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
P32027 UniProt NPD GO	CROC_DROME	Fork head domain-containing protein crocodile (FKH protein FD1)	0.59	+	nuc	0	Nucleus	nucleus [IDA]			508
O60548 UniProt NPD GO	FOXD2_HUMAN	Forkhead box protein D2 (Forkhead-related protein FKHL17) (Forkhead-related transcription factor 9) ...	0.59	-	nuc	0	Nucleus (By similarity)		602211		497
Q12946 UniProt NPD GO	FOXF1_HUMAN	Forkhead box protein F1 (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1) ( ...	0.59	-	nuc	0	Nucleus	nucleus [TAS] transcription factor complex [TAS]	601089		354
Q63244 UniProt NPD GO	FOXQ1_RAT	Forkhead box protein Q1 (Hepatocyte nuclear factor 3 forkhead homolog 1) (HNF-3/forkhead-like protei ...	0.59	-	nuc	0	Nucleus			1KQ8	392
Q96I76 UniProt NPD GO	GPTC3_HUMAN	G patch domain-containing protein 3	0.59	-	nuc	0					525
Q8BIY1 UniProt NPD GO	GPTC3_MOUSE	G patch domain-containing protein 3	0.59	-	nuc	0					525
Q50DM7 UniProt NPD GO	GPR56_PANTR	G-protein coupled receptor 56 precursor	0.59	-	end	7 *	Membrane; multi-pass membrane protein				687
Q96HU8 UniProt NPD GO	DIRA2_HUMAN	GTP-binding protein Di-Ras2 (Distinct subgroup of the Ras family member 2)	0.59	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		607863	2ERX	199
Q99578 UniProt NPD GO	RIT2_HUMAN	GTP-binding protein Rit2 (Ras-like protein expressed in neurons) (Ras-like without CAAX protein 2)	0.59	+	cyt	0	Cell membrane	plasma membrane [TAS]	609592		217
P32559 UniProt NPD GO	MSS1_YEAST	GTPase MSS1, mitochondrial precursor	0.59	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA]			526
Q8K3K9 UniProt NPD GO	GIMA4_RAT	GTPase, IMAP family member 4 (Immunity-associated protein 4) (Immunity-associated nucleotide 1 prote ...	0.59	-	nuc	0					310
P38785 UniProt NPD GO	GIC1_YEAST	GTPase-interacting component 1	0.59	-	nuc	0	Concentrated at the incipient bud site of unbudded cells, at the bud tip and mother-bud neck of budd ...	actin cap [IDA] bud neck [IDA] bud tip [IDA] incipient bud site [IDA] mating projection tip [IDA]			314
Q92052 UniProt NPD GO	CXA7_BRARE	Gap junction alpha-7 protein (Connexin-43.4) (Cx43.4)	0.59	-	end	4 *	Membrane; multi-pass membrane protein				380
O60763 UniProt NPD GO	VDP_HUMAN	General vesicular transport factor p115 (Transcytosis-associated protein) (TAP) (Vesicle docking pro ...	0.59	-	nuc	0	Cytoplasm; cytosol. Golgi apparatus; Golgi membrane; peripheral membrane protein. Recycles between t ...	Golgi membrane [TAS]	603344		962
P01274 UniProt NPD GO	GLUC_PIG	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.59	-	vac	0	Secreted protein			1GCN	180
Q8MJ25 UniProt NPD GO	GLUC_SHEEP	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.59	-	exc	0	Secreted protein				176
Q9Y761 UniProt NPD GO	GNT1A_KLULA	Glucose N-acetyltransferase 1-A (EC 2.4.1.-) (N-acetylglucosaminyltransferase A)	0.59	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				460
Q94900 UniProt NPD GO	GLUCL_DROME	Glutamate-gated chloride channel precursor	0.59	+	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IC]			456
P48077 UniProt NPD GO	HEM1_CYAPA	Glutamyl-tRNA reductase (EC 1.2.1.70) (GluTR)	0.59	-	nuc	0	Plastid; cyanelle				432
P23900 UniProt NPD GO	FPS1_YEAST	Glycerol uptake/efflux facilitator protein	0.59	-	end	5	Membrane; multi-pass membrane protein (Probable)	cytoplasm [IDA] plasma membrane [IDA] vacuole (sensu Fungi) [IDA]			669
Q00743 UniProt NPD GO	GPA1_EMENI	Guanine nucleotide-binding protein subunit alpha	0.59	-	cyt	0					352
P61574 UniProt NPD GO	REC5_HUMAN	HERV-K_19p13.11 provirus Rec protein (HERV-K113 Rec protein)	0.59	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
Q96PI4 UniProt NPD GO	GAK7_HUMAN	HERV-K_1q23.3 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K18 Gag protein) (HERV-K110 ...	0.59	-	nuc	0					252
P61581 UniProt NPD GO	NP11_HUMAN	HERV-K_22q11.21 provirus Np9 protein (HERV-K101 Np9 protein)	0.59	-	nuc	0	Nucleus. When overexpressed				75
Q9UKH3 UniProt NPD GO	ENK4_HUMAN	HERV-K_6q14.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K109 envelop ...	0.59	-	mit	2					698
P10321 UniProt NPD GO	1C07_HUMAN	HLA class I histocompatibility antigen, Cw-7 alpha chain precursor (MHC class I antigen Cw*7)	0.59	-	end	1	Membrane; single-pass type I membrane protein		142840		366
P57101 UniProt NPD GO	HAND2_XENLA	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.59	+	nuc	0					210
Q00613 UniProt NPD GO	HSF1_HUMAN	Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)	0.59	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic during normal growth and moves to the nucleus upon activation		140580		529
Q12931 UniProt NPD GO	TRAP1_HUMAN	Heat shock protein 75 kDa, mitochondrial precursor (HSP 75) (Tumor necrosis factor type 1 receptor-a ...	0.59	-	mit	0	Mitochondrion		606219		704
Q02576 UniProt NPD GO	HEN1_MOUSE	Helix-loop-helix protein 1 (HEN1) (Nescient helix loop helix 1) (NSCL-1)	0.59	+	nuc	0					133
Q5NVR8 UniProt NPD GO	HEPC_PONPY	Hepcidin precursor	0.59	-	exc	1 *	Secreted protein (By similarity)				84
O43390 UniProt NPD GO	HNRPR_HUMAN	Heterogeneous nuclear ribonucleoprotein R (hnRNP R)	0.59	+	nuc	0	Nucleus; nucleoplasm	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]	607201		633
P30681 UniProt NPD GO	HMGB2_MOUSE	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.59	-	nuc	0	Nucleus	condensed chromosome [ISS] cytoplasm [ISS] nucleus [ISS] perinuclear region [ISS]			209
P17741 UniProt NPD GO	HMGB2_PIG	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.59	-	nuc	0	Nucleus	condensed chromosome [ISS] cytoplasm [ISS] nucleus [ISS] perinuclear region [ISS]		1J3X	209
Q92522 UniProt NPD GO	H1X_HUMAN	Histone H1x	0.59	-	nuc	0	Nucleus	nucleosome [NAS]	602785		213
P14001 UniProt NPD GO	H2B_CAIMO	Histone H2B	0.59	+	nuc	0	Nucleus				125
Q64478 UniProt NPD GO	H2B1H_MOUSE	Histone H2B type 1-H (h2B-221)	0.59	+	nuc	0	Nucleus				125
P23527 UniProt NPD GO	H2B1O_HUMAN	Histone H2B type 1-O (H2B.n) (H2B/n) (H2B.2)	0.59	+	nuc	0	Nucleus	nucleosome [NAS]	602808		125
Q16778 UniProt NPD GO	H2B2E_HUMAN	Histone H2B type 2-E (H2B.q) (H2B/q) (H2B-GL105)	0.59	+	nuc	0	Nucleus	nucleosome [NAS]	601831		125
Q9SGE3 UniProt NPD GO	H2B2_ARATH	Histone H2B.2 (HTB8)	0.59	+	nuc	0	Nucleus (By similarity)				243
Q03828 UniProt NPD GO	EVX2_HUMAN	Homeobox even-skipped homolog protein 2 (EVX-2)	0.59	+	nuc	0	Nucleus	nucleus [NAS]	142991		476
Q61658 UniProt NPD GO	HESX1_MOUSE	Homeobox expressed in ES cells 1 (Homeobox protein ANF) (Anterior-restricted homeobox protein) (Rath ...	0.59	+	nuc	0	Nucleus (Probable)				185
Q05095 UniProt NPD GO	CDX1_RAT	Homeobox protein CDX-1 (Caudal-type homeobox protein 1) (Fragment)	0.59	+	nuc	0	Nucleus				123
P50577 UniProt NPD GO	DLX5_CHICK	Homeobox protein DLX-5 (cDlx)	0.59	+	nuc	0	Nucleus (Potential)				286
Q01702 UniProt NPD GO	DLX3B_BRARE	Homeobox protein Dlx3b (DLX-3) (Distal-less homeobox protein 3b)	0.59	+	nuc	0	Nucleus (Potential)				269
Q04741 UniProt NPD GO	EMX1_HUMAN	Homeobox protein EMX1 (Empty spiracles homolog 1) (Empty spiracles-like protein 1)	0.59	+	cyt	0	Nucleus (Probable)	nucleus [NAS]	600034		257
Q28598 UniProt NPD GO	HXA4_SHEEP	Homeobox protein Hox-A4 (Fragment)	0.59	+	nuc	0	Nucleus				87
P31312 UniProt NPD GO	HXC11_MOUSE	Homeobox protein Hox-C11 (Hox-3.7) (Fragment)	0.59	+	nuc	0	Nucleus				60
P28359 UniProt NPD GO	HXD10_MOUSE	Homeobox protein Hox-D10 (Hox-4.5) (Hox-5.3)	0.59	+	nuc	0	Nucleus				340
Q03356 UniProt NPD GO	MSXB_BRARE	Homeobox protein MSH-B	0.59	+	nuc	0	Nucleus				257

You are viewing entries 19551 to 19600 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.)

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