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
P17801 UniProt NPD GO	KPRO_MAIZE	Putative receptor protein kinase ZmPK1 precursor (EC 2.7.11.1)	0.23	-	end	2 *	Membrane; single-pass type I membrane protein				817
Q08485 UniProt NPD GO	THIX_YEAST	Putative thiamine transporter YOR071C	0.23	-	end	10 *	Membrane; multi-pass membrane protein				598
Q12084 UniProt NPD GO	YD020_YEAST	Putative uridine kinase YDR020C (EC 2.7.1.48)	0.23	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			232
Q8R107 UniProt NPD GO	PX19_MOUSE	Px19-like protein	0.23	-	cyt	0					217
P79076 UniProt NPD GO	P2OX_TRAVE	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.23	-	mit	0	Hyphal periplasmic space (By similarity)				623
Q8J2V8 UniProt NPD GO	P2OX_TRIMT	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.23	-	nuc	0					564
Q5E9K3 UniProt NPD GO	PNPO_BOVIN	Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) (Pyridoxamine-phosphate oxidase)	0.23	-	mit	0					261
P32585 UniProt NPD GO	MED18_YEAST	RNA polymerase II mediator complex subunit 18 (Suppressor of RNA polymerase B 5)	0.23	-	nuc	0	Nucleus	mediator complex [IDA]			307
O65155 UniProt NPD GO	KELP_ARATH	RNA polymerase II transcriptional coactivator KELP	0.23	-	nuc	0	Nucleus (By similarity)				165
Q08473 UniProt NPD GO	SQD_DROME	RNA-binding protein squid (Heterogeneous nuclear ribonucleoprotein 40) (HNRNP 40)	0.23	+	cyt	0	Nucleus. Cytoplasm. It is possible that some isoforms are found only in one of these locations	chromatin [IDA] cytoplasm [TAS] nucleus [IDA] omega speckle [IDA] polytene chromosome puff [IDA]			344
Q9H0Z9 UniProt NPD GO	RNPC1_HUMAN	RNA-binding region-containing protein 1 (HSRNASEB) (ssDNA-binding protein SEB4) (CLL-associated anti ...	0.23	-	cyt	0				2CQD	216
P51153 UniProt NPD GO	RAB13_HUMAN	Ras-related protein Rab-13	0.23	-	nuc	0	Cell membrane; cell-cell junction; tight junction; lipid-anchor; cytoplasmic side. Cytoplasmic vesic ...	tight junction [TAS]	602672		203
Q9JKM7 UniProt NPD GO	RAB37_MOUSE	Ras-related protein Rab-37	0.23	-	cyt	0	Secretory granules	secretory granule [IDA]			223
Q92930 UniProt NPD GO	RAB8B_HUMAN	Ras-related protein Rab-8B	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q39434 UniProt NPD GO	RB2BV_BETVU	Ras-related protein Rab2BV	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
Q9BQQ7 UniProt NPD GO	RTP3_HUMAN	Receptor-transporting protein 3 (Transmembrane protein 7)	0.23	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)		607181		232
Q18211 UniProt NPD GO	RCC1_CAEEL	Regulator of chromosome condensation (Cell cycle regulatory protein) (RCC1 homolog)	0.23	-	nuc	0	Nucleus				569
Q5U2W9 UniProt NPD GO	RENAL_RAT	Renalase precursor (EC 1.4.-.-)	0.23	-	mit	0	Secreted protein (By similarity)				315
Q9TSZ1 UniProt NPD GO	RENI_CALJA	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.23	-	mit	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				400
Q5ZJJ2 UniProt NPD GO	RFA1_CHICK	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (p70 ...	0.23	-	nuc	0	Nucleus (By similarity)				614
Q8BP92 UniProt NPD GO	RCN2_MOUSE	Reticulocalbin-2 precursor (Taipoxin-associated calcium-binding protein 49) (TCBP-49)	0.23	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				320
Q8BYK4 UniProt NPD GO	RDH12_MOUSE	Retinol dehydrogenase 12 (EC 1.1.1.-)	0.23	-	nuc	1 *		intracellular [ISS]			316
P08134 UniProt NPD GO	RHOC_HUMAN	Rho-related GTP-binding protein RhoC precursor (H9)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		165380	1Z2C	193
Q62159 UniProt NPD GO	RHOC_MOUSE	Rho-related GTP-binding protein RhoC precursor (Silica-induced gene 61 protein) (SIG-61)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	nucleus [IDA] plasma membrane [IDA]			193
Q9H4E5 UniProt NPD GO	RHOJ_HUMAN	Rho-related GTP-binding protein RhoJ (Tc10-like GTP-binding protein TCL)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		607653		214
P25791 UniProt NPD GO	RBTN2_HUMAN	Rhombotin-2 (Cysteine-rich protein TTG-2) (T-cell translocation protein 2) (LIM-only protein 2)	0.23	-	nuc	0	Nucleus (Potential)		180385		158
P25801 UniProt NPD GO	RBTN2_MOUSE	Rhombotin-2 (Cysteine-rich protein TTG-2) (T-cell translocation protein 2) (LIM-only protein 2)	0.23	-	nuc	0	Nucleus (Potential)			1J2O	158
O80322 UniProt NPD GO	RNS1_PYRPY	Ribonuclease S-1 precursor (EC 3.1.27.1) (S1-RNase)	0.23	-	nuc	1 *					228
Q01796 UniProt NPD GO	RNS2_SOLTU	Ribonuclease S-2 precursor (EC 3.1.27.1) (Stylar glycoprotein 2) (S2-RNase)	0.23	-	vac	0	Secreted protein; extracellular space				223
P36159 UniProt NPD GO	RNZ_YEAST	Ribonuclease Z (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease)	0.23	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			838
P07847 UniProt NPD GO	RNAS1_AEPME	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.23	-	nuc	0	Secreted protein				124
P00672 UniProt NPD GO	RNAS1_HIPAM	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.23	-	nuc	0	Secreted protein				124
P00682 UniProt NPD GO	RNAS1_MESAU	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.23	-	nuc	0	Secreted protein				124
P16137 UniProt NPD GO	RBS4_ACEME	Ribulose bisphosphate carboxylase small chain 4, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.23	-	mit	0	Plastid; chloroplast				182
Q9P7E3 UniProt NPD GO	DCAM_SCHPO	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.23	-	cyt	0					378
Q42613 UniProt NPD GO	DCAM1_BRAJU	S-adenosylmethionine decarboxylase proenzyme 1 (EC 4.1.1.50) (AdoMetDC 1) (SamDC 1) [Contains: S-ade ...	0.23	-	nuc	0					368
Q9SL48 UniProt NPD GO	SLY1_ARATH	SEC1-family transport protein SLY1 (AtSLY1)	0.23	-	nuc	0					627
Q91VW3 UniProt NPD GO	SH3L3_MOUSE	SH3 domain-binding glutamic acid-rich-like protein 3	0.23	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)			1T1V	93
Q8NBJ9 UniProt NPD GO	SIDT2_HUMAN	SID1 transmembrane family member 2 precursor	0.23	-	end	9	Membrane; multi-pass membrane protein (Potential)				832
Q9GZT3 UniProt NPD GO	SLIRP_HUMAN	SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor	0.23	-	mit	0	Mitochondrion; predominantly. Nucleus; some fraction is nuclear. In the nucleus, it is recruited to ...		610211		109
P40666 UniProt NPD GO	CH02_CHICK	SRY-related protein CH2 (Fragment)	0.23	-	nuc	0	Nucleus (Potential)				54
Q8BTY8 UniProt NPD GO	SCFD2_MOUSE	Sec1 family domain-containing protein 2 (Syntaxin-binding protein 1-like 1) (Neuronal Sec1)	0.23	-	vac	0					684
Q8N474 UniProt NPD GO	SFRP1_HUMAN	Secreted frizzled-related protein 1 precursor (sFRP-1) (Frizzled-related protein 1) (FRP-1) (Secrete ...	0.23	-	exc	1 *	Secreted protein. Cell membrane or extracellular matrix-associated. Released by heparin-binding		604156		314
Q3SZ20 UniProt NPD GO	GLYM_BOVIN	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.23	-	mit	0	Mitochondrion (By similarity)				504
Q9JIY5 UniProt NPD GO	HTRA2_MOUSE	Serine protease HTRA2, mitochondrial precursor (EC 3.4.21.-) (High temperature requirement protein A ...	0.23	-	mit	1	Mitochondrion; mitochondrial intermembrane space. Predominantly present in the intermembrane space. ...				458
O77416 UniProt NPD GO	ASP1_ANISI	Serine protease inhibitor 1 precursor (ASPI-1)	0.23	-	exc	0	Secreted protein (By similarity)				77
O77418 UniProt NPD GO	ASP3_ANISI	Serine protease inhibitor 3 precursor (ASPI-3)	0.23	-	exc	0	Secreted protein (By similarity)				77
P87179 UniProt NPD GO	YB1E_SCHPO	Serine-rich protein C30B4.01c precursor	0.23	-	mit	1 *	Membrane; single-pass membrane protein				374
Q60EX6 UniProt NPD GO	BSL1_ORYSA	Serine/threonine protein phosphatase BSL1 homolog (EC 3.1.3.16) (BSU1-like protein 1 homolog)	0.23	-	cyt	0	Nucleus (By similarity)				883
P50530 UniProt NPD GO	SCK1_SCHPO	Serine/threonine-protein kinase sck1 (EC 2.7.11.1)	0.23	-	nuc	0					696

You are viewing entries 47851 to 47900 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.