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
Q9NB31 UniProt NPD GO	CST1_CAEEL	Serine/threonine-protein kinase cst-1 (EC 2.7.11.1) (STE20-like kinase 1) (STE20-like kinase MST) (c ...	0.82	+	nuc	0					497
Q6FR44 UniProt NPD GO	PP4R3_CANGA	Serine/threonine-protein phosphatase 4 regulatory subunit 3 (PP4R3)	0.82	+	nuc	0	Nucleus (By similarity)				842
O74508 UniProt NPD GO	SPP1_SCHPO	Set1 complex component spp1 (Set1C component spp1) (COMPASS component spp1) (Complex proteins associ ...	0.82	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA]			424
Q9UHB9 UniProt NPD GO	SRP68_HUMAN	Signal recognition particle 68 kDa protein (SRP68)	0.82	-	cyt	0	Cytoplasm. Nucleus; nucleolus	endoplasmic reticulum [TAS] nucleolus [TAS] ribosome [TAS] signal recognition particle (sensu Eukaryota) [TAS]	604858		627
P52631 UniProt NPD GO	STAT3_RAT	Signal transducer and activator of transcription 3	0.82	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				770
P40763 UniProt NPD GO	STAT3_HUMAN	Signal transducer and activator of transcription 3 (Acute-phase response factor)	0.82	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [TAS] nucleus [TAS]	102582		770
P42227 UniProt NPD GO	STAT3_MOUSE	Signal transducer and activator of transcription 3 (Acute-phase response factor)	0.82	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]		1BG1	770
Q9R1B9 UniProt NPD GO	SLIT2_MOUSE	Slit homolog 2 protein precursor (Slit-2) [Contains: Slit homolog 2 protein N-product; Slit homolog ...	0.82	-	nuc	0	Secreted protein (By similarity). The C-terminal cleavage protein is more diffusible than the larger ...	extracellular space [IDA]			1521
Q4PHC3 UniProt NPD GO	MVP1_USTMA	Sorting nexin MVP1	0.82	-	nuc	0	Cytoplasm (By similarity)				683
Q9H254 UniProt NPD GO	SPTN4_HUMAN	Spectrin beta chain, brain 3 (Spectrin, non-erythroid beta chain 3) (Beta-IV spectrin)	0.82	+	nuc	0		cytoplasm [IDA] nuclear matrix [IDA] PML body [IDA] spectrin [IDA]	606214		2564
P15340 UniProt NPD GO	HSP1_CHICK	Sperm histone (Protamine) (Galline)	0.82	+	nuc	0	Nucleus				61
Q8WMD3 UniProt NPD GO	HSP1_EPTBN	Sperm protamine P1	0.82	+	nuc	0	Nucleus (By similarity)				45
Q866P6 UniProt NPD GO	HSP1_LAGFA	Sperm protamine P1	0.82	+	nuc	0	Nucleus (By similarity)				61
Q9GKQ3 UniProt NPD GO	HSP1_NASLA	Sperm protamine P1	0.82	+	nuc	0	Nucleus (By similarity)				50
Q7JH04 UniProt NPD GO	HSP1_PIPSA	Sperm protamine P1	0.82	+	nuc	0	Nucleus (By similarity)				45
O18747 UniProt NPD GO	HSP1_PLAGI	Sperm protamine P1	0.82	+	mit	0	Nucleus				61
O18746 UniProt NPD GO	HSP1_PLAMS	Sperm protamine P1	0.82	+	mit	0	Nucleus				61
Q9GLQ8 UniProt NPD GO	HSP1_THYST	Sperm protamine P1	0.82	+	nuc	0	Nucleus				61
Q9GKQ2 UniProt NPD GO	HSP1_TRACR	Sperm protamine P1	0.82	+	mit	0	Nucleus (By similarity)				50
Q7JIX9 UniProt NPD GO	HSP1_TRAOB	Sperm protamine P1	0.82	+	mit	0	Nucleus (By similarity)				50
Q8MHZ2 UniProt NPD GO	HSP1_TRAPH	Sperm protamine P1	0.82	+	mit	0	Nucleus (By similarity)				49
P04553 UniProt NPD GO	HSP1_HUMAN	Sperm protamine P1 (Cysteine-rich protamine)	0.82	+	mit	0	Nucleus	nucleoplasm [TAS]	182880		50
P35306 UniProt NPD GO	HSP1_HYLLA	Sperm protamine P1 (Cysteine-rich protamine)	0.82	+	mit	0	Nucleus	nucleoplasm [ISS]			50
Q07617 UniProt NPD GO	SPAG1_HUMAN	Sperm-associated antigen 1 (Infertility-related sperm protein Spag-1) (HSD-3.8)	0.82	-	nuc	0	Cytoplasm		603395		926
P09430 UniProt NPD GO	STP1_HUMAN	Spermatid nuclear transition protein 1 (STP-1) (TP-1)	0.82	-	nuc	0	Nucleus	nucleosome [IDA]	190231		54
P22613 UniProt NPD GO	STP1_SHEEP	Spermatid nuclear transition protein 1 (STP-1) (TP-1) (Protein T)	0.82	-	nuc	0	Nucleus	nucleosome [ISS]			54
P02317 UniProt NPD GO	STP1_RAT	Spermatid nuclear transition protein 1 (STP-1) (TP-1) (Testis-specific basic protein)	0.82	-	nuc	0	Nucleus	male germ cell nucleus [IDA] nucleosome [ISS]			54
P13275 UniProt NPD GO	SSS1_SCYCA	Spermatid-specific protein S1	0.82	+	nuc	0	Nucleus				87
Q9D9T6 UniProt NPD GO	SPTA3_MOUSE	Spermatogenesis-associated protein 3 (Testis spermatocyte apoptosis-related protein 1) (Testis and s ...	0.82	-	nuc	0					193
Q96I25 UniProt NPD GO	SPF45_HUMAN	Splicing factor 45 (45 kDa-splicing factor) (RNA-binding motif protein 17)	0.82	-	nuc	0	Nucleus		606935		401
Q8JZX4 UniProt NPD GO	SPF45_MOUSE	Splicing factor 45 (45 kDa-splicing factor) (RNA-binding motif protein 17)	0.82	-	nuc	0	Nucleus (By similarity)	spliceosome complex [TAS]			405
Q5R1W5 UniProt NPD GO	SFRS2_PANTR	Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 kDa)	0.82	+	nuc	0	Nucleus (By similarity)				220
P84103 UniProt NPD GO	SFRS3_HUMAN	Splicing factor, arginine/serine-rich 3 (Pre-mRNA-splicing factor SRP20)	0.82	+	nuc	0	Nucleus		603364		164
P84104 UniProt NPD GO	SFRS3_MOUSE	Splicing factor, arginine/serine-rich 3 (Pre-mRNA-splicing factor SRP20) (X16 protein)	0.82	+	nuc	0	Nucleus				164
Q9P2P6 UniProt NPD GO	STAR9_HUMAN	StAR-related lipid transfer protein 9 (StARD9) (START domain-containing protein 9) (Fragment)	0.82	-	nuc	0					1820
Q95LV5 UniProt NPD GO	SAMD4_MACFA	Sterile alpha motif domain-containing protein 4	0.82	-	nuc	0					617
Q5B4C9 UniProt NPD GO	ATG26_EMENI	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.82	-	nuc	0	Membrane; peripheral membrane protein (Potential)				1396
P70302 UniProt NPD GO	STIM1_MOUSE	Stromal interaction molecule 1 precursor	0.82	+	end	1	Cell membrane; single-pass type I membrane protein (Potential)				685
P50532 UniProt NPD GO	SMC4_XENLA	Structural maintenance of chromosome 4 (Chromosome-associated protein C) (Chromosome assembly protei ...	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...	condensin complex [ISS] nucleus [ISS]			1290
Q8CG47 UniProt NPD GO	SMC4_MOUSE	Structural maintenance of chromosomes 4-like 1 protein (Chromosome-associated polypeptide C) (XCAP-C ...	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...	condensin complex [ISS] nucleus [ISS]			1286
O43426 UniProt NPD GO	SYNJ1_HUMAN	Synaptojanin-1 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1)	0.82	-	nuc	0	Cytoplasm (By similarity)		604297		1575
Q9SWH4 UniProt NPD GO	SYP42_ARATH	Syntaxin-42 (AtSYP42) (AtTLG2b)	0.82	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				323
Q9Y458 UniProt NPD GO	TBX22_HUMAN	T-box transcription factor TBX22 (T-box protein 22)	0.82	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	303400		520
O97790 UniProt NPD GO	TBCD1_BOVIN	TBC1 domain family member 1 (Lyncein) (Fragment)	0.82	-	nuc	0	Nucleus (By similarity)				556
Q9DBA9 UniProt NPD GO	TF2H1_MOUSE	TFIIH basal transcription factor complex p62 subunit (Basic transcription factor 62 kDa subunit) (BT ...	0.82	-	nuc	0	Nucleus	nucleus [IDA]			547
Q9Y228 UniProt NPD GO	T3JAM_HUMAN	TRAF3-interacting JNK-activating modulator (TRAF3-interacting protein 3)	0.82	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)		608255		551
Q99973 UniProt NPD GO	TEP1_HUMAN	Telomerase protein component 1 (Telomerase-associated protein 1) (Telomerase protein 1) (p240) (p80 ...	0.82	-	nuc	0		cytoplasm [IDA] nuclear matrix [IDA] soluble fraction [ISS] telomerase holoenzyme complex [IDA]	601686		2627
Q803M3 UniProt NPD GO	TEX10_BRARE	Testis-expressed sequence 10 protein homolog	0.82	+	end	0	Nucleus; nucleolus (By similarity)				933
O95049 UniProt NPD GO	ZO3_HUMAN	Tight junction protein ZO-3 (Zonula occludens 3 protein) (Zona occludens 3 protein) (Tight junction ...	0.82	-	nuc	0					933
P25644 UniProt NPD GO	PAT1_YEAST	Topoisomerase II-associated protein PAT1	0.82	-	nuc	0	Cytoplasm	cytoplasmic mRNA processing body [IDA] cytosolic small ribosomal subunit (sensu Eu... [IDA]			796

You are viewing entries 8101 to 8150 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.