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
Q922Q4 UniProt NPD GO	P5CR2_MOUSE	Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2) (P5CR 2) (P5C reductase 2)	0.04	-	cyt	0					320
Q6AY23 UniProt NPD GO	P5CR2_RAT	Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2) (P5CR 2) (P5C reductase 2)	0.04	-	cyt	0					320
Q9D051 UniProt NPD GO	ODPB_MOUSE	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			359
O00330 UniProt NPD GO	ODPX_HUMAN	Pyruvate dehydrogenase protein X component, mitochondrial precursor (Dihydrolipoamide dehydrogenase- ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix		245349	2F60	501
Q875M9 UniProt NPD GO	KPYK_KLULA	Pyruvate kinase (EC 2.7.1.40) (PK)	0.04	-	cyt	0					501
Q27788 UniProt NPD GO	KPYK_TRYBO	Pyruvate kinase (EC 2.7.1.40) (PK)	0.04	-	mit	0					498
P30616 UniProt NPD GO	KPYK2_TRYBB	Pyruvate kinase 2 (EC 2.7.1.40) (PK 2)	0.04	-	cyt	0					499
Q5NVN0 UniProt NPD GO	KPYM_PONPY	Pyruvate kinase isozyme M1 (EC 2.7.1.40)	0.04	-	cyt	0					530
P11974 UniProt NPD GO	KPYM_RABIT	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) (Pyruvate kinase muscle isozyme)	0.04	-	cyt	0				2G50	530
P30613 UniProt NPD GO	KPYR_HUMAN	Pyruvate kinase isozymes R/L (EC 2.7.1.40) (R-type/L-type pyruvate kinase) (Red cell/liver pyruvate ...	0.04	-	nuc	0			102900	1LIY	574
P25415 UniProt NPD GO	DHQA_EMENI	Quinate dehydrogenase (EC 1.1.1.24)	0.04	-	cyt	0					329
Q7SIG0 UniProt NPD GO	PHEA_GRACH	R-phycoerythrin alpha chain	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1EYX	164
O36005 UniProt NPD GO	PHEA_GRIMO	R-phycoerythrin alpha chain	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1B8D	164
P51367 UniProt NPD GO	PHEB_PORPU	R-phycoerythrin beta chain	0.04	-	mit	0	Periphery of the rods of the phycobilisome				177
P34145 UniProt NPD GO	RAC1B_DICDI	RAS-related protein rac1B	0.04	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
Q9GPR7 UniProt NPD GO	RACH_DICDI	RAS-related protein racH	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
Q99LJ7 UniProt NPD GO	RCBT2_MOUSE	RCC1 and BTB domain-containing protein 2 (Regulator of chromosome condensation and BTB domain-contai ...	0.04	-	cyt	0					551
Q9H9V4 UniProt NPD GO	RN122_HUMAN	RING finger protein 122	0.04	-	nuc	1 *	Golgi apparatus. Endoplasmic reticulum. Membrane; single-pass membrane protein (Potential)				155
Q8BP31 UniProt NPD GO	RN122_MOUSE	RING finger protein 122	0.04	-	nuc	1 *	Golgi apparatus. Endoplasmic reticulum (By similarity). Membrane; single-pass membrane protein (Pote ...				155
P34162 UniProt NPD GO	MED20_YEAST	RNA polymerase II mediator complex subunit 20 (Suppressor of RNA polymerase B 2) (Hyper-recombinatio ...	0.04	-	cyt	0	Nucleus	mediator complex [IDA]			210
Q6C1B5 UniProt NPD GO	TFB5_YARLI	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.04	-	nuc	0	Nucleus (By similarity)				75
P31843 UniProt NPD GO	RRPO_OENBE	RNA-directed DNA polymerase homolog (Reverse transcriptase homolog)	0.04	-	cyt	0					142
P92985 UniProt NPD GO	RBP1C_ARATH	Ran-binding protein 1 homolog c	0.04	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				219
P39084 UniProt NPD GO	RLXN_RANCA	Ranalexin precursor	0.04	-	end	0	Secreted protein				66
P22691 UniProt NPD GO	TKND_RANCA	Ranatachykinin-D (RTK D)	0.04	-		0	Secreted protein				11
P08952 UniProt NPD GO	RANR_RANRU	Ranatensin-R	0.04	-		0	Secreted protein				17
Q8QFQ3 UniProt NPD GO	RN2PA_RANPI	Ranatuerin-2Pa precursor	0.04	-	exc	0	Secreted protein				70
O88931 UniProt NPD GO	RAC2_CAVPO	Ras-related C3 botulinum toxin substrate 2 precursor (p21-Rac2)	0.04	-	cyt	0	Cytoplasm (By similarity). Membrane-associated when activated (By similarity)				192
P25766 UniProt NPD GO	RGP1_ORYSA	Ras-related protein RGP1 (GTP-binding regulatory protein RGP1)	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				226
P40393 UniProt NPD GO	RIC2_ORYSA	Ras-related protein RIC2	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q9TVU5 UniProt NPD GO	RAB1_THEPA	Ras-related protein Rab-1 (Small GTP-binding protein rab1) (TpRab1)	0.04	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential). Located in the vicinity of the schizont n ...				220
Q9H0T7 UniProt NPD GO	RAB17_HUMAN	Ras-related protein Rab-17	0.04	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		602206		212
P35293 UniProt NPD GO	RAB18_MOUSE	Ras-related protein Rab-18	0.04	-	cyt	0	Highly enriched on apical endocytic structures in polarized epithelial cells of kidney proximal tubu ...				206
Q05974 UniProt NPD GO	RAB1A_LYMST	Ras-related protein Rab-1A	0.04	-	cyt	0	Golgi apparatus (By similarity)				205
P49104 UniProt NPD GO	RAB2B_MAIZE	Ras-related protein Rab-2-B	0.04	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				210
Q99P74 UniProt NPD GO	RB27B_RAT	Ras-related protein Rab-27B	0.04	-	cyt	0	Membrane; lipid-anchor (By similarity)	zymogen granule membrane [IDA]			217
Q40195 UniProt NPD GO	RB11E_LOTJA	Ras-related protein Rab11E	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
Q39572 UniProt NPD GO	YPTC6_CHLRE	Ras-related protein YPTC6	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P61232 UniProt NPD GO	TXR3_MACRV	Raventoxin-3 (Raventoxin III)	0.04	-	nuc	0	Secreted protein (By similarity)				29
Q9WTJ5 UniProt NPD GO	RAMP1_MOUSE	Receptor activity-modifying protein 1 precursor	0.04	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				148
O60894 UniProt NPD GO	RAMP1_HUMAN	Receptor activity-modifying protein 1 precursor (CRLR activity-modifying protein 1) (Calcitonin-rece ...	0.04	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605153		148
P26338 UniProt NPD GO	CYAA_TRYEQ	Receptor-type adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) (Fragment) ...	0.04	-	mit	1	Cell membrane; multi-pass membrane protein (By similarity)				469
P11185 UniProt NPD GO	RELX_BALED	Relaxin [Contains: Relaxin B chain; Relaxin A chain]	0.04	-	nuc	0	Secreted protein				54
Q8WXF3 UniProt NPD GO	REL3_HUMAN	Relaxin-3 precursor (Prorelaxin H3) (Insulin-like peptide INSL7) (Insulin-like peptide 7) [Contains: ...	0.04	-	exc	0	Secreted protein		606855	2FHW	142
Q5CZK2 UniProt NPD GO	REL3_PANTR	Relaxin-3 precursor (Prorelaxin H3) [Contains: Relaxin-3 B chain; Relaxin-3 A chain]	0.04	-	vac	0	Secreted protein (By similarity)				142
Q6DYE7 UniProt NPD GO	RENI_CANFA	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.04	-	end	1 *	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				403
P80760 UniProt NPD GO	PRP_PHAVU	Repetitive proline-rich cell wall protein (Fragment)	0.04	-	nuc	0	Cell wall				25
Q99P87 UniProt NPD GO	RSN_MOUSE	Resistin precursor (Cysteine-rich secreted protein FIZZ3) (Adipose tissue-specific secretory factor) ...	0.04	-	exc	0	Secreted protein	extracellular region [IDA]		1RGX	114
Q99P85 UniProt NPD GO	RSNA_RAT	Resistin-like alpha precursor (RELMalpha) (Cysteine-rich secreted protein FIZZ1)	0.04	-	nuc	0	Secreted protein				111
P24549 UniProt NPD GO	AL1A1_MOUSE	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.04	-	cyt	0	Cytoplasm				500

You are viewing entries 78301 to 78350 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.