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
Q74ZJ5 UniProt NPD GO	SEN54_ASHGO	tRNA-splicing endonuclease subunit SEN54 (tRNA-intron endonuclease SEN54)	0.54	-	cyt	0					455
Q28295 UniProt NPD GO	VWF_CANFA	von Willebrand factor precursor (vWF)	0.54	-	nuc	0	Secreted protein. Localized to storage granules				2813
Q28833 UniProt NPD GO	VWF_PIG	von Willebrand factor precursor (vWF) (Fragment)	0.54	-	nuc	0	Secreted protein (By similarity). Localized to storage granules (By similarity)				2482
P11178 UniProt NPD GO	ODBA_BOVIN	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial precursor (EC 1.2.4.4) (Branched-chain a ...	0.53	-	mit	0	Mitochondrion; mitochondrial matrix				455
P82673 UniProt NPD GO	RT35_HUMAN	28S ribosomal protein S35, mitochondrial precursor (S35mt) (MRP-S35) (Mitochondrial ribosomal protei ...	0.53	-	nuc	0	Mitochondrion (By similarity)	mitochondrial small ribosomal subunit [NAS]			323
Q9VMX0 UniProt NPD GO	RM28_DROME	39S ribosomal protein L28, mitochondrial precursor (L28mt)	0.53	-	mit	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [NAS]			302
P02407 UniProt NPD GO	RS17A_YEAST	40S ribosomal protein S17-A (RP51A)	0.53	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			136
Q5RBK1 UniProt NPD GO	RS27_PONPY	40S ribosomal protein S27	0.53	+	nuc	0					83
P62992 UniProt NPD GO	RS27A_BOVIN	40S ribosomal protein S27a	0.53	+	nuc	0					80
P62978 UniProt NPD GO	RS27A_CAVPO	40S ribosomal protein S27a	0.53	+	nuc	0					80
P79781 UniProt NPD GO	RS27A_CHICK	40S ribosomal protein S27a	0.53	+	nuc	0					80
P62979 UniProt NPD GO	RS27A_HUMAN	40S ribosomal protein S27a	0.53	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	191343		80
Q5RDH5 UniProt NPD GO	AAPK1_PONPY	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMPK alpha-1 chain)	0.53	-	nuc	0					550
Q5R4S0 UniProt NPD GO	AAKG2_PONPY	5'-AMP-activated protein kinase subunit gamma-2 (AMPK gamma-2 chain) (AMPK gamma2)	0.53	-	nuc	0					524
P79400 UniProt NPD GO	5HT1D_PIG	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D) (5-HT1D) (Fragment)	0.53	-	end	6 *	Membrane; multi-pass membrane protein				291
Q25414 UniProt NPD GO	5HTR_LYMST	5-hydroxytryptamine receptor (5-HT receptor) (Serotonin receptor)	0.53	+	end	7	Membrane; multi-pass membrane protein				509
Q15646 UniProt NPD GO	OASL_HUMAN	59 kDa 2'-5'-oligoadenylate synthetase-like protein (p59 OASL) (p59OASL) (Thyroid receptor-interacti ...	0.53	-	cyt	0		cytoplasm [TAS] nucleolus [TAS]	603281	1WH3	514
P53026 UniProt NPD GO	RL10A_MOUSE	60S ribosomal protein L10a (CSA-19) (Protein NEDD6) (Neural precursor cell expressed developmentally ...	0.53	+	nuc	0					216
P35427 UniProt NPD GO	RL13A_RAT	60S ribosomal protein L13a	0.53	+	cyt	0		ribosome [NAS]			202
Q10192 UniProt NPD GO	RL18A_SCHPO	60S ribosomal protein L18-A	0.53	-	nuc	0					187
Q6BIE4 UniProt NPD GO	RM02_DEBHA	60S ribosomal protein L2, mitochondrial precursor	0.53	-	mit	0	Mitochondrion (By similarity)				394
P39872 UniProt NPD GO	RL3_BOVIN	60S ribosomal protein L3	0.53	-	mit	0	Cytoplasm				402
O16797 UniProt NPD GO	RL3_DROME	60S ribosomal protein L3	0.53	-	mit	0	Cytoplasm				415
P36584 UniProt NPD GO	RL3B_SCHPO	60S ribosomal protein L3-B	0.53	-	mit	0	Cytoplasm				387
Q8SSA2 UniProt NPD GO	RL34_ENCCU	60S ribosomal protein L34	0.53	-	mit	0					110
Q9SF53 UniProt NPD GO	RL351_ARATH	60S ribosomal protein L35-1	0.53	-	nuc	0					123
P31027 UniProt NPD GO	RL44_KLULA	60S ribosomal protein L44 (60S ribosomal protein L41)	0.53	-	nuc	0					105
O01802 UniProt NPD GO	RL7_CAEEL	60S ribosomal protein L7	0.53	+	cyt	0					244
O88987 UniProt NPD GO	AKAP3_MOUSE	A-kinase anchor protein 3 (Protein kinase A-anchoring protein 3) (PRKA3) (A-kinase anchor protein 11 ...	0.53	-	nuc	0	Localizes to the ribs of the fibrous sheath in the principal piece of the sperm tail (By similarity) ...	flagellum (sensu Eukaryota) [IDA]			864
P14197 UniProt NPD GO	AAC3_DICDI	AAC-rich mRNA clone AAC3 protein (Fragment)	0.53	-	nuc	0					437
Q7Z4H4 UniProt NPD GO	ADM2_HUMAN	ADM2 precursor (Intermedin) [Contains: Adrenomedullin-2 (Intermedin-long) (IMDL); Intermedin-short ( ...	0.53	-	exc	0	Secreted protein		608682		148
O35284 UniProt NPD GO	BATF_MOUSE	ATF-like basic leucine zipper transcription factor B-ATF	0.53	-	nuc	0	Nucleus				125
Q16520 UniProt NPD GO	BATF_HUMAN	ATF-like basic leucine zipper transcriptional factor B-ATF (SF-HT-activated gene 2) (SFA-2)	0.53	-	nuc	0	Nucleus				125
P41234 UniProt NPD GO	ABCA2_MOUSE	ATP-binding cassette sub-family A member 2 (ATP-binding cassette transporter 2) (ATP-binding cassett ...	0.53	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				2434
O76031 UniProt NPD GO	CLPX_HUMAN	ATP-dependent Clp protease ATP-binding subunit ClpX-like, mitochondrial precursor	0.53	-	mit	0	Mitochondrion	mitochondrion [TAS]			633
O70133 UniProt NPD GO	DHX9_MOUSE	ATP-dependent RNA helicase A (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II) (DEAH box protein 9) (m ...	0.53	+	mit	0	Nucleus; nucleolus	nucleolus [IDA]		1WHQ	1380
Q6CT46 UniProt NPD GO	DBP3_KLULA	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.53	+	nuc	0	Nucleus; nucleolus (By similarity)				504
Q5RF43 UniProt NPD GO	DDX3Y_PONPY	ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (DEAD box protein 3, Y-chromosomal)	0.53	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm i ...				658
P15424 UniProt NPD GO	MS116_YEAST	ATP-dependent RNA helicase MSS116, mitochondrial precursor (EC 3.6.1.-)	0.53	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IMP]			664
Q6FQQ6 UniProt NPD GO	IF4A_CANGA	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.53	-	cyt	0	Cytoplasm (By similarity)				396
P09052 UniProt NPD GO	VASA_DROME	ATP-dependent RNA helicase vasa (EC 3.6.1.-) (Antigen Mab46F11)	0.53	-	cyt	0		polar granule [IDA]		2DB3	661
P32386 UniProt NPD GO	YBT1_YEAST	ATP-dependent bile acid permease	0.53	-	end	14 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			1661
Q5B5E7 UniProt NPD GO	RRP3_EMENI	ATP-dependent rRNA helicase rrp3 (EC 3.6.1.-)	0.53	-	nuc	0	Nucleus (Probable)				465
P12219 UniProt NPD GO	ACCD_TOBAC	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.53	-	nuc	0	Plastid; chloroplast				512
P15891 UniProt NPD GO	ABP1_YEAST	Actin-binding protein	0.53	-	nuc	0	Actin patch. Cortical actin patches	cell cortex [IDA] cytoplasm [IDA] cytoskeleton [TAS]		1JO8	591
Q80US4 UniProt NPD GO	ARP5_MOUSE	Actin-related protein 5	0.53	-	cyt	0					605
Q20952 UniProt NPD GO	ADD2_CAEEL	Adducin-related protein 2	0.53	-	nuc	0					611
Q9DGG6 UniProt NPD GO	ADCY9_CHICK	Adenylate cyclase type 9 (EC 4.6.1.1) (Adenylate cyclase type IX) (ATP pyrophosphate-lyase 9) (Adeny ...	0.53	-	end	10	Membrane; multi-pass membrane protein (By similarity)				1334
P51830 UniProt NPD GO	ADCY9_MOUSE	Adenylate cyclase type 9 (EC 4.6.1.1) (Adenylate cyclase type IX) (ATP pyrophosphate-lyase 9) (Adeny ...	0.53	-	end	11	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1353
Q6ULP2 UniProt NPD GO	AFTIN_HUMAN	Aftiphilin	0.53	-	nuc	0	Cytoplasm. Colocalizes with AP1G1 and clathrin	AP-1 adaptor complex [IDA] cytosol [IDA]			937

You are viewing entries 22901 to 22950 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.