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
Q58DT1 UniProt NPD GO	RL7_BOVIN	60S ribosomal protein L7	0.67	+	nuc	0					248
Q28628 UniProt NPD GO	AKAP9_RABIT	A-kinase anchor protein 9 (Protein kinase A-anchoring protein 9) (PRKA9) (A-kinase anchor protein 12 ...	0.67	-	nuc	0					1087
P38817 UniProt NPD GO	GGA2_YEAST	ADP-ribosylation factor-binding protein GGA2 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.67	-	nuc	0		Golgi trans face [IDA]			585
P27351 UniProt NPD GO	AP2B_YEAST	AP-2 complex subunit beta (Beta-adaptin) (Clathrin assembly protein large beta chain) (Clathrin asse ...	0.67	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				700
Q5KHB7 UniProt NPD GO	DBP3_CRYNE	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				605
Q4IJH1 UniProt NPD GO	DBP3_GIBZE	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				581
Q6CEB8 UniProt NPD GO	DRS1_YARLI	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				753
Q4X0C2 UniProt NPD GO	DBP9_ASPFU	ATP-dependent RNA helicase dbp9 (EC 3.6.1.-)	0.67	-	mit	0	Nucleus; nucleolus (By similarity)				649
Q7S2N9 UniProt NPD GO	HAS1_NEUCR	ATP-dependent RNA helicase has-1 (EC 3.6.1.-)	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				578
P19109 UniProt NPD GO	RM62_DROME	ATP-dependent RNA helicase p62 (EC 3.6.1.-)	0.67	+	nuc	0	Nucleus (Potential)	nucleus [IC]			719
Q9QZM5 UniProt NPD GO	ABI1_RAT	Abl interactor 1 (Abelson interactor 1) (Abi-1) (Eps8 SH3 domain-binding protein) (Eps8-binding prot ...	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized to protruding lamellipodia and filopod ...				475
Q8CBW3 UniProt NPD GO	ABI1_MOUSE	Abl interactor 1 (Abelson interactor 1) (Abi-1) (Spectrin SH3 domain-binding protein 1) (Eps8 SH3 do ...	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized to protruding lamellipodia and filopod ...	lamellipodium [IDA]			480
Q6FJV8 UniProt NPD GO	ARP4_CANGA	Actin-like protein ARP4	0.67	-	nuc	0	Nucleus (By similarity)				493
Q63396 UniProt NPD GO	TCP4_RAT	Activated RNA polymerase II transcriptional coactivator p15 precursor (SUB1 homolog) (Positive cofac ...	0.67	+	nuc	0	Nucleus				126
Q4KLM5 UniProt NPD GO	ABT1_RAT	Activator of basal transcription 1	0.67	-	cyt	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity)				268
Q12979 UniProt NPD GO	ABR_HUMAN	Active breakpoint cluster region-related protein	0.67	-	cyt	0			600365		859
Q01513 UniProt NPD GO	CYAA_PODAN	Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.67	-	nuc	0					2145
Q38837 UniProt NPD GO	AGL13_ARATH	Agamous-like MADS-box protein AGL13	0.67	-	nuc	0	Nucleus (By similarity)				244
Q1XGV5 UniProt NPD GO	ASIP_GORGO	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.67	-	nuc	0	Secreted protein (By similarity)				132
Q1XGV6 UniProt NPD GO	ASIP_PANPA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.67	-	nuc	0	Secreted protein (By similarity)				132
Q1XGV7 UniProt NPD GO	ASIP_PANTR	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.67	-	nuc	0	Secreted protein (By similarity)				132
P12814 UniProt NPD GO	ACTN1_HUMAN	Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin-1) (F-actin cross lin ...	0.67	-	nuc	0	Cytoplasm. Colocalizes with MYOZ2 and PPP3CA at the Z-line of heart and skeletal muscle	actin cytoskeleton [TAS]	102575		892
P57780 UniProt NPD GO	ACTN4_MOUSE	Alpha-actinin-4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein)	0.67	-	cyt	0		cortical cytoskeleton [IDA] cytoplasm [IDA]			912
Q5RCS6 UniProt NPD GO	ACTN4_PONPY	Alpha-actinin-4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein)	0.67	-	nuc	0					911
O08838 UniProt NPD GO	AMPH_RAT	Amphiphysin	0.67	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein; cytoplasmic side (By simil ...				683
Q7Z5R6 UniProt NPD GO	AB1IP_HUMAN	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1-interacting p ...	0.67	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Colocalizes with ENA/VASP proteins at la ...		609036		666
Q3V0J1 UniProt NPD GO	AL2S4_MOUSE	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 4 protein homolog	0.67	+	nuc	4	Membrane; multi-pass membrane protein (Potential)				427
P53886 UniProt NPD GO	APC1_YEAST	Anaphase-promoting complex subunit 1	0.67	-	nuc	0	Nucleus. Cytoplasm. And spindle pole	anaphase-promoting complex [TAS]			1748
Q9URV2 UniProt NPD GO	APC1_SCHPO	Anaphase-promoting complex subunit 1 (20S cyclosome/APC complex protein apc1) (Cell untimely torn pr ...	0.67	-	end	0		anaphase-promoting complex [IDA]			1458
Q12107 UniProt NPD GO	APC9_YEAST	Anaphase-promoting complex subunit 9	0.67	-	nuc	0	Cytoplasm. Nucleus	anaphase-promoting complex [TAS]			265
Q6P9J5 UniProt NPD GO	ANR38_MOUSE	Ankyrin repeat domain-containing protein 38	0.67	-	nuc	0					1016
Q9ULJ7 UniProt NPD GO	ANR50_HUMAN	Ankyrin repeat domain-containing protein 50	0.67	-	nuc	0					1375
P61802 UniProt NPD GO	APTX_CIOIN	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.67	-	nuc	0	Nucleus (Probable)				380
Q9NWT8 UniProt NPD GO	AKIP_HUMAN	Aurora kinase A-interacting protein (AURKA-interacting protein)	0.67	-	mit	0	Nucleus	nucleus [IDA]	609183		199
Q4WHN5 UniProt NPD GO	ATG13_ASPFU	Autophagy-related protein 13	0.67	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				958
Q5BBK4 UniProt NPD GO	ATG13_EMENI	Autophagy-related protein 13	0.67	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				974
Q06628 UniProt NPD GO	ATG13_YEAST	Autophagy-related protein 13	0.67	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	extrinsic to membrane [IDA]			738
Q75BE5 UniProt NPD GO	ATG14_ASHGO	Autophagy-related protein 14	0.67	-	mit	0	Membrane; peripheral membrane protein (By similarity)				308
O42651 UniProt NPD GO	ATG17_SCHPO	Autophagy-related protein 17	0.67	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				481
Q6CQ43 UniProt NPD GO	ATG2_KLULA	Autophagy-related protein 2	0.67	-	nuc	0	Perivacuolar compartment (By similarity)				1502
Q6CWA7 UniProt NPD GO	ATG23_KLULA	Autophagy-related protein 23	0.67	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				426
Q94JM3 UniProt NPD GO	ARFB_ARATH	Auxin response factor 2 (ARF1-binding protein) (ARF1-BP)	0.67	-	nuc	0	Nucleus				859
P21855 UniProt NPD GO	CD72_MOUSE	B-cell differentiation antigen CD72 (Lyb-2) (Antigen Ly-32)	0.67	-	nuc	1	Membrane; single-pass type II membrane protein				354
Q99933 UniProt NPD GO	BAG1_HUMAN	BAG family molecular chaperone regulator 1 (BCL-2-binding athanogene-1) (BAG-1) (Glucocorticoid rece ...	0.67	-	nuc	0		cytoplasm [TAS]	601497	1WXV	274
Q8CI32 UniProt NPD GO	BAG5_MOUSE	BAG family molecular chaperone regulator 5 (BCL2-associated athanogene 5) (BAG-5)	0.67	-	cyt	0				1UGO	447
P25307 UniProt NPD GO	BLT4_HORVU	BLT4 protein precursor	0.67	-	mit	0					130
Q96SI1 UniProt NPD GO	KCD15_HUMAN	BTB/POZ domain-containing protein KCTD15	0.67	-	nuc	0					283
Q9QUK4 UniProt NPD GO	BIR1B_MOUSE	Baculoviral IAP repeat-containing protein 1b (Neuronal apoptosis inhibitory protein 2)	0.67	-	nuc	0					1447
Q9H329 UniProt NPD GO	E41LB_HUMAN	Band 4.1-like protein 4B (Protein EHM2) (FERM-containing protein CG1)	0.67	-	nuc	0		cytoskeleton [TAS]			913
O62703 UniProt NPD GO	CTBL1_BOVIN	Beta-catenin-like protein 1 (Nuclear-associated protein) (NAP) (p14)	0.67	-	cyt	0	Nucleus (By similarity)				563

You are viewing entries 15101 to 15150 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.