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
Q7RYI3 UniProt NPD GO	SWC5_NEUCR	SWR1-complex protein 5	0.79	+	nuc	0	Nucleus (By similarity)				342
O42236 UniProt NPD GO	SEM3C_CHICK	Semaphorin-3C precursor (Collapsin-3) (COLL-3)	0.79	-	nuc	0	Secreted protein				751
Q9UPE1 UniProt NPD GO	STK23_HUMAN	Serine/threonine-protein kinase 23 (EC 2.7.11.1) (Muscle-specific serine kinase 1) (MSSK-1)	0.79	-	cyt	0					533
Q9JI11 UniProt NPD GO	STK4_MOUSE	Serine/threonine-protein kinase 4 (EC 2.7.11.1) (STE20-like kinase MST1) (MST-1) (Mammalian STE20-li ...	0.79	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			487
Q4I5U9 UniProt NPD GO	BUR1_GIBZE	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.79	-	nuc	0	Nucleus (By similarity)				473
O96017 UniProt NPD GO	CHK2_HUMAN	Serine/threonine-protein kinase Chk2 (EC 2.7.11.1) (Cds1)	0.79	-	nuc	0	Isoform 2, isoform 4, isoform 7, isoform 9, isoform 12: Nucleus. Isoform 10 is present throughout th ...	nucleus [NAS]	176807	1GXC	543
P51955 UniProt NPD GO	NEK2_HUMAN	Serine/threonine-protein kinase Nek2 (EC 2.7.11.1) (NimA-related protein kinase 2) (NimA-like protei ...	0.79	-	nuc	0	Nucleus. Isoform 1: Nucleus; nucleolus. Isoform 2: Cytoplasm. Isoform 1 has a nucleolar targeting/ r ...	centrosome [TAS]	604043		445
Q4P5N0 UniProt NPD GO	STE20_USTMA	Serine/threonine-protein kinase SMU1 (EC 2.7.11.1)	0.79	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				746
Q9BYP7 UniProt NPD GO	WNK3_HUMAN	Serine/threonine-protein kinase WNK3 (EC 2.7.11.1) (Protein kinase with no lysine 3) (Protein kinase ...	0.79	-	nuc	0			300358		1743
Q96VK3 UniProt NPD GO	BUR1_EMENI	Serine/threonine-protein kinase bur1 (EC 2.7.11.22) (EC 2.7.11.23) (PITALRE-like kinase A)	0.79	-	nuc	0	Nucleus (By similarity)				544
P34331 UniProt NPD GO	PLK1_CAEEL	Serine/threonine-protein kinase plk-1 (EC 2.7.11.21) (Polo-like kinase 1)	0.79	-	nuc	0	Centrosome. In mitosis, remains associated with centrosomes entering prophase through to anaphase. D ...	centrosome [IDA] nucleus [IEP]			649
Q5TM61 UniProt NPD GO	PP1RA_MACMU	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (MHC class I region proline-rich protei ...	0.79	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli (By similarity)				940
O14830 UniProt NPD GO	PPE2_HUMAN	Serine/threonine-protein phosphatase with EF-hands 2 (EC 3.1.3.16) (PPEF-2)	0.79	-	nuc	0	Localized to photoreceptors, PPEF-2(L) is at least 2 fold more abundant in rod inner segments than i ...		602256		753
Q6TC44 UniProt NPD GO	SRY_ARCGZ	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				220
Q6TC37 UniProt NPD GO	SRY_CYSCR	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				221
Q864P9 UniProt NPD GO	SRY_DELDE	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				201
Q864P8 UniProt NPD GO	SRY_LAGOL	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				201
Q864P6 UniProt NPD GO	SRY_PENEL	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				201
Q864Q0 UniProt NPD GO	SRY_TURTR	Sex-determining region Y protein (Testis-determining factor)	0.79	+	nuc	0	Nucleus				201
Q24141 UniProt NPD GO	SGO1_DROME	Shugoshin (Meiotic protein S332)	0.79	-	nuc	0	Nucleus. Localizes to the centromere of meiotic and mitotic chromosomes. During meiosis, it assemble ...	chromosome [IDA] chromosome, pericentric region [IDA]			401
Q6BMV4 UniProt NPD GO	SRP68_DEBHA	Signal recognition particle subunit SRP68 (Signal recognition particle 68 kDa protein homolog)	0.79	-	nuc	0	Cytoplasm (By similarity)				587
P46062 UniProt NPD GO	SIPA1_MOUSE	Signal-induced proliferation-associated protein 1 (Sipa-1) (GTPase-activating protein Spa-1)	0.79	-	nuc	0	Nucleus. Mostly	nucleus [ISS]			1037
O75094 UniProt NPD GO	SLIT3_HUMAN	Slit homolog 3 protein precursor (Slit-3) (Multiple epidermal growth factor-like domains 5)	0.79	-	nuc	0	Secreted protein (By similarity)	extracellular space [TAS]	603745		1523
Q9H2S1 UniProt NPD GO	KCNN2_HUMAN	Small conductance calcium-activated potassium channel protein 2 (SK2)	0.79	+	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]	605879		579
P70604 UniProt NPD GO	KCNN2_RAT	Small conductance calcium-activated potassium channel protein 2 (SK2)	0.79	+	end	7	Membrane; multi-pass membrane protein			1QX7	580
P18340 UniProt NPD GO	SCYB9_MOUSE	Small inducible cytokine B9 precursor (CXCL9) (Gamma interferon-induced monokine) (MIG) (M119)	0.79	-	nuc	0	Secreted protein				126
Q9Y5W8 UniProt NPD GO	SNX13_HUMAN	Sorting nexin-13 (RGS domain- and PHOX domain-containing protein) (RGS-PX1)	0.79	-	end	2 *			606589		968
Q969T3 UniProt NPD GO	SNX21_HUMAN	Sorting nexin-21 (Sorting nexin L) (SNX-L)	0.79	-	nuc	0					373
Q5H7C3 UniProt NPD GO	SNX4_PICPA	Sorting nexin-4 (Autophagy-related protein 24) (Pexophagy zeocin-resistant mutant protein 16)	0.79	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral membrane pr ...				661
Q07528 UniProt NPD GO	ATG20_YEAST	Sorting nexin-42 (Autophagy-related protein 20) (Cytoplasm to vacuole targeting protein 20)	0.79	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Endosome; endosomal membrane; peripheral membrane ...	membrane [IPI]			640
P14402 UniProt NPD GO	HSP1_COTJA	Sperm histone (Protamine)	0.79	+	nuc	0	Nucleus				56
Q8MJT0 UniProt NPD GO	HSP1_COLBA	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				50
Q8WNY8 UniProt NPD GO	HSP1_MYODA	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				46
Q8WNZ3 UniProt NPD GO	HSP1_NATST	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				49
P35307 UniProt NPD GO	HSP1_ORNAN	Sperm protamine P1	0.79	+	nuc	0	Nucleus				60
Q8WNZ0 UniProt NPD GO	HSP1_PLETO	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				47
Q9GJR3 UniProt NPD GO	HSP1_SEMEN	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				49
Q7JIY0 UniProt NPD GO	HSP1_TRAVT	Sperm protamine P1	0.79	+	nuc	0	Nucleus (By similarity)				49
P04101 UniProt NPD GO	HSP1_PIG	Sperm protamine P1 (Cysteine-rich protamine)	0.79	+	nuc	0	Nucleus				49
P83264 UniProt NPD GO	PRT1_SCOSC	Sperm protamine alpha isoform 1 (Scombrine alpha-1)	0.79	+	nuc	0	Nucleus	nucleosome [TAS] nucleus [TAS]			34
Q05831 UniProt NPD GO	H1L_MYTTR	Sperm-specific protein PHI-2B (PL-II*) (Sperm-specific linker histone H1-like protein) [Contains: Sp ...	0.79	+	nuc	0	Nucleus				202
Q8BL97 UniProt NPD GO	SFRS7_MOUSE	Splicing factor, arginine/serine-rich 7	0.79	+	nuc	0	Nucleus (By similarity)				267
P11475 UniProt NPD GO	ERR2_RAT	Steroid hormone receptor ERR2 (Estrogen-related receptor, beta) (ERR-beta) (Estrogen receptor-like 2 ...	0.79	-	nuc	0	Nucleus (Potential)				433
Q8CDJ8 UniProt NPD GO	STON1_MOUSE	Stonin-1 (Stoned B-like factor)	0.79	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Some fraction is membrane-associated (By simila ...				730
Q9BPZ7 UniProt NPD GO	SIN1_HUMAN	Stress-activated map kinase-interacting protein 1 (SAPK-interacting protein 1) (Putative Ras inhibit ...	0.79	+	nuc	0					522
P49031 UniProt NPD GO	SPS_BETVU	Sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase)	0.79	-	nuc	0					1045
Q6P3Y5 UniProt NPD GO	SUHW3_MOUSE	Suppressor of hairy wing homolog 3	0.79	+	nuc	0	Nucleus (Potential)				742
Q6N043 UniProt NPD GO	SUHW4_HUMAN	Suppressor of hairy wing homolog 4	0.79	-	nuc	0	Nucleus (Potential)				979
Q9USV1 UniProt NPD GO	SFR1_SCHPO	Swi5-dependent recombination DNA repair protein 1 (DNA repair protein dds20)	0.79	-	nuc	0					299
Q62910 UniProt NPD GO	SYNJ1_RAT	Synaptojanin-1 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1)	0.79	-	nuc	0	Cytoplasm (By similarity)				1574

You are viewing entries 9601 to 9650 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.