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
Q66WF5 UniProt NPD GO	RL24_FELCA	60S ribosomal protein L24 (Ribosomal protein L30)	0.78	+	nuc	0					157
P83731 UniProt NPD GO	RL24_HUMAN	60S ribosomal protein L24 (Ribosomal protein L30)	0.78	+	nuc	0			604180		157
P38666 UniProt NPD GO	RL242_ARATH	60S ribosomal protein L24-2 (Protein SHORT VALVE 1)	0.78	-	nuc	0	Cytoplasm				163
Q9JII1 UniProt NPD GO	INP5E_MOUSE	72 kDa inositol polyphosphate 5-phosphatase (EC 3.1.3.36) (Phosphatidylinositol-4,5-bisphosphate 5-p ...	0.78	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein; cytoplasmic side. P ...	Golgi membrane [IDA]			647
Q9H013 UniProt NPD GO	ADA19_HUMAN	ADAM 19 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 19) (Meltrin beta) (Meta ...	0.78	-	exc	1	Membrane; single-pass type I membrane protein		603640		956
Q9P0K1 UniProt NPD GO	ADA22_HUMAN	ADAM 22 precursor (A disintegrin and metalloproteinase domain 22) (Metalloproteinase-like, disintegr ...	0.78	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	603709		906
Q9NP61 UniProt NPD GO	ARFG3_HUMAN	ADP-ribosylation factor GTPase-activating protein 3 (ARF GAP 3)	0.78	-	nuc	0	Cytoplasm; perinuclear region	cytosol [IDA]		2CRW	516
P36120 UniProt NPD GO	DBP7_YEAST	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-) (DEAD box protein 7)	0.78	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			742
Q8N8A6 UniProt NPD GO	DDX51_HUMAN	ATP-dependent RNA helicase DDX51 (EC 3.6.1.-) (DEAD box protein 51)	0.78	+	end	0	Nucleus; nucleolus (By similarity)				666
Q5B3H7 UniProt NPD GO	DBP8_EMENI	ATP-dependent RNA helicase dbp8 (EC 3.6.1.-)	0.78	+	nuc	0	Nucleus; nucleolus (By similarity)				525
Q4WRV2 UniProt NPD GO	DRS1_ASPFU	ATP-dependent RNA helicase drs1 (EC 3.6.1.-)	0.78	+	nuc	0	Nucleus; nucleolus (By similarity)				830
P19359 UniProt NPD GO	ASCL1_RAT	Achaete-scute homolog 1	0.78	-	nuc	0	Nucleus (Probable)				233
P50553 UniProt NPD GO	ASCL1_HUMAN	Achaete-scute homolog 1 (HASH1)	0.78	-	nuc	0	Nucleus (Probable)		100790		236
Q38838 UniProt NPD GO	AGL14_ARATH	Agamous-like MADS-box protein AGL14	0.78	-	nuc	0	Nucleus (By similarity)				221
P29383 UniProt NPD GO	AGL3_ARATH	Agamous-like MADS-box protein AGL3	0.78	-	nuc	0	Nucleus				258
Q95MP2 UniProt NPD GO	ASIP_HORSE	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.78	-	nuc	0	Secreted protein (By similarity)				133
Q03288 UniProt NPD GO	ASIP_MOUSE	Agouti signaling protein precursor (ASP) (Agouti switch protein) (Agouti coat color protein)	0.78	-	nuc	0	Secreted protein				131
P37089 UniProt NPD GO	SCNNA_RAT	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.78	-	nuc	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...	integral to membrane [NAS]			698
Q4VCS5 UniProt NPD GO	AMOT_HUMAN	Angiomotin	0.78	-	nuc	0	Cell membrane; cell-cell junction. Localized on the cell surface. May act as a transmembrane protein ...	actin filament [IDA] cytoplasmic vesicle [IDA] lamellipodium [IDA]	300410		1084
P23352 UniProt NPD GO	KALM_HUMAN	Anosmin-1 precursor (Kallmann syndrome protein) (Adhesion molecule-like X-linked)	0.78	+	nuc	0	Cell surface	extracellular matrix (sensu Metazoa) [TAS] extracellular space [TAS]	308700	1ZLG	680
P15179 UniProt NPD GO	SYDM_YEAST	Aspartyl-tRNA synthetase, mitochondrial (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.78	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			658
Q59TN9 UniProt NPD GO	ATG20_CANAL	Autophagy-related protein 20	0.78	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				407
Q05764 UniProt NPD GO	ADDB_RAT	Beta-adducin (Erythrocyte adducin subunit beta) (Adducin 63)	0.78	+	nuc	0		cytoskeleton [NAS]			724
Q58DL5 UniProt NPD GO	BCAR3_BOVIN	Breast cancer anti-estrogen resistance protein 3	0.78	-	nuc	0					826
Q4R8R1 UniProt NPD GO	BCAR3_MACFA	Breast cancer anti-estrogen resistance protein 3	0.78	-	nuc	0					825
Q02637 UniProt NPD GO	CEBP_DROME	CCAAT/enhancer-binding protein (C/EBP) (Slow border cell protein)	0.78	+	nuc	0	Nucleus				449
P43132 UniProt NPD GO	BRE2_YEAST	COMPASS component BRE2 (Complex proteins associated with SET1 protein BRE2) (Set1C component BRE2) ( ...	0.78	-	nuc	0	Nucleus (Probable)	COMPASS complex [IPI]			505
Q9H159 UniProt NPD GO	CAD19_HUMAN	Cadherin-19 precursor	0.78	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	603016		772
Q00366 UniProt NPD GO	P53_MESAU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				396
Q9TU23 UniProt NPD GO	CE290_BOVIN	Centrosomal protein Cep290	0.78	-	nuc	0	Centrosome (By similarity)				1453
Q99127 UniProt NPD GO	CHSY_USTMA	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.78	-	exc	0	Cell membrane; multi-pass membrane protein				738
P41641 UniProt NPD GO	RR14_PINTH	Chloroplast 30S ribosomal protein S14	0.78	-	nuc	0	Plastid; chloroplast				99
P06371 UniProt NPD GO	RR14_TOBAC	Chloroplast 30S ribosomal protein S14	0.78	-	nuc	0	Plastid; chloroplast				100
Q6YXM5 UniProt NPD GO	RK20_PHYPA	Chloroplast 50S ribosomal protein L20	0.78	-	nuc	0	Plastid; chloroplast				115
P19948 UniProt NPD GO	RK20_SOYBN	Chloroplast 50S ribosomal protein L20	0.78	+	nuc	0	Plastid; chloroplast				130
P35790 UniProt NPD GO	CHKA_HUMAN	Choline kinase alpha (EC 2.7.1.32) (CK) (CHETK-alpha)	0.78	-	nuc	0	Cytoplasm		118491		457
Q59QC2 UniProt NPD GO	EAF6_CANAL	Chromatin modification-related protein EAF6	0.78	-	nuc	0	Nucleus (By similarity)				211
O00257 UniProt NPD GO	CBX4_HUMAN	Chromobox protein homolog 4 (Polycomb 2 homolog) (Pc2) (hPc2)	0.78	-	nuc	0	Nucleus	nucleus [TAS]	603079		558
O55187 UniProt NPD GO	CBX4_MOUSE	Chromobox protein homolog 4 (Polycomb 2 homolog) (Pc2) (mPc2)	0.78	-	nuc	0	Nucleus				551
Q9QYC3 UniProt NPD GO	BHLH8_MOUSE	Class B basic helix-loop-helix protein 8 (bHLHB8) (Muscle, intestine and stomach expression 1) (MIST ...	0.78	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			197
P70562 UniProt NPD GO	BHLH8_RAT	Class B basic helix-loop-helix protein 8 (bHLHB8) (Muscle, intestine and stomach expression 1) (MIST ...	0.78	-	mit	0	Nucleus (Probable)	nucleus [IDA]			197
Q6AYJ5 UniProt NPD GO	CLUA1_RAT	Clusterin-associated protein 1	0.78	-	nuc	0	Nucleus (By similarity)				402
Q96M95 UniProt NPD GO	CCD42_HUMAN	Coiled-coil domain-containing protein 42	0.78	-	nuc	0					316
Q6PFL6 UniProt NPD GO	CCD43_BRARE	Coiled-coil domain-containing protein 43	0.78	+	nuc	0					213
Q3ZAV0 UniProt NPD GO	CCD60_RAT	Coiled-coil domain-containing protein 60	0.78	-	nuc	0					542
Q5ZKI4 UniProt NPD GO	CCD93_CHICK	Coiled-coil domain-containing protein 93	0.78	-	nuc	0					617
Q95LS7 UniProt NPD GO	CCD96_MACFA	Coiled-coil domain-containing protein 96	0.78	-	nuc	0					560
P13671 UniProt NPD GO	CO6_HUMAN	Complement component C6 precursor	0.78	-	mit	0	Secreted protein		217050		934
Q06680 UniProt NPD GO	CND3_YEAST	Condensin complex subunit 3 (CAPG homolog)	0.78	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	nuclear condensin complex [IGI]			1035
Q04632 UniProt NPD GO	COG8_YEAST	Conserved oligomeric Golgi complex subunit 8 (COG complex subunit 8)	0.78	-	nuc	0		Golgi transport complex [IPI]			607

You are viewing entries 9751 to 9800 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.