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
P38346 UniProt NPD GO	YB9O_YEAST	Uncharacterized protein YBR270C	0.75	-	mit	0					545
P38966 UniProt NPD GO	YD089_YEAST	Uncharacterized protein YDR089W	0.75	-	nuc	3					869
P32900 UniProt NPD GO	YHU9_YEAST	Uncharacterized protein YHR149C	0.75	-	nuc	1		bud neck [IDA] bud tip [IDA]			734
P40492 UniProt NPD GO	YIJ7_YEAST	Uncharacterized protein YIL097W	0.75	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			516
Q04322 UniProt NPD GO	YM52_YEAST	Uncharacterized protein YMR192W	0.75	-	nuc	0		bud neck [IDA] bud tip [IDA] cytoplasm [IDA] Golgi-associated vesicle [IDA] incipient bud site [IDA] mitochondrion [IDA] plasma membrane [IDA]			720
Q12182 UniProt NPD GO	YO342_YEAST	Uncharacterized protein YOR342C	0.75	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			319
Q08816 UniProt NPD GO	YO352_YEAST	Uncharacterized protein YOR352W	0.75	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			343
Q02606 UniProt NPD GO	YP014_YEAST	Uncharacterized protein YPL014W	0.75	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			381
Q5KE13 UniProt NPD GO	BRO1_CRYNE	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.75	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				957
P09799 UniProt NPD GO	VCLA_GOSHI	Vicilin GC72-A precursor (Alpha-globulin A)	0.75	-	exc	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				605
Q9GMA3 UniProt NPD GO	VSX1_BOVIN	Visual system homeobox 1 (Transcription factor VSX1) (Retinal inner nuclear layer homeobox protein) ...	0.75	+	nuc	0	Nucleus (By similarity)				365
Q27309 UniProt NPD GO	VIT_BOMMO	Vitellogenin precursor [Contains: Vitellin light chain (VL); Vitellin light chain rare isoform; Vite ...	0.75	-	exc	0	Secreted protein				1782
O13046 UniProt NPD GO	WDHD1_XENLA	WD repeat and HMG-box DNA-binding protein 1 (Acidic nucleoplasmic DNA-binding protein 1) (And-1)	0.75	+	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Transiently cytoplasmic during mitosis				1127
Q9C0J8 UniProt NPD GO	WDR33_HUMAN	WD repeat protein 33 (WD repeat protein WDC146)	0.75	-	nuc	0	Nucleus	nucleus [IDA]			1336
P47817 UniProt NPD GO	WEE1A_XENLA	Wee1-like protein kinase (EC 2.7.10.2)	0.75	-	end	0	Nucleus (By similarity)				555
Q8SWF6 UniProt NPD GO	Z231_ENCCU	Zinc finger C2H2 protein ECU02_0310	0.75	-	nuc	0					104
Q64321 UniProt NPD GO	ZBT7B_MOUSE	Zinc finger and BTB domain-containing protein 7B (Zinc finger protein 67) (Zfp-67) (Zinc finger prot ...	0.75	+	nuc	0	Nucleus				544
P17026 UniProt NPD GO	ZNF22_HUMAN	Zinc finger protein 22 (Zinc finger protein KOX15) (Krox-26 protein)	0.75	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]	194529		224
Q9UK10 UniProt NPD GO	ZN225_HUMAN	Zinc finger protein 225	0.75	-	nuc	0	Nucleus (Probable)				706
Q5R5U3 UniProt NPD GO	ZN271_PONPY	Zinc finger protein 271	0.75	-	nuc	0	Nucleus (By similarity)				672
Q9HBE1 UniProt NPD GO	ZN278_HUMAN	Zinc finger protein 278 (POZ-, AT hook-, and zinc finger-containing protein) (Zinc finger sarcoma ge ...	0.75	+	nuc	0	Nucleus	nucleus [TAS]	605165		687
Q5JVG2 UniProt NPD GO	ZN484_HUMAN	Zinc finger protein 484	0.75	-	nuc	0	Nucleus (Probable)				852
Q7Z340 UniProt NPD GO	ZN551_HUMAN	Zinc finger protein 551 (Zinc finger protein KOX23)	0.75	-	nuc	0	Nucleus (Probable)				670
Q9NPA5 UniProt NPD GO	ZF64A_HUMAN	Zinc finger protein 64, isoforms 1 and 2 (Zinc finger protein 338)	0.75	-	nuc	0	Nucleus (Probable)			1X5W	681
Q99LH4 UniProt NPD GO	ZN672_MOUSE	Zinc finger protein 672	0.75	-	nuc	0	Nucleus (Probable)				468
Q642B2 UniProt NPD GO	ZN672_RAT	Zinc finger protein 672	0.75	-	nuc	0	Nucleus (Probable)				468
Q6ZN79 UniProt NPD GO	Z705A_HUMAN	Zinc finger protein 705A	0.75	-	nuc	0	Nucleus (Potential)				300
Q96C28 UniProt NPD GO	ZN707_HUMAN	Zinc finger protein 707	0.75	+	nuc	0	Nucleus (Potential)				369
Q3U288 UniProt NPD GO	ZN710_MOUSE	Zinc finger protein 710	0.75	-	nuc	0	Nucleus (Potential)				666
Q9Z1D8 UniProt NPD GO	ZFP95_MOUSE	Zinc finger protein 95 (Zfp-95)	0.75	-	nuc	0	Nucleus (Potential)				819
Q9C469 UniProt NPD GO	GRT1_SCHPO	Zinc finger protein grt1	0.75	-	mit	2	Nucleus				648
Q9Y493 UniProt NPD GO	ZAN_HUMAN	Zonadhesin precursor	0.75	+	nuc	1	Cell membrane; single-pass type I membrane protein. Exclusively on the apical region of the sperm he ...	apical plasma membrane [NAS] plasma membrane [NAS]	602372		2812
Q28983 UniProt NPD GO	ZAN_PIG	Zonadhesin precursor	0.75	+	cyt	1 *	Cell membrane; single-pass type I membrane protein. Exclusively on the apical region of the sperm he ...				2476
P54748 UniProt NPD GO	PDE4A_RAT	cAMP-specific 3',5'-cyclic phosphodiesterase 4A (EC 3.1.4.17) (DPDE2)	0.75	-	nuc	0				1LOI	844
Q6CQ07 UniProt NPD GO	PACC_KLULA	pH-response transcription factor pacC/RIM101	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				517
Q5B8X0 UniProt NPD GO	TRM10_EMENI	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				415
O94295 UniProt NPD GO	PUS2_SCHPO	tRNA pseudouridine synthase 2 (EC 5.4.99.-) (tRNA-uridine isomerase 2) (tRNA pseudouridylate synthas ...	0.75	-	nuc	0	Nucleus (By similarity)				451
P49199 UniProt NPD GO	RS8_ORYSA	40S ribosomal protein S8	0.74	+	nuc	0					220
P23326 UniProt NPD GO	RK35_SPIOL	50S ribosomal protein L35, chloroplast precursor (CL35)	0.74	-	mit	0	Plastid; chloroplast				159
Q9Z313 UniProt NPD GO	RL13_CRIGR	60S ribosomal protein L13	0.74	-	nuc	0					210
Q8X034 UniProt NPD GO	RL15_NEUCR	60S ribosomal protein L15	0.74	-	nuc	0					203
P53881 UniProt NPD GO	RM22_YEAST	60S ribosomal protein L22, mitochondrial precursor	0.74	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			309
Q6Y263 UniProt NPD GO	RL24_PAGMA	60S ribosomal protein L24	0.74	-	nuc	0					157
Q962T5 UniProt NPD GO	RL24_SPOFR	60S ribosomal protein L24	0.74	-	nuc	0					155
P04449 UniProt NPD GO	RL24A_YEAST	60S ribosomal protein L24-A (L30A) (RP29) (YL21)	0.74	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	155
Q4N756 UniProt NPD GO	RL35_THEPA	60S ribosomal protein L35	0.74	-	nuc	0					123
Q2VA69 UniProt NPD GO	RL36_THELE	60S ribosomal protein L35	0.74	-	nuc	0					123
Q5R9D2 UniProt NPD GO	RL36L_PONPY	60S ribosomal protein L36a-like	0.74	-	nuc	0	Cytoplasm (Probable)				105
P40909 UniProt NPD GO	RL40_CRYNE	60S ribosomal protein L40 (CEP52) (CEP53)	0.74	-	nuc	0					53
Q9NB33 UniProt NPD GO	RL44_AEDTR	60S ribosomal protein L44	0.74	-	nuc	0					103

You are viewing entries 11651 to 11700 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.