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
P20165 UniProt NPD GO	HR2_TRIFL	Trimerelysin-2 (EC 3.4.24.53) (Trimerelysin II) (H2 metalloproteinase)	0.11	-	nuc	0				1WNI	201
Q7KQM0 UniProt NPD GO	TPIS_PLAF7	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.11	-	cyt	0					248
Q07412 UniProt NPD GO	TPIS_PLAFA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.11	-	cyt	0				2FI6	248
P00761 UniProt NPD GO	TRYP_PIG	Trypsin precursor (EC 3.4.21.4)	0.11	-	nuc	0	Secreted protein; extracellular space			1Z7K	231
P13228 UniProt NPD GO	TRP_NEUCR	Tryptophan synthase (EC 4.2.1.20)	0.11	-	nuc	0					708
P53372 UniProt NPD GO	TBA1_PNECA	Tubulin alpha chain	0.11	-	cyt	0					449
P87066 UniProt NPD GO	TBA_CANAL	Tubulin alpha chain	0.11	-	cyt	0					448
P33625 UniProt NPD GO	TBA_EUGGR	Tubulin alpha chain	0.11	-	cyt	0					451
P28268 UniProt NPD GO	TBA_EUPVA	Tubulin alpha chain	0.11	-	cyt	0					450
Q92335 UniProt NPD GO	TBA_SORMA	Tubulin alpha chain	0.11	-	cyt	0					449
P04106 UniProt NPD GO	TBA_TRYBR	Tubulin alpha chain	0.11	-	cyt	0					451
P08537 UniProt NPD GO	TBA_XENLA	Tubulin alpha chain	0.11	-	cyt	0					449
P18288 UniProt NPD GO	TBAT_ONCMY	Tubulin alpha chain, testis-specific	0.11	-	cyt	0					450
P06603 UniProt NPD GO	TBA1_DROME	Tubulin alpha-1 chain	0.11	-	cyt	0					450
P31017 UniProt NPD GO	TBA1_ENTHI	Tubulin alpha-1 chain	0.11	-	cyt	0					455
Q40831 UniProt NPD GO	TBA1_PELFA	Tubulin alpha-1 chain	0.11	-	cyt	0					453
Q25008 UniProt NPD GO	TBA1_HOMAM	Tubulin alpha-1 chain (Alpha-I tubulin)	0.11	-	cyt	0					451
P09243 UniProt NPD GO	TBA2_STYLE	Tubulin alpha-2 chain	0.11	-	cyt	0					449
Q94570 UniProt NPD GO	TBA2_HOMAM	Tubulin alpha-2 chain (Alpha-II tubulin)	0.11	-	cyt	0					451
Q13748 UniProt NPD GO	TBA2_HUMAN	Tubulin alpha-2 chain (Alpha-tubulin 2)	0.11	-	cyt	0		microtubule [NAS]	602528		450
P06605 UniProt NPD GO	TBA3_DROME	Tubulin alpha-3 chain	0.11	-	cyt	0					450
Q68FR8 UniProt NPD GO	TBA3_RAT	Tubulin alpha-3 chain (Alpha-tubulin 3)	0.11	-	cyt	0					450
P68365 UniProt NPD GO	TBA3_CRIGR	Tubulin alpha-3 chain (Alpha-tubulin 3) (Alpha-tubulin III)	0.11	-	cyt	0					449
P05214 UniProt NPD GO	TBA3_MOUSE	Tubulin alpha-3/alpha-7 chain (Alpha-tubulin 3/7) (Alpha-tubulin isotype M-alpha-3/7)	0.11	-	cyt	0					450
Q9BQE3 UniProt NPD GO	TBA6_HUMAN	Tubulin alpha-6 chain (Alpha-tubulin 6)	0.11	-	cyt	0					449
Q6AYZ1 UniProt NPD GO	TBA6_RAT	Tubulin alpha-6 chain (Alpha-tubulin 6)	0.11	-	cyt	0					449
P68373 UniProt NPD GO	TBA6_MOUSE	Tubulin alpha-6 chain (Alpha-tubulin 6) (Alpha-tubulin isotype M-alpha-6)	0.11	-	cyt	0		mitochondrion [IDA]			449
P33127 UniProt NPD GO	TBB_ACRCO	Tubulin beta chain (Beta tubulin)	0.11	-	cyt	0					448
P41741 UniProt NPD GO	TBB_CEPAC	Tubulin beta chain (Beta tubulin)	0.11	-	cyt	0					447
P79008 UniProt NPD GO	TBB_COPCI	Tubulin beta chain (Beta tubulin)	0.11	-	cyt	0					445
P17938 UniProt NPD GO	TBB_EPITY	Tubulin beta chain (Beta tubulin)	0.11	-	cyt	0					448
Q9ZSW1 UniProt NPD GO	TBB1_CYAPA	Tubulin beta-1 chain (Beta-1 tubulin)	0.11	-	cyt	0					447
Q9YHC3 UniProt NPD GO	TBB1_GADMO	Tubulin beta-1 chain (Beta-1 tubulin)	0.11	-	cyt	0					445
Q6EVK8 UniProt NPD GO	TBB1_SUIBO	Tubulin beta-1 chain (Beta-1 tubulin)	0.11	-	cyt	0					446
Q9NFZ6 UniProt NPD GO	TBB2_ECHMU	Tubulin beta-2 chain (Beta-tubulin 2)	0.11	-	cyt	0					445
P30883 UniProt NPD GO	TBB4_XENLA	Tubulin beta-4 chain	0.11	-	cyt	0					445
Q9D6T1 UniProt NPD GO	TBE_MOUSE	Tubulin epsilon chain (Epsilon tubulin)	0.11	-	cyt	0	Centrosome. Associated with pericentriolar material				475
P01375 UniProt NPD GO	TNFA_HUMAN	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.11	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...	soluble fraction [TAS]	191160	5TSW	233
Q9Y274 UniProt NPD GO	SIA10_HUMAN	Type 2 lactosamine alpha-2,3-sialyltransferase (EC 2.4.99.-) (CMP-NeuAc:beta-galactoside alpha-2,3-s ...	0.11	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS]	607156		331
O42411 UniProt NPD GO	IOD1_CHICK	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI) (Fragm ...	0.11	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				245
P79747 UniProt NPD GO	IOD2_FUNHE	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.11	-	mit	0					266
P28209 UniProt NPD GO	PTP17_STYPL	Tyrosine-protein phosphatase 17 (EC 3.1.3.48) (Fragment)	0.11	-	cyt	0					112
P28216 UniProt NPD GO	PTP24_STYPL	Tyrosine-protein phosphatase 24 (EC 3.1.3.48) (Fragment)	0.11	-	cyt	0					115
P43333 UniProt NPD GO	RU2A_ARATH	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.11	-	cyt	0	Nucleus (Potential)				249
P53178 UniProt NPD GO	ALG13_YEAST	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.11	-	cyt	0	Endoplasmic reticulum	cytoplasm [IDA] cytosol [IDA] endoplasmic reticulum [IDA] extrinsic to endoplasmic reticulum membrane [IDA] membrane fraction [IDA] nucleus [IDA] UDP-N-acetylglucosamine transferase complex [IPI]			202
P38197 UniProt NPD GO	YBD6_YEAST	UPF0001 protein YBL036C	0.11	-	cyt	0		intracellular [IC]		1CT5	257
P90838 UniProt NPD GO	YT6J_CAEEL	UPF0027 protein F16A11.2	0.11	-	cyt	0					505
Q09896 UniProt NPD GO	YAI9_SCHPO	UPF0041 protein C24B11.09	0.11	-	nuc	1					118
Q20069 UniProt NPD GO	U171_CAEEL	UPF0171 protein F35H10.7	0.11	-	cyt	0					511
Q8X1T0 UniProt NPD GO	HAG1_SCHPO	UPF0326 protein hag1	0.11	-	nuc	0					201

You are viewing entries 63651 to 63700 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.