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
Q76FD7 UniProt NPD GO	H2B_DROSE	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
P59782 UniProt NPD GO	H2B_DROSI	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
Q76FF3 UniProt NPD GO	H2B_DROTE	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
Q8I1N0 UniProt NPD GO	H2B_DROYA	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
P0C1H5 UniProt NPD GO	H2B7_CHICK	Histone H2B 7 (H2B VII)	0.60	+	nuc	0	Nucleus				125
Q9PSW9 UniProt NPD GO	H2B8_CHICK	Histone H2B 8 (H2B VIII)	0.60	+	nuc	0	Nucleus				125
P10853 UniProt NPD GO	H2B1F_MOUSE	Histone H2B type 1-F/J/L (H2B 291A)	0.60	+	nuc	0	Nucleus				125
Q32L48 UniProt NPD GO	H2B1N_BOVIN	Histone H2B type 1-N	0.60	+	nuc	0	Nucleus				125
Q99877 UniProt NPD GO	H2B1N_HUMAN	Histone H2B type 1-N (H2B.d) (H2B/d)	0.60	+	nuc	0	Nucleus	nucleosome [NAS]	602801		125
Q64524 UniProt NPD GO	H2B2E_MOUSE	Histone H2B type 2-E (H2b 613)	0.60	+	nuc	0	Nucleus				125
P57053 UniProt NPD GO	H2BFS_HUMAN	Histone H2B type F-S (H2B.s) (H2B/s)	0.60	-	nuc	0	Nucleus				125
Q2UEX1 UniProt NPD GO	HAT1_ASPOR	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.60	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				511
Q8X225 UniProt NPD GO	DIM5_NEUCR	Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.60	-	nuc	0	Nucleus (By similarity)			1PEG	318
P09635 UniProt NPD GO	HXA4_RAT	Homeobox protein Hox-A4 (R2) (Fragment)	0.60	+	nuc	0	Nucleus				67
P79937 UniProt NPD GO	MEIS1_XENLA	Homeobox protein Meis1 (XMeis1)	0.60	-	nuc	0	Nucleus				390
Q63410 UniProt NPD GO	OTX1_RAT	Homeobox protein OTX1	0.60	-	nuc	0	Nucleus (Probable)				355
Q8MIE6 UniProt NPD GO	TF2LX_HYLLA	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.60	-	nuc	0	Nucleus (By similarity)				241
P56662 UniProt NPD GO	KNOX4_MAIZE	Homeobox protein knotted-1-like 4 (Fragment)	0.60	-	nuc	0	Nucleus (Probable)				85
P46604 UniProt NPD GO	HAT22_ARATH	Homeobox-leucine zipper protein HAT22 (HD-ZIP protein 22)	0.60	+	nuc	0	Nucleus (Potential)				278
Q5RF31 UniProt NPD GO	F10A1_PONPY	Hsc70-interacting protein (Hip) (Protein ST13 homolog) (Protein FAM10A1)	0.60	-	nuc	0	Cytoplasm (By similarity)				369
P50502 UniProt NPD GO	F10A1_HUMAN	Hsc70-interacting protein (Hip) (Suppression of tumorigenicity protein 13) (Putative tumor suppresso ...	0.60	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]	606796		369
P06101 UniProt NPD GO	CDC37_YEAST	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (Cell division control p ...	0.60	-	nuc	0	Cytoplasm	cytoplasm [IDA]			506
P53222 UniProt NPD GO	YG1O_YEAST	Hypothetical 12.9 kDa protein in RPL26B-ACB1 intergenic region	0.60	-	nuc	0					116
P53892 UniProt NPD GO	YNQ4_YEAST	Hypothetical 40.0 kDa protein in SKO1-RPL44A intergenic region	0.60	-	nuc	0		nucleus [NAS]			351
Q03652 UniProt NPD GO	YM61_YEAST	Hypothetical 55.3 kDa protein in RAR1-SCJ1 intergenic region	0.60	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			475
P53140 UniProt NPD GO	YGK7_YEAST	Hypothetical 74.6 kDa protein in TAF60-MLC1 intergenic region	0.60	-	mit	0		mitochondrion [IDA]			646
P47046 UniProt NPD GO	YJF1_YEAST	Hypothetical 91.3 kDa protein in TDH1-MTR4 intergenic region	0.60	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)	bud tip [IDA]			822
O94394 UniProt NPD GO	YQF1_SCHPO	Hypothetical WD repeat protein C126.01c in chromosome III	0.60	-	nuc	0					369
Q19124 UniProt NPD GO	YDEM_CAEEL	Hypothetical WD repeat protein F02E8.5	0.60	-	nuc	1 *					578
P05469 UniProt NPD GO	YKP3_KLULA	Hypothetical killer plasmid pGKl-2 protein 3	0.60	-	nuc	0					594
Q94CC0 UniProt NPD GO	Y5994_ARATH	Hypothetical protein At5g49945 precursor	0.60	-	mit	0	Membrane; single-pass membrane protein (Potential)				480
P42001 UniProt NPD GO	YKC0_CAEEL	Hypothetical protein B0280.10	0.60	-	cyt	0					345
Q9UTR0 UniProt NPD GO	YL33_SCHPO	Hypothetical protein C1071.03c in chromosome I	0.60	-	nuc	1 *					338
Q09264 UniProt NPD GO	YQD4_CAEEL	Hypothetical protein C32D5.4	0.60	-	nuc	0					369
Q8STJ4 UniProt NPD GO	Y603_ENCCU	Hypothetical protein ECU06_0030/ECU06_1690/ECU11_0020	0.60	-	mit	2					248
Q93591 UniProt NPD GO	YUBO_CAEEL	Hypothetical protein F26A3.7	0.60	-	nuc	0					297
Q03606 UniProt NPD GO	YN02_CAEEL	Hypothetical protein T23G5.2 in chromosome III	0.60	-	nuc	0					719
P38244 UniProt NPD GO	YBS4_YEAST	Hypothetical protein YBR074W	0.60	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				976
P38462 UniProt NPD GO	YMF19_MARPO	Hypothetical protein ymf19 (ORF 172)	0.60	-	nuc	1 *	Mitochondrion (Potential)				172
P78318 UniProt NPD GO	IGBP1_HUMAN	Immunoglobulin-binding protein 1 (CD79a-binding protein 1) (B cell signal transduction molecule alph ...	0.60	-	nuc	0	Cytoplasm (Potential)	cytoplasm [NAS]	300472		339
Q27295 UniProt NPD GO	EAT5_CAEEL	Innexin eat-5	0.60	+	end	3 *	Membrane; multi-pass membrane protein				423
Q96DU7 UniProt NPD GO	IP3KC_HUMAN	Inositol-trisphosphate 3-kinase C (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase C) (InsP 3-k ...	0.60	-	nuc	0	Nucleus. Cytoplasm. Shuttles actively between nucleus and cytoplasm with both nuclear import and nuc ...		606476	2A98	683
Q6INW9 UniProt NPD GO	IGF2B_XENLA	Insulin-like growth factor II-B precursor (IGF-II-B) (Insulin-like growth factor 2-B)	0.60	-	nuc	0	Secreted protein (By similarity)				217
P47878 UniProt NPD GO	IBP3_MOUSE	Insulin-like growth factor-binding protein 3 precursor (IGFBP-3) (IBP-3) (IGF-binding protein 3)	0.60	-	exc	0	Secreted protein	extracellular region [ISS]			291
P05014 UniProt NPD GO	IFNA4_HUMAN	Interferon alpha-4 precursor (Interferon alpha-4B) (Interferon alpha-M1) (Interferon alpha-76)	0.60	-	mit	0	Secreted protein		147564		189
P49876 UniProt NPD GO	IFNAF_BOVIN	Interferon alpha-F precursor	0.60	-	mit	1 *	Secreted protein				189
P01580 UniProt NPD GO	IFNG_MOUSE	Interferon gamma precursor (IFN-gamma)	0.60	-	exc	0	Secreted protein	extracellular space [IDA]			155
Q3SZP0 UniProt NPD GO	IRF1_BOVIN	Interferon regulatory factor 1 (IRF-1)	0.60	+	nuc	0	Nucleus (By similarity)				322
P15261 UniProt NPD GO	INGR1_MOUSE	Interferon-gamma receptor alpha chain precursor (IFN-gamma-R1) (CD119 antigen)	0.60	-	exc	1	Membrane; single-pass type I membrane protein				477
Q12894 UniProt NPD GO	IFRD2_HUMAN	Interferon-related developmental regulator 2 (SKMC15 protein)	0.60	-	mit	0			602725		442

You are viewing entries 19051 to 19100 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.