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
P54777 UniProt NPD GO	PEX6_RAT	Peroxisome assembly factor 2 (PAF-2) (Peroxisomal-type ATPase 1) (Peroxin-6) (Peroxisomal biogenesis ...	0.21	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane. Associated with peroxisomal membranes				978
Q6BMZ7 UniProt NPD GO	PEX22_DEBHA	Peroxisome assembly protein 22 (Peroxin-22)	0.21	-	mit	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein (By similarity)				196
Q7Z412 UniProt NPD GO	PEX26_HUMAN	Peroxisome assembly protein 26 (Peroxin-26)	0.21	-	cyt	0	Peroxisome; peroxisomal membrane; single-pass type II membrane protein		608666		305
P37230 UniProt NPD GO	PPARA_RAT	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.21	+	nuc	0	Nucleus				468
Q01861 UniProt NPD GO	PAL1_PEA	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.21	-	nuc	0	Cytoplasm (Probable)				723
Q9WUA2 UniProt NPD GO	SYFB_MOUSE	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.21	-	cyt	0	Cytoplasm (By similarity)				589
Q8VIN1 UniProt NPD GO	PEBP2_MOUSE	Phosphatidylethanolamine-binding protein 2 (PEBP-2)	0.21	+	cyt	0	Cytoplasm. At the cell periphery in pachytene spermatocytes and round spermatids, in the distal dors ...			1KN3	187
Q9QYT7 UniProt NPD GO	PIGQ_MOUSE	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q (EC 2.4.1.198) (Phosphatidylinositol- ...	0.21	-	end	5	Membrane; multi-pass membrane protein (Potential)				580
Q8BSF4 UniProt NPD GO	PISD_MOUSE	Phosphatidylserine decarboxylase proenzyme (EC 4.1.1.65) [Contains: Phosphatidylserine decarboxylase ...	0.21	-	mit	0	Mitochondrion (By similarity)				406
P21642 UniProt NPD GO	PPCKM_CHICK	Phosphoenolpyruvate carboxykinase [GTP], mitochondrial precursor (EC 4.1.1.32) (Phosphoenolpyruvate ...	0.21	-	mit	0	Mitochondrion			2FAH	640
Q9SM59 UniProt NPD GO	PGMP_PEA	Phosphoglucomutase, chloroplast precursor (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.21	-	mit	0	Plastid; chloroplast				626
P70089 UniProt NPD GO	PA27_TRIGA	Phospholipase A2 isozyme 7 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme VII) (Phosphatidylcholin ...	0.21	-	exc	0	Secreted protein				138
P31482 UniProt NPD GO	PA2GA_MOUSE	Phospholipase A2, membrane associated precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ( ...	0.21	-	nuc	0	Membrane; peripheral membrane protein				146
P58195 UniProt NPD GO	PLS1_RAT	Phospholipid scramblase 1 (PL scramblase 1) (Ca(2+)-dependent phospholipid scramblase 1)	0.21	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				335
Q9NRY7 UniProt NPD GO	PLS2_HUMAN	Phospholipid scramblase 2 (PL scramblase 2) (Ca(2+)-dependent phospholipid scramblase 2)	0.21	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)	plasma membrane [NAS]	607610		224
Q8S9F1 UniProt NPD GO	PCYAB_EUGGR	Photoactivated adenylate cyclase subunit beta (EC 4.6.1.1) (Photoactivated adenylyl cyclase beta sub ...	0.21	-	mit	0	Paraflagellar body, flagellum and paraxonemal bodies (PABs)	flagellum [IDA]			859
Q8S8X3 UniProt NPD GO	YCF3_ATRBE	Photosystem I assembly protein ycf3	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q7YJX1 UniProt NPD GO	YCF3_CALFE	Photosystem I assembly protein ycf3	0.21	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q5SD07 UniProt NPD GO	YCF3_HUPLU	Photosystem I assembly protein ycf3	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				169
Q7YJW2 UniProt NPD GO	YCF4_CALFE	Photosystem I assembly protein ycf4	0.21	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P29302 UniProt NPD GO	PSAD_NICSY	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				204
P12353 UniProt NPD GO	PSAD_SPIOL	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.21	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side				212
Q5Z5A8 UniProt NPD GO	P2SAF_ORYSA	Photosystem II stability/assembly factor HCF136, chloroplast precursor	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; lumenal side (By ...				416
P55004 UniProt NPD GO	PHYE_IPONI	Phytochrome E	0.21	-	cyt	0					1115
P36955 UniProt NPD GO	PEDF_HUMAN	Pigment epithelium-derived factor precursor (PEDF) (EPC-1)	0.21	-	end	0	Secreted protein	extracellular region [IDA]	172860	1IMV	418
Q9SEE4 UniProt NPD GO	PIRL_LYCES	Pirin-like protein	0.21	-	mit	0	Nucleus (By similarity)				291
P20020 UniProt NPD GO	AT2B1_HUMAN	Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) (PMCA1) (Plasma membrane calcium pump iso ...	0.21	-	end	7	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	108731	1CFF	1258
P11505 UniProt NPD GO	AT2B1_RAT	Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) (PMCA1) (Plasma membrane calcium pump iso ...	0.21	-	end	7	Cell membrane; multi-pass membrane protein				1258
P58165 UniProt NPD GO	AT2B2_OREMO	Plasma membrane calcium-transporting ATPase 2 (EC 3.6.3.8) (PMCA2) (Plasma membrane calcium pump iso ...	0.21	+	end	7	Cell membrane; multi-pass membrane protein (By similarity)				1112
P40088 UniProt NPD GO	FTR1_YEAST	Plasma membrane iron permease	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			404
Q14651 UniProt NPD GO	PLSI_HUMAN	Plastin-1 (I-plastin) (Intestine-specific plastin)	0.21	-	cyt	0	Cytoplasm		602734		629
Q6DE92 UniProt NPD GO	PXDC2_XENLA	Plexin domain-containing protein 2 precursor	0.21	-	end	1	Membrane; single-pass type I membrane protein (Potential)				513
Q9NQS3 UniProt NPD GO	PVRL3_HUMAN	Poliovirus receptor-related protein 3 precursor (Nectin-3) (CDw113 antigen)	0.21	-	end	1	Membrane; single-pass membrane protein (Potential)		607147		549
P58822 UniProt NPD GO	PGIP2_PHAVU	Polygalacturonase inhibitor 2 precursor (Polygalacturonase-inhibiting protein) (PGIP-2)	0.21	-	exc	0	Cell wall; peripheral membrane protein			1OGQ	342
Q8TCS8 UniProt NPD GO	PNPT1_HUMAN	Polyribonucleotide nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.8) (PNPase 1) (Polynu ...	0.21	-	mit	0	Mitochondrion				783
P97438 UniProt NPD GO	KCNK2_MOUSE	Potassium channel subfamily K member 2 (Outward rectifying potassium channel protein TREK-1) (Two-po ...	0.21	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	voltage-gated potassium channel complex [IDA]			411
O88454 UniProt NPD GO	KCNK4_MOUSE	Potassium channel subfamily K member 4 (TWIK-related arachidonic acid-stimulated potassium channel p ...	0.21	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				398
Q9ES08 UniProt NPD GO	KCNK9_RAT	Potassium channel subfamily K member 9 (Acid-sensitive potassium channel protein TASK-3) (TWIK-relat ...	0.21	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				396
P22460 UniProt NPD GO	KCNA5_HUMAN	Potassium voltage-gated channel subfamily A member 5 (Voltage-gated potassium channel subunit Kv1.5) ...	0.21	-	end	3	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176267		613
P17658 UniProt NPD GO	KCNA6_HUMAN	Potassium voltage-gated channel subfamily A member 6 (Voltage-gated potassium channel subunit Kv1.6) ...	0.21	-	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176257		529
Q8TAE7 UniProt NPD GO	KCNG3_HUMAN	Potassium voltage-gated channel subfamily G member 3 (Voltage-gated potassium channel subunit Kv6.3) ...	0.21	+	end	7	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. Has to be associa ...	endoplasmic reticulum [IDA] plasma membrane [IDA]	606767		436
P50992 UniProt NPD GO	ATP4B_MOUSE	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.21	-	nuc	1 *	Membrane; single-pass type II membrane protein				294
Q75EF0 UniProt NPD GO	SYF1_ASHGO	Pre-mRNA-splicing factor SYF1	0.21	-	cyt	0	Nucleus (By similarity)				803
O13615 UniProt NPD GO	PRP46_SCHPO	Pre-mRNA-splicing factor prp46 (Pre-mRNA-processing protein 5) (Complexed with cdc5 protein 1)	0.21	-	cyt	0	Nucleus (Probable)	spliceosome complex [IDA]			473
Q2KHV4 UniProt NPD GO	PARL_BOVIN	Presenilins-associated rhomboid-like protein, mitochondrial precursor (EC 3.4.21.105) (Mitochondrial ...	0.21	-	nuc	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Mitochondrion; mitochondri ...				377
Q5TZ07 UniProt NPD GO	PPC2A_BRARE	Presqualene diphosphate phosphatase A (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-cont ...	0.21	-	end	3	Membrane; multi-pass membrane protein (Potential)				288
Q27483 UniProt NPD GO	K6PF_CAEEL	Probable 6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.21	-	nuc	0					756
Q8SQI1 UniProt NPD GO	3MG_ENCCU	Probable DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase)	0.21	-	cyt	0	Nucleus (Potential)				208
Q7TQN8 UniProt NPD GO	GP119_RAT	Probable G-protein coupled receptor 119	0.21	-	end	7 *	Membrane; multi-pass membrane protein				468
Q9UNW8 UniProt NPD GO	GP132_HUMAN	Probable G-protein coupled receptor 132 (G2 accumulation protein)	0.21	+	end	7 *	Membrane; multi-pass membrane protein (Probable). Internalized and accumulated in endosomal compartm ...		606167		380

You are viewing entries 49851 to 49900 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.