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
Q10353 UniProt NPD GO	RLP24_SCHPO	Ribosome biogenesis protein rlp24	0.61	-	nuc	0	Nucleus; nucleolus (By similarity)				192
P13830 UniProt NPD GO	RESA_PLAFF	Ring-infected erythrocyte surface antigen precursor	0.61	+	mit	0	Cell membrane; cytoplasmic side. Probably located on the cytoplasmic face of the membrane where it a ...				1073
P17708 UniProt NPD GO	DCAM_RAT	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.61	-	cyt	0					333
P38810 UniProt NPD GO	SFB3_YEAST	SED5-binding protein 3 (SEC24-related protein 3) (Lethal with SEC13 protein 1)	0.61	-	nuc	0	Cytoplasm (By similarity)	COPII vesicle coat [IGI] endoplasmic reticulum [IDA] peripheral to membrane of membrane fraction [IDA]			929
Q9JL10 UniProt NPD GO	SRTD1_MOUSE	SERTA domain-containing protein 1 (Transcriptional regulator interacting with the PHD-bromodomain 1) ...	0.61	-	nuc	0					236
O95248 UniProt NPD GO	MTMR5_HUMAN	SET-binding factor 1 (Sbf1) (Myotubularin-related protein 5)	0.61	-	cyt	0	Nucleus	integral to membrane [TAS]	603560		1866
Q39618 UniProt NPD GO	SFAS_CHLRE	SF-assemblin	0.61	-	nuc	0					276
Q810C1 UniProt NPD GO	SLIK1_MOUSE	SLIT and NTRK-like protein 1 precursor	0.61	-	end	1	Membrane; single-pass membrane protein (Potential)				696
Q9VEB5 UniProt NPD GO	SRR1L_DROME	SRR1-like protein	0.61	-	cyt	0					276
P50079 UniProt NPD GO	HSV2_YEAST	SVP1-like protein 2	0.61	-	nuc	0	Vacuole (Potential). Cytoplasmic vesicle (Potential). Vesicular and vacuolar (Potential). Found in p ...	cytoplasm [IDA] vacuole (sensu Fungi) [IDA]			448
Q62991 UniProt NPD GO	SCFD1_RAT	Sec1 family domain-containing protein 1 (Syntaxin-binding protein 1-like 2) (Vesicle transport-relat ...	0.61	-	nuc	0	Cytoplasm. Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi ...			1Y9J	637
Q13275 UniProt NPD GO	SEM3F_HUMAN	Semaphorin-3F precursor (Semaphorin IV) (Sema IV) (Sema III/F)	0.61	-	exc	0	Secreted protein (By similarity)	extracellular space [TAS]	601124		785
P48008 UniProt NPD GO	SPN3_SCHPO	Septin homolog spn3	0.61	-	cyt	0		septin complex [IDA] septin ring (sensu Fungi) [IDA]			412
P07664 UniProt NPD GO	SRYD_DROME	Serendipity locus protein delta	0.61	-	nuc	0	Nucleus	nucleus [IDA] polytene chromosome interband [IDA]			433
Q9GM70 UniProt NPD GO	ST17A_RABIT	Serine/threonine-protein kinase 17A (EC 2.7.11.1) (DAP kinase-related apoptosis-inducing protein kin ...	0.61	-	cyt	0	Nucleus				397
Q8TDR2 UniProt NPD GO	STK35_HUMAN	Serine/threonine-protein kinase 35 (EC 2.7.11.1) (CLP-36-interacting kinase) (Clik1) (PDLIM1-interac ...	0.61	-	nuc	0	Nucleus. Cytoplasm. When associated with PDLIM1, it is mostly found in cytoplasm, localized to actin ...		609370		401
Q8K045 UniProt NPD GO	PKN3_MOUSE	Serine/threonine-protein kinase N3 (EC 2.7.11.13) (Protein kinase PKN-beta) (Protein-kinase C-relate ...	0.61	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear and perinuclear Golg ...				878
Q8C0Q4 UniProt NPD GO	NEK11_MOUSE	Serine/threonine-protein kinase Nek11 (EC 2.7.11.1) (NimA-related protein kinase 11) (Never in mitos ...	0.61	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Nuclear during interphase but moves to ...	nucleolus [ISS]			628
Q9H4B4 UniProt NPD GO	PLK3_HUMAN	Serine/threonine-protein kinase PLK3 (EC 2.7.11.21) (Polo-like kinase 3) (PLK-3) (Cytokine-inducible ...	0.61	-	nuc	0	Membrane; peripheral membrane protein		602913		646
Q86Y07 UniProt NPD GO	VRK2_HUMAN	Serine/threonine-protein kinase VRK2 (EC 2.7.11.1) (Vaccinia-related kinase 2)	0.61	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)		602169		508
P28006 UniProt NPD GO	GAC1_YEAST	Serine/threonine-protein phosphatase 1 regulatory subunit GAC1	0.61	-	nuc	0		protein phosphatase type 1 complex [IDA]			793
Q925E7 UniProt NPD GO	2ABD_MOUSE	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform (PP2A, subunit B, ...	0.61	-	nuc	0	Cytoplasm (By similarity)				453
Q8K2V1 UniProt NPD GO	PP4R1_MOUSE	Serine/threonine-protein phosphatase 4 regulatory subunit 1	0.61	-	nuc	0					951
Q6FUC3 UniProt NPD GO	PP4R2_CANGA	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2)	0.61	-	nuc	0	Nucleus (By similarity)				402
O60070 UniProt NPD GO	ASH2_SCHPO	Set1 complex component ash2 (Set1C component ash2) (COMPASS component ash2) (Complex proteins associ ...	0.61	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA] Lid2 complex [IDA]			652
O18784 UniProt NPD GO	TRPC1_BOVIN	Short transient receptor potential channel 1 (TrpC1) (TRP-1 protein)	0.61	-	end	7	Membrane; multi-pass membrane protein (Probable)				793
P48995 UniProt NPD GO	TRPC1_HUMAN	Short transient receptor potential channel 1 (TrpC1) (TRP-1 protein)	0.61	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	602343		793
Q61056 UniProt NPD GO	TRPC1_MOUSE	Short transient receptor potential channel 1 (TrpC1) (Transient receptor protein 1) (Mtrp1) (Trp-rel ...	0.61	-	end	8	Membrane; multi-pass membrane protein (Probable)				809
P42226 UniProt NPD GO	STAT6_HUMAN	Signal transducer and activator of transcription 6 (IL-4 Stat)	0.61	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation		601512	1OJ5	847
P25559 UniProt NPD GO	DCC1_YEAST	Sister chromatid cohesion protein DCC1 (Defective in sister chromatid cohesion protein 1)	0.61	-	cyt	0		DNA replication factor C complex [IPI]			380
Q24179 UniProt NPD GO	SLY1_DROME	Sly1 protein homolog	0.61	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [ISS] membrane [ISS]			657
P35498 UniProt NPD GO	SCN1A_HUMAN	Sodium channel protein type 1 subunit alpha (Sodium channel protein type I subunit alpha) (Voltage-g ...	0.61	+	end	19	Membrane; multi-pass membrane protein	integral to membrane [NAS]	609634		2009
O01352 UniProt NPD GO	DJ_DROME	Sperm-specific protein Don juan	0.61	+	nuc	0	Nucleus. Predominantly. Mitochondrion. Some fraction is associated with mitochondria	flagellum (sensu Eukaryota) [IDA] mitochondrial derivative [IDA] nucleus [IDA]			248
P35422 UniProt NPD GO	PHI1_MYTCA	Sperm-specific protein Phi-1 (PL-III) (Sperm-specific protamine-like protein) (Fragment)	0.61	-	nuc	0	Nucleus				35
P60008 UniProt NPD GO	HILS1_HUMAN	Spermatid-specific linker histone H1-like protein	0.61	+	nuc	0	Nucleus	male germ cell nucleus [IDA] nucleosome [IDA]	608101		231
O94534 UniProt NPD GO	ALP14_SCHPO	Spindle pole body component alp14 (Altered polarity protein 14)	0.61	-	nuc	0	Spindle pole body. And the periphery of the kinetochores				809
Q09825 UniProt NPD GO	SAD1_SCHPO	Spindle pole body-associated protein sad1	0.61	-	nuc	1	Nucleus; nuclear membrane; single-pass membrane protein	nuclear membrane [TAS] spindle pole body [IDA]			514
Q924S7 UniProt NPD GO	SPRE2_MOUSE	Sprouty-related, EVH1 domain-containing protein 2 (Spred-2)	0.61	-	nuc	0	Membrane; peripheral membrane protein	plasma membrane [IDA]			410
Q5R4C5 UniProt NPD GO	STMN4_PONPY	Stathmin-4	0.61	-	nuc	0					189
Q9H169 UniProt NPD GO	STMN4_HUMAN	Stathmin-4 (Stathmin-like protein B3) (RB3)	0.61	-	nuc	0					189
Q20924 UniProt NPD GO	SUN1_CAEEL	Sun domain protein 1	0.61	-	mit	0					473
Q6XYQ8 UniProt NPD GO	SYT10_HUMAN	Synaptotagmin-10 (Synaptotagmin X) (SytX)	0.61	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				523
Q9R0N5 UniProt NPD GO	SYT5_MOUSE	Synaptotagmin-5 (Synaptotagmin V) (SytV) (Synaptotagmin IX)	0.61	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Endosome; recycling endoso ...	cell soma [IDA] neuron projection [IDA] perinuclear region [IDA]			386
P57082 UniProt NPD GO	TBX4_HUMAN	T-box transcription factor TBX4 (T-box protein 4)	0.61	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	601719		545
O93366 UniProt NPD GO	TLX1_CHICK	T-cell leukemia homeobox protein 1 (Homeobox protein Hox-11) (Homeobox TLX-1)	0.61	+	nuc	0	Nucleus (By similarity)				297
P56846 UniProt NPD GO	TCL6_HUMAN	T-cell leukemia/lymphoma 6 protein (Protein TNG1)	0.61	-	nuc	0			604412		141
Q9Z1A9 UniProt NPD GO	TBCD8_MOUSE	TBC1 domain family member 8 (Vascular Rab-GAP/TBC-containing protein) (BUB2-like protein 1)	0.61	-	mit	0					891
Q61471 UniProt NPD GO	TOB1_MOUSE	Tob1 protein (Transducer of erbB-2 1)	0.61	-	nuc	0		cytoplasm [IDA]			363
Q6R5N8 UniProt NPD GO	TLR13_MOUSE	Toll-like receptor 13 precursor	0.61	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)				991
Q9EQU3 UniProt NPD GO	TLR9_MOUSE	Toll-like receptor 9 precursor (CD289 antigen)	0.61	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1032

You are viewing entries 18751 to 18800 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.