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
O80988 UniProt NPD GO	GCSP_ARATH	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.25	-	mit	0	Mitochondrion				1044
Q4WIQ0 UniProt NPD GO	GPI11_ASPFU	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.25	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				297
P34763 UniProt NPD GO	NMT_AJECA	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.25	-	cyt	0	Cytoplasm				529
P51655 UniProt NPD GO	GPC4_MOUSE	Glypican-4 precursor (K-glypican)	0.25	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				557
P23785 UniProt NPD GO	GRN_RAT	Granulins precursor [Contains: Acrogranin; Granulin-1 (Granulin G); Granulin-2 (Granulin F); Granuli ...	0.25	-	exc	0	Secreted protein				588
Q9EPR2 UniProt NPD GO	PG12A_MOUSE	Group XIIA secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GX ...	0.25	-	exc	0	Secreted protein	endoplasmic reticulum [IDA] Golgi apparatus [IDA] intracellular [IDA]			192
Q5USV6 UniProt NPD GO	GDF8_SYLGR	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.25	-	cyt	0	Secreted protein (By similarity)				375
Q6BTP9 UniProt NPD GO	GRPE_DEBHA	GrpE protein homolog, mitochondrial precursor	0.25	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				243
P62879 UniProt NPD GO	GBB2_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 2 (Transducin beta chain 2) (G protei ...	0.25	-	cyt	0			139390		339
P62880 UniProt NPD GO	GBB2_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 2 (Transducin beta chain 2) (G protei ...	0.25	-	cyt	0					339
P54313 UniProt NPD GO	GBB2_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 2 (Transducin beta chain 2) (G protei ...	0.25	-	cyt	0					339
P10824 UniProt NPD GO	GNAI1_RAT	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.25	-	cyt	0		heterotrimeric G-protein complex [TAS]		1SVS	353
Q870G5 UniProt NPD GO	GBG_LENED	Guanine nucleotide-binding protein subunit gamma	0.25	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				82
P16068 UniProt NPD GO	GCYB1_BOVIN	Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) (GCS-beta-1) (Soluble guanylate cyclase small ...	0.25	-	cyt	0	Cytoplasm			1AWN	619
Q02153 UniProt NPD GO	GCYB1_HUMAN	Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) (GCS-beta-1) (Soluble guanylate cyclase small ...	0.25	-	cyt	0	Cytoplasm	guanylate cyclase complex, soluble [TAS]	139397		619
Q9UMX6 UniProt NPD GO	GUC1B_HUMAN	Guanylyl cyclase-activating protein 2 (GCAP 2) (Guanylate cyclase activator 1B)	0.25	-	cyt	0	Membranes of outer segment		602275		199
Q15034 UniProt NPD GO	HERC3_HUMAN	HECT domain and RCC1-like domain protein 3	0.25	-	cyt	0	Cytoplasm. Cytoplasmic vesicle. Also found in vesicular-like structures		605200		1050
Q01766 UniProt NPD GO	HAL1_YEAST	Halotolerance protein HAL1	0.25	-	nuc	0	Cytoplasm	cytoplasm [IDA]			294
P48722 UniProt NPD GO	HS74L_MOUSE	Heat shock 70 kDa protein 4L (Osmotic stress protein 94) (Heat shock 70-related protein APG-1)	0.25	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). May translocate to the nucleus after heat shock ...	cytoplasm [ISS] nucleus [ISS]			838
P37900 UniProt NPD GO	HSP7M_PEA	Heat shock 70 kDa protein, mitochondrial precursor	0.25	-	mit	0	Mitochondrion				675
P63017 UniProt NPD GO	HSP7C_MOUSE	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.25	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				646
P63018 UniProt NPD GO	HSP7C_RAT	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.25	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...			7HSC	646
Q3ZC22 UniProt NPD GO	HSBP1_BOVIN	Heat shock factor-binding protein 1	0.25	-	nuc	0	Nucleus (By similarity)				76
Q5RDI2 UniProt NPD GO	HSBP1_PONPY	Heat shock factor-binding protein 1	0.25	-	nuc	0	Nucleus (By similarity)				76
O75506 UniProt NPD GO	HSBP1_HUMAN	Heat shock factor-binding protein 1 (Nasopharyngeal carcinoma-associated antigen 13) (NPC-A-13)	0.25	-	nuc	0	Nucleus	nucleus [TAS]	604553		76
P22202 UniProt NPD GO	HSP74_YEAST	Heat shock protein SSA4	0.25	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			641
P40150 UniProt NPD GO	HSP76_YEAST	Heat shock protein SSB2	0.25	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide	cytoplasm [IDA] polysome [IDA]			612
P32339 UniProt NPD GO	HMX1_YEAST	Heme-binding protein HMX1	0.25	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	endoplasmic reticulum [IDA] integral to membrane [NAS] membrane [IDA]			317
Q8TG40 UniProt NPD GO	HBR1_CANAL	Hemoglobin and proliferation-regulated protein HBR1 (Hb-regulated protein 1)	0.25	-	mit	0					248
Q90YK5 UniProt NPD GO	HPSE_CHICK	Heparanase precursor (EC 3.2.-.-)	0.25	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				523
Q3Y598 UniProt NPD GO	HNF3G_BOVIN	Hepatocyte nuclear factor 3-gamma (HNF-3G) (Forkhead box protein A3)	0.25	+	nuc	0	Nucleus (By similarity)				351
Q99729 UniProt NPD GO	ROAA_HUMAN	Heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) (APOBEC-1-binding protein 1) (ABBP-1)	0.25	+	cyt	0	Nucleus		602688		331
Q3SZF3 UniProt NPD GO	HNRH2_BOVIN	Heterogeneous nuclear ribonucleoprotein H' (hnRNP H')	0.25	-	cyt	0	Nucleus; nucleoplasm (By similarity)				449
P70333 UniProt NPD GO	HNRH2_MOUSE	Heterogeneous nuclear ribonucleoprotein H' (hnRNP H')	0.25	-	cyt	0	Nucleus; nucleoplasm (By similarity)				449
P55795 UniProt NPD GO	HNRH2_HUMAN	Heterogeneous nuclear ribonucleoprotein H' (hnRNP H') (FTP-3)	0.25	-	cyt	0	Nucleus; nucleoplasm	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]	601036	1WG5	449
P50506 UniProt NPD GO	HXK_DEBOC	Hexokinase (EC 2.7.1.1)	0.25	-	cyt	0					478
P10870 UniProt NPD GO	SNF3_YEAST	High-affinity glucose transporter SNF3	0.25	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			818
Q9ZNV9 UniProt NPD GO	AHP1_ARATH	Histidine-containing phosphotransfer protein 1	0.25	-	nuc	0					154
Q61035 UniProt NPD GO	SYH_MOUSE	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.25	-	nuc	0					509
Q02539 UniProt NPD GO	H11_HUMAN	Histone H1.1	0.25	+	nuc	0	Nucleus		142709		214
Q4IMD1 UniProt NPD GO	H2AZ_GIBZE	Histone H2A.Z	0.25	-	nuc	0	Nucleus (By similarity)				144
P50565 UniProt NPD GO	H2B1_CHLRE	Histone H2B.1 (H2B-I)	0.25	-	nuc	0	Nucleus				152
P40283 UniProt NPD GO	H2B11_ARATH	Histone H2B.11 (HTB4)	0.25	-	nuc	0	Nucleus				149
O23629 UniProt NPD GO	H2B6_ARATH	Histone H2B.6 (HTB9) (H2BAt)	0.25	-	nuc	0	Nucleus (By similarity)				149
Q9LZT0 UniProt NPD GO	H2B7_ARATH	Histone H2B.7 (HTB11)	0.25	-	nuc	0	Nucleus (By similarity)				144
P80738 UniProt NPD GO	H4Y_BLEJA	Histone H4 (Fragment)	0.25	-	nuc	0	Nucleus (By similarity)				47
Q92769 UniProt NPD GO	HDAC2_HUMAN	Histone deacetylase 2 (HD2)	0.25	-	nuc	0	Nucleus	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]	605164		488
P70288 UniProt NPD GO	HDAC2_MOUSE	Histone deacetylase 2 (HD2) (YY1 transcription factor-binding protein)	0.25	-	nuc	0	Nucleus	cytoplasm [TAS] heterochromatin [IDA] histone deacetylase complex [TAS] nucleus [TAS] replication fork [IDA]			488
Q56WH4 UniProt NPD GO	HD2B_ARATH	Histone deacetylase 2b (HD-tuins protein 2)	0.25	-	nuc	0	Nucleus; nucleolus				306
Q8SW50 UniProt NPD GO	HD7_ENCCU	Homeobox protein HD-7 (EcHD-7)	0.25	-	nuc	0	Nucleus				148

You are viewing entries 45251 to 45300 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.