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
Q80Z36 UniProt NPD GO	ZHX3_RAT	Zinc finger and homeodomain protein 3 (Fragment)	0.44	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			522
Q2KI58 UniProt NPD GO	ZN181_BOVIN	Zinc finger protein 181	0.44	-	nuc	0	Nucleus (Probable)				570
Q5REF1 UniProt NPD GO	ZN181_PONPY	Zinc finger protein 181	0.44	-	nuc	0	Nucleus (Probable)				615
P17031 UniProt NPD GO	ZNF26_HUMAN	Zinc finger protein 26 (Zinc finger protein KOX20)	0.44	-	nuc	0	Nucleus (Potential)		194537		199
Q62513 UniProt NPD GO	ZF260_MOUSE	Zinc finger protein 260 (Zfp-260)	0.44	-	nuc	0	Nucleus (By similarity)				407
P17041 UniProt NPD GO	ZNF32_HUMAN	Zinc finger protein 32 (Zinc finger protein KOX30) (C2H2-546)	0.44	-	nuc	0	Nucleus (Potential)		194539		273
P13682 UniProt NPD GO	ZNF35_HUMAN	Zinc finger protein 35 (Zinc finger protein HF.10)	0.44	-	nuc	0	Nucleus (Potential)		194533		519
P17032 UniProt NPD GO	ZN37A_HUMAN	Zinc finger protein 37A (Zinc finger protein KOX21)	0.44	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			561
Q8BKX7 UniProt NPD GO	ZN410_MOUSE	Zinc finger protein 410 (Zinc finger protein APA-1) (Another partner for ARF 1)	0.44	-	nuc	0	Nucleus (Probable)				478
Q8N8E2 UniProt NPD GO	ZN513_HUMAN	Zinc finger protein 513	0.44	-	nuc	0	Nucleus (Probable)				479
Q8TBZ8 UniProt NPD GO	ZN564_HUMAN	Zinc finger protein 564	0.44	-	nuc	0	Nucleus (Probable)				553
Q8CJ78 UniProt NPD GO	ZN628_MOUSE	Zinc finger protein 628 (Zinc finger protein expressed in embryonal cells and certain adult organs)	0.44	-	nuc	0	Nucleus	nucleus [IDA]			1031
Q9FHH8 UniProt NPD GO	COL5_ARATH	Zinc finger protein CONSTANS-LIKE 5	0.44	-	nuc	0	Nucleus (Potential)				355
O43623 UniProt NPD GO	SLUG_HUMAN	Zinc finger protein SLUG (Neural crest transcription factor Slug) (Snail homolog 2)	0.44	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	608890		268
Q6Q2W4 UniProt NPD GO	ZPBP1_CHICK	Zona pellucida-binding protein 1 (Fragment)	0.44	-	exc	0	Secreted protein (Potential)				320
Q15942 UniProt NPD GO	ZYX_HUMAN	Zyxin (Zyxin-2)	0.44	-	nuc	0	Cytoplasm. Cytoskeleton. Associates with the actin cytoskeleton near the adhesion plaques	cell-cell adherens junction [IDA] integral to plasma membrane [TAS] plasma membrane [TAS]	602002		572
Q8SR66 UniProt NPD GO	MCES_ENCCU	mRNA cap guanine-N7 methyltransferase (mRNA (guanine-N(7)-)-methyltransferase) (EC 2.1.1.56)	0.44	-	nuc	0				1Z3C	298
Q5EA99 UniProt NPD GO	PK1IP_BOVIN	p21-activated protein kinase-interacting protein 1 (PAK1-interacting protein 1)	0.44	+	cyt	0	Nucleus; nucleolus (By similarity)				392
Q9UVF6 UniProt NPD GO	PALH_YARLI	pH-response regulator protein palH/RIM21	0.44	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				632
P51383 UniProt NPD GO	TILS_PORPU	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.44	-	cyt	0	Plastid; chloroplast				327
Q3KRC5 UniProt NPD GO	DUS3L_RAT	tRNA-dihydrouridine synthase 3-like (EC 1.-.-.-)	0.44	-	cyt	0					640
O23880 UniProt NPD GO	13S2_FAGES	13S globulin seed storage protein 2 precursor (Legumin-like protein 2) [Contains: 13S globulin seed ...	0.43	-	mit	0					504
P16180 UniProt NPD GO	RR17_ARATH	30S ribosomal protein S17, chloroplast precursor (CS17)	0.43	-	mit	0	Plastid; chloroplast (Probable)				149
Q5ZI69 UniProt NPD GO	RM37_CHICK	39S ribosomal protein L37, mitochondrial precursor (L37mt) (MRP-L37)	0.43	-	mit	0	Mitochondrion (By similarity)				429
Q9BRJ2 UniProt NPD GO	RM45_HUMAN	39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45)	0.43	-	mit	0	Mitochondrion	mitochondrion [NAS]			306
Q9W237 UniProt NPD GO	RS16_DROME	40S ribosomal protein S16	0.43	-	cyt	0					148
Q9P7J6 UniProt NPD GO	RS17B_SCHPO	40S ribosomal protein S17-B	0.43	-	nuc	0					132
P27085 UniProt NPD GO	RS26_OCTVU	40S ribosomal protein S26	0.43	-	nuc	0					127
P37164 UniProt NPD GO	RS27A_CAEBR	40S ribosomal protein S27a	0.43	+	nuc	0					93
Q20228 UniProt NPD GO	RS9_CAEEL	40S ribosomal protein S9	0.43	-	mit	0					189
P16118 UniProt NPD GO	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6PF-2-K/Fru-2,6-P2ASE liver isozyme) [Include ...	0.43	-	cyt	0		6-phosphofructo-2-kinase/fructose-2,6-bipho... [IDA]	311790	1K6M	471
Q9JJH5 UniProt NPD GO	F262_RAT	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6PF-2-K/Fru-2,6-P2ASE heart-type isozyme) (PF ...	0.43	-	nuc	0					557
Q16875 UniProt NPD GO	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6PF-2-K/Fru-2,6-P2ASE brain/placenta-type iso ...	0.43	-	nuc	0			605319	2AXN	520
Q876B2 UniProt NPD GO	RL13_SACEX	60S ribosomal protein L13	0.43	-	nuc	0					199
Q91487 UniProt NPD GO	RL13A_SALTR	60S ribosomal protein L13a (Transplantation antigen P198 homolog) (Fragment)	0.43	+	cyt	0					189
P79324 UniProt NPD GO	RL15_PIG	60S ribosomal protein L15 (Fragment)	0.43	-	mit	0					153
P46289 UniProt NPD GO	RL15_BRANA	60S ribosomal protein L15 (RL10) (Fragment)	0.43	-	nuc	0					88
Q90YV0 UniProt NPD GO	RL18_ICTPU	60S ribosomal protein L18	0.43	-	nuc	0	Cytoplasm				187
P41960 UniProt NPD GO	RL26_BRUPA	60S ribosomal protein L26 (Fragment)	0.43	-	nuc	0					60
Q58DW3 UniProt NPD GO	RL29_BOVIN	60S ribosomal protein L29	0.43	-	nuc	0					151
Q759R7 UniProt NPD GO	RL3_ASHGO	60S ribosomal protein L3	0.43	+	mit	0	Cytoplasm (By similarity)				388
Q8SQI3 UniProt NPD GO	RL3_ENCCU	60S ribosomal protein L3	0.43	-	mit	0	Cytoplasm				383
P36516 UniProt NPD GO	RM03_YEAST	60S ribosomal protein L3, mitochondrial precursor (YmL3)	0.43	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			390
Q9HFR7 UniProt NPD GO	RL36_TRIHM	60S ribosomal protein L36 (TRP36)	0.43	-	mit	0					105
O59870 UniProt NPD GO	RL44_PHARH	60S ribosomal protein L44 (60S ribosomal protein L41)	0.43	+	nuc	0					105
P26321 UniProt NPD GO	RL5_YEAST	60S ribosomal protein L5 (L1) (YL3) (Ribosomal 5S RNA-binding protein)	0.43	-	mit	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	296
P49227 UniProt NPD GO	RL52_ARATH	60S ribosomal protein L5-2	0.43	-	mit	0					301
Q6C603 UniProt NPD GO	RL7_YARLI	60S ribosomal protein L7	0.43	+	cyt	0					250
Q99128 UniProt NPD GO	AP1G1_USTMA	AP-1 complex subunit gamma-1 (Gamma(1)-adaptin) (Clathrin assembly protein large gamma-1 chain) (Cla ...	0.43	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				853
Q09718 UniProt NPD GO	AP2M_SCHPO	AP-2 complex subunit mu (Probable clathrin coat assembly protein AP50) (Clathrin coat-associated pro ...	0.43	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...				446

You are viewing entries 29401 to 29450 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.