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
Q27380 UniProt NPD GO	TBB_EIMTE	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					449
Q9UV72 UniProt NPD GO	TBB_PESMI	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					446
P24637 UniProt NPD GO	TBB_PNECA	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					442
Q5UBX3 UniProt NPD GO	TBB_TRIRU	Tubulin beta chain (Beta tubulin)	0.10	-	cyt	0					447
P28551 UniProt NPD GO	TBB3_SOYBN	Tubulin beta chain (Beta tubulin) (Fragment)	0.10	-	cyt	0					408
P20365 UniProt NPD GO	TBB_EUPCR	Tubulin beta chain (Beta-tubulin)	0.10	-	cyt	0					446
Q08115 UniProt NPD GO	TBB_EUPOC	Tubulin beta chain (Beta-tubulin)	0.10	-	cyt	0					444
Q875L3 UniProt NPD GO	TBB1_TRIVE	Tubulin beta-1 chain (Beta-1 tubulin)	0.10	-	cyt	0					445
P33631 UniProt NPD GO	TBB2_ANEPH	Tubulin beta-2 chain (Beta-2 tubulin) (Fragment)	0.10	-	cyt	0					411
P41937 UniProt NPD GO	TBB4_CAEEL	Tubulin beta-4 chain (Beta-4 tubulin)	0.10	-	cyt	0					444
P50262 UniProt NPD GO	TBB4_PORPU	Tubulin beta-4 chain (Beta-4 tubulin)	0.10	-	cyt	0					451
O95922 UniProt NPD GO	TTLL1_HUMAN	Tubulin--tyrosine ligase-like protein 1	0.10	-	cyt	0			608955		423
O95150 UniProt NPD GO	TNF15_HUMAN	Tumor necrosis factor ligand superfamily member 15 (Vascular endothelial cell growth inhibitor) (TNF ...	0.10	-	mit	0	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS] plasma membrane [IDA]	604052		174
P79374 UniProt NPD GO	TNFA_TRIVU	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.10	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P51743 UniProt NPD GO	TNFA_CEREL	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.10	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				229
Q7YRL5 UniProt NPD GO	TNR5_CANFA	Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antig ...	0.10	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				274
Q5I3B2 UniProt NPD GO	IOD2_BOVIN	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.10	-	end	0					269
Q8QZR1 UniProt NPD GO	ATTY_MOUSE	Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)	0.10	-	cyt	0		mitochondrion [IDA]			454
Q4KM49 UniProt NPD GO	SYYC_RAT	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.10	-	cyt	0	Cytoplasm (By similarity)				527
P38203 UniProt NPD GO	LSM2_YEAST	U6 snRNA-associated Sm-like protein LSm2 (Small nuclear ribonucleoprotein D homolog SNP3)	0.10	-	mit	0	Nucleus. Cytoplasm (Probable)	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			95
Q6BMD0 UniProt NPD GO	ALG14_DEBHA	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.10	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				232
Q62452 UniProt NPD GO	UD17_MOUSE	UDP-glucuronosyltransferase 1-7 precursor (EC 2.4.1.17) (UDPGT) (UGT1*7) (UGT1-07) (UGT1.7) (UGT1A7) ...	0.10	-	end	1	Microsome				520
Q84KI6 UniProt NPD GO	SQD1_SPIOL	UDP-sulfoquinovose synthase, chloroplast precursor (EC 3.13.1.1) (Sulfite:UDP-glucose sulfotransfera ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast stroma				482
Q29561 UniProt NPD GO	KCY_PIG	UMP-CMP kinase (EC 2.7.4.14) (Cytidylate kinase) (Deoxycytidylate kinase) (Cytidine monophosphate ki ...	0.10	-	cyt	0	Nucleus (By similarity). Mainly. Cytoplasm (By similarity)				196
P38295 UniProt NPD GO	YB27_YEAST	UPF0017 protein YBR177C	0.10	-	cyt	0		lipid particle [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			451
Q02891 UniProt NPD GO	YP095_YEAST	UPF0017 protein YPL095C	0.10	-	cyt	0					456
O17606 UniProt NPD GO	YK4P_CAEEL	UPF0160 protein C27H6.8	0.10	-	cyt	0					340
Q8J0M6 UniProt NPD GO	YCB2_SACBA	UPF0357 protein YCL012C precursor	0.10	-	nuc	1 *					132
P49727 UniProt NPD GO	UCRI_MAIZE	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane				273
P53318 UniProt NPD GO	COQ6_YEAST	Ubiquinone biosynthesis monooxygenase COQ6 (EC 1.14.13.-)	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [IDA] mitochondrion [IDA]			479
Q9UUB6 UniProt NPD GO	UBLH2_SCHPO	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15)	0.10	-	cyt	0	Nucleus				300
Q6SEG5 UniProt NPD GO	UCHL1_PIG	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.10	-	nuc	0	Cytoplasm (By similarity)				223
Q7SYL3 UniProt NPD GO	SIAH2_BRARE	Ubiquitin ligase Siah2 (EC 6.3.2.-) (Seven in absentia homolog 2-like) (Siah-2)	0.10	-	exc	0					331
Q32PA5 UniProt NPD GO	UBE2C_BOVIN	Ubiquitin-conjugating enzyme E2 C (EC 6.3.2.19) (Ubiquitin-protein ligase C) (Ubiquitin carrier prot ...	0.10	-	nuc	0					179
Q9D2M8 UniProt NPD GO	UB2V2_MOUSE	Ubiquitin-conjugating enzyme E2 variant 2 (Ubc-like protein MMS2)	0.10	-	nuc	0					144
Q7M767 UniProt NPD GO	UB2V2_RAT	Ubiquitin-conjugating enzyme E2 variant 2 (Ubiquitin-conjugating enzyme variant MMS2)	0.10	-	nuc	0					144
P15732 UniProt NPD GO	UBC5_YEAST	Ubiquitin-conjugating enzyme E2-16 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.10	-	nuc	0		proteasome complex (sensu Eukaryota) [IPI]			148
P35135 UniProt NPD GO	UBC4_LYCES	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.10	-	nuc	0					148
P35133 UniProt NPD GO	UBC10_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 10/12 (EC 6.3.2.19) (Ubiquitin-protein ligase 10/12) (Ubiquit ...	0.10	-	nuc	0					148
Q99942 UniProt NPD GO	RNF5_HUMAN	Ubiquitin-protein ligase RMA1 (EC 6.3.2.-) (HsRma1) (RING finger protein 5) (Protein G16)	0.10	-	cyt	2	Membrane; multi-pass membrane protein (Potential). Predominantly located in the plasma membrane, wit ...		602677		180
Q7Z6K5 UniProt NPD GO	CO038_HUMAN	Uncharacterized protein C15orf38	0.10	-	cyt	0					226
Q8NB54 UniProt NPD GO	CR023_HUMAN	Uncharacterized protein C18orf23	0.10	-	nuc	0					160
Q9P6M2 UniProt NPD GO	YKQ3_SCHPO	Uncharacterized protein C688.03c	0.10	-	nuc	0					204
P38347 UniProt NPD GO	YB9P_YEAST	Uncharacterized protein YBR271W	0.10	-	cyt	0		cytoplasm [IDA]			419
P25361 UniProt NPD GO	YCT3_YEAST	Uncharacterized protein YCR043C	0.10	-	nuc	1		Golgi apparatus [IDA]			127
Q03941 UniProt NPD GO	YD196_YEAST	Uncharacterized protein YDR196C	0.10	-	mit	0		endoplasmic reticulum [IDA] nuclear envelope [IDA]			241
Q3E7A2 UniProt NPD GO	YE078_YEAST	Uncharacterized protein YER078W-A	0.10	-	mit	0					54
Q45U48 UniProt NPD GO	YG035_YEAST	Uncharacterized protein YGR035W-A	0.10	-	cyt	0					73
P40533 UniProt NPD GO	YID9_YEAST	Uncharacterized protein YIL039W	0.10	-	cyt	1 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			473
P40165 UniProt NPD GO	YNU0_YEAST	Uncharacterized protein YNL200C	0.10	-	cyt	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]		1JZT	246

You are viewing entries 65401 to 65450 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.