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
Q949M3 UniProt NPD GO	FABG3_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase 3, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ...	0.14	-	cyt	0	Plastid; chloroplast (By similarity). Plastid (By similarity). And non-photosynthetic plastids (By s ...				315
Q93X68 UniProt NPD GO	FABG5_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase 5, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ...	0.14	-	cyt	0	Plastid; chloroplast (By similarity). Plastid (By similarity). And non-photosynthetic plastids (By s ...				317
Q8L3X9 UniProt NPD GO	KASM_ARATH	3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial precursor (EC 2.3.1.41) (Beta-ketoacyl-ACP ...	0.14	-	nuc	0	Mitochondrion			1W0I	461
P34752 UniProt NPD GO	PHYA_ASPNG	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.14	-	exc	0	Secreted protein			1IHP	467
P53707 UniProt NPD GO	CSP37_CANAL	37 kDa cell surface protein	0.14	-	nuc	0	Cell wall				321
Q3T0J3 UniProt NPD GO	RM16_BOVIN	39S ribosomal protein L16, mitochondrial precursor (L16mt) (MRP-L16)	0.14	-	mit	0	Mitochondrion (By similarity)				251
Q99N94 UniProt NPD GO	RM09_MOUSE	39S ribosomal protein L9, mitochondrial precursor (L9mt) (MRP-L9)	0.14	-	cyt	0	Mitochondrion				265
Q9S777 UniProt NPD GO	4CL3_ARATH	4-coumarate--CoA ligase 3 (EC 6.2.1.12) (4CL 3) (At4CL3) (4-coumaroyl-CoA synthase 3)	0.14	-	nuc	0					561
P49429 UniProt NPD GO	HPPD_MOUSE	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (4-hydroxyphenylpyruvic acid oxida ...	0.14	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				392
Q02110 UniProt NPD GO	HPPD_PIG	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.14	-	cyt	0					392
P06147 UniProt NPD GO	RS12_TETTH	40S ribosomal protein S12	0.14	-	mit	0					142
P52811 UniProt NPD GO	RS13_ANOGA	40S ribosomal protein S13	0.14	-	nuc	0					150
P34788 UniProt NPD GO	RS18_ARATH	40S ribosomal protein S18	0.14	-	nuc	0	Cytoplasm				152
P39018 UniProt NPD GO	RS19A_DROME	40S ribosomal protein S19a	0.14	-	cyt	0					155
P46297 UniProt NPD GO	RS23_FRAAN	40S ribosomal protein S23 (S12)	0.14	-	nuc	0					142
Q9W334 UniProt NPD GO	RS28_DROME	40S ribosomal protein S28	0.14	-	cyt	0					65
Q949H0 UniProt NPD GO	RS7_HORVU	40S ribosomal protein S7	0.14	-	cyt	0					191
P79399 UniProt NPD GO	5HT1B_PIG	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B) (Fragment)	0.14	-	mit	2	Membrane; multi-pass membrane protein				150
Q13639 UniProt NPD GO	5HT4R_HUMAN	5-hydroxytryptamine 4 receptor (5-HT-4) (Serotonin receptor 4) (5-HT4)	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA]	602164		388
O50061 UniProt NPD GO	RK4_ARATH	50S ribosomal protein L4, chloroplast precursor (R-protein L4)	0.14	-	mit	0	Plastid; chloroplast				282
Q40592 UniProt NPD GO	RL10_TOBAC	60S ribosomal protein L10 (QM protein homolog) (Fragment)	0.14	-	nuc	0					150
P45635 UniProt NPD GO	RL101_ORYSA	60S ribosomal protein L10-1 (Putative tumor suppressor SC34) (Protein QM)	0.14	-	mit	0					224
Q75AP7 UniProt NPD GO	RL2_ASHGO	60S ribosomal protein L2	0.14	-	mit	0					254
Q6FPN7 UniProt NPD GO	RL2_CANGA	60S ribosomal protein L2	0.14	-	mit	0					254
P05736 UniProt NPD GO	RL2_YEAST	60S ribosomal protein L2 (YL6) (L5) (RP8)	0.14	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	253
Q02984 UniProt NPD GO	RL27_PYRST	60S ribosomal protein L27	0.14	-	cyt	0					134
Q9LR33 UniProt NPD GO	R27A2_ARATH	60S ribosomal protein L27a-2	0.14	+	cyt	0					146
P49637 UniProt NPD GO	R27A3_ARATH	60S ribosomal protein L27a-3	0.14	+	mit	0					146
P34091 UniProt NPD GO	RL6_MESCR	60S ribosomal protein L6 (YL16-like)	0.14	-	nuc	0					234
P25998 UniProt NPD GO	RL8_TOBAC	60S ribosomal protein L8 (60S ribosomal protein L2)	0.14	-	mit	0	Cytoplasm				260
P08253 UniProt NPD GO	MMP2_HUMAN	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.14	-	mit	0		extracellular space [TAS]	120360	1RTG	660
Q9UKJ8 UniProt NPD GO	ADA21_HUMAN	ADAM 21 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 21)	0.14	-	end	2 *	Membrane; single-pass type I membrane protein		603713		722
P27080 UniProt NPD GO	ADT_CHLRE	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT)	0.14	-	nuc	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				308
P02723 UniProt NPD GO	ADT_NEUCR	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT)	0.14	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				313
Q8SQH8 UniProt NPD GO	ARF_ENCCU	ADP-ribosylation factor	0.14	-	cyt	0					206
P36579 UniProt NPD GO	ARF1_SCHPO	ADP-ribosylation factor 1	0.14	-	cyt	0					179
Q64240 UniProt NPD GO	AMBP_RAT	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.14	-	nuc	0	Secreted protein	extracellular region [ISS] microsome [IDA] plasma membrane [ISS]			349
Q62577 UniProt NPD GO	AMBP_MERUN	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.14	-	exc	0	Secreted protein	extracellular region [ISS] plasma membrane [ISS]			346
P61966 UniProt NPD GO	AP1S1_HUMAN	AP-1 complex subunit sigma-1A (Adapter-related protein complex 1 sigma-1A subunit) (Sigma-adaptin 1A ...	0.14	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [TAS] Golgi trans face [ISS]	603531		158
P61967 UniProt NPD GO	AP1S1_MOUSE	AP-1 complex subunit sigma-1A (Adapter-related protein complex 1 sigma-1A subunit) (Sigma-adaptin 1A ...	0.14	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [NAS] Golgi trans face [NAS]		1W63	158
Q9LSZ0 UniProt NPD GO	APO4_ARATH	APO protein 4, mitochondrial precursor	0.14	-	nuc	0	Mitochondrion (Potential)				337
Q9DCX2 UniProt NPD GO	ATP5H_MOUSE	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.14	-	nuc	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			160
O78476 UniProt NPD GO	ATPD_GUITH	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.14	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane				185
Q8M9X7 UniProt NPD GO	ATPE_CHAGL	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.14	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				136
P41292 UniProt NPD GO	ATP8_BALMU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				63
P24947 UniProt NPD GO	ATP8_BALPH	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				63
Q9TEG7 UniProt NPD GO	ATP8_CAVPO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q34801 UniProt NPD GO	ATP8_HYLSY	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q9MEI6 UniProt NPD GO	ATP8_LAMPA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P14570 UniProt NPD GO	ATP8_LOCMI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52

You are viewing entries 57901 to 57950 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.