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
P46599 UniProt NPD GO	STE7_CANAL	Serine/threonine-protein kinase STE7 homolog (EC 2.7.12.2)	0.86	-	nuc	0					589
Q751J3 UniProt NPD GO	ATM_ASHGO	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.86	+	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2768
Q2VWQ3 UniProt NPD GO	STE20_PENMA	Serine/threonine-protein kinase pakA (EC 2.7.11.1)	0.86	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				642
Q6TC50 UniProt NPD GO	SRY_FELCA	Sex-determining region Y protein (Testis-determining factor)	0.86	+	nuc	0	Nucleus				234
Q28447 UniProt NPD GO	SRY_HYLLA	Sex-determining region Y protein (Testis-determining factor)	0.86	+	nuc	0	Nucleus				204
Q864Q5 UniProt NPD GO	SRY_KOGSI	Sex-determining region Y protein (Testis-determining factor)	0.86	+	nuc	0	Nucleus				216
Q28783 UniProt NPD GO	SRY_PONPY	Sex-determining region Y protein (Testis-determining factor)	0.86	+	nuc	0	Nucleus				233
P79100 UniProt NPD GO	TRPC4_BOVIN	Short transient receptor potential channel 4 (TrpC4) (Capacitative calcium entry channel 1) (CCE1)	0.86	-	end	8	Membrane; multi-pass membrane protein (Probable)				981
Q18412 UniProt NPD GO	SGO1_CAEEL	Shugoshin	0.86	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				307
Q8BMA6 UniProt NPD GO	SRP68_MOUSE	Signal recognition particle 68 kDa protein (SRP68)	0.86	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				625
Q13596 UniProt NPD GO	SNX1_HUMAN	Sorting nexin-1	0.86	-	nuc	0			601272		522
Q7SB54 UniProt NPD GO	SNX41_NEUCR	Sorting nexin-41	0.86	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				604
P45970 UniProt NPD GO	LIN5_CAEEL	Spindle apparatus protein lin-5 (Abnormal cell lineage protein 5)	0.86	+	nuc	0	Spindle. Kinetochore. Centrosome. Located to the spindle apparatus in a cell cycle- and microtubule- ...				821
P23246 UniProt NPD GO	SFPQ_HUMAN	Splicing factor, proline- and glutamine-rich (Polypyrimidine tract-binding protein-associated-splici ...	0.86	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Predominantly in nuclear matrix		605199		707
Q10411 UniProt NPD GO	SPO15_SCHPO	Sporulation-specific protein 15	0.86	+	nuc	0	Spindle pole body				1957
Q9NZ72 UniProt NPD GO	STMN3_HUMAN	Stathmin-3 (SCG10-like protein)	0.86	-	nuc	0					180
Q86DA5 UniProt NPD GO	SARM1_CAEEL	Sterile alpha and TIR motif-containing protein tir-1 (Neuronal symmetry protein 2) (SARM1 homolog)	0.86	-	mit	0	Cytoplasm				1000
O94383 UniProt NPD GO	SMC1_SCHPO	Structural maintenance of chromosome 1 (Cohesin complex subunit psm1) (Chromosome segregation protei ...	0.86	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. At anapha ...	chromosome [IDA] mitotic cohesin complex [TAS]			1233
P59817 UniProt NPD GO	SUHW1_HUMAN	Suppressor of hairy wing homolog 1 (3'OY11.1)	0.86	-	nuc	0	Nucleus (Potential)				542
Q9P347 UniProt NPD GO	YIP1_SCHPO	Survival of motor neuron protein-interacting protein yip1 (SMN-interacting protein yip1) (Yab8-inter ...	0.86	-	nuc	0	Nucleus	nucleus [IDA]			235
P0C1G6 UniProt NPD GO	SWP70_BOVIN	Switch-associated protein 70 (SWAP-70)	0.86	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Nucleus (By similarity). In resting B-cell ...				585
P31111 UniProt NPD GO	ZIP1_YEAST	Synaptonemal complex protein ZIP1	0.86	+	nuc	0	Synapsed meiotic chromosomes	transverse filament [IDA]			875
Q812E4 UniProt NPD GO	SYTL5_RAT	Synaptotagmin-like protein 5	0.86	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				753
Q9Y6H5 UniProt NPD GO	SNCAP_HUMAN	Synphilin-1 (Alpha-synuclein-interacting protein)	0.86	-	nuc	0		cell soma [NAS] cytoplasm [IDA] presynaptic membrane [NAS]	603779		919
Q15572 UniProt NPD GO	TAF1C_HUMAN	TATA box-binding protein-associated factor RNA polymerase I subunit C (TATA box-binding protein-asso ...	0.86	+	nuc	0	Nucleus		604905		869
Q9D305 UniProt NPD GO	THAP2_MOUSE	THAP domain-containing protein 2	0.86	-	nuc	0					217
Q01550 UniProt NPD GO	TANA_XENLA	Tanabin	0.86	-	nuc	0					1744
Q6JPI3 UniProt NPD GO	T240L_MOUSE	Thyroid hormone receptor-associated protein 2 (Thyroid hormone receptor-associated protein complex 2 ...	0.86	-	nuc	0	Nucleus (By similarity)	mediator complex [IDA]			2207
Q9NR97 UniProt NPD GO	TLR8_HUMAN	Toll-like receptor 8 precursor	0.86	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [IC]	300366		1041
Q8NIV6 UniProt NPD GO	SPT6_NEUCR	Transcription elongation factor spt-6 (Chromatin elongation factor spt-6)	0.86	+	nuc	0	Nucleus (By similarity)				1402
O55170 UniProt NPD GO	SOX10_RAT	Transcription factor SOX-10	0.86	+	nuc	0	Nucleus				466
P48435 UniProt NPD GO	SOX11_CHICK	Transcription factor SOX-11	0.86	+	nuc	0	Nucleus				396
P48432 UniProt NPD GO	SOX2_MOUSE	Transcription factor SOX-2	0.86	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1GT0	319
P48433 UniProt NPD GO	SOX3_CHICK	Transcription factor SOX-3	0.86	+	nuc	0	Nucleus				312
Q9BT81 UniProt NPD GO	SOX7_HUMAN	Transcription factor SOX-7	0.86	+	nuc	0	Nucleus (Probable)				388
Q04886 UniProt NPD GO	SOX8_MOUSE	Transcription factor SOX-8	0.86	+	nuc	0	Nucleus (Potential)				464
P36631 UniProt NPD GO	STE11_SCHPO	Transcription factor ste11	0.86	-	nuc	0	Nucleus. Cytoplasm. Accumulates in the nucleus under conditions of nitrogen starvation and in the pr ...				468
O94416 UniProt NPD GO	T2FA_SCHPO	Transcription initiation factor IIF alpha subunit (EC 2.7.11.1) (TFIIF-alpha) (TFIIF large subunit)	0.86	-	nuc	0	Nucleus (By similarity)				490
Q9VHY5 UniProt NPD GO	TAF7_DROME	Transcription initiation factor TFIID subunit 7 (Transcription initiation factor TFIID 55 kDa subuni ...	0.86	-	nuc	0	Nucleus	nucleus [NAS]			479
P38255 UniProt NPD GO	RXT2_YEAST	Transcriptional regulatory protein RXT2	0.86	-	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			430
P34586 UniProt NPD GO	TRPL_CAEEL	Transient-receptor-potential-like protein (TRP homologous cation channel protein 1)	0.86	-	end	6	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			1027
Q80W04 UniProt NPD GO	TMCC2_MOUSE	Transmembrane and coiled-coil domains protein 2	0.86	-	end	2	Membrane; multi-pass membrane protein (Potential)				706
P13789 UniProt NPD GO	TNNT2_BOVIN	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.86	+	nuc	0					284
P45378 UniProt NPD GO	TNNT3_HUMAN	Troponin T, fast skeletal muscle (TnTf) (Fast skeletal muscle troponin T) (fTnT) (Beta TnTF)	0.86	-	nuc	0			601680		268
O88346 UniProt NPD GO	TNNT1_MOUSE	Troponin T, slow skeletal muscle (TnTs) (Slow skeletal muscle troponin T) (sTnT)	0.86	-	nuc	0					261
Q7TNB2 UniProt NPD GO	TNNT1_RAT	Troponin T, slow skeletal muscle (TnTs) (Slow skeletal muscle troponin T) (sTnT)	0.86	-	nuc	0					260
Q9NRJ4 UniProt NPD GO	TULP4_HUMAN	Tubby-like protein 4 (Tubby superfamily protein)	0.86	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1544
Q14679 UniProt NPD GO	TTLL4_HUMAN	Tubulin--tyrosine ligase-like protein 4	0.86	-	nuc	0					1199
O96642 UniProt NPD GO	TWIST_BRABE	Twist-related protein (BBtwist)	0.86	+	nuc	0	Nucleus	nucleus [ISS]			196
Q9FGT7 UniProt NPD GO	ARR18_ARATH	Two-component response regulator ARR18	0.86	+	nuc	0	Nucleus				635

You are viewing entries 6301 to 6350 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.