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
Q9CU62 UniProt NPD GO	SMC1A_MOUSE	Structural maintenance of chromosome 1-like 1 protein (SMC1alpha protein) (Chromosome segregation pr ...	0.92	+	nuc	0	Nucleus. Associates with chromatin. The phosphorylated form on Ser-957 and Ser-966 associates with c ...	cohesin core heterodimer [ISS] kinetochore [ISS] nucleus [ISS]			1233
Q14683 UniProt NPD GO	SMC1A_HUMAN	Structural maintenance of chromosome 1-like 1 protein (SMC1alpha protein) (DXS423E protein) (Sb1.8)	0.92	+	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	cohesin core heterodimer [TAS] condensed nuclear chromosome [TAS] kinetochore [IDA] nucleus [IDA]	300590		1233
P28159 UniProt NPD GO	SUH_DROME	Suppressor of hairless protein (J kappa-recombination signal-binding protein) (RBP-J kappa)	0.92	-	nuc	0	Nucleus. Cytoplasm. In imaginal disk, at the onset of differentiation of socket cell, it is also pre ...	cytoplasm [IDA] nucleus [IDA]			594
Q04673 UniProt NPD GO	SSL1_YEAST	Suppressor of stem-loop protein 1 (General transcription and DNA repair factor IIH subunit SSL1) (TF ...	0.92	+	nuc	0	Nucleus (Potential)	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [IDA]			461
P09926 UniProt NPD GO	SURF2_MOUSE	Surfeit locus protein 2 (Surf-2)	0.92	-	nuc	0					257
Q9VDS6 UniProt NPD GO	SURF6_DROME	Surfeit locus protein 6 homolog	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [NAS]			324
Q9CUU3 UniProt NPD GO	SYCP2_MOUSE	Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein) (Fragment)	0.92	-	nuc	0	Nucleus (By similarity). In axial/lateral elements of the tripartite segments of synaptonemal comple ...				557
Q99N80 UniProt NPD GO	SYTL1_MOUSE	Synaptotagmin-like protein 1 (Exophilin-7)	0.92	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein	extrinsic to plasma membrane [IDA] melanosome [IDA] membrane fraction [IDA] soluble fraction [IDA]			567
Q99N48 UniProt NPD GO	SYTL3_MOUSE	Synaptotagmin-like protein 3 (Exophilin-6)	0.92	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein	extrinsic to plasma membrane [IDA] membrane fraction [IDA]			607
Q01965 UniProt NPD GO	LY9_MOUSE	T-lymphocyte surface antigen Ly-9 precursor (Lymphocyte antigen 9) (Cell-surface molecule Ly-9)	0.92	-	end	1 *	Membrane; single-pass type I membrane protein				654
Q8C1B2 UniProt NPD GO	PARPT_MOUSE	TCDD-inducible poly [ADP-ribose] polymerase (EC 2.4.2.30)	0.92	-	nuc	0					657
Q7Z3E1 UniProt NPD GO	PARPT_HUMAN	TCDD-inducible poly [ADP-ribose] polymerase (EC 2.4.2.30) (Poly [ADP-ribose] polymerase 7) (PARP-7)	0.92	-	nuc	0					657
Q9H175 UniProt NPD GO	TAI12_HUMAN	TGF-beta-induced apoptosis protein 12 (TAIP-12)	0.92	-	nuc	0	Nucleus (Potential)				543
Q8BGQ2 UniProt NPD GO	TAI12_MOUSE	TGF-beta-induced apoptosis protein 12 (TAIP-12)	0.92	-	nuc	0	Nucleus (Potential)				534
P59055 UniProt NPD GO	TAIP2_MOUSE	TGF-beta-induced apoptosis protein 2 (TAIP-2)	0.92	-	nuc	0	Nucleus (Potential)				585
Q8VCZ3 UniProt NPD GO	THAP7_MOUSE	THAP domain-containing protein 7	0.92	-	nuc	0					309
Q5RDK1 UniProt NPD GO	TEX10_PONPY	Testis-expressed sequence 10 protein	0.92	+	end	0	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				929
O54887 UniProt NPD GO	TSKS_MOUSE	Testis-specific serine kinase substrate (Testis-specific kinase substrate) (STK22 substrate 1)	0.92	-	nuc	0					585
P38141 UniProt NPD GO	THI2_YEAST	Thiamine biosynthesis regulatory protein	0.92	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			450
Q98867 UniProt NPD GO	THA1_BRARE	Thyroid hormone receptor alpha 1	0.92	+	nuc	0	Nucleus				427
Q28570 UniProt NPD GO	THA1_SHEEP	Thyroid hormone receptor alpha-1	0.92	+	nuc	0	Nucleus				410
P15204 UniProt NPD GO	THAA_XENLA	Thyroid hormone receptor alpha-A	0.92	+	nuc	0	Nucleus				418
P18115 UniProt NPD GO	THAB_XENLA	Thyroid hormone receptor alpha-B	0.92	+	nuc	0	Nucleus				418
O97758 UniProt NPD GO	ZO1_CANFA	Tight junction protein ZO-1 (Zonula occludens 1 protein) (Zona occludens 1 protein) (Tight junction ...	0.92	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Movement of ZO-1 from ...				1769
Q9UNS1 UniProt NPD GO	TIM_HUMAN	Timeless homolog (hTIM)	0.92	+	nuc	0	Nucleus (By similarity)	nucleus [IC]	603887		1208
Q9Z2Y1 UniProt NPD GO	TIM_RAT	Timeless homolog (rTIM) (Timeless-like protein) (rTLP)	0.92	+	nuc	0	Nucleus	nucleus [IDA]			1205
Q9UTN3 UniProt NPD GO	CID14_SCHPO	Topoisomerase 1-related protein cid14 (Caffeine-induced death protein 14)	0.92	+	nuc	0		nucleus [IDA] protein complex [IDA]			684
Q7KZ85 UniProt NPD GO	SPT6H_HUMAN	Transcription elongation factor SPT6 (hSPT6) (Tat-cotransactivator 2 protein) (Tat-CT2 protein)	0.92	+	nuc	0	Nucleus (Probable)	nucleus [NAS]	601333		1726
Q9BQ70 UniProt NPD GO	TCF25_HUMAN	Transcription factor 25 (Nuclear localized protein 1)	0.92	+	nuc	0	Nucleus				676
P34694 UniProt NPD GO	TF3A_BUFAM	Transcription factor IIIA (Factor A) (TFIIIA)	0.92	-	nuc	0	Nucleus				339
Q6CGB2 UniProt NPD GO	IWS1_YARLI	Transcription factor IWS1	0.92	+	nuc	0	Nucleus (By similarity)				414
P12383 UniProt NPD GO	PDR1_YEAST	Transcription factor PDR1 (Pleiotropic drug resistance protein 1)	0.92	-	nuc	0	Nucleus	nucleus [IPI]			1063
Q06149 UniProt NPD GO	PDR8_YEAST	Transcription factor PDR8 (Pleiotropic drug resistance protein 8)	0.92	+	end	0	Cytoplasm. Nucleus	nucleus [IPI]			701
P31363 UniProt NPD GO	POU1_XENLA	Transcription factor POU1 (XLPOU1) (Homeotic protein NRL-22/NRL-34)	0.92	+	nuc	0	Nucleus				356
Q7M3M8 UniProt NPD GO	CAS_DROME	Transcription factor castor (Protein ming)	0.92	+	nuc	0	Nucleus	nucleus [IDA]			793
Q27403 UniProt NPD GO	GCM_DROME	Transcription factor glial cells missing (Protein glide)	0.92	+	nuc	0	Nucleus	nucleus [IDA]			504
Q870S2 UniProt NPD GO	IWS1_NEUCR	Transcription factor iws-1	0.92	+	nuc	0	Nucleus (By similarity)				430
O42964 UniProt NPD GO	IWS1_SCHPO	Transcription factor iws1	0.92	-	nuc	0	Nucleus (By similarity)				428
P21525 UniProt NPD GO	FOSL_DROME	Transcription factor kayak (Fos-related antigen) (dFra) (AP-1)	0.92	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			722
P33339 UniProt NPD GO	TFC4_YEAST	Transcription factor tau 131 kDa subunit (TFIIIC 131 kDa subunit)	0.92	-	nuc	0	Nucleus	transcription factor TFIIIC complex [TAS]			1025
P97303 UniProt NPD GO	BACH2_MOUSE	Transcription regulator protein BACH2 (BTB and CNC homolog 2)	0.92	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			716
P54785 UniProt NPD GO	MOT3_YEAST	Transcriptional activator/repressor MOT3 (Modulator of transcription protein 3) (Hypoxic gene repres ...	0.92	-	nuc	0	Nucleus	nucleus [IDA]			490
Q9P326 UniProt NPD GO	PRO1_NEUCR	Transcriptional regulatory protein pro-1	0.92	+	nuc	0	Nucleus (By similarity)				696
Q9HCF6 UniProt NPD GO	TRPM3_HUMAN	Transient receptor potential cation channel subfamily M member 3 (Long transient receptor potential ...	0.92	-	end	7 *	Membrane; multi-pass membrane protein		608961		1732
Q03434 UniProt NPD GO	YMD9_YEAST	Transposon Ty1 protein B	0.92	-	nuc	0					1328
Q04214 UniProt NPD GO	YMT5_YEAST	Transposon Ty1 protein B	0.92	-	nuc	0					1328
Q04670 UniProt NPD GO	YMU0_YEAST	Transposon Ty1 protein B	0.92	-	nuc	0					1328
Q13428 UniProt NPD GO	TCOF_HUMAN	Treacle protein (Treacher Collins syndrome protein)	0.92	+	nuc	0	Nucleus; nucleolus (Potential)	nucleolus [IDA]	606847		1411
Q6PCX9 UniProt NPD GO	TRI37_MOUSE	Tripartite motif-containing protein 37	0.92	-	nuc	0	Cytoplasm (By similarity). Peroxisome (By similarity). Found in vesicles of the peroxisome (By simil ...				961
O94972 UniProt NPD GO	TRI37_HUMAN	Tripartite motif-containing protein 37 (Mulibrey nanism protein)	0.92	-	nuc	0	Cytoplasm. Peroxisome. Found in vesicles of the peroxisome		605073		964

You are viewing entries 3501 to 3550 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.