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
Q23919 UniProt NPD GO	PGM_DICDI	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.16	-	mit	0	Cytoplasm (By similarity)				572
P33401 UniProt NPD GO	PGM1_YEAST	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.16	-	cyt	0	Cytoplasm				570
Q8UW30 UniProt NPD GO	PA27_LAPHA	Phospholipase A2 73 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.16	-	nuc	0	Secreted protein (By similarity)				118
P60044 UniProt NPD GO	PA22_NAJSG	Phospholipase A2 isoform 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.16	-	mit	0	Secreted protein			1XXW	126
P43434 UniProt NPD GO	PA21B_CAVPO	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.16	-	exc	0	Secreted protein				146
P04417 UniProt NPD GO	PA21B_AGKHA	Phospholipase A2, basic (EC 3.1.1.4) (PA2-I) (Phosphatidylcholine 2-acylhydrolase)	0.16	-	nuc	0	Secreted protein			1C1J	122
Q9PTA6 UniProt NPD GO	PA2C_BUNMU	Phospholipase A2, beta bungarotoxin A-AL3 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhy ...	0.16	-	nuc	0	Secreted protein (By similarity)				138
P47711 UniProt NPD GO	PA2GA_CAVPO	Phospholipase A2, membrane associated precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ( ...	0.16	-	exc	0	Membrane; peripheral membrane protein				145
P23026 UniProt NPD GO	PA2A_PSETE	Phospholipase A2, textilotoxin A chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.16	-	nuc	0	Secreted protein				118
P23027 UniProt NPD GO	PA2B_PSETE	Phospholipase A2, textilotoxin B chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.16	-	nuc	0	Secreted protein				121
O82549 UniProt NPD GO	PLDA1_BRAOC	Phospholipase D alpha 1 precursor (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine- ...	0.16	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				810
Q9SSQ9 UniProt NPD GO	PLDA2_ARATH	Phospholipase D alpha 2 (EC 3.1.4.4) (AtPLDalpha2) (PLD alpha 2) (Choline phosphatase 2) (Phosphatid ...	0.16	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found in vacuoles and also associated with plasma, ...				810
P55058 UniProt NPD GO	PLTP_HUMAN	Phospholipid transfer protein precursor (Lipid transfer protein II)	0.16	-	exc	0	Secreted protein	extracellular region [TAS]	172425		493
P52423 UniProt NPD GO	PUR3_VIGUN	Phosphoribosylglycinamide formyltransferase, chloroplast precursor (EC 2.1.2.2) (GART) (GAR transfor ...	0.16	-	mit	0	Plastid; chloroplast				312
P27774 UniProt NPD GO	KPPR_MESCR	Phosphoribulokinase, chloroplast precursor (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK)	0.16	-	mit	0	Plastid; chloroplast				397
P84738 UniProt NPD GO	PAL1F_EUGGR	Photoactivated adenylate cyclase subunit alpha-like protein 1224-5/1F	0.16	-	cyt	0	Flagellum. Paraxonemal body. And paraxonemal bodies (PABs)	flagellum [IDA]			1019
O78490 UniProt NPD GO	YCF3_GUITH	Photosystem I assembly protein ycf3	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				172
Q9M3M5 UniProt NPD GO	YCF3_SPIOL	Photosystem I assembly protein ycf3	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				165
Q6B8P5 UniProt NPD GO	YCF4_GRATL	Photosystem I assembly protein ycf4	0.16	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q8WI09 UniProt NPD GO	YCF4_PSINU	Photosystem I assembly protein ycf4	0.16	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q9S7H1 UniProt NPD GO	PSAD1_ARATH	Photosystem I reaction center subunit II-1, chloroplast precursor (Photosystem I 20 kDa subunit 1) ( ...	0.16	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side	thylakoid membrane (sensu Viridiplantae) [IDA]			208
P31336 UniProt NPD GO	PST2_GOSHI	Photosystem II 5 kDa protein, chloroplast precursor (PSII-T) (Light-regulated unknown 11 kDa protein ...	0.16	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				105
Q07356 UniProt NPD GO	CRTI_ARATH	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.16	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast				566
P33578 UniProt NPD GO	PRLPD_RAT	Placental prolactin-like protein D precursor (PRL-like protein D) (PLP-D) (Growth hormone-related pr ...	0.16	-	mit	0	Secreted protein				240
P27068 UniProt NPD GO	RR2_EPIVI	Plastid 30S ribosomal protein S2	0.16	-	mit	0	Plastid				237
P82412 UniProt NPD GO	RRP3_SPIOL	Plastid-specific 30S ribosomal protein 3, chloroplast precursor (PSRP-3)	0.16	-	mit	0	Plastid; chloroplast. Plastid				179
Q96CS7 UniProt NPD GO	PKHB2_HUMAN	Pleckstrin homology domain-containing family B member 2 (Evectin-2)	0.16	-	mit	0	Membrane; peripheral membrane protein (Potential)				222
O13340 UniProt NPD GO	CARP_PODAN	Podosporapepsin precursor (EC 3.4.23.-)	0.16	-	cyt	0					425
P32506 UniProt NPD GO	PVR_CERAE	Poliovirus receptor precursor (CD155 antigen)	0.16	-	end	1	Isoform alpha: Cell membrane; single-pass type I membrane protein. Isoform beta, isoform gamma: Secr ...				417
P57723 UniProt NPD GO	PCBP4_HUMAN	Poly(rC)-binding protein 4 (Alpha-CP4)	0.16	-	nuc	0	Cytoplasm				403
P14216 UniProt NPD GO	PPM2_LIMPO	Polyphemusin-2 (Polyphemusin II)	0.16	-		0	Secreted protein				18
Q8K1R3 UniProt NPD GO	PNPT1_MOUSE	Polyribonucleotide nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.8) (PNPase 1) (Polynu ...	0.16	-	end	0	Mitochondrion (By similarity)			1WHU	783
P12027 UniProt NPD GO	PSGP_ONCMY	Polysialoglycoprotein precursor (PSGP) (Apopolysialoglycoprotein) (apoPSGP)	0.16	-	nuc	0					542
P08397 UniProt NPD GO	HEM3_HUMAN	Porphobilinogen deaminase (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogen ...	0.16	-	cyt	0	Cytoplasm (Probable)		609806		361
Q9HB14 UniProt NPD GO	KCNKD_HUMAN	Potassium channel subfamily K member 13 (Tandem pore domain halothane-inhibited potassium channel 1) ...	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)		607367		408
P55927 UniProt NPD GO	KAX71_PANIM	Potassium channel toxin alpha-KTx 7.1 precursor (Toxin PiTX-K-alpha) (Pandinotoxin-alpha) (Potassium ...	0.16	-	nuc	0	Secreted protein			2PTA	47
Q9XT97 UniProt NPD GO	PSN1_BOVIN	Presenilin-1 (EC 3.4.23.-) (PS-1) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit; Pre ...	0.16	+	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			478
P49794 UniProt NPD GO	MCH_OREMO	Pro-MCH precursor [Contains: Melanin-concentrating hormone (MCH)]	0.16	-	end	1 *					136
P20382 UniProt NPD GO	MCH_HUMAN	Pro-MCH precursor [Contains: Neuropeptide-glycine-glutamic acid (NGE) (Neuropeptide G-E); Neuropepti ...	0.16	-	exc	1 *	Secreted protein	extracellular region [NAS]	176795		165
Q9US13 UniProt NPD GO	RPN9_SCHPO	Probable 26S proteasome regulatory subunit rpn9	0.16	-	cyt	0		nucleus [TAS]			381
Q8SV74 UniProt NPD GO	PSF2_ENCCU	Probable DNA replication complex GINS protein PSF2	0.16	-	cyt	0	Nucleus (By similarity)				175
Q9UTC3 UniProt NPD GO	PSF3_SCHPO	Probable DNA replication complex GINS protein psf3	0.16	-	nuc	0	Nucleus (By similarity)				166
Q3U487 UniProt NPD GO	HECD3_MOUSE	Probable E3 ubiquitin-protein ligase HECTD3 (HECT domain-containing protein 3)	0.16	-	cyt	0					861
Q10434 UniProt NPD GO	CAPZA_SCHPO	Probable F-actin capping protein subunit alpha	0.16	-	nuc	0		actin cortical patch [IDA] actin filament [IDA] cell tip [IDA] F-actin capping protein complex [IDA]			256
Q80T62 UniProt NPD GO	GP101_MOUSE	Probable G-protein coupled receptor 101	0.16	-	end	7 *	Membrane; multi-pass membrane protein				511
Q10306 UniProt NPD GO	CISY_SCHPO	Probable citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				473
P55933 UniProt NPD GO	CKS1_PHYPO	Probable cyclin-dependent kinases regulatory subunit	0.16	-	nuc	0					84
Q6FP20 UniProt NPD GO	ATG4_CANGA	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.16	-	cyt	0	Cytoplasm (By similarity)				483
P43295 UniProt NPD GO	A494_ARATH	Probable cysteine proteinase A494 precursor (EC 3.4.22.-)	0.16	-	gol	0					361
Q9VLZ7 UniProt NPD GO	C4D21_DROME	Probable cytochrome P450 4d21 (EC 1.14.-.-) (CYPIVD21)	0.16	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				511

You are viewing entries 56051 to 56100 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.