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
Q9VSF4 UniProt NPD GO	DHYS_DROME	Probable deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.20	-	cyt	0					368
Q9SSR8 UniProt NPD GO	DRL6_ARATH	Probable disease resistance protein At1g52660	0.20	-	cyt	0					375
O23317 UniProt NPD GO	DRL24_ARATH	Probable disease resistance protein At4g14610 (pCol1)	0.20	-	cyt	0					719
Q9W2D9 UniProt NPD GO	IF3C_DROME	Probable eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.20	-	cyt	0					222
Q19706 UniProt NPD GO	IF34_CAEEL	Probable eukaryotic translation initiation factor 3 subunit 4 (eIF-3 delta) (eIF3 p44) (eIF-3 RNA-bi ...	0.20	-	cyt	0					256
P36001 UniProt NPD GO	FOLC_YEAST	Probable folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Te ...	0.20	-	nuc	0	Mitochondrion	mitochondrion [IDA]			430
O14057 UniProt NPD GO	GUAD_SCHPO	Probable guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH)	0.20	-	cyt	0					527
Q8TGG8 UniProt NPD GO	GDA1_ASPFU	Probable guanosine-diphosphatase (EC 3.6.1.42) (GDPase)	0.20	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				503
Q6BXB6 UniProt NPD GO	SPC24_DEBHA	Probable kinetochore protein SPC24	0.20	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				227
Q9P601 UniProt NPD GO	MOB1_NEUCR	Probable maintenance of ploidy protein mob1	0.20	-	nuc	0					219
Q09632 UniProt NPD GO	YOF5_CAEEL	Probable oxidoreductase ZK1290.5 (EC 1.-.-.-)	0.20	-	nuc	0					321
Q8IVQ6 UniProt NPD GO	ZDH21_HUMAN	Probable palmitoyltransferase ZDHHC21 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 21) ( ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				265
Q5RB84 UniProt NPD GO	ZDH21_PONPY	Probable palmitoyltransferase ZDHHC21 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 21) ( ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				265
Q9D270 UniProt NPD GO	ZDH21_MOUSE	Probable palmitoyltransferase ZDHHC21 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 21) ( ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				265
Q9UUD8 UniProt NPD GO	YOD1_SCHPO	Probable peptidase C18A7.01 (EC 3.4.-.-)	0.20	-	mit	1 *					451
P90925 UniProt NPD GO	PH4H_CAEEL	Probable phenylalanine-4-hydroxylase 1 (EC 1.14.16.1) (PAH) (Phe-4-monooxygenase) (Biogenic amine sy ...	0.20	-	cyt	0					457
O16129 UniProt NPD GO	SYFM_DROME	Probable phenylalanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.20) (Phenylalanine--tRNA li ...	0.20	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)	mitochondrion [ISS]			453
Q6DBV4 UniProt NPD GO	PHOP1_BRARE	Probable phosphatase phospho1 (EC 3.1.3.-)	0.20	-	cyt	0					279
P98196 UniProt NPD GO	AT11A_HUMAN	Probable phospholipid-transporting ATPase IH (EC 3.6.3.1) (ATPase class I type 11A) (ATPase IS)	0.20	-	end	7	Membrane; multi-pass membrane protein		605868		1134
Q9UTD4 UniProt NPD GO	PFD4_SCHPO	Probable prefoldin subunit 4	0.20	-	nuc	0					123
Q09682 UniProt NPD GO	PSA4_SCHPO	Probable proteasome subunit alpha type 4 (EC 3.4.25.1)	0.20	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				248
O78428 UniProt NPD GO	YCF27_GUITH	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.20	-	cyt	0	Plastid; chloroplast				254
Q6FWD4 UniProt NPD GO	MCH1_CANGA	Probable transporter MCH1	0.20	+	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				489
Q07376 UniProt NPD GO	MCH1_YEAST	Probable transporter MCH1 (Monocarboxylate transporter homolog 1)	0.20	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein				486
Q17413 UniProt NPD GO	UCK_CAEEL	Probable uridine-cytidine kinase (EC 2.7.1.48) (UCK) (Uridine monophosphokinase) (Cytidine monophosp ...	0.20	-	exc	0					248
Q9LX65 UniProt NPD GO	VATH_ARATH	Probable vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump su ...	0.20	-	cyt	0					441
Q20666 UniProt NPD GO	VATH1_CAEEL	Probable vacuolar ATP synthase subunit H 1 (EC 3.6.3.14) (V-ATPase H subunit 1) (Vacuolar proton pum ...	0.20	-	nuc	0					451
Q8LF99 UniProt NPD GO	XTH6_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 6 precursor (EC 2.4.1.207) (At-XTH6) (XTH ...	0.20	-	vac	1 *	Secreted protein; extracellular space; apoplast (Probable)				292
P93349 UniProt NPD GO	XTH_TOBAC	Probable xyloglucan endotransglucosylase/hydrolase protein precursor (EC 2.4.1.207)	0.20	-	mit	0	Secreted protein; extracellular space; apoplast				295
Q02809 UniProt NPD GO	PLOD1_HUMAN	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.20	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...		225400		727
O09163 UniProt NPD GO	GON1_MESAU	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.20	-	nuc	0	Secreted protein				63
Q91330 UniProt NPD GO	GON2_RUTRU	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.20	-	exc	0	Secreted protein				86
P51922 UniProt NPD GO	GON3_PORNO	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.20	-	exc	1 *	Secreted protein				89
Q9Z0X1 UniProt NPD GO	PDCD8_MOUSE	Programmed cell death protein 8, mitochondrial precursor (EC 1.-.-.-) (Apoptosis-inducing factor)	0.20	-	nuc	0	Mitochondrion; mitochondrial intermembrane space. Nucleus. Translocated to the nucleus upon inductio ...	cytosol [TAS] microsome [IDA] mitochondrial intermembrane space [TAS] mitochondrial outer membrane [TAS] mitochondrion [IDA] nucleus [TAS] soluble fraction [IDA]		1GV4	612
Q9JM53 UniProt NPD GO	PDCD8_RAT	Programmed cell death protein 8, mitochondrial precursor (EC 1.-.-.-) (Apoptosis-inducing factor)	0.20	-	nuc	0	Mitochondrion; mitochondrial intermembrane space. Nucleus. Translocated to the nucleus upon inductio ...	mitochondrion [IDA] nucleus [IDA]			612
P58368 UniProt NPD GO	ANKH_BRARE	Progressive ankylosis protein homolog (ANK)	0.20	+	end	8 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS] outer membrane [ISS]			501
Q8TCW9 UniProt NPD GO	PKR1_HUMAN	Prokineticin receptor 1 (PK-R1) (G-protein coupled receptor 73) (GPR73a) (G-protein coupled receptor ...	0.20	+	end	7	Membrane; multi-pass membrane protein		607122		393
P81264 UniProt NPD GO	PRRP_BOVIN	Prolactin-releasing peptide precursor (PrRP) (Prolactin-releasing hormone) [Contains: Prolactin-rele ...	0.20	-	exc	1 *	Secreted protein				98
Q810F0 UniProt NPD GO	PRIMA_MOUSE	Proline-rich membrane anchor 1 precursor (PRiMA)	0.20	-	exc	1	Membrane; single-pass type I membrane protein				153
P13674 UniProt NPD GO	P4HA1_HUMAN	Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2- ...	0.20	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]	176710	1TJC	534
Q5RAG8 UniProt NPD GO	P4HA1_PONPY	Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2- ...	0.20	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				534
Q62786 UniProt NPD GO	FPRP_RAT	Prostaglandin F2 receptor negative regulator precursor (Prostaglandin F2-alpha receptor regulatory p ...	0.20	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Golgi ap ...				879
P97371 UniProt NPD GO	PSME1_MOUSE	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) ( ...	0.20	-	cyt	0					249
Q5R9L9 UniProt NPD GO	POMP_PONPY	Proteasome maturation protein (Proteassemblin)	0.20	-	nuc	0	Cytoplasm; cytosol (By similarity). Nucleus (By similarity)				141
Q9Y244 UniProt NPD GO	POMP_HUMAN	Proteasome maturation protein (Proteassemblin) (Protein UMP1 homolog) (hUMP1) (Voltage-gated K chann ...	0.20	-	nuc	0	Cytoplasm; cytosol. Nucleus				141
O82530 UniProt NPD GO	PSA4_PETHY	Proteasome subunit alpha type 4 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome subun ...	0.20	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
O82531 UniProt NPD GO	PSB1_PETHY	Proteasome subunit beta type 1 (EC 3.4.25.1) (20S proteasome alpha subunit F) (20S proteasome subuni ...	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				223
Q4PFI5 UniProt NPD GO	AF9_USTMA	Protein AF-9 homolog	0.20	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				431
P16550 UniProt NPD GO	APA1_YEAST	Protein APA1 [Includes: 5',5'''-P-1,P-4-tetraphosphate phosphorylase (EC 2.7.7.53) (Diadenosine 5',5 ...	0.20	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			320
Q9D2V5 UniProt NPD GO	CT004_MOUSE	Protein C20orf4 homolog	0.20	-	cyt	0					384

You are viewing entries 51051 to 51100 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.