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
Q13084 UniProt NPD GO	RM28_HUMAN	39S ribosomal protein L28, mitochondrial precursor (L28mt) (MRP-L28) (Melanoma antigen p15) (Melanom ...	0.36	-	cyt	0	Mitochondrion	mitochondrial ribosome [NAS]	604853		256
Q96X22 UniProt NPD GO	HPPD_MAGGR	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase)	0.36	-	cyt	0					419
P35687 UniProt NPD GO	RS21_ORYSA	40S ribosomal protein S21	0.36	-	cyt	0					82
O93931 UniProt NPD GO	RS26_SCHCO	40S ribosomal protein S26	0.36	-	nuc	0					126
Q6PBY1 UniProt NPD GO	RS3A_BRARE	40S ribosomal protein S3a	0.36	+	nuc	0					266
Q5RT64 UniProt NPD GO	RS7_FELCA	40S ribosomal protein S7	0.36	-	nuc	0					194
P62081 UniProt NPD GO	RS7_HUMAN	40S ribosomal protein S7	0.36	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA] nucleolus [IDA] ribosome [IDA]	603658		194
P62082 UniProt NPD GO	RS7_MOUSE	40S ribosomal protein S7	0.36	-	nuc	0					194
Q962S0 UniProt NPD GO	RS7_SPOFR	40S ribosomal protein S7	0.36	-	nuc	0					190
P62083 UniProt NPD GO	RS7_RAT	40S ribosomal protein S7 (S8)	0.36	-	nuc	0					194
P26786 UniProt NPD GO	RS7A_YEAST	40S ribosomal protein S7-A (RP30)	0.36	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]			189
Q13702 UniProt NPD GO	RAPSN_HUMAN	43 kDa receptor-associated protein of the synapse (RAPsyn) (Acetylcholine receptor-associated 43 kDa ...	0.36	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of postsynaptic me ...		608931		411
O35552 UniProt NPD GO	F263_RAT	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6PF-2-K/Fru-2,6-P2ASE brain-type isozyme) (RB ...	0.36	-	nuc	0					555
P41093 UniProt NPD GO	RL18A_DROME	60S ribosomal protein L18a	0.36	-	cyt	0					177
Q9LUD4 UniProt NPD GO	R18A3_ARATH	60S ribosomal protein L18a-3	0.36	-	nuc	0					178
O00822 UniProt NPD GO	RL28_TRYCR	60S ribosomal protein L28	0.36	-	nuc	0					146
Q9M0E2 UniProt NPD GO	RL282_ARATH	60S ribosomal protein L28-2	0.36	-	nuc	0					143
Q751I7 UniProt NPD GO	RL32_ASHGO	60S ribosomal protein L32	0.36	-	nuc	0					131
Q9D1R9 UniProt NPD GO	RL34_MOUSE	60S ribosomal protein L34	0.36	-	mit	0					116
Q29223 UniProt NPD GO	RL34_PIG	60S ribosomal protein L34	0.36	-	mit	0					116
P47834 UniProt NPD GO	RL36_CANAL	60S ribosomal protein L36 (L39)	0.36	-	nuc	0					99
P49633 UniProt NPD GO	RL40_ACACA	60S ribosomal protein L40 (CEP52)	0.36	-	nuc	0					52
Q2TBW6 UniProt NPD GO	ARL3_BOVIN	ADP-ribosylation factor-like protein 3	0.36	-	cyt	0					182
Q9Y7J4 UniProt NPD GO	ARPC3_SCHPO	ARP2/3 complex 21 kDa subunit (p21-ARC)	0.36	-	nuc	0					174
Q5MB13 UniProt NPD GO	ABCG2_MACMU	ATP-binding cassette sub-family G member 2	0.36	-	end	5	Cell membrane; multi-pass membrane protein (By similarity)				654
P58428 UniProt NPD GO	ABCG8_RAT	ATP-binding cassette sub-family G member 8 (Sterolin-2)	0.36	-	end	6	Membrane; multi-pass membrane protein (Probable)	ATP-binding cassette (ABC) transporter complex [TAS]			694
P49574 UniProt NPD GO	CLPC_ODOSI	ATP-dependent Clp protease ATP-binding subunit clpA homolog	0.36	-	cyt	0	Plastid; chloroplast				885
Q2UGK3 UniProt NPD GO	DED1_ASPOR	ATP-dependent RNA helicase ded1 (EC 3.6.1.-)	0.36	-	nuc	0	Cytoplasm (By similarity)				675
Q15842 UniProt NPD GO	IRK8_HUMAN	ATP-sensitive inward rectifier potassium channel 8 (Potassium channel, inwardly rectifying subfamily ...	0.36	-	end	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	600935		424
Q13085 UniProt NPD GO	COA1_HUMAN	Acetyl-CoA carboxylase 1 (EC 6.4.1.2) (ACC-alpha) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.36	-	nuc	0	Cytoplasm		200350		2346
Q28559 UniProt NPD GO	COA1_SHEEP	Acetyl-CoA carboxylase 1 (EC 6.4.1.2) (ACC-alpha) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.36	-	nuc	0	Cytoplasm				2346
P58154 UniProt NPD GO	ACHP_LYMST	Acetylcholine-binding protein precursor (ACh-binding protein) (AchBP)	0.36	-	exc	0	Secreted protein. In synaptic cleft. Released in an acetylcholine-dependent manner in the synaptic c ...			1YI5	229
Q27459 UniProt NPD GO	ACE1_CAEBR	Acetylcholinesterase 1 precursor (EC 3.1.1.7) (AChE 1)	0.36	-	exc	0	Secreted protein (Potential). Membrane; peripheral membrane protein (Potential). May be secreted or ...				620
Q43694 UniProt NPD GO	ADF2_MAIZE	Actin-depolymerizing factor 2 (ADF 2) (ZmABP2) (ZmADF2)	0.36	-	nuc	0					139
Q4P2E8 UniProt NPD GO	ARP4_USTMA	Actin-like protein ARP4	0.36	-	cyt	0	Nucleus (By similarity)				534
Q01771 UniProt NPD GO	STADS_BRANA	Acyl-[acyl-carrier-protein] desaturase, seed specific, chloroplast precursor (EC 1.14.19.2) (Stearoy ...	0.36	-	mit	0	Plastid; chloroplast (Probable)				399
Q9LLH9 UniProt NPD GO	ACOX3_ARATH	Acyl-coenzyme A oxidase 3, peroxisomal precursor (EC 1.3.3.6) (AOX 3) (Medium-chain acyl-CoA oxidase ...	0.36	-	mit	0	Peroxisome				675
Q63495 UniProt NPD GO	RAGE_RAT	Advanced glycosylation end product-specific receptor precursor (Receptor for advanced glycosylation ...	0.36	-	end	1 *	Membrane; single-pass type I membrane protein				402
P43652 UniProt NPD GO	AFAM_HUMAN	Afamin precursor (Alpha-albumin) (Alpha-Alb)	0.36	-	exc	0	Secreted protein	extracellular region [TAS]	104145		599
P16112 UniProt NPD GO	PGCA_HUMAN	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP) (Chondroitin ...	0.36	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		155760		2415
P56413 UniProt NPD GO	AGRP_BOVIN	Agouti-related protein precursor	0.36	-	exc	0	Secreted protein (By similarity)				134
P21786 UniProt NPD GO	ALLT_MANSE	Allatotropin precursor (AT)	0.36	-	vac	0	Secreted protein				204
P02507 UniProt NPD GO	CRYAA_RANES	Alpha crystallin A chain (Fragments)	0.36	-	nuc	0					167
P02487 UniProt NPD GO	CRYAA_BRAVA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.36	-	mit	0					170
P02479 UniProt NPD GO	CRYAA_CERSI	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.36	-	mit	0					173
P02488 UniProt NPD GO	CRYAA_MACMU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.36	-	cyt	0					172
P23928 UniProt NPD GO	CRYAB_RAT	Alpha crystallin B chain (Alpha(B)-crystallin)	0.36	-	mit	0					175
Q5ENY9 UniProt NPD GO	CRYAB_SHEEP	Alpha crystallin B chain (Alpha(B)-crystallin)	0.36	-	mit	0					175
Q9GKU6 UniProt NPD GO	FUT6_PONPY	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.36	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
Q9UNA3 UniProt NPD GO	A4GCT_HUMAN	Alpha-1,4-N-acetylglucosaminyltransferase (EC 2.4.1.-) (Alpha4GnT)	0.36	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [TAS] membrane fraction [TAS]			340

You are viewing entries 34701 to 34750 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.