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
Q7XYA7 UniProt NPD GO	RL14_GRIJA	60S ribosomal protein L14	0.12	-	mit	0					133
Q56K03 UniProt NPD GO	RL27A_BOVIN	60S ribosomal protein L27a	0.12	+	mit	0					147
P18445 UniProt NPD GO	RL27A_RAT	60S ribosomal protein L27a	0.12	+	mit	0					147
P47830 UniProt NPD GO	RL27A_XENLA	60S ribosomal protein L27a (L22)	0.12	+	mit	0					147
P57728 UniProt NPD GO	RL28B_SCHPO	60S ribosomal protein L28-B	0.12	+	mit	0					148
P67883 UniProt NPD GO	RL30_CHICK	60S ribosomal protein L30	0.12	-	mit	0					114
P67884 UniProt NPD GO	RL30_OPHHA	60S ribosomal protein L30	0.12	-	mit	0					114
P10664 UniProt NPD GO	RL4A_YEAST	60S ribosomal protein L4-A (L2A) (RP2)	0.12	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	361
Q9P784 UniProt NPD GO	RL4B_SCHPO	60S ribosomal protein L4-B	0.12	-	mit	0					363
P49626 UniProt NPD GO	RL4B_YEAST	60S ribosomal protein L4-B (L2B) (RP2)	0.12	-	mit	0		cytoplasm [IDA] cytosolic large ribosomal subunit (sensu Eu... [TAS]		1S1I	361
Q6FRG6 UniProt NPD GO	RL43_CANGA	60S ribosomal protein L43	0.12	-	mit	0					92
O15595 UniProt NPD GO	RL6_ENTHI	60S ribosomal protein L6 (Fragment)	0.12	-	nuc	0					92
P05739 UniProt NPD GO	RL6B_YEAST	60S ribosomal protein L6-B (L17) (YL16) (RP18)	0.12	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			175
Q90YW0 UniProt NPD GO	RL9_ICTPU	60S ribosomal protein L9	0.12	-	cyt	0					192
P22010 UniProt NPD GO	GRP78_KLULA	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.12	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				679
P78695 UniProt NPD GO	GRP78_NEUCR	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.12	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				661
P81281 UniProt NPD GO	TRGS_TACTR	8.6 kDa transglutaminase substrate	0.12	-	nuc	0					81
P84179 UniProt NPD GO	ABP1_PHYPO	87 kDa annexin-binding protein (Fragments)	0.12	-	cyt	0					112
P32781 UniProt NPD GO	AGA2_YEAST	A-agglutinin precursor	0.12	-	exc	0		cell wall (sensu Fungi) [TAS]			87
Q02356 UniProt NPD GO	AMPD2_RAT	AMP deaminase 2 (EC 3.5.4.6) (AMP deaminase isoform L) (Fragment)	0.12	-	nuc	0					88
Q32Q06 UniProt NPD GO	AP1M1_RAT	AP-1 complex subunit mu-1 (Adaptor-related protein complex 1 mu-1 subunit) (Mu-adaptin 1) (Adaptor p ...	0.12	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				422
P35585 UniProt NPD GO	AP1M1_MOUSE	AP-1 complex subunit mu-1 (Adaptor-related protein complex 1 mu-1 subunit) (Mu-adaptin 1) (Adaptor p ...	0.12	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]		1W63	422
Q09905 UniProt NPD GO	AP3S_SCHPO	AP-3 complex subunit sigma (Adapter-related protein complex 3 sigma subunit) (Sigma-adaptin 3A) (AP- ...	0.12	-	nuc	0					165
Q9WV76 UniProt NPD GO	AP4B1_MOUSE	AP-4 complex subunit beta-1 (Adapter-related protein complex 4 beta-1 subunit) (Beta subunit of AP-4 ...	0.12	-	cyt	0	Golgi apparatus; trans-Golgi network (By similarity). Associated with the trans-Golgi network. Found ...	Golgi trans face [IDA]			739
P50654 UniProt NPD GO	ATP6_ANAPL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.12	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q68S00 UniProt NPD GO	ATPE_PANGI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.12	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				140
Q06645 UniProt NPD GO	AT5G1_RAT	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.12	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [NAS]			136
Q06056 UniProt NPD GO	AT5G2_SHEEP	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.12	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				143
Q8HFZ6 UniProt NPD GO	ATP8_ALOGU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
Q9MQJ9 UniProt NPD GO	ATP8_CEREH	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
P50682 UniProt NPD GO	ATP8_COTJA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P14414 UniProt NPD GO	ATP8_CRIGR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
O21329 UniProt NPD GO	ATP8_DASNO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P38592 UniProt NPD GO	ATP8_HALGR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9TA07 UniProt NPD GO	ATP8_LAMFL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q38PR8 UniProt NPD GO	ATP8_MAMPR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
Q9XMI9 UniProt NPD GO	ATP8_ORYAF	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q35537 UniProt NPD GO	ATP8_PETMA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P48882 UniProt NPD GO	ATP8_PICCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.12	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q03672 UniProt NPD GO	ATP9_PODAN	ATP synthase protein 9, mitochondrial precursor (EC 3.6.3.14) (Lipid-binding protein)	0.12	-	end	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				144
Q6FRW0 UniProt NPD GO	ATPF_CANGA	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.12	-	nuc	2	Mitochondrion (By similarity)				242
P56294 UniProt NPD GO	ATPA_CHLVU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.12	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				506
O03070 UniProt NPD GO	ATPB_HYPHO	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.12	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				208
Q12233 UniProt NPD GO	ATPN_YEAST	ATP synthase subunit g, mitochondrial (EC 3.6.3.14)	0.12	-	mit	0		proton-transporting ATP synthase complex, c... [IMP]			115
Q641Y8 UniProt NPD GO	DDX1_RAT	ATP-dependent RNA helicase DDX1 (EC 3.6.1.-) (DEAD box protein 1)	0.12	-	cyt	0					740
Q92499 UniProt NPD GO	DDX1_HUMAN	ATP-dependent RNA helicase DDX1 (EC 3.6.1.-) (DEAD box protein 1) (DEAD box protein retinoblastoma) ...	0.12	-	cyt	0			601257		740
O02822 UniProt NPD GO	IRK11_RABIT	ATP-sensitive inward rectifier potassium channel 11 (Potassium channel, inwardly rectifying subfamil ...	0.12	-	end	2	Membrane; multi-pass membrane protein				390
Q6FMR7 UniProt NPD GO	ACN9_CANGA	Acetate non-utilizing protein 9, mitochondrial precursor	0.12	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				137
O19929 UniProt NPD GO	ILVB_CYACA	Acetolactate synthase large subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase large subunit) ( ...	0.12	-	nuc	0	Plastid; chloroplast				585
Q85FL3 UniProt NPD GO	ACCD_ADICA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.12	-	cyt	0	Plastid; chloroplast				310

You are viewing entries 60751 to 60800 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.