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
Q6L3Y2 UniProt NPD GO	R1B11_SOLDE	Putative late blight resistance protein homolog R1B-11	0.44	-	cyt	0	Cytoplasm (By similarity)				1252
Q6L3L0 UniProt NPD GO	R1B23_SOLDE	Putative late blight resistance protein homolog R1B-23	0.44	-	cyt	0	Cytoplasm (By similarity)				1262
Q9SX33 UniProt NPD GO	ALA9_ARATH	Putative phospholipid-transporting ATPase 9 (EC 3.6.3.1) (Aminophospholipid flippase 9)	0.44	+	end	10	Membrane; multi-pass membrane protein				1200
P36093 UniProt NPD GO	PHD1_YEAST	Putative transcription factor PHD1	0.44	-	nuc	0	Nucleus	nucleus [IDA]			366
Q6XXX2 UniProt NPD GO	CU024_HUMAN	Putative uncharacterized protein C21orf24	0.44	-	nuc	0					140
Q12322 UniProt NPD GO	YO114_YEAST	Putative uncharacterized protein YOL114C	0.44	-	nuc	0					202
P11637 UniProt NPD GO	QA1S_NEUCR	Quinate repressor	0.44	-	cyt	0					919
O64763 UniProt NPD GO	ATL2G_ARATH	RING-H2 finger protein ATL2G precursor (RING-H2 finger protein ATL9)	0.44	-	exc	2 *					378
Q9NTZ6 UniProt NPD GO	RBM12_HUMAN	RNA-binding protein 12 (RNA-binding motif protein 12) (SH3/WW domain anchor protein in the nucleus) ...	0.44	+	nuc	0	Nucleus		607179	2CPY	932
Q5E999 UniProt NPD GO	DUS11_BOVIN	RNA/RNP complex-1-interacting phosphatase (EC 3.1.3.-) (Phosphatase that interacts with RNA/RNP comp ...	0.44	-	nuc	0	Nucleus (By similarity)				331
O93831 UniProt NPD GO	RAEP_CANAL	Rab proteins geranylgeranyltransferase component A (Rab escort protein) (REP)	0.44	-	nuc	0					640
P53107 UniProt NPD GO	YRB30_YEAST	Ran-specific GTPase-activating protein 30 (Ran-binding protein 30) (RANBP30)	0.44	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and cytoplasm	cytoplasm [IDA] nucleus [IMP]			440
Q6NTA4 UniProt NPD GO	RRAGB_MOUSE	Ras-related GTP-binding protein B (Rag B) (RagB)	0.44	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			374
Q63487 UniProt NPD GO	RRAGB_RAT	Ras-related GTP-binding protein B (Rag B) (RagB)	0.44	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			374
Q9LJM4 UniProt NPD GO	IKU2_ARATH	Receptor-like protein kinase HAIKU2 precursor (EC 2.7.11.1)	0.44	-	end	1	Membrane; single-pass membrane protein (Potential)				991
Q5IS59 UniProt NPD GO	RTN1_PANTR	Reticulon-1	0.44	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				776
O70622 UniProt NPD GO	RTN2_MOUSE	Reticulon-2 (Neuroendocrine-specific protein-like 1) (NSP-like protein 1) (NSPLI)	0.44	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				471
Q86UN2 UniProt NPD GO	R4RL1_HUMAN	Reticulon-4 receptor-like 1 precursor (Nogo-66 receptor homolog 2) (Nogo-66 receptor-related protein ...	0.44	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. Localized to the surface of neurons, including axons	anchored to plasma membrane [IDA]			441
Q5TM57 UniProt NPD GO	RPP21_MACMU	Ribonuclease P protein subunit p21 (EC 3.1.26.5) (RNaseP protein p21)	0.44	-	nuc	0	Nucleus; nucleolus (By similarity)				154
Q9BUL9 UniProt NPD GO	RPP25_HUMAN	Ribonuclease P protein subunit p25 (EC 3.1.26.5) (RNase P protein subunit p25)	0.44	-	nuc	0	Nucleus				199
Q03604 UniProt NPD GO	RIR1_CAEEL	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleotide reductase large cha ...	0.44	-	nuc	0					788
P32895 UniProt NPD GO	KPR1_YEAST	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 1)	0.44	-	cyt	0		cytoplasm [IDA]			427
Q9UBS0 UniProt NPD GO	KS6B2_HUMAN	Ribosomal protein S6 kinase beta-2 (EC 2.7.11.1) (S6K2) (70 kDa ribosomal protein S6 kinase 2) (p70- ...	0.44	-	cyt	0			608939		482
Q6BLC3 UniProt NPD GO	RRF1_DEBHA	Ribosomal recycling factor, mitochondrial precursor	0.44	-	mit	0	Mitochondrion (By similarity)				257
Q9XSB7 UniProt NPD GO	RUNX2_HORSE	Runt-related transcription factor 2 (Core-binding factor, alpha 1 subunit) (CBF-alpha 1) (Fragment)	0.44	-	nuc	0	Nucleus (By similarity)				131
Q13761 UniProt NPD GO	RUNX3_HUMAN	Runt-related transcription factor 3 (Core-binding factor, alpha 3 subunit) (CBF-alpha 3) (Acute myel ...	0.44	-	nuc	0	Nucleus	nucleus [NAS]	600210		415
Q9DE27 UniProt NPD GO	RUVB2_XENLA	RuvB-like 2 (EC 3.6.1.-) (Reptin)	0.44	-	nuc	0	Nucleus (By similarity)				462
P27009 UniProt NPD GO	SCRY1_OCTDO	S-crystallin 1 (OL1)	0.44	-	nuc	0					215
Q5F3V0 UniProt NPD GO	SMYD4_CHICK	SET and MYND domain-containing protein 4	0.44	-	nuc	0					742
Q9Y371 UniProt NPD GO	SHLB1_HUMAN	SH3 domain GRB2-like protein B1 (EC 2.3.1.-) (Endophilin B1) (Bax-interacting factor 1) (Bif-1)	0.44	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with internal membranes				365
O94901 UniProt NPD GO	UN84A_HUMAN	Sad1/unc-84 protein-like 1 (Unc-84 homolog A)	0.44	-	mit	2	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Membrane; perinuclear region; mu ...		607723		812
Q8WXD2 UniProt NPD GO	SCG3_HUMAN	Secretogranin-3 precursor (Secretogranin III) (SgIII)	0.44	-	nuc	0	Secreted protein. Neuroendocrine and endocrine secretory granules				468
P42209 UniProt NPD GO	SEPT1_MOUSE	Septin-1 (Differentiation protein 6) (Diff6 protein)	0.44	-	cyt	0					365
O00506 UniProt NPD GO	STK25_HUMAN	Serine/threonine-protein kinase 25 (EC 2.7.11.1) (Sterile 20/oxidant stress-response kinase 1) (Ste2 ...	0.44	-	cyt	0	Cytoplasm. Golgi apparatus. Localizes to the Golgi apparatus		602255		426
Q9NY57 UniProt NPD GO	ST32B_HUMAN	Serine/threonine-protein kinase 32B (EC 2.7.11.1) (YANK2)	0.44	-	nuc	0					414
Q8K4T3 UniProt NPD GO	AL2S2_MOUSE	Serine/threonine-protein kinase ALS2CR2 (EC 2.7.11.1) (Amyotrophic lateral sclerosis 2 chromosomal r ...	0.44	-	nuc	0	Cytoplasm (Potential)				418
Q8N568 UniProt NPD GO	DCAK2_HUMAN	Serine/threonine-protein kinase DCAMKL2 (EC 2.7.11.1) (Doublecortin-like and CAM kinase-like 2)	0.44	+	nuc	0					766
Q9P289 UniProt NPD GO	MST4_HUMAN	Serine/threonine-protein kinase MST4 (EC 2.7.11.1) (STE20-like kinase MST4) (MST-4) (Mammalian STE20 ...	0.44	-	cyt	0	Cytoplasm. Golgi apparatus. Localizes to the Golgi apparatus	Golgi apparatus [IPI]	300547		416
Q04735 UniProt NPD GO	PCTK1_MOUSE	Serine/threonine-protein kinase PCTAIRE-1 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 1) (CRK5)	0.44	-	nuc	0					496
Q9ERE3 UniProt NPD GO	SGK3_MOUSE	Serine/threonine-protein kinase Sgk3 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 3) (Serum/ ...	0.44	-	cyt	0	Cytoplasmic vesicle. Endosome; early endosome. Localized in vesicle-like structures and in the early ...	cytoplasmic membrane-bound vesicle [IDA]		1XTN	496
Q28647 UniProt NPD GO	2A5B_RABIT	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform (PP2A, B subunit, B' ...	0.44	-	cyt	0	Nucleus (By similarity)				500
Q4WSA8 UniProt NPD GO	PTPA2_ASPFU	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.44	-	cyt	0	Cytoplasm (By similarity)				422
P32598 UniProt NPD GO	PP12_YEAST	Serine/threonine-protein phosphatase PP1-2 (EC 3.1.3.16)	0.44	-	cyt	0	Cytoplasm. Nucleus	bud neck [IDA] mating projection base [IDA] mRNA cleavage and polyadenylation specifici... [IPI] nucleolus [IDA] protein phosphatase type 1 complex [IDA] spindle pole body [IDA]			312
P49591 UniProt NPD GO	SYS_HUMAN	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.44	-	cyt	0			607529		513
Q9JJL8 UniProt NPD GO	SYSM_MOUSE	Seryl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.11) (Serine--tRNA ligase) (SerRSmt)	0.44	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			518
O23145 UniProt NPD GO	KSG2_ARATH	Shaggy-related protein kinase beta (EC 2.7.11.1) (ASK-beta)	0.44	-	mit	0					431
P01431 UniProt NPD GO	NXS1_NAJMO	Short neurotoxin 1 (Neurotoxin I) (NMM I)	0.44	-	nuc	0	Secreted protein				62
Q62230 UniProt NPD GO	SN_MOUSE	Sialoadhesin precursor (Sialic acid-binding Ig-like lectin-1) (Siglec-1) (Sheep erythrocyte receptor ...	0.44	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3: Secreted protei ...	integral to membrane [ISS]		1URL	1694
O60232 UniProt NPD GO	SSA27_HUMAN	Sjoegren syndrome/scleroderma autoantigen 1 (Autoantigen p27)	0.44	-	nuc	0			606044		199
Q92952 UniProt NPD GO	KCNN1_HUMAN	Small conductance calcium-activated potassium channel protein 1 (SK1)	0.44	+	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	602982		561

You are viewing entries 29251 to 29300 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.