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
P62946 UniProt NPD GO	RL41_FELCA	60S ribosomal protein L41	0.86	+	nuc	0					25
P62949 UniProt NPD GO	RL41_FUGRU	60S ribosomal protein L41	0.86	+	nuc	0					25
Q90YS7 UniProt NPD GO	RL41_ICTPU	60S ribosomal protein L41	0.86	+	nuc	0					25
P62947 UniProt NPD GO	RL41_MOUSE	60S ribosomal protein L41	0.86	+	nuc	0					25
P62948 UniProt NPD GO	RL41_RAT	60S ribosomal protein L41	0.86	+	nuc	0					25
P62945 UniProt NPD GO	RL41_HUMAN	60S ribosomal protein L41 (HG12)	0.86	+	nuc	0					25
P05746 UniProt NPD GO	RL41_YEAST	60S ribosomal protein L41 (YL41) (YL47)	0.86	+	nuc	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS]			25
Q08287 UniProt NPD GO	NOP8_YEAST	60S ribosome subunit biogenesis protein NOP8 (Nucleolar protein 8)	0.86	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			484
Q10159 UniProt NPD GO	MYH1_SCHPO	A/G-specific adenine DNA glycosylase (EC 3.2.2.-)	0.86	-	nuc	0					461
P97297 UniProt NPD GO	ADML_MOUSE	ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (P ...	0.86	-	nuc	0	Secreted protein				184
Q5KMS9 UniProt NPD GO	DBP10_CRYNE	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.86	+	nuc	0	Nucleus; nucleolus (By similarity)				802
Q75C76 UniProt NPD GO	DBP4_ASHGO	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.86	+	nuc	0	Nucleus; nucleolus (By similarity)				763
Q4IEK8 UniProt NPD GO	HAS1_GIBZE	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.86	+	nuc	0	Nucleus; nucleolus (By similarity)				590
O54967 UniProt NPD GO	ACK1_MOUSE	Activated CDC42 kinase 1 (EC 2.7.10.2) (ACK-1) (Non-receptor protein tyrosine kinase Ack) (Tyrosine ...	0.86	-	nuc	0		axon [IDA] cell soma [IDA] dendrite [IDA] growth cone [IDA]			1055
Q9QXN3 UniProt NPD GO	TRIP4_MOUSE	Activating signal cointegrator 1 (ASC-1) (Thyroid receptor-interacting protein 4) (Trip-4)	0.86	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Cytoplasmic under conditions of serum deprivatio ...				581
Q6BNQ8 UniProt NPD GO	SPB1_DEBHA	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.86	+	nuc	0	Nucleus; nucleolus (By similarity)				831
Q6C9Q1 UniProt NPD GO	SPB1_YARLI	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.86	-	nuc	0	Nucleus; nucleolus (By similarity)				850
Q5BH88 UniProt NPD GO	SPB1_EMENI	AdoMet-dependent rRNA methyltransferase spb1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.86	-	nuc	0	Nucleus; nucleolus (By similarity)				806
P27046 UniProt NPD GO	MA2A1_MOUSE	Alpha-mannosidase 2 (EC 3.2.1.114) (Alpha-mannosidase II) (Mannosyl-oligosaccharide 1,3-1,6-alpha-ma ...	0.86	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [IDA]			1150
P69527 UniProt NPD GO	AMPO_RAT	Aminopeptidase O (EC 3.4.11.-) (AP-O)	0.86	-	cyt	0	Cytoplasm (Potential)				816
O35431 UniProt NPD GO	APBA2_RAT	Amyloid beta A4 precursor protein-binding family A member 2 (Neuron-specific X11L protein) (Neuronal ...	0.86	-	nuc	0		plasma membrane [IDA]			750
Q9Y2J4 UniProt NPD GO	AMOL2_HUMAN	Angiomotin-like protein 2 (Leman coiled-coil protein) (LCCP)	0.86	-	nuc	0					779
P59672 UniProt NPD GO	ANKS1_MOUSE	Ankyrin repeat and SAM domain-containing protein 1A	0.86	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic before and after growth factor treatment (By similarity)				1149
Q8K3X6 UniProt NPD GO	ANS4B_MOUSE	Ankyrin repeat and SAM domain-containing protein 4B (Harmonin-interacting ankyrin repeat-containing ...	0.86	-	nuc	0		plasma membrane [IDA]			423
Q5TYW2 UniProt NPD GO	A20A1_HUMAN	Ankyrin repeat domain-containing protein 20A1	0.86	+	nuc	0					823
Q4UJ75 UniProt NPD GO	A20A2_HUMAN	Ankyrin repeat domain-containing protein 20A2	0.86	+	nuc	0					823
Q8N283 UniProt NPD GO	ANR35_HUMAN	Ankyrin repeat domain-containing protein 35	0.86	-	nuc	0					1001
P53327 UniProt NPD GO	SLH1_YEAST	Antiviral helicase SLH1 (EC 3.6.1.-) (SKI2-like helicase 1)	0.86	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1967
Q26657 UniProt NPD GO	ALX_STRPU	Aristaless homeobox protein (ALX) (SpPrx-1) (Fragment)	0.86	+	nuc	0	Nucleus (By similarity)				327
Q5XIX3 UniProt NPD GO	DCR1C_RAT	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein) (SNM1-like protein)	0.86	-	nuc	0	Nucleus (By similarity)				698
O88529 UniProt NPD GO	BMAL1_MESAU	Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Brain and muscle ARNT-like 1)	0.86	-	nuc	0	Nucleus (By similarity)				626
Q5AMN3 UniProt NPD GO	ATG11_CANAL	Autophagy-related protein 11	0.86	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1165
Q6BHF8 UniProt NPD GO	ATG23_DEBHA	Autophagy-related protein 23	0.86	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				905
Q9BLJ6 UniProt NPD GO	BAGS_BOMMO	BAG domain-containing protein Samui	0.86	-	nuc	0					677
O16867 UniProt NPD GO	TAP_DROME	Basic helix-loop-helix neural transcription factor TAP (Target of Poxn protein) (Protein biparous)	0.86	-	nuc	0	Nucleus (Potential)				398
Q6H1V1 UniProt NPD GO	VMDL3_MOUSE	Bestrophin-4 (Vitelliform macular dystrophy 2-like protein 3)	0.86	-	end	4 *	Cell membrane; multi-pass membrane protein				669
P13916 UniProt NPD GO	GLCA_SOYBN	Beta-conglycinin, alpha chain precursor	0.86	-	exc	1 *	Embryo axis, and cotyledonary membrane-bound vacuolar protein bodies				605
Q9QZK2 UniProt NPD GO	BCAR3_MOUSE	Breast cancer anti-estrogen resistance protein 3 (p130Cas-binding protein AND-34)	0.86	-	nuc	0					820
Q99N20 UniProt NPD GO	BRMS1_MOUSE	Breast cancer metastasis-suppressor 1 homolog	0.86	-	nuc	0					246
O75175 UniProt NPD GO	CNOT3_HUMAN	CCR4-NOT transcription complex subunit 3 (CCR4-associated factor 3)	0.86	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)		604910		753
O75122 UniProt NPD GO	CLAP2_HUMAN	CLIP-associating protein 2 (Cytoplasmic linker-associated protein 2)	0.86	-	nuc	0	Cytoplasm. Localizes to microtubule tips. Polarized accumulation is subject to regulation by positio ...	cytoplasmic microtubule [IDA] Golgi apparatus [IDA] kinetochore microtubule [TAS]	605853		1294
Q60PC0 UniProt NPD GO	CAPS_CAEBR	Calcium-dependent secretion activator (Uncoordinated protein 31)	0.86	-	cyt	0	Cytoplasmic vesicle (By similarity). Membrane-associated to vesicles (By similarity). Strongly enric ...				1261
Q9NHE5 UniProt NPD GO	CAPS_DROME	Calcium-dependent secretion activator (dCAPS)	0.86	-	nuc	0	Cytoplasmic vesicle. Membrane-associated to vesicles. Restricted to all classes of presynaptic termi ...	synapse [IDA] synaptic vesicle [NAS]			1436
Q6DD51 UniProt NPD GO	CSKI2_XENLA	Caskin-2	0.86	-	nuc	0					1205
Q9BXL7 UniProt NPD GO	CAR11_HUMAN	Caspase recruitment domain-containing protein 11 (CARD-containing MAGUK protein 3) (Carma 1)	0.86	-	nuc	0	Cytoplasm	membrane fraction [NAS]	607210		1147
Q5R652 UniProt NPD GO	RAD17_PONPY	Cell cycle checkpoint protein RAD17	0.86	-	nuc	0	Nucleus. Phosphorylated form redistributes to discrete nuclear foci upon DNA damage (By similarity)				681
Q9USK4 UniProt NPD GO	CWF20_SCHPO	Cell cycle control protein cwf20	0.86	-	nuc	0	Nucleus (Probable)	spliceosome complex [TAS]			290
O89033 UniProt NPD GO	CDC6_MOUSE	Cell division control protein 6 homolog (CDC6-related protein) (p62(cdc6))	0.86	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). The protein is nuclear in G1 and cytoplasmic in ...	cytoplasm [IDA] spindle [IDA]			562
Q6AYK5 UniProt NPD GO	LYAR_RAT	Cell growth-regulating nucleolar protein	0.86	+	nuc	0	Nucleus; nucleolus (By similarity)				386
Q8R5G7 UniProt NPD GO	CEND3_MOUSE	Centaurin-delta 3 (Cnt-d3) (Arf-GAP, Rho-GAP, ankyrin repeat and pleckstrin homology domain-containi ...	0.86	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Cytoplasmic, and associated with F-actin-rich ...	cytoplasm [IDA] lamellipodium [IDA] ruffle [IDA]			1538

You are viewing entries 5951 to 6000 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.