GI85 UniProt NPD GO	MATK_ADELA	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				511
O09410 UniProt NPD GO	MATK_APOAN	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				505
Q9GF61 UniProt NPD GO	MATK_ARALP	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				504
Q7YM31 UniProt NPD GO	MATK_ASITR	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				507
Q9GF62 UniProt NPD GO	MATK_BARVU	Maturase K (Intron maturase)	0.74	-	mit	0	Plastid; chloroplast				504
Q8WJQ9 UniProt NPD GO	MATK_CRAMN	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				506
Q9TIB3 UniProt NPD GO	MATK_CYNDA	Maturase K (Intron maturase)	0.74	+	nuc	0	Plastid; chloroplast				513
Q8WKM6 UniProt NPD GO	MATK_HYDMC	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				506
Q8M9H0 UniProt NPD GO	MATK_JACMI	Maturase K (Intron maturase)	0.74	-	pox	0	Plastid; chloroplast				509
Q9TKB8 UniProt NPD GO	MATK_KUNER	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				505
O47128 UniProt NPD GO	MATK_LYOLI	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				507
Q4LAM6 UniProt NPD GO	MATK_MALDO	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				485
Q8M9A9 UniProt NPD GO	MATK_MANZA	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				508

You are viewing entries 11851 to 11900 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.