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
Q6DFC6 UniProt NPD GO	WDR75_XENLA	WD repeat protein 75	0.63	-	nuc	0	Nucleus; nucleolus (By similarity)				832
Q6X7J4 UniProt NPD GO	WOX9_ARATH	WUSCHEL-related homeobox 9	0.63	-	nuc	0	Nucleus (By similarity)				378
Q61048 UniProt NPD GO	WBP4_MOUSE	WW domain-binding protein 4 (WBP-4) (Formin-binding protein 21)	0.63	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle	spliceosome complex [IDA]			376
Q803A8 UniProt NPD GO	WWOX_BRARE	WW domain-containing oxidoreductase (EC 1.1.1.-)	0.63	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				412
Q5DX34 UniProt NPD GO	RPGRH_CAEEL	X-linked retinitis pigmentosa GTPase regulator homolog (Gut granule loss protein 4)	0.63	-	nuc	0					1392
Q9Y2T7 UniProt NPD GO	YBOX2_HUMAN	Y-box-binding protein 2 (Germ cell-specific Y-box-binding protein) (Contrin) (MSY2 homolog)	0.63	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [TAS] nucleus [TAS]			364
Q5R9F0 UniProt NPD GO	ZNF14_PONPY	Zinc finger protein 14	0.63	-	nuc	0	Nucleus (Probable)				642
O14628 UniProt NPD GO	ZN195_HUMAN	Zinc finger protein 195	0.63	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	602187		629
O14771 UniProt NPD GO	ZN213_HUMAN	Zinc finger protein 213 (Putative transcription factor CR53)	0.63	-	nuc	0	Nucleus (Potential)		608387		459
Q9R0B7 UniProt NPD GO	ZN346_MOUSE	Zinc finger protein 346 (Just another zinc finger protein)	0.63	-	nuc	0	Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). Nuclear at steady state, primarily in ...	nucleolus [IDA]			294
Q8IYI8 UniProt NPD GO	ZN440_HUMAN	Zinc finger protein 440	0.63	-	nuc	0	Nucleus (Potential)				595
Q8N720 UniProt NPD GO	ZN655_HUMAN	Zinc finger protein 655 (Vav-interacting Krueppel-like protein)	0.63	-	nuc	0	Nucleus (Probable)				491
Q9LUA9 UniProt NPD GO	COL10_ARATH	Zinc finger protein CONSTANS-LIKE 10	0.63	-	nuc	0	Nucleus (Potential)				373
P32432 UniProt NPD GO	SFP1_YEAST	Zinc finger protein SFP1	0.63	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			683
P38621 UniProt NPD GO	ZN12_MICSA	Zinc finger protein ZFMSA12A	0.63	-	nuc	0	Nucleus (Probable)				415
P17029 UniProt NPD GO	ZKSC1_HUMAN	Zinc finger with KRAB and SCAN domain-containing protein 1 (Zinc finger protein 36) (Zinc finger pro ...	0.63	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	601260		563
P18619 UniProt NPD GO	DISF_TRIFL	Zinc metalloproteinase flavoridin precursor (EC 3.4.24.-) [Contains: Disintegrin flavoridin]	0.63	+	nuc	0	Secreted protein			1FVL	483
Q20191 UniProt NPD GO	NAS13_CAEEL	Zinc metalloproteinase nas-13 precursor (EC 3.4.24.21) (Nematode astacin 13)	0.63	-	mit	0	Secreted protein (Potential)				527
Q9W747 UniProt NPD GO	DRL_BRARE	Zinc-finger protein draculin	0.63	-	nuc	0					411
Q9BS86 UniProt NPD GO	ZPBP1_HUMAN	Zona pellucida-binding protein 1 precursor (Sp38)	0.63	-	mit	1 *	Secreted protein (Potential)		608498		351
O54735 UniProt NPD GO	PDE5A_RAT	cGMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) (CGB-PDE) (cGMP-binding cGMP-specific pho ...	0.63	-	cyt	0					833
O60942 UniProt NPD GO	MCE1_HUMAN	mRNA capping enzyme (HCE) (HCAP1) [Includes: Polynucleotide 5'-triphosphatase (EC 3.1.3.33) (mRNA 5' ...	0.63	+	nuc	0	Nucleus (By similarity)	nucleus [TAS]	603512	2C46	597
Q9P904 UniProt NPD GO	PALH_EMENI	pH-response regulator protein palH/RIM21	0.63	+	end	4	Cell membrane; multi-pass membrane protein				760
P33753 UniProt NPD GO	TRM2_YEAST	tRNA (uracil-5-)-methyltransferase (EC 2.1.1.35) (tRNA(M-5-U54)-methyltransferase) (Transfer RNA met ...	0.63	-	nuc	0					639
P19594 UniProt NPD GO	2SS_SOYBN	2S albumin precursor (GM2S-1) [Contains: 2S albumin small chain (Aspartic acid-rich peptide); 2S alb ...	0.62	-	exc	0					158
Q8SRY0 UniProt NPD GO	RS6_ENCCU	40S ribosomal protein S6	0.62	+	nuc	0					203
Q4UIF8 UniProt NPD GO	RL35_THEAN	60S ribosomal protein L35	0.62	-	nuc	0					142
Q3T051 UniProt NPD GO	RL39_BOVIN	60S ribosomal protein L39	0.62	-	mit	0					50
Q6BHV8 UniProt NPD GO	RL39_DEBHA	60S ribosomal protein L39	0.62	-	mit	0					51
P62891 UniProt NPD GO	RL39_HUMAN	60S ribosomal protein L39	0.62	-	mit	0			601904		50
Q90YS9 UniProt NPD GO	RL39_ICTPU	60S ribosomal protein L39	0.62	-	mit	0					51
P62892 UniProt NPD GO	RL39_MOUSE	60S ribosomal protein L39	0.62	-	mit	0					50
Q6F482 UniProt NPD GO	RL39_PLUXY	60S ribosomal protein L39	0.62	-	nuc	0					51
P62893 UniProt NPD GO	RL39_RAT	60S ribosomal protein L39	0.62	-	mit	0					50
Q962S4 UniProt NPD GO	RL39_SPOFR	60S ribosomal protein L39	0.62	-	nuc	0					51
Q58DW0 UniProt NPD GO	RL4_BOVIN	60S ribosomal protein L4	0.62	+	nuc	0					421
P14695 UniProt NPD GO	RL40_CHLRE	60S ribosomal protein L40 (CEP52)	0.62	-	nuc	0					52
Q13444 UniProt NPD GO	ADA15_HUMAN	ADAM 15 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 15) (Metalloproteinase-l ...	0.62	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	605548		814
Q63180 UniProt NPD GO	ADAM7_RAT	ADAM 7 precursor (A disintegrin and metalloproteinase domain 7) (Epididymal apical protein I) (EAP I ...	0.62	-	nuc	1	Membrane; single-pass type I membrane protein				789
Q96FJ0 UniProt NPD GO	STALP_HUMAN	AMSH-like protease (EC 3.1.2.15) (AMSH-LP) (STAM-binding protein-like 1)	0.62	-	nuc	0					436
Q5R558 UniProt NPD GO	STALP_PONPY	AMSH-like protease (EC 3.1.2.15) (AMSH-LP) (STAM-binding protein-like 1)	0.62	-	nuc	0					436
Q80V94 UniProt NPD GO	AP4E1_MOUSE	AP-4 complex subunit epsilon-1 (Adapter-related protein complex 4 epsilon-1 subunit) (Epsilon subuni ...	0.62	-	cyt	0	Golgi apparatus; trans-Golgi network (By similarity). Associated with the trans-Golgi network. Found ...	Golgi trans face [TAS]			1122
Q5RF63 UniProt NPD GO	RECQ1_PONPY	ATP-dependent DNA helicase Q1 (EC 3.6.1.-) (DNA-dependent ATPase Q1)	0.62	+	cyt	0	Nucleus (By similarity)				649
Q757I6 UniProt NPD GO	MAK5_ASHGO	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.62	-	nuc	0	Nucleus; nucleolus (By similarity)				752
O01836 UniProt NPD GO	GLH3_CAEEL	ATP-dependent RNA helicase glh-3 (EC 3.6.1.-) (Germline helicase 3)	0.62	-	nuc	0		P granule [IDA]			720
P38712 UniProt NPD GO	RRP3_YEAST	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-) (Ribosomal RNA-processing protein RRP3)	0.62	-	nuc	0	Nucleus (Probable)	nucleolus [TAS]			501
Q2UNB7 UniProt NPD GO	RRP3_ASPOR	ATP-dependent rRNA helicase rrp3 (EC 3.6.1.-)	0.62	-	nuc	0	Nucleus (Probable)				472
P06518 UniProt NPD GO	AGN1_APLCA	Abdominal ganglion neuropeptide L11 precursor	0.62	-	nuc	1 *	Secreted protein				151
P54246 UniProt NPD GO	ACR5_CAEEL	Acetylcholine receptor subunit alpha-type acr-5 precursor	0.62	-	end	3	Membrane; multi-pass membrane protein				548
O94929 UniProt NPD GO	ABLM3_HUMAN	Actin-binding LIM protein 3 (Actin-binding LIM protein family member 3) (abLIM-3)	0.62	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]		1UJS	683

You are viewing entries 17751 to 17800 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.