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
P08016 UniProt NPD GO	EGGS_SCHMA	Putative eggshell protein (Fragment)	0.16	-	nuc	0					149
Q9VKA5 UniProt NPD GO	GR33A_DROME	Putative gustatory receptor 33a	0.16	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			475
Q6C7U1 UniProt NPD GO	CCPR3_YARLI	Putative heme-binding peroxidase (EC 1.11.1.-)	0.16	-	mit	0					297
Q09440 UniProt NPD GO	HDA2_CAEEL	Putative histone deacetylase 2	0.16	-	nuc	0	Nucleus (By similarity)				507
Q6CU02 UniProt NPD GO	ATG15_KLULA	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.16	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				531
P82771 UniProt NPD GO	LCR57_ARATH	Putative low-molecular-weight cysteine-rich protein LCR57 precursor	0.16	-	exc	1 *					120
P53257 UniProt NPD GO	YG2O_YEAST	Putative mitochondrial carrier YGR096W	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial envelope [IDA]			314
Q9V9I4 UniProt NPD GO	OR42B_DROME	Putative odorant receptor 42b	0.16	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			399
Q9VT08 UniProt NPD GO	OR67A_DROME	Putative odorant receptor 67a	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			407
P53439 UniProt NPD GO	CDS1_CAEEL	Putative phosphatidate cytidylyltransferase (EC 2.7.7.41) (CDP-diglyceride synthetase) (CDP-diglycer ...	0.16	-	end	8	Membrane; multi-pass membrane protein (Potential)				455
Q9SA05 UniProt NPD GO	POT10_ARATH	Putative potassium transporter 10 (AtPOT10)	0.16	-	end	11	Cell membrane; multi-pass membrane protein (Potential)				787
P38708 UniProt NPD GO	YHI0_YEAST	Putative prolyl-tRNA synthetase YHR020W (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS)	0.16	-	cyt	0					688
Q3E6S8 UniProt NPD GO	DGP14_ARATH	Putative protease Do-like 14 (EC 3.4.21.-)	0.16	-	mit	0					459
Q9FRX4 UniProt NPD GO	RIP1_CUCFI	Putative ribosome-inactivating protein precursor (EC 3.2.2.22) (rRNA N-glycosidase)	0.16	-	mit	0					286
Q00674 UniProt NPD GO	STCE_EMENI	Putative sterigmatocystin biosynthesis ketoreductase stcE (EC 1.1.1.-)	0.16	-	cyt	0					260
O16925 UniProt NPD GO	DHBY_CAEEL	Putative steroid dehydrogenase F25G6.5 (EC 1.1.1.-)	0.16	-	nuc	1 *					314
Q8NFU3 UniProt NPD GO	KAT_HUMAN	Putative thiosulfate sulfurtransferase KAT (EC 2.8.1.1)	0.16	-	cyt	0	Cytoplasm; perinuclear region. Localized around the nuclear membranes	cytoplasm [IDA]			114
Q05451 UniProt NPD GO	YH50_YEAST	Putative uncharacterized protein YHR050W-A	0.16	-	mit	0					56
Q75ZP8 UniProt NPD GO	P2OX_LYOSH	Pyranose 2-oxidase (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:oxygen 2-oxi ...	0.16	+	cyt	0					618
Q05920 UniProt NPD GO	PYC_MOUSE	Pyruvate carboxylase, mitochondrial precursor (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			1178
P22221 UniProt NPD GO	PPDK_FLATR	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.16	-	cyt	0	Plastid; chloroplast				953
P47196 UniProt NPD GO	AKT1_RAT	RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-alpha) (Protein kinase B) (PKB)	0.16	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus after activation by integrin-linked prot ...	cytoplasm [IDA]			480
Q5ZM74 UniProt NPD GO	RN141_CHICK	RING finger protein 141	0.16	-	cyt	0					230
Q6IV57 UniProt NPD GO	RN141_RAT	RING finger protein 141	0.16	-	nuc	0					230
Q99MB7 UniProt NPD GO	RN141_MOUSE	RING finger protein 141 (Zinc finger protein 230)	0.16	-	nuc	0					230
Q9BY78 UniProt NPD GO	RNF26_HUMAN	RING finger protein 26	0.16	-	end	4 *			606130		433
Q9ZT50 UniProt NPD GO	RHA2A_ARATH	RING-H2 zinc finger protein RHA2a	0.16	-	nuc	1 *	Cytoplasm. Nucleus				155
O94503 UniProt NPD GO	SRB11_SCHPO	RNA polymerase II holoenzyme cyclin-like subunit (Suppressor of RNA polymerase B srb11)	0.16	-	cyt	0	Nucleus (Probable)			1ZP2	228
O74366 UniProt NPD GO	TFB4_SCHPO	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.16	-	cyt	0	Nucleus (By similarity)				297
Q4P985 UniProt NPD GO	TFB5_USTMA	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.16	-	cyt	0	Nucleus (By similarity)				62
P23640 UniProt NPD GO	RB27A_RAT	Ras-related protein Rab-27A (Rab-27) (GTP-binding protein Ram) (Ram p25)	0.16	-	cyt	0	Membrane; lipid-anchor				221
Q86YS6 UniProt NPD GO	RAB43_HUMAN	Ras-related protein Rab-43 (Ras-related protein Rab-41)	0.16	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				212
P51147 UniProt NPD GO	RAB5C_CANFA	Ras-related protein Rab-5C	0.16	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...				216
O60895 UniProt NPD GO	RAMP2_HUMAN	Receptor activity-modifying protein 2 precursor (CRLR activity-modifying protein 2) (Calcitonin-rece ...	0.16	-	nuc	1	Membrane; single-pass type I membrane protein	coated pit [TAS] integral to plasma membrane [TAS] lysosome [TAS] plasma membrane [TAS]	605154		175
Q99KK1 UniProt NPD GO	REEP3_MOUSE	Receptor expression-enhancing protein 3	0.16	-	nuc	3 *	Membrane; multi-pass membrane protein (By similarity)				254
Q9SYQ8 UniProt NPD GO	CLV1_ARATH	Receptor protein kinase CLAVATA1 precursor (EC 2.7.11.1)	0.16	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				980
Q27675 UniProt NPD GO	CYAA_LEIDO	Receptor-type adenylate cyclase A (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.16	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				1380
Q8WXD0 UniProt NPD GO	RXFP2_HUMAN	Relaxin receptor 2 (Relaxin family peptide receptor 2) (Leucine-rich repeat-containing G-protein cou ...	0.16	-	end	8 *	Membrane; multi-pass membrane protein		606655		754
Q91ZZ5 UniProt NPD GO	RXFP2_MOUSE	Relaxin receptor 2 (Relaxin family peptide receptor 2) (Leucine-rich repeat-containing G-protein cou ...	0.16	-	end	7	Membrane; multi-pass membrane protein				737
Q8BGE9 UniProt NPD GO	RL3R1_MOUSE	Relaxin-3 receptor 1 (RLN3 receptor 1) (Relaxin family peptide receptor 3) (G protein-coupled recept ...	0.16	-	end	7	Membrane; multi-pass membrane protein				472
P81191 UniProt NPD GO	RELX_DASSA	Relaxin-like protein AGF [Contains: Relaxin-like protein AGF B chain; Relaxin-like protein AGF A cha ...	0.16	-	nuc	0	Secreted protein				81
P00796 UniProt NPD GO	RENI2_MOUSE	Renin-2 precursor (EC 3.4.23.15) (Angiotensinogenase) (Submandibular gland renin) [Contains: Renin-2 ...	0.16	-	end	0	Secreted protein			1SMR	401
P35249 UniProt NPD GO	RFC4_HUMAN	Replication factor C subunit 4 (Replication factor C 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37) ( ...	0.16	-	cyt	0	Nucleus (Probable)	DNA replication factor C complex [TAS]	102577		363
Q24492 UniProt NPD GO	RFA1_DROME	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (Sin ...	0.16	-	cyt	0	Nucleus	DNA replication factor A complex [IDA] nucleus [IDA]			603
P27694 UniProt NPD GO	RFA1_HUMAN	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (Sin ...	0.16	-	cyt	0	Nucleus	DNA replication factor A complex [TAS]	179835	2B3G	616
Q05186 UniProt NPD GO	RCN1_MOUSE	Reticulocalbin-1 precursor	0.16	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				325
P22571 UniProt NPD GO	CNCG_BOVIN	Retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GM ...	0.16	-	nuc	0					83
P18545 UniProt NPD GO	CNRG_HUMAN	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.16	-	cyt	0			180073		87
P32608 UniProt NPD GO	RTG2_YEAST	Retrograde regulation protein 2	0.16	-	cyt	0		cytoplasm [IDA] SLIK (SAGA-like) complex [IPI]			588
Q03269 UniProt NPD GO	PO11_NASVI	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 (Retrovirus-related Pol ...	0.16	-	cyt	0					337

You are viewing entries 56201 to 56250 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.