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
Q9M2V7 UniProt NPD GO	WBC16_ARATH	Probable white-brown complex homolog protein 16	0.39	-	end	7	Membrane; multi-pass membrane protein (By similarity)				720
P01212 UniProt NPD GO	PENKA_XENLA	Proenkephalin A-A precursor [Contains: Synenkephalin; Met-enkephalin; Met-enkephalin-Arg-Gly-Tyr; Me ...	0.39	-	exc	0	Secreted protein				262
Q9WU79 UniProt NPD GO	PROD_MOUSE	Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase)	0.39	+	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA]			497
Q5U1W2 UniProt NPD GO	PRR13_RAT	Proline-rich protein 13	0.39	+	nuc	0					139
O19183 UniProt NPD GO	PGH2_HORSE	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.39	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] nucleus [ISS]			604
Q6S545 UniProt NPD GO	POT22_HUMAN	Prostate, ovary, testis-expressed protein on chromosome 22	0.39	-	nuc	0			608913		288
P40013 UniProt NPD GO	BIM1_YEAST	Protein BIM1	0.39	-	cyt	0		cytoplasmic microtubule [IDA] kinetochore [TAS] spindle pole body [IDA]			344
Q8WVF2 UniProt NPD GO	CJ049_HUMAN	Protein C10orf49 precursor	0.39	-	exc	0					138
Q96DM3 UniProt NPD GO	MIC1_HUMAN	Protein C18orf8 (Colon cancer-associated protein Mic1) (Mic-1)	0.39	-	cyt	0					657
Q5SQH8 UniProt NPD GO	CF136_HUMAN	Protein C6orf136	0.39	-	nuc	0					315
Q9NWS8 UniProt NPD GO	CF096_HUMAN	Protein C6orf96	0.39	-	cyt	0					449
Q5ZJB7 UniProt NPD GO	CHMP7_CHICK	Protein CHMP7	0.39	-	cyt	0					448
P47187 UniProt NPD GO	COS5_YEAST	Protein COS5	0.39	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			383
P13007 UniProt NPD GO	D7_XENLA	Protein D7	0.39	-	nuc	0	Cytoplasm				278
Q6Q560 UniProt NPD GO	ISD11_YEAST	Protein ISD11 (Iron-sulfur protein biogenesis, desulfurase-interacting protein 11)	0.39	-	nuc	0	Mitochondrion	extrinsic to mitochondrial inner membrane [IDA] mitochondrial matrix [IDA] mitochondrion [IDA]			94
O43156 UniProt NPD GO	K0406_HUMAN	Protein KIAA0406	0.39	-	cyt	0					1089
Q07887 UniProt NPD GO	LDB18_YEAST	Protein LDB18 (Low dye-binding protein 18)	0.39	-	cyt	0					179
Q8NHV4 UniProt NPD GO	NEDD1_HUMAN	Protein NEDD1	0.39	-	nuc	0			600372		660
Q9QZQ5 UniProt NPD GO	NOV_RAT	Protein NOV homolog precursor (NovH) (Nephroblastoma overexpressed gene protein homolog)	0.39	-	mit	0	Secreted protein				351
O55126 UniProt NPD GO	NIPS2_MOUSE	Protein NipSnap2 (Glioblastoma amplified sequence)	0.39	-	mit	0		mitochondrion [ISS]			281
Q02771 UniProt NPD GO	PT117_YEAST	Protein PET117, mitochondrial precursor	0.39	-	mit	1 *	Mitochondrion (Probable)	mitochondrial inner membrane [TAS]			107
P25365 UniProt NPD GO	SED4_YEAST	Protein SED4	0.39	-	nuc	0	Membrane; single-pass type II membrane protein	endoplasmic reticulum [TAS] integral to endoplasmic reticulum membrane [IDA]			1065
Q6BK59 UniProt NPD GO	SEY1_DEBHA	Protein SEY1	0.39	-	end	1	Membrane; multi-pass membrane protein (Potential)				847
P56847 UniProt NPD GO	TNG2_HUMAN	Protein TNG2	0.39	-	nuc	0			604412		110
Q91YQ7 UniProt NPD GO	U2508_MOUSE	Protein UNQ2508/PRO5996 homolog	0.39	-	cyt	0					393
Q8NJR0 UniProt NPD GO	URE2_CANMA	Protein URE2	0.39	-	nuc	0					328
P49339 UniProt NPD GO	WNT11_CHICK	Protein Wnt-11 precursor	0.39	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				354
O74851 UniProt NPD GO	ADG3_SCHPO	Protein adg3 precursor	0.39	-	nuc	0	Secreted protein (Potential)				1131
Q9VG55 UniProt NPD GO	HUGIN_DROME	Protein hugin precursor [Contains: Hug-gamma; Hug-peptide; PK-2 (Drm-PK-2) (Pyrokinin-2) (Myotrophin ...	0.39	-	nuc	0	Secreted protein	extracellular region [NAS]			191
O46262 UniProt NPD GO	HUNB_DRODA	Protein hunchback (Fragments)	0.39	-	nuc	0	Nucleus (By similarity)				195
O19111 UniProt NPD GO	KPCZ_RABIT	Protein kinase C zeta type (EC 2.7.11.13) (nPKC-zeta)	0.39	-	cyt	0	Cytoplasm (By similarity). In the retina, localizes in the terminals of the rod bipolar cells. Endos ...				591
P34885 UniProt NPD GO	KPC1B_CAEEL	Protein kinase C-like 1B (EC 2.7.11.13) (PKC1B)	0.39	-	cyt	0	Membrane; peripheral membrane protein. Associated with membranes and the cytoskeleton				707
P34705 UniProt NPD GO	KUP1_CAEEL	Protein kup-1	0.39	-	cyt	0					385
Q8BWG9 UniProt NPD GO	ORAI1_MOUSE	Protein orai-1	0.39	-	nuc	3	Cell membrane; multi-pass membrane protein (By similarity)				304
Q5XIP1 UniProt NPD GO	PELO_RAT	Protein pelota homolog	0.39	-	cyt	0	Nucleus (Potential)				385
Q4WKB2 UniProt NPD GO	PPME1_ASPFU	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.39	-	nuc	0					420
Q3UH53 UniProt NPD GO	SDK1_MOUSE	Protein sidekick-1 precursor	0.39	-	nuc	1	Membrane; single-pass membrane protein (Potential)				2193
Q9Y5G0 UniProt NPD GO	PCDGH_HUMAN	Protocadherin gamma B5 precursor (PCDH-gamma-B5)	0.39	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606302		923
Q5DRA7 UniProt NPD GO	PCDGH_PANTR	Protocadherin gamma B5 precursor (PCDH-gamma-B5)	0.39	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				923
Q9BZA8 UniProt NPD GO	PC11Y_HUMAN	Protocadherin-11 Y-linked precursor (Protocadherin-11) (Protocadherin-22) (Protocadherin on the Y ch ...	0.39	+	exc	2 *	Membrane; single-pass membrane protein (Potential)		400022		1340
Q4I5G1 UniProt NPD GO	COX10_GIBZE	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.39	-	end	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				507
O24164 UniProt NPD GO	PPOM_TOBAC	Protoporphyrinogen oxidase, mitochondrial (EC 1.3.3.4) (PPO II) (Protoporphyrinogen IX oxidase isozy ...	0.39	-	nuc	0	Mitochondrion			1SEZ	504
Q9S7C9 UniProt NPD GO	ESCA_ARATH	Putative DNA-binding protein ESCAROLA	0.39	-	nuc	0					311
Q9M0R5 UniProt NPD GO	ATL4C_ARATH	Putative RING-H2 finger protein ATL4C precursor	0.39	-	end	2 *					345
Q9XID4 UniProt NPD GO	ARFL_ARATH	Putative auxin response factor 12	0.39	-	cyt	0	Nucleus				593
Q9SX38 UniProt NPD GO	DRL4_ARATH	Putative disease resistance protein At1g50180	0.39	-	cyt	0					839
Q9SZG1 UniProt NPD GO	GT6_ARATH	Putative glycosyltransferase 6 (EC 2.4.-.-) (AtGT6)	0.39	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				432
P58962 UniProt NPD GO	GR58A_DROME	Putative gustatory receptor 58a	0.39	+	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			395
Q09828 UniProt NPD GO	SYLM_SCHPO	Putative leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS) ...	0.39	-	nuc	0	Mitochondrion; mitochondrial matrix				874
Q9VFN2 UniProt NPD GO	OR88A_DROME	Putative odorant receptor 88a	0.39	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				401

You are viewing entries 32901 to 32950 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.