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
P46942 UniProt NPD GO	DB10_NICSY	ATP-dependent RNA helicase-like protein DB10 (EC 3.6.1.-)	0.60	+	nuc	0					607
P53706 UniProt NPD GO	HST6_CANAL	ATP-dependent permease HST6 (STE6 homolog)	0.60	-	end	11 *	Membrane; multi-pass membrane protein				1323
Q6CN92 UniProt NPD GO	SPB4_KLULA	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.60	-	nuc	0	Nucleus; nucleolus (By similarity)				596
Q9P6N8 UniProt NPD GO	RRP3_SCHPO	ATP-dependent rRNA helicase rrp3 (EC 3.6.1.-)	0.60	+	cyt	0	Nucleus (Probable)				465
Q754G5 UniProt NPD GO	ARP4_ASHGO	Actin-like protein ARP4	0.60	-	cyt	0	Nucleus (By similarity)				479
Q03100 UniProt NPD GO	CYAA_DICDI	Adenylate cyclase, aggregation specific (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.60	+	end	11	Membrane; multi-pass membrane protein				1407
Q920R0 UniProt NPD GO	ALS2_MOUSE	Alsin (Amyotrophic lateral sclerosis protein 2 homolog)	0.60	-	nuc	0		cytosol [ISS] early endosome [ISS] vesicular fraction [ISS]			1651
O35240 UniProt NPD GO	ACCN3_RAT	Amiloride-sensitive cation channel 3 (Acid-sensing ion channel 3) (ASIC3) (Dorsal root ASIC) (DRASIC ...	0.60	-	nuc	0	Cytoplasm (By similarity). Cell membrane; multi-pass membrane protein (By similarity). In part cytop ...	integral to plasma membrane [IDA]			533
P37088 UniProt NPD GO	SCNNA_HUMAN	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.60	-	nuc	1	Cell membrane; apical cell membrane; multi-pass membrane protein. Apical membrane of epithelial cell ...		600228		669
O97741 UniProt NPD GO	SCNNA_RABIT	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.60	-	nuc	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				640
Q08683 UniProt NPD GO	APC5_YEAST	Anaphase-promoting complex subunit 5	0.60	-	nuc	0	Nucleus	anaphase-promoting complex [TAS]			685
Q7T1K4 UniProt NPD GO	ANDR_RANCA	Androgen receptor (Dihydrotestosterone receptor) (bfAR)	0.60	+	nuc	0	Nucleus	nucleus [IDA]			777
Q6Q4G4 UniProt NPD GO	ACE_THETS	Angiotensin-converting enzyme precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase I) (Kininase II) ...	0.60	-	cyt	0	Secreted protein; extracellular space (Probable)				616
Q68DC2 UniProt NPD GO	ANKS6_HUMAN	Ankyrin repeat and SAM domain-containing protein 6 (Sterile alpha motif domain-containing protein 6) ...	0.60	-	nuc	0					871
Q812A3 UniProt NPD GO	ANR23_MOUSE	Ankyrin repeat domain-containing protein 23 (Diabetes-related ankyrin repeat protein)	0.60	+	cyt	0	Nucleus. Sarcomeric I-band and some intercalated disks (By similarity)	nucleus [IDA]			306
P16157 UniProt NPD GO	ANK1_HUMAN	Ankyrin-1 (Erythrocyte ankyrin) (Ankyrin-R)	0.60	+	nuc	0	Isoform Er1: Cytoplasm. Probably the other erythrocyte (Er) isoforms, are located near the surface o ...	basolateral plasma membrane [NAS] plasma membrane [NAS]	182900	1N11	1880
Q28995 UniProt NPD GO	APOE_SAISC	Apolipoprotein E (Apo-E) (Fragment)	0.60	-	nuc	0	Secreted protein				107
Q7TQC5 UniProt NPD GO	APTX_MOUSE	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.60	+	nuc	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...	nucleoplasm [TAS]			342
Q5ZMQ0 UniProt NPD GO	ARMC1_CHICK	Armadillo repeat-containing protein 1	0.60	-	nuc	0					279
Q5FYB0 UniProt NPD GO	ARSJ_HUMAN	Arylsulfatase J precursor (EC 3.1.6.-) (ASJ)	0.60	+	nuc	0	Secreted protein (Potential)		610010		599
Q8WWM7 UniProt NPD GO	ATX2L_HUMAN	Ataxin-2-like protein (Ataxin-2 domain protein) (Ataxin-2-related protein)	0.60	-	nuc	0	Membrane; peripheral membrane protein		607931		1075
P48985 UniProt NPD GO	ATOH1_MOUSE	Atonal protein homolog 1 (Helix-loop-helix protein mATH-1) (MATH1)	0.60	-	nuc	0	Nucleus (Probable)				351
Q805E9 UniProt NPD GO	ANF_OREMO	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.60	-	exc	0	Secreted protein				140
P56213 UniProt NPD GO	ALR_MOUSE	Augmenter of liver regeneration	0.60	-	nuc	0		mitochondrion [IDA]			125
Q4FZV3 UniProt NPD GO	IDLC_RAT	Axonemal dynein light intermediate polypeptide 1 (Inner dynein arm light chain, axonemal)	0.60	-	nuc	0					258
P41183 UniProt NPD GO	BCL6_MOUSE	B-cell lymphoma 6 protein homolog	0.60	-	nuc	0	Nucleus	nucleus [IDA]			707
Q9HB09 UniProt NPD GO	B2L12_HUMAN	Bcl-2-related proline-rich protein (Bcl-2-like 12 protein)	0.60	-	nuc	0					334
O46576 UniProt NPD GO	BMP4_RABIT	Bone morphogenetic protein 4 precursor (BMP-4)	0.60	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				409
P87350 UniProt NPD GO	RNBR_AXIPR	Brain ribonuclease (EC 3.1.27.-) (BRB)	0.60	-	nuc	0	Secreted protein				151
Q5HZE8 UniProt NPD GO	BSMAP_RAT	Brain-specific membrane-anchored protein precursor	0.60	-	exc	1	Membrane (Potential). Could be associated with an intracellular organelle or membrane (Potential)				331
Q9USK6 UniProt NPD GO	CBP3_SCHPO	CBP3-like protein	0.60	-	mit	0					283
Q12348 UniProt NPD GO	CSN10_YEAST	COP9 signalosome complex subunit 10	0.60	-	mit	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IDA]			645
P46963 UniProt NPD GO	CTK3_YEAST	CTD kinase subunit gamma (CTD kinase 32 kDa subunit) (CTDK-I gamma subunit)	0.60	-	nuc	0	Nucleus	nucleus [IPI]			296
Q12791 UniProt NPD GO	KCMA1_HUMAN	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.60	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [NAS] voltage-gated potassium channel complex [TAS]	609446		1236
O15865 UniProt NPD GO	CDPK2_PLAFK	Calcium-dependent protein kinase 2 (EC 2.7.11.1) (PfCDPK2)	0.60	+	nuc	0					512
Q7RJG2 UniProt NPD GO	CDPK4_PLAYO	Calcium-dependent protein kinase 4 (EC 2.7.11.1)	0.60	-	cyt	0					527
P52825 UniProt NPD GO	CPT2_MOUSE	Carnitine O-palmitoyltransferase 2, mitochondrial precursor (EC 2.3.1.21) (Carnitine palmitoyltransf ...	0.60	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			658
Q9H078 UniProt NPD GO	CLPB_HUMAN	Caseinolytic peptidase B protein homolog (Suppressor of potassium transport defect 3)	0.60	-	mit	0					707
P55215 UniProt NPD GO	CASP2_RAT	Caspase-2 precursor (EC 3.4.22.-) (CASP-2) (ICH-1 protease) [Contains: Caspase-2 subunit p18; Caspas ...	0.60	-	nuc	0					452
O09185 UniProt NPD GO	P53_CRIGR	Cellular tumor antigen p53 (Tumor suppressor p53)	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
Q39079 UniProt NPD GO	DNJ13_ARATH	Chaperone protein dnaJ 13 (AtJ13) (AtDjB13)	0.60	-	cyt	0	Membrane; single-pass membrane protein (Potential)				538
Q6GL11 UniProt NPD GO	CHM4B_XENTR	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b)	0.60	-	nuc	0	Cytoplasm (By similarity)				222
P51295 UniProt NPD GO	RR13_PORPU	Chloroplast 30S ribosomal protein S13	0.60	-	nuc	0	Plastid; chloroplast				126
P11538 UniProt NPD GO	RR14_EUGGR	Chloroplast 30S ribosomal protein S14	0.60	-	mit	0	Plastid; chloroplast				100
Q5QA75 UniProt NPD GO	RR18_ACOGR	Chloroplast 30S ribosomal protein S18	0.60	-	nuc	0	Plastid; chloroplast				101
Q6KGX3 UniProt NPD GO	RR7_PEA	Chloroplast 30S ribosomal protein S7	0.60	-	nuc	0	Plastid; chloroplast				156
P59032 UniProt NPD GO	RR8_CHAGL	Chloroplast 30S ribosomal protein S8	0.60	-	nuc	0	Plastid; chloroplast				132
Q42362 UniProt NPD GO	RR8_MUSAC	Chloroplast 30S ribosomal protein S8 (Fragment)	0.60	-	nuc	0	Plastid; chloroplast				116
Q6EN83 UniProt NPD GO	RK2_ORYNI	Chloroplast 50S ribosomal protein L2	0.60	+	nuc	0	Plastid; chloroplast				273
P17351 UniProt NPD GO	RK2_ORYSA	Chloroplast 50S ribosomal protein L2	0.60	+	nuc	0	Plastid; chloroplast				273

You are viewing entries 18901 to 18950 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.