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
Q925Q9 UniProt NPD GO	SH3K1_RAT	SH3-domain kinase-binding protein 1 (SH3-containing, expressed in tumorigenic astrocytes) (Regulator ...	0.80	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Nucleus (By similarity)				709
Q5ZHY5 UniProt NPD GO	STUB1_CHICK	STIP1 homology and U box-containing protein 1 (EC 6.3.2.-) (STIP1 homology and U-box-containing prot ...	0.80	-	nuc	0	Cytoplasm (By similarity)				314
Q9CQN4 UniProt NPD GO	SOSD1_MOUSE	Sclerostin domain-containing protein 1 precursor (Ectodermal BMP inhibitor) (Ectodin) (Uterine sensi ...	0.80	-	exc	0	Secreted protein	extracellular space [IDA]			206
Q642G2 UniProt NPD GO	SOSD1_RAT	Sclerostin domain-containing protein 1 precursor (Uterine sensitization-associated gene 1 protein) ( ...	0.80	-	nuc	0	Secreted protein				206
Q62217 UniProt NPD GO	SEM5A_MOUSE	Semaphorin-5A precursor (Semaphorin F) (Sema F)	0.80	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [IDA]			1077
Q9P7Y8 UniProt NPD GO	MID2_SCHPO	Septin ring organizing protein mid2	0.80	-	nuc	0	Localizes to the medial ring at the cell cortex	medial ring [IDA] septin ring (sensu Fungi) [IDA]			704
O94768 UniProt NPD GO	ST17B_HUMAN	Serine/threonine-protein kinase 17B (EC 2.7.11.1) (DAP kinase-related apoptosis-inducing protein kin ...	0.80	-	mit	0	Nucleus	nucleus [IEP]	604727		372
Q86UX6 UniProt NPD GO	ST32C_HUMAN	Serine/threonine-protein kinase 32C (EC 2.7.11.1) (PKE) (YANK3)	0.80	-	mit	0					486
Q8BYR2 UniProt NPD GO	LATS1_MOUSE	Serine/threonine-protein kinase LATS1 (EC 2.7.11.1) (Large tumor suppressor homolog 1) (WARTS protei ...	0.80	-	nuc	0	Centrosome (By similarity). Localizes to the centrosomes throughout interphase but migrates to the m ...	spindle pole [ISS]			1129
Q7YQL4 UniProt NPD GO	PAK3_PANTR	Serine/threonine-protein kinase PAK 3 (EC 2.7.11.1) (p21-activated kinase 3) (PAK-3)	0.80	-	nuc	0					559
Q7YQL3 UniProt NPD GO	PAK3_PONPY	Serine/threonine-protein kinase PAK 3 (EC 2.7.11.1) (p21-activated kinase 3) (PAK-3)	0.80	-	nuc	0					559
O75914 UniProt NPD GO	PAK3_HUMAN	Serine/threonine-protein kinase PAK 3 (EC 2.7.11.1) (p21-activated kinase 3) (PAK-3) (Beta-PAK) (Oli ...	0.80	-	nuc	0			300558		559
P62205 UniProt NPD GO	PLK1_XENTR	Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-1) (Plx1)	0.80	-	cyt	0	Nucleus (By similarity). Centrosome (By similarity). Localized at centrosomes at prophase, spindles ...				598
Q8CFH6 UniProt NPD GO	SN1L2_MOUSE	Serine/threonine-protein kinase SNF1-like kinase 2 (EC 2.7.11.1) (Salt-inducible kinase 2)	0.80	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			931
Q9N2L7 UniProt NPD GO	PLK2_CAEEL	Serine/threonine-protein kinase plk-2 (EC 2.7.11.21) (Polo-like kinase 2)	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]			632
P38193 UniProt NPD GO	PP4R2_YEAST	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2)	0.80	+	nuc	0	Nucleus	nucleus [IDA]			441
Q6T723 UniProt NPD GO	SRY_ARCAU	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				220
Q6T724 UniProt NPD GO	SRY_ARCFO	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				220
Q6TC43 UniProt NPD GO	SRY_CALUR	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				220
Q6TC27 UniProt NPD GO	SRY_ENHLU	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				219
Q6TC46 UniProt NPD GO	SRY_EUMJU	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				220
P36390 UniProt NPD GO	SRY_HALGR	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				232
Q6TC34 UniProt NPD GO	SRY_PHOCA	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				232
Q6TC36 UniProt NPD GO	SRY_PHOGR	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				221
Q6TC32 UniProt NPD GO	SRY_PHOHI	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				232
Q6TC31 UniProt NPD GO	SRY_PHOLR	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				232
Q6TC33 UniProt NPD GO	SRY_PHOVI	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				232
Q6TC45 UniProt NPD GO	SRY_ZALCA	Sex-determining region Y protein (Testis-determining factor)	0.80	+	nuc	0	Nucleus				220
Q96LC7 UniProt NPD GO	SIG10_HUMAN	Sialic acid-binding Ig-like lectin 10 precursor (Siglec-10) (Siglec-like protein 2)	0.80	-	end	1	Isoform 1, isoform 2, isoform 3, isoform 4: Cell membrane; single-pass type I membrane protein. Isof ...		606091		697
Q17237 UniProt NPD GO	SGF3_BOMMO	Silk gland factor 3 (SGF-3) (POU domain protein M1)	0.80	+	nuc	0	Nucleus				351
Q12158 UniProt NPD GO	SCC1_YEAST	Sister chromatid cohesion protein 1	0.80	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	nuclear cohesin complex [TAS] nucleus [IDA]		1W1W	566
O94813 UniProt NPD GO	SLIT2_HUMAN	Slit homolog 2 protein precursor (Slit-2) [Contains: Slit homolog 2 protein N-product; Slit homolog ...	0.80	-	nuc	0	Secreted protein. The C-terminal cleavage protein is more diffusible than the larger N-terminal prot ...	extracellular region [IEP]	603746		1529
Q02260 UniProt NPD GO	SMD1_YEAST	Small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1)	0.80	-	nuc	0	Nucleus	commitment complex [IPI] snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			146
Q9JI13 UniProt NPD GO	SAS10_MOUSE	Something about silencing protein 10 (Disrupter of silencing SAS10) (Charged amino acid-rich leucine ...	0.80	-	nuc	0	Nucleus	nucleus [IPI]			469
P15342 UniProt NPD GO	PRM2_HORSE	Sperm histone P2a (Protamine 2a) (ST2a)	0.80	+	nuc	0	Nucleus				62
P42142 UniProt NPD GO	HSP1_MACRU	Sperm protamine P1	0.80	+	nuc	0	Nucleus				59
Q8WNZ5 UniProt NPD GO	HSP1_MORME	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)				47
P42143 UniProt NPD GO	HSP1_NOTTY	Sperm protamine P1	0.80	+	nuc	0	Nucleus				60
P79990 UniProt NPD GO	HSP1_PHACI	Sperm protamine P1	0.80	+	nuc	0	Nucleus				59
Q8WNZ6 UniProt NPD GO	HSP1_RHIHA	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)				48
Q9GKQ4 UniProt NPD GO	HSP1_TRAFR	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)	nucleoplasm [ISS]			50
Q7JHM8 UniProt NPD GO	HSP1_TRAGE	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)	nucleoplasm [ISS]			50
Q8MJS8 UniProt NPD GO	HSP1_TRAJO	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)				50
Q7JHM9 UniProt NPD GO	HSP1_TRAPL	Sperm protamine P1	0.80	+	nuc	0	Nucleus (By similarity)	nucleoplasm [ISS]			50
P10118 UniProt NPD GO	HSP1_RAT	Sperm protamine P1 (Cysteine-rich protamine)	0.80	+	nuc	0	Nucleus				50
Q7LZB2 UniProt NPD GO	HSP1_CHRPI	Sperm protamine P1-type (Protamine I-1)	0.80	+	nuc	0	Nucleus (By similarity)				58
P83212 UniProt NPD GO	HSP2_MURBR	Sperm protamine P2	0.80	+	nuc	0	Nucleus				58
Q86QH9 UniProt NPD GO	H1L1_OSTED	Sperm-specific H1/protamine-like protein type 1 precursor [Contains: Sperm-specific protein OE1 (Spe ...	0.80	-	mit	0	Nucleus (By similarity)				202
P10856 UniProt NPD GO	STP1_MOUSE	Spermatid nuclear transition protein 1 (STP-1) (TP-1)	0.80	-	nuc	0	Nucleus	male germ cell nucleus [TAS] nucleosome [ISS] nucleus [TAS]			54
P80001 UniProt NPD GO	PRT1_SEPOF	Spermatid-specific protein T1 [Contains: Spermatid-specific protein T1B; Sperm protamine SP1]	0.80	+	nuc	0	Nucleus				78

You are viewing entries 9101 to 9150 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.