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
P15622 UniProt NPD GO	ZN250_HUMAN	Zinc finger protein 250 (Zinc finger protein 647)	0.55	-	nuc	0	Nucleus (Probable)				560
Q8BZ89 UniProt NPD GO	Z322A_MOUSE	Zinc finger protein 322A	0.55	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				410
Q922H9 UniProt NPD GO	ZN330_MOUSE	Zinc finger protein 330 (Nucleolar cysteine-rich protein) (Nucleolar autoantigen 36)	0.55	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Predominantly expressed in nucleolus. I ...	chromosome, pericentric region [ISS] midbody [ISS] nucleolus [ISS]			316
Q5R741 UniProt NPD GO	ZN394_PONPY	Zinc finger protein 394	0.55	-	nuc	0	Nucleus (Potential)				574
Q9UPU6 UniProt NPD GO	ZN409_HUMAN	Zinc finger protein 409	0.55	-	nuc	0	Nucleus (Probable)				862
Q86V71 UniProt NPD GO	ZN429_HUMAN	Zinc finger protein 429	0.55	-	nuc	0	Nucleus (Potential)				588
Q9Y2A4 UniProt NPD GO	ZN443_HUMAN	Zinc finger protein 443 (Krueppel-type zinc finger protein ZK1)	0.55	-	nuc	0	Nucleus (Potential)				671
Q5R5S6 UniProt NPD GO	ZN540_PONPY	Zinc finger protein 540	0.55	-	nuc	0	Nucleus (Potential)				660
Q96NG5 UniProt NPD GO	ZN558_HUMAN	Zinc finger protein 558	0.55	-	nuc	0	Nucleus (Potential)				402
Q96NG8 UniProt NPD GO	ZN582_HUMAN	Zinc finger protein 582	0.55	-	nuc	0	Nucleus (Probable)				517
Q96LX8 UniProt NPD GO	ZN597_HUMAN	Zinc finger protein 597	0.55	-	nuc	0	Nucleus (Potential)				424
P51508 UniProt NPD GO	ZNF81_HUMAN	Zinc finger protein 81 (HFZ20)	0.55	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	314998		661
Q8RWD0 UniProt NPD GO	COL16_ARATH	Zinc finger protein CONSTANS-LIKE 16	0.55	+	nuc	0	Nucleus (Potential)				417
Q61467 UniProt NPD GO	ZIC4_MOUSE	Zinc finger protein ZIC 4 (Zinc finger protein of the cerebellum 4)	0.55	-	mit	0	Nucleus	nucleus [IDA]			341
P83912 UniProt NPD GO	DIST_TRIJE	Zinc metalloproteinase jerdonitin precursor (EC 3.4.24.-) [Contains: Disintegrin jerdonitin]	0.55	-	nuc	0	Secreted protein				484
Q80Y81 UniProt NPD GO	RNZ2_MOUSE	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.55	-	mit	0	Nucleus (Probable)				831
Q9GL72 UniProt NPD GO	RNZ2_PANTR	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.55	+	cyt	0	Nucleus (Probable)				826
Q498J7 UniProt NPD GO	MC6ZA_XENLA	Zygotic DNA replication licensing factor mcm6-A (Zygotic minichromosome maintenance protein 6-A) (zM ...	0.55	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	MCM complex [IPI]			823
Q9DBC7 UniProt NPD GO	KAP0_MOUSE	cAMP-dependent protein kinase type I-alpha regulatory subunit	0.55	-	cyt	0		cytoplasm [TAS]			380
Q59S63 UniProt NPD GO	PUS1_CANAL	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.55	-	nuc	0	Nucleus (By similarity)				450
P12615 UniProt NPD GO	SSG1_AVESA	12S seed storage globulin 1 precursor [Contains: 12S seed storage globulin 1 acidic chain; 12S seed ...	0.54	-	mit	0					518
Q7RZR2 UniProt NPD GO	TSC10_NEUCR	3-ketodihydrosphingosine reductase tsc-10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduc ...	0.54	-	end	0	Endoplasmic reticulum (By similarity)				969
Q26630 UniProt NPD GO	IDLC_STRPU	33 kDa inner dynein arm light chain, axonemal (p33)	0.54	-	nuc	0					260
P21772 UniProt NPD GO	RS26_NEUCR	40S ribosomal protein S26E (CRP5) (13.6 kDa ribosomal protein)	0.54	-	nuc	0					119
O96269 UniProt NPD GO	RS30_PLAF7	40S ribosomal protein S30	0.54	-	nuc	0					58
O15612 UniProt NPD GO	RS9_ENTHI	40S ribosomal protein S9	0.54	-	nuc	0					185
O57405 UniProt NPD GO	TYRP1_CHICK	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.54	-	nuc	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)				535
Q61224 UniProt NPD GO	5HT1D_MOUSE	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D)	0.54	-	end	7 *	Membrane; multi-pass membrane protein				374
P28565 UniProt NPD GO	5HT1D_RAT	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D)	0.54	-	end	7 *	Membrane; multi-pass membrane protein				374
Q27274 UniProt NPD GO	RO60_CAEEL	60 kDa SS-A/Ro ribonucleoprotein homolog	0.54	+	nuc	0	Cytoplasm (By similarity)				643
Q9US22 UniProt NPD GO	RL15B_SCHPO	60S ribosomal protein L15-B	0.54	-	nuc	0					201
Q5E973 UniProt NPD GO	RL18_BOVIN	60S ribosomal protein L18	0.54	-	nuc	0	Cytoplasm (By similarity)				187
Q07020 UniProt NPD GO	RL18_HUMAN	60S ribosomal protein L18	0.54	-	nuc	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS]	604179		187
P49667 UniProt NPD GO	RL21_PYUST	60S ribosomal protein L21 (Fragment)	0.54	+	nuc	0					155
P47914 UniProt NPD GO	RL29_HUMAN	60S ribosomal protein L29 (Cell surface heparin-binding protein HIP)	0.54	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	601832		158
Q4R5Q0 UniProt NPD GO	RL3_MACFA	60S ribosomal protein L3	0.54	-	mit	0					402
O18602 UniProt NPD GO	RL31_DROVI	60S ribosomal protein L31	0.54	-	nuc	0					128
Q9URX6 UniProt NPD GO	RL31_SCHPO	60S ribosomal protein L31	0.54	-	nuc	0					113
Q9NB34 UniProt NPD GO	RL34_AEDTR	60S ribosomal protein L34	0.54	-	mit	0					138
Q9LZ41 UniProt NPD GO	RL354_ARATH	60S ribosomal protein L35-4	0.54	-	nuc	0					123
P51425 UniProt NPD GO	RL39_MAIZE	60S ribosomal protein L39	0.54	-	nuc	0					51
P51426 UniProt NPD GO	RL39_ORYSA	60S ribosomal protein L39	0.54	-	nuc	0					51
P05767 UniProt NPD GO	RL39_SCHPO	60S ribosomal protein L39 (YL36)	0.54	-	mit	0					50
P51424 UniProt NPD GO	RL391_ARATH	60S ribosomal protein L39-1	0.54	-	nuc	0					51
P49625 UniProt NPD GO	RL51_ORYSA	60S ribosomal protein L5-1	0.54	-	nuc	0					304
P46938 UniProt NPD GO	YAP1_MOUSE	65 kDa Yes-associated protein (YAP65)	0.54	-	nuc	0		transcription factor complex [IGI]			472
O77797 UniProt NPD GO	AKAP3_BOVIN	A-kinase anchor protein 3 (Protein kinase A-anchoring protein 3) (PRKA3) (A-kinase anchor protein 11 ...	0.54	-	nuc	0	Localizes to the ribs of the fibrous sheath in the principal piece of the sperm tail (By similarity) ...				854
P34358 UniProt NPD GO	CED7_CAEEL	ABC transporter ced-7 (Cell death protein 7)	0.54	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS] plasma membrane [IDA]			1704
O14241 UniProt NPD GO	ARPC2_SCHPO	ARP2/3 complex 34 kDa subunit (p34-ARC)	0.54	-	cyt	0					317
Q09747 UniProt NPD GO	DBP5_SCHPO	ATP-dependent RNA helicase dbp5 (EC 3.6.1.-)	0.54	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				503

You are viewing entries 22301 to 22350 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.