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
P34070 UniProt NPD GO	TA1_TREBR	Tremerogen A-I	0.09	-		0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				15
P79110 UniProt NPD GO	TXTP_BOVIN	Tricarboxylate transport protein, mitochondrial precursor (Citrate transport protein) (CTP) (Tricarb ...	0.09	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				311
Q9UVI4 UniProt NPD GO	THYD_CLAFS	Trihydrophobin precursor (CFTH1)	0.09	-	nuc	0	Secreted protein	hyphal cell wall [IDA]			394
Q9EQV6 UniProt NPD GO	TPP1_RAT	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.09	-	end	0	Lysosome				563
O89023 UniProt NPD GO	TPP1_MOUSE	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.09	-	cyt	0	Lysosome	mitochondrion [IDA]			562
P50165 UniProt NPD GO	TRNH_DATST	Tropinone reductase homolog (EC 1.1.1.-) (P29X)	0.09	-	cyt	0					268
P47948 UniProt NPD GO	TNNC2_DROME	Troponin C, isoform 2	0.09	-	cyt	0					155
P35042 UniProt NPD GO	TRYP_CHOFU	Trypsin CFT-1 precursor (EC 3.4.21.4)	0.09	-	exc	0	Secreted protein; extracellular space				256
P54629 UniProt NPD GO	TRYU_DROER	Trypsin eta precursor (EC 3.4.21.4)	0.09	-	end	1 *	Secreted protein; extracellular space				258
P42279 UniProt NPD GO	TRYU_DROME	Trypsin eta precursor (EC 3.4.21.4)	0.09	-	vac	1 *	Secreted protein; extracellular space				262
P19398 UniProt NPD GO	ITR1_ASCSU	Trypsin inhibitor (ATI)	0.09	-	nuc	0	Secreted protein			1ATE	62
P11969 UniProt NPD GO	ITR1_CITLA	Trypsin inhibitor 1 (Trypsin inhibitor I) (CVTI-I)	0.09	-	nuc	0	Secreted protein				30
P82409 UniProt NPD GO	ITR2_MOMCO	Trypsin inhibitor 2 (Trypsin inhibitor II) (MCoTI-II)	0.09	-	nuc	0	Secreted protein			2C4B	34
P83396 UniProt NPD GO	ITR5_CYCPE	Trypsin inhibitor 5 (Trypsin inhibitor V) (CyPTI-V) [Contains: Trypsin inhibitor 2 (Trypsin inhibito ...	0.09	-	nuc	0	Secreted protein				29
P35045 UniProt NPD GO	TRYA_MANSE	Trypsin, alkaline A precursor (EC 3.4.21.4)	0.09	-	exc	0	Secreted protein; extracellular space				256
P35812 UniProt NPD GO	ITC_ALOMA	Trypsin/chymotrypsin inhibitor	0.09	-	nuc	0					184
P38967 UniProt NPD GO	TAT2_YEAST	Tryptophan permease (Tryptophan amino acid transporter)	0.09	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IDA]			592
P50258 UniProt NPD GO	TBAD_PHYPO	Tubulin alpha-1A chain	0.09	-	cyt	0	Spindle. Mitosis in the slime mold Plasmodium differs from the process in many eukaryotes. The tubul ...				450
Q4R9N3 UniProt NPD GO	TBB_COCHE	Tubulin beta chain (Beta tubulin)	0.09	-	cyt	0					447
Q8SS99 UniProt NPD GO	TBB_ENCCU	Tubulin beta chain (Beta tubulin)	0.09	-	cyt	0					439
P05220 UniProt NPD GO	TBB_NEUCR	Tubulin beta chain (Beta tubulin)	0.09	-	cyt	0					447
P10653 UniProt NPD GO	TBB1_EMENI	Tubulin beta-1 chain (Beta-1 tubulin)	0.09	-	cyt	0					447
P07436 UniProt NPD GO	TBB1_PHYPO	Tubulin beta-1 chain (Beta-1 tubulin)	0.09	-	cyt	0	Spindle. Mitosis in the slime mold Plasmodium differs from the process in many eukaryotes. The tubul ...				467
P69893 UniProt NPD GO	TBB1_CRIGR	Tubulin beta-1 chain (Beta-tubulin isotype I) (Class I beta tubulin)	0.09	-	cyt	0					444
P07437 UniProt NPD GO	TBB2_HUMAN	Tubulin beta-2 chain	0.09	-	cyt	0			191130		444
P69895 UniProt NPD GO	TBB2_MACMU	Tubulin beta-2 chain	0.09	-	cyt	0					444
Q7JJU6 UniProt NPD GO	TBB2_PANTR	Tubulin beta-2 chain	0.09	-	cyt	0					444
P52275 UniProt NPD GO	TBB2_CAEEL	Tubulin beta-2 chain (Beta-2 tubulin)	0.09	-	cyt	0					450
P50261 UniProt NPD GO	TBB3_PORPU	Tubulin beta-3 chain (Beta-3 tubulin)	0.09	-	cyt	0					445
P09206 UniProt NPD GO	TBB3_CHICK	Tubulin beta-3 chain (Beta-tubulin class-IV)	0.09	-	cyt	0					445
P99024 UniProt NPD GO	TBB5_MOUSE	Tubulin beta-5 chain	0.09	-	cyt	0		tubulin [NAS]			444
P69897 UniProt NPD GO	TBB5_RAT	Tubulin beta-5 chain	0.09	-	cyt	0					444
P09244 UniProt NPD GO	TBB7_CHICK	Tubulin beta-7 chain (Tubulin beta 4')	0.09	-	cyt	0					444
Q8SRD2 UniProt NPD GO	TBG_ENCCU	Tubulin gamma chain (Gamma tubulin)	0.09	-	cyt	0					434
Q7TQD2 UniProt NPD GO	P25A_MOUSE	Tubulin polymerization-promoting protein (TPPP)	0.09	-	nuc	0					218
Q91V51 UniProt NPD GO	TTLL1_MOUSE	Tubulin--tyrosine ligase-like protein 1	0.09	-	cyt	0					423
P23510 UniProt NPD GO	TNFL4_HUMAN	Tumor necrosis factor ligand superfamily member 4 (OX40 ligand) (OX40L) (Glycoprotein Gp34) (TAX tra ...	0.09	-	nuc	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	603594		183
P19101 UniProt NPD GO	TNFA_FELCA	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.09	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P48094 UniProt NPD GO	TNFA_MACMU	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.09	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
Q9ER63 UniProt NPD GO	TNR23_MOUSE	Tumor necrosis factor receptor superfamily member 23 precursor (Tumor necrosis factor receptor p60 h ...	0.09	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				176
P61943 UniProt NPD GO	SIA10_RAT	Type 2 lactosamine alpha-2,3-sialyltransferase (EC 2.4.99.-) (CMP-NeuAc:beta-galactoside alpha-2,3-s ...	0.09	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				331
P17713 UniProt NPD GO	STK_HYDAT	Tyrosine-protein kinase STK (EC 2.7.10.2) (P57-STK)	0.09	-	nuc	0					509
Q64725 UniProt NPD GO	KSYK_RAT	Tyrosine-protein kinase SYK (EC 2.7.10.2) (Spleen tyrosine kinase)	0.09	-	cyt	0					629
P28194 UniProt NPD GO	PTP2_STYPL	Tyrosine-protein phosphatase 2 (EC 3.1.3.48) (Fragment)	0.09	-	nuc	0					127
P28195 UniProt NPD GO	PTP3_STYPL	Tyrosine-protein phosphatase 3 (EC 3.1.3.48) (Fragment)	0.09	-	cyt	0					110
Q5ZJ08 UniProt NPD GO	SYYC_CHICK	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.09	-	cyt	0	Cytoplasm (By similarity)				527
P54577 UniProt NPD GO	SYYC_HUMAN	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.09	-	cyt	0	Cytoplasm	cytoplasm [TAS] extracellular space [TAS] soluble fraction [TAS]	603623	1Q11	527
Q5R8T5 UniProt NPD GO	SYYC_PONPY	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.09	-	cyt	0	Cytoplasm (By similarity)				527
Q969L4 UniProt NPD GO	LSM10_HUMAN	U7 snRNA-associated Sm-like protein LSm10	0.09	-	mit	0	Nucleus				123
Q750J3 UniProt NPD GO	ALG13_ASHGO	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.09	-	cyt	0	Endoplasmic reticulum (By similarity)				203

You are viewing entries 67201 to 67250 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.