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
Q9GK08 UniProt NPD GO	MSX2_CANFA	Homeobox protein MSX-2 (Hox-8)	0.48	+	nuc	0	Nucleus				267
P35548 UniProt NPD GO	MSX2_HUMAN	Homeobox protein MSX-2 (Hox-8)	0.48	+	nuc	0	Nucleus		604757		267
P34766 UniProt NPD GO	PAL1_CAEEL	Homeobox protein pal-1 (Homeobox protein ceh-3) (Posterior alae in males protein 1)	0.48	+	nuc	0	Nucleus (Probable)				208
P32475 UniProt NPD GO	YG3Z_YEAST	Hypothetical 13.7 kDa protein in ERG1-ATF2 intergenic region	0.48	-	exc	0					115
P39991 UniProt NPD GO	YEC5_YEAST	Hypothetical 136.1 kDa protein in VMA3-RIP1 intergenic region	0.48	-	mit	1	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] nucleus [IDA]			1188
P15607 UniProt NPD GO	YM06_PARTE	Hypothetical 20.7 kDa protein (ORF6)	0.48	+	mit	1					178
Q04659 UniProt NPD GO	YMT8_YEAST	Hypothetical 36.4 kDa protein in NUP116-FAR3 intergenic region	0.48	-	cyt	0		nucleus [IDA]			317
P53293 UniProt NPD GO	YG3W_YEAST	Hypothetical 44.3 kDa protein in CLC1-PDS2 intergenic region	0.48	+	end	5 *	Membrane; multi-pass membrane protein (Potential)				376
P47114 UniProt NPD GO	YJ24_YEAST	Hypothetical 57.5 kDa protein in RAD7-HIT1 intergenic region	0.48	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			497
P34284 UniProt NPD GO	YKK7_CAEEL	Hypothetical F-box/LRR-repeat protein C02F5.7	0.48	-	nuc	0					466
P93308 UniProt NPD GO	M530_ARATH	Hypothetical mitochondrial protein AtMg00530 (ORF109)	0.48	-	nuc	0	Mitochondrion (Potential)				109
P92542 UniProt NPD GO	M1100_ARATH	Hypothetical mitochondrial protein AtMg01100 (ORF105a)	0.48	-	mit	0	Mitochondrion (Potential)				105
Q751T1 UniProt NPD GO	YF43_ASHGO	Hypothetical protein AFR743C-A	0.48	-	nuc	0					101
Q4WPU9 UniProt NPD GO	YA530_ASPFU	Hypothetical protein Afu4g10530	0.48	-	nuc	0					371
Q10950 UniProt NPD GO	YMP6_CAEEL	Hypothetical protein B0361.6	0.48	-	nuc	0					378
Q11182 UniProt NPD GO	YPD2_CAEEL	Hypothetical protein C05D11.2	0.48	-	nuc	0					852
Q10108 UniProt NPD GO	YAQ9_SCHPO	Hypothetical protein C18G6.09c in chromosome I	0.48	-	nuc	0					312
P87117 UniProt NPD GO	YDKA_SCHPO	Hypothetical protein C20G8.10c in chromosome I	0.48	-	nuc	0					499
Q09281 UniProt NPD GO	YQIA_CAEEL	Hypothetical protein C45G9.10	0.48	-	mit	0					971
Q10257 UniProt NPD GO	YD29_SCHPO	Hypothetical protein C56F8.09 in chromosome I	0.48	+	cyt	0					318
O14219 UniProt NPD GO	YDTE_SCHPO	Hypothetical protein C6B12.14c in chromosome I	0.48	-	nuc	0					154
Q8STB5 UniProt NPD GO	Y111_ENCCU	Hypothetical protein ECU01_0110/ECU01_1500/ECU08_0040	0.48	-	cyt	0					592
Q8SV60 UniProt NPD GO	Y6G5_ENCCU	Hypothetical protein ECU06_1650	0.48	-	end	8 *					391
O17811 UniProt NPD GO	YSZI_CAEEL	Hypothetical protein F15A4.10	0.48	-	nuc	0					79
P83351 UniProt NPD GO	YMQ5_CAEEL	Hypothetical protein K02D10.5 on chromosome III	0.48	-	nuc	0					277
P34509 UniProt NPD GO	YMX1_CAEEL	Hypothetical protein K06H7.1	0.48	-	nuc	0					316
P13999 UniProt NPD GO	YIPP_KLULA	Hypothetical protein KLLA0E17732g	0.48	-	nuc	0					91
P82637 UniProt NPD GO	SCR18_ARATH	Hypothetical protein SCRL18 precursor	0.48	-	mit	1 *					97
Q22695 UniProt NPD GO	YOP3_CAEEL	Hypothetical protein T23F11.3 in chromosome III	0.48	-	nuc	0					356
P34587 UniProt NPD GO	YN53_CAEEL	Hypothetical protein ZC21.3	0.48	-	mit	0					321
Q03152 UniProt NPD GO	YMF19_BRANA	Hypothetical protein ymf19 (ORF158)	0.48	-	mit	1 *	Mitochondrion (Potential)				158
Q06564 UniProt NPD GO	YMF19_RAPSA	Hypothetical protein ymf19 (ORFB)	0.48	-	mit	1 *	Mitochondrion (Potential)				158
P01880 UniProt NPD GO	IGHD_HUMAN	Ig delta chain C region	0.48	-	nuc	0			147170	1ZVO	383
P06336 UniProt NPD GO	IGHE_MOUSE	Ig epsilon chain C region	0.48	-	nuc	0					421
Q8R035 UniProt NPD GO	ICT1_MOUSE	Immature colon carcinoma transcript 1 protein precursor	0.48	-	mit	0				1J26	206
Q14197 UniProt NPD GO	ICT1_HUMAN	Immature colon carcinoma transcript 1 protein precursor (Digestion substraction 1) (DS-1)	0.48	-	mit	0			603000		206
Q8NI35 UniProt NPD GO	INADL_HUMAN	InaD-like protein (Inadl protein) (hINADL) (Pals1-associated tight junction protein) (Protein associ ...	0.48	-	nuc	0	Localized in the paranodal region of myelinating Schwann cells (By similarity). Membrane-associated. ...		603199	2DB5	1801
Q6Q629 UniProt NPD GO	DPP10_RAT	Inactive dipeptidyl peptidase 10 (Dipeptidyl peptidase X) (Kv4 potassium channel auxiliary subunit)	0.48	-	gol	1 *	Membrane; single-pass type II membrane protein (By similarity)				796
O09107 UniProt NPD GO	INSL3_MOUSE	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.48	-	exc	0	Secreted protein				122
P01344 UniProt NPD GO	IGF2_HUMAN	Insulin-like growth factor II precursor (IGF-II) (Somatomedin A) [Contains: Insulin-like growth fact ...	0.48	-	exc	0	Secreted protein		147470	1IGL	180
P05013 UniProt NPD GO	IFNA6_HUMAN	Interferon alpha-6 precursor (Interferon alpha-K) (LeIF K) (Interferon alpha-54)	0.48	-	exc	0	Secreted protein		147566		189
Q9P0W0 UniProt NPD GO	IFNK_HUMAN	Interferon kappa precursor (IFN-kappa)	0.48	-	nuc	1 *	Secreted protein	extracellular region [IC]			207
P05001 UniProt NPD GO	IFNW1_HORSE	Interferon omega-1 precursor (Interferon alpha-II-1)	0.48	-	nuc	0	Secreted protein				195
Q90597 UniProt NPD GO	MX_CHICK	Interferon-induced GTP-binding protein Mx	0.48	-	mit	0	Cytoplasm				705
Q28267 UniProt NPD GO	IL12A_CANFA	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.48	-	exc	0	Secreted protein				222
Q28233 UniProt NPD GO	IL12A_CEREL	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.48	-	mit	0	Secreted protein				221
Q566E5 UniProt NPD GO	KDEL2_RAT	KDEL motif-containing protein 2 precursor	0.48	-	exc	0	Endoplasmic reticulum; Endoplasmic reticulum lumen (Potential)				508
Q8H0T9 UniProt NPD GO	KTNB1_ARATH	Katanin p80 WD40-containing subunit B1 homolog 1	0.48	-	nuc	0					837
Q15323 UniProt NPD GO	K1H1_HUMAN	Keratin, type I cuticular Ha1 (Hair keratin, type I Ha1)	0.48	-	nuc	0		intermediate filament [TAS]	601077		416
Q14525 UniProt NPD GO	K1HB_HUMAN	Keratin, type I cuticular Ha3-II (Hair keratin, type I Ha3-II)	0.48	-	nuc	0			602762		404

You are viewing entries 26301 to 26350 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.