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
Q10471 UniProt NPD GO	GALT2_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.35	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Resides pr ...		602274	2FFV	571
Q38998 UniProt NPD GO	AKT1_ARATH	Potassium channel AKT1	0.35	+	end	5	Membrane; multi-pass membrane protein				857
Q94A76 UniProt NPD GO	GORK_ARATH	Potassium channel GORK (Guard cell outward rectifying K(+) channel) (AtGORK)	0.35	-	end	5	Membrane; multi-pass membrane protein				820
Q63ZI0 UniProt NPD GO	KCNK9_XENLA	Potassium channel subfamily K member 9	0.35	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				374
P16389 UniProt NPD GO	KCNA2_HUMAN	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.35	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176262		499
P16390 UniProt NPD GO	KCNA3_MOUSE	Potassium voltage-gated channel subfamily A member 3 (Voltage-gated potassium channel subunit Kv1.3) ...	0.35	-	end	4	Membrane; multi-pass membrane protein				528
P20648 UniProt NPD GO	ATP4A_HUMAN	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.35	-	end	8	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137216		1034
Q75B95 UniProt NPD GO	BRR1_ASHGO	Pre-mRNA-splicing factor BRR1	0.35	-	cyt	0	Nucleus (By similarity)				322
Q74ZN9 UniProt NPD GO	SLU7_ASHGO	Pre-mRNA-splicing factor SLU7	0.35	-	nuc	0	Nucleus (By similarity)				266
Q03958 UniProt NPD GO	PFD6_MOUSE	Prefoldin subunit 6 (Protein Ke2)	0.35	-	nuc	0	Nucleus				127
Q9UQ74 UniProt NPD GO	PSG8_HUMAN	Pregnancy-specific beta-1-glycoprotein 8 precursor (PSBG-8)	0.35	-	nuc	0	Secreted protein (Potential)		176397		426
P46502 UniProt NPD GO	PRS6B_CAEEL	Probable 26S protease regulatory subunit 6B	0.35	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				414
Q25278 UniProt NPD GO	RL14_LEIDO	Probable 60S ribosomal protein L14 (23 kDa cell surface protein) (LDP 23)	0.35	-	nuc	0					175
P54824 UniProt NPD GO	DDX6_XENLA	Probable ATP-dependent RNA helicase DDX6 (EC 3.6.1.-) (DEAD box protein 6) (ATP-dependent RNA helica ...	0.35	-	nuc	0	Cytoplasm. Mostly. Nucleus				481
O95800 UniProt NPD GO	GPR75_HUMAN	Probable G-protein coupled receptor 75	0.35	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606704		540
Q3ZC80 UniProt NPD GO	GPR92_BOVIN	Probable G-protein coupled receptor 92	0.35	+	end	7 *	Membrane; multi-pass membrane protein				367
Q09580 UniProt NPD GO	GUAA_CAEEL	Probable GMP synthase [glutamine-hydrolyzing] (EC 6.3.5.2) (Glutamine amidotransferase)	0.35	-	nuc	0					792
O15746 UniProt NPD GO	RTC1_DICDI	Probable RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) (RNA-3'-phosphate cyclase) (RNA cyclase)	0.35	-	nuc	0	Nucleus; nucleoplasm (By similarity)				433
Q93WU9 UniProt NPD GO	WRK51_ARATH	Probable WRKY transcription factor 51 (WRKY DNA-binding protein 51)	0.35	-	nuc	0	Nucleus (Probable)				194
P58798 UniProt NPD GO	ARPC4_CAEEL	Probable actin-related protein 2/3 complex subunit 4 (ARP2/3 complex 20 kDa subunit) (p20-ARC)	0.35	-	cyt	0					169
Q8MZC4 UniProt NPD GO	CRLS1_DROME	Probable cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS)	0.35	-	nuc	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			322
Q9NQ11 UniProt NPD GO	AT132_HUMAN	Probable cation-transporting ATPase 13A2 (EC 3.6.3.-)	0.35	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				1180
Q9GP34 UniProt NPD GO	CCNH_ECHMU	Probable cyclin-H	0.35	-	cyt	0	Nucleus (By similarity)				335
Q9VYQ7 UniProt NPD GO	CP311_DROME	Probable cytochrome P450 311a1 (EC 1.14.-.-) (CYPCCCXIA1)	0.35	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				483
Q9V979 UniProt NPD GO	CP6U1_DROME	Probable cytochrome P450 6u1 (EC 1.14.-.-) (CYPVIU1)	0.35	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				488
Q9SI85 UniProt NPD GO	DRL14_ARATH	Probable disease resistance protein At1g62630 (pNd4)	0.35	-	cyt	0					893
Q7X7L3 UniProt NPD GO	ELP3_ORYSA	Probable histone acetyltransferase ELP3 (EC 2.3.1.48) (Elongator component 3) (Elongation protein 3) ...	0.35	+	cyt	0	Nucleus (Probable)				573
Q5XI06 UniProt NPD GO	MYST1_RAT	Probable histone acetyltransferase MYST1 (EC 2.3.1.48) (MYST protein 1) (MOZ, YBF2/SAS3, SAS2 and TI ...	0.35	-	cyt	0	Nucleus (By similarity)				458
O64644 UniProt NPD GO	SAP18_ARATH	Probable histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa)	0.35	-	mit	0					152
Q9VT50 UniProt NPD GO	INSL1_DROME	Probable insulin-like peptide 1 precursor (Insulin-related peptide) (DILP1) [Contains: Probable insu ...	0.35	-	nuc	0	Secreted protein (Potential)	extracellular region [ISS]			154
Q9VT51 UniProt NPD GO	INSL2_DROME	Probable insulin-like peptide 2 precursor (Insulin-related peptide) (DILP2) [Contains: Probable insu ...	0.35	-	nuc	0	Secreted protein (Potential)	extracellular region [NAS]			137
Q9W4Z4 UniProt NPD GO	INSL6_DROME	Probable insulin-like peptide 6 precursor (Insulin-related peptide) (DILP6) [Contains: Probable insu ...	0.35	-	exc	1 *	Secreted protein (Potential)	extracellular region [ISS]			107
Q60YU0 UniProt NPD GO	LCMT1_CAEBR	Probable leucine carboxyl methyltransferase 1 (EC 2.1.1.-)	0.35	-	cyt	0					331
P40051 UniProt NPD GO	YEQ8_YEAST	Probable peptidase YER078C (EC 3.4.-.-)	0.35	-	mit	0		mitochondrial matrix [NAS] mitochondrion [IDA]			511
Q7XBW5 UniProt NPD GO	PAP3_ORYSA	Probable plastid-lipid-associated protein 3, chloroplast precursor	0.35	-	mit	0	Plastid; chloroplast (Potential)				374
P52554 UniProt NPD GO	PFD6_CAEEL	Probable prefoldin subunit 6	0.35	-	nuc	0					126
O78411 UniProt NPD GO	DNAB_GUITH	Probable replicative DNA helicase (EC 3.6.1.-) [Contains: Gth dnaB intein]	0.35	-	cyt	0	Plastid; chloroplast				599
Q05652 UniProt NPD GO	KPEL_DROME	Probable serine/threonine-protein kinase pelle (EC 2.7.11.1)	0.35	-	nuc	0		cytoplasm [IDA] plasma membrane [IDA]		1YGO	501
Q9MUN1 UniProt NPD GO	CYSA_MESVI	Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATP ...	0.35	-	cyt	0	Plastid; chloroplast				348
P60319 UniProt NPD GO	KEN_DROYA	Probable transcription factor Ken (Protein Ken and Barbie) (Fragment)	0.35	-	nuc	0	Nucleus (Probable)				205
Q9NEF6 UniProt NPD GO	VATD2_DROME	Probable vacuolar ATP synthase subunit D 2 (EC 3.6.3.14) (V-ATPase D subunit 2) (Vacuolar proton pum ...	0.35	-	cyt	0					249
Q9R0E1 UniProt NPD GO	PLOD3_MOUSE	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH ...	0.35	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				741
P47969 UniProt NPD GO	PENK_CAVPO	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.35	-	exc	0	Secreted protein				268
O97686 UniProt NPD GO	GON2_SUNMU	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.35	-	nuc	0	Secreted protein				110
Q5XIH7 UniProt NPD GO	PHB2_RAT	Prohibitin-2 (B-cell receptor-associated protein BAP37) (BAP-37)	0.35	-	mit	0	Mitochondrion; mitochondrial inner membrane. Cytoplasm. Nucleus. Also cytoplasmic and nuclear	mitochondrial inner membrane [ISS] nucleus [ISS]			299
P58294 UniProt NPD GO	PROK1_HUMAN	Prokineticin-1 precursor (Endocrine-gland-derived vascular endothelial growth factor) (EG-VEGF) (Mam ...	0.35	-	exc	0	Secreted protein		606233		105
Q90374 UniProt NPD GO	PRLR_COLLI	Prolactin receptor precursor (PRL-R)	0.35	-	exc	1 *	Membrane; single-pass type I membrane protein				830
O54990 UniProt NPD GO	PROM1_MOUSE	Prominin-1 precursor (Prominin-like protein 1) (Antigen AC133 homolog)	0.35	-	end	5	Membrane; multi-pass membrane protein (Potential)	brush border [IDA] extracellular space [IDA] integral to plasma membrane [IDA] microvillus [IDA]			867
P35375 UniProt NPD GO	PE2R1_MOUSE	Prostaglandin E2 receptor, EP1 subtype (Prostanoid EP1 receptor) (PGE receptor, EP1 subtype)	0.35	-	end	6 *	Membrane; multi-pass membrane protein				405
P50131 UniProt NPD GO	PE2R3_PIG	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype)	0.35	+	end	6 *	Membrane; multi-pass membrane protein				373

You are viewing entries 36101 to 36150 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.