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
Q6GM65 UniProt NPD GO	PLAP_XENLA	Phospholipase A-2-activating protein (PLAP)	0.17	-	nuc	0					799
Q9C5Y0 UniProt NPD GO	PLDD1_ARATH	Phospholipase D delta (EC 3.1.4.4) (AtPLDdelta) (PLD delta)	0.17	-	cyt	0	Membrane; peripheral membrane protein. Colocalization with cortical microtubules also occurs				868
Q9T051 UniProt NPD GO	PLDG2_ARATH	Phospholipase D gamma 2 (EC 3.1.4.4) (AtPLDgamma2) (PLD gamma 2)	0.17	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found mainly associated with intracellular membran ...				824
Q9T052 UniProt NPD GO	PLDG3_ARATH	Phospholipase D gamma 3 (EC 3.1.4.4) (AtPLDgamma3) (PLD gamma 3)	0.17	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found mainly associated with intracellular membran ...				866
Q9NRQ2 UniProt NPD GO	PLS4_HUMAN	Phospholipid scramblase 4 (PL scramblase 4) (Ca(2+)-dependent phospholipid scramblase 4) (TRA1)	0.17	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)	integral to membrane [NAS]	607612		329
O08618 UniProt NPD GO	KPRB_RAT	Phosphoribosyl pyrophosphate synthetase-associated protein 2 (PRPP synthetase-associated protein 2) ...	0.17	-	cyt	0					369
P09559 UniProt NPD GO	KPPR_SPIOL	Phosphoribulokinase, chloroplast precursor (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK)	0.17	-	nuc	0	Plastid; chloroplast				402
P84737 UniProt NPD GO	PALFB_EUGGR	Photoactivated adenylate cyclase subunit alpha-like protein FB	0.17	-	mit	0	Flagellum. Paraxonemal body. And paraxonemal bodies (PABs)	flagellum [IDA]			1019
Q08814 UniProt NPD GO	YCF3_GALSU	Photosystem I assembly protein ycf3	0.17	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
P56312 UniProt NPD GO	YCF4_CHLVU	Photosystem I assembly protein ycf4	0.17	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				183
P48192 UniProt NPD GO	YCF4_CYAPA	Photosystem I assembly protein ycf4	0.17	-	nuc	2 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				187
P12372 UniProt NPD GO	PSAD_LYCES	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.17	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				208
O81003 UniProt NPD GO	PSK2_ARATH	Phytosulfokines 2 precursor (AtPSK2) [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); ...	0.17	-	nuc	0	Secreted protein				87
Q7ZTA0 UniProt NPD GO	CRVP_AGKPI	Piscivorin precursor	0.17	-	exc	0	Secreted protein				240
Q04785 UniProt NPD GO	GP1BB_PAPCY	Platelet glycoprotein Ib beta chain precursor (GP-Ib beta) (GPIbB) (GPIb-beta) (Antigen CD42b-beta) ...	0.17	+	end	1	Membrane; single-pass type I membrane protein				208
Q28017 UniProt NPD GO	PAFA_BOVIN	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.17	-	exc	0	Secreted protein; extracellular space				444
P32507 UniProt NPD GO	PVRL2_MOUSE	Poliovirus receptor-related protein 2 precursor (Murine herpesvirus entry protein B) (mHveB) (Nectin ...	0.17	-	end	1	Membrane; single-pass type I membrane protein	intercellular junction [IDA]			530
Q8VZY6 UniProt NPD GO	FIE2_MAIZE	Polycomb group protein FIE2 (FERTILIZATION-INDEPENDENT ENDOSPERM 2)	0.17	-	cyt	0					379
Q91VA6 UniProt NPD GO	PDIP2_MOUSE	Polymerase delta-interacting protein 2	0.17	-	mit	0	Nucleus (Probable)	mitochondrion [IDA]			368
P22907 UniProt NPD GO	HEM3_MOUSE	Porphobilinogen deaminase (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogen ...	0.17	-	cyt	0					361
Q6MW51 UniProt NPD GO	HEM3_NEUCR	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.17	-	cyt	0					337
Q9FE38 UniProt NPD GO	POT3_ARATH	Potassium transporter 3 (AtPOT3) (AtKUP4) (AtKT3) (Tiny root hair 1 protein)	0.17	-	end	14 *	Cell membrane; multi-pass membrane protein (Potential)				775
Q9TUH9 UniProt NPD GO	KCNE1_PIG	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.17	-	mit	1 *	Membrane; single-pass type I membrane protein				130
Q9BDR0 UniProt NPD GO	KCNE2_RABIT	Potassium voltage-gated channel subfamily E member 2 (Minimum potassium ion channel-related peptide ...	0.17	-	nuc	1 *	Membrane; single-pass type I membrane protein				71
Q9ULS6 UniProt NPD GO	KCNS2_HUMAN	Potassium voltage-gated channel subfamily S member 2 (Voltage-gated potassium channel subunit Kv9.2) ...	0.17	-	end	4	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...		602906		477
O35174 UniProt NPD GO	KCNS2_MOUSE	Potassium voltage-gated channel subfamily S member 2 (Voltage-gated potassium channel subunit Kv9.2) ...	0.17	-	end	4	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. May not reach the ...				477
Q9ER26 UniProt NPD GO	KCNS2_RAT	Potassium voltage-gated channel subfamily S member 2 (Voltage-gated potassium channel subunit Kv9.2) ...	0.17	-	end	4	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...				477
P28540 UniProt NPD GO	SECY_PAVLU	Preprotein translocase secY subunit	0.17	-	end	10 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				419
Q6RH31 UniProt NPD GO	PSN1_CANFA	Presenilin-1 (EC 3.4.23.-) (PS-1) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit; Pre ...	0.17	+	end	9	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]			466
Q9JKQ2 UniProt NPD GO	S26A5_MERUN	Prestin (Solute carrier family 26 member 5)	0.17	-	end	10	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Basolateral wall of outer hai ...				744
Q99NH7 UniProt NPD GO	S26A5_MOUSE	Prestin (Solute carrier family 26 member 5)	0.17	-	end	10	Integral membrane protein; lateral wall of outer hair cells (By similarity)	basolateral plasma membrane [IDA]			744
Q5KMX3 UniProt NPD GO	1A1D_CRYNE	Probable 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) (ACC deaminase) (ACCD)	0.17	-	mit	0					345
Q8X097 UniProt NPD GO	ACL1_NEUCR	Probable ATP-citrate synthase subunit 1 (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase 1) (Citrate cleavag ...	0.17	-	cyt	0	Cytoplasm (By similarity)				670
P43569 UniProt NPD GO	YFC8_YEAST	Probable ATP-dependent transporter YFL028C	0.17	-	cyt	0		CCR4-NOT complex [IPI] cytoplasm [IDA]			289
O44441 UniProt NPD GO	ATIF2_CAEEL	Probable ATPase inhibitor B0546.1, mitochondrial precursor	0.17	-	mit	0	Mitochondrion (Potential)				109
P31941 UniProt NPD GO	ABC3A_HUMAN	Probable DNA dC->dU-editing enzyme APOBEC-3A (EC 3.5.4.-) (Phorbolin-1)	0.17	-	cyt	0			607109		199
O94553 UniProt NPD GO	RPC6_SCHPO	Probable DNA-directed RNA polymerase III 34 kDa polypeptide (EC 2.7.7.6)	0.17	-	nuc	0	Nucleus (Probable)				301
Q9SCY3 UniProt NPD GO	FKBP4_ARATH	Probable FKBP-type peptidyl-prolyl cis-trans isomerase 4, chloroplast precursor (EC 5.2.1.8) (PPIase ...	0.17	-	mit	0	Plastid; chloroplast (Potential)	thylakoid membrane (sensu Viridiplantae) [IDA]			217
Q96P66 UniProt NPD GO	GP101_HUMAN	Probable G-protein coupled receptor 101	0.17	-	end	7 *	Membrane; multi-pass membrane protein		300393		508
Q8BXS7 UniProt NPD GO	GP152_MOUSE	Probable G-protein coupled receptor 152	0.17	-	end	7 *	Membrane; multi-pass membrane protein				511
Q66H29 UniProt NPD GO	GP160_RAT	Probable G-protein coupled receptor 160	0.17	-	end	7 *	Membrane; multi-pass membrane protein				336
Q61121 UniProt NPD GO	GPR19_MOUSE	Probable G-protein coupled receptor 19	0.17	-	end	7	Membrane; multi-pass membrane protein				415
Q9UTS7 UniProt NPD GO	ASPG2_SCHPO	Probable L-asparaginase 2 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 2)	0.17	-	nuc	1 *	Cell wall (By similarity)				356
Q8TFF8 UniProt NPD GO	ASPG4_SCHPO	Probable L-asparaginase 4 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 4)	0.17	-	nuc	1 *	Cell wall (By similarity)				356
Q8H930 UniProt NPD GO	ARAE1_ORYSA	Probable UDP-arabinose 4-epimerase 1 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 1) (UDP-galactose 4-epim ...	0.17	+	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				421
P91134 UniProt NPD GO	PURA_CAEEL	Probable adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)	0.17	-	cyt	0	Cytoplasm (By similarity)				434
Q7Y1E6 UniProt NPD GO	PIP28_ORYSA	Probable aquaporin PIP2.8 (Plasma membrane intrinsic protein 2.8) (OsPIP2.8)	0.17	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				280
Q9W5U3 UniProt NPD GO	CHIT1_DROME	Probable chitinase 1 (EC 3.2.1.14)	0.17	-	cyt	0					508
Q9VAI1 UniProt NPD GO	CIA30_DROME	Probable complex I intermediate-associated protein 30, mitochondrial precursor	0.17	-	mit	0	Mitochondrion (Probable)	respiratory chain complex I (sensu Eukaryota) [ISS]			296
Q09736 UniProt NPD GO	CP51_SCHPO	Probable cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanos ...	0.17	-	end	2 *					495

You are viewing entries 54701 to 54750 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.