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
Q4QQQ4 UniProt NPD GO	RM45_XENTR	39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45)	0.35	-	mit	0	Mitochondrion (By similarity)				309
Q9H2W6 UniProt NPD GO	RM46_HUMAN	39S ribosomal protein L46, mitochondrial precursor (L46mt) (MRP-L46) (P2ECSL)	0.35	-	exc	0	Mitochondrion				279
O22584 UniProt NPD GO	RS14_LUPLU	40S ribosomal protein S14	0.35	-	mit	0					150
Q967G1 UniProt NPD GO	RS17_THEAN	40S ribosomal protein S17	0.35	-	mit	0					130
Q90YQ0 UniProt NPD GO	RS24_ICTPU	40S ribosomal protein S24	0.35	-	mit	0					131
P59233 UniProt NPD GO	R27AC_ARATH	40S ribosomal protein S27a-3	0.35	+	nuc	0					81
Q98TX2 UniProt NPD GO	RS3A_OPHHA	40S ribosomal protein S3a	0.35	+	nuc	0					263
P48164 UniProt NPD GO	RS7B_YEAST	40S ribosomal protein S7-B	0.35	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]			190
Q8WN57 UniProt NPD GO	TYRP1_BOVIN	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.35	-	end	2 *	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)	melanosome [ISS]			537
P11894 UniProt NPD GO	RK9_PEA	50S ribosomal protein L9, chloroplast precursor (CL13)	0.35	-	mit	0	Plastid; chloroplast				194
Q92448 UniProt NPD GO	K6PF1_PICPA	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.35	-	cyt	0	Cytoplasm (By similarity)				990
O94201 UniProt NPD GO	K6PF1_CANAL	6-phosphofructokinase subunit alpha (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (6PF-1 ...	0.35	-	cyt	0	Cytoplasm (By similarity)				987
Q01813 UniProt NPD GO	K6PP_HUMAN	6-phosphofructokinase type C (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosphofruct ...	0.35	+	cyt	0		6-phosphofructokinase complex [NAS]	171840		784
O65729 UniProt NPD GO	RL18_CICAR	60S ribosomal protein L18 (Fragment)	0.35	-	nuc	0					183
P42791 UniProt NPD GO	RL182_ARATH	60S ribosomal protein L18-2	0.35	-	cyt	0	Cytoplasm				187
Q940B0 UniProt NPD GO	RL183_ARATH	60S ribosomal protein L18-3	0.35	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			187
Q24JY1 UniProt NPD GO	RL23A_BOVIN	60S ribosomal protein L23a	0.35	-	nuc	0					156
P62750 UniProt NPD GO	RL23A_HUMAN	60S ribosomal protein L23a	0.35	-	nuc	0			602326		156
P62751 UniProt NPD GO	RL23A_MOUSE	60S ribosomal protein L23a	0.35	-	nuc	0					156
P62752 UniProt NPD GO	RL23A_RAT	60S ribosomal protein L23a	0.35	-	nuc	0					156
Q9BI06 UniProt NPD GO	R27A1_ENTHI	60S ribosomal protein L27a-1	0.35	-	mit	0					149
Q90YT7 UniProt NPD GO	RL31_ICTPU	60S ribosomal protein L31	0.35	-	nuc	0					125
P46290 UniProt NPD GO	RL31_NICGU	60S ribosomal protein L31	0.35	-	nuc	0					120
P11250 UniProt NPD GO	RL34_RAT	60S ribosomal protein L34	0.35	-	mit	0					116
P49181 UniProt NPD GO	RL36_CAEEL	60S ribosomal protein L36	0.35	+	nuc	0		ribosome [NAS]			103
Q95276 UniProt NPD GO	RL5_PIG	60S ribosomal protein L5 (Fragment)	0.35	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				124
Q9LZH9 UniProt NPD GO	RL7A2_ARATH	60S ribosomal protein L7a-2	0.35	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			256
Q3SYR7 UniProt NPD GO	RL9_BOVIN	60S ribosomal protein L9	0.35	-	cyt	0					192
P32969 UniProt NPD GO	RL9_HUMAN	60S ribosomal protein L9	0.35	-	cyt	0		ribosome [TAS]	603686	2CQL	192
Q5IFJ7 UniProt NPD GO	RL9_MACFA	60S ribosomal protein L9	0.35	-	cyt	0					192
P17077 UniProt NPD GO	RL9_RAT	60S ribosomal protein L9	0.35	-	cyt	0					192
Q06068 UniProt NPD GO	HSP97_STRPU	97 kDa heat shock protein (Egg sperm receptor)	0.35	-	nuc	0					889
Q9Y3Q7 UniProt NPD GO	ADA18_HUMAN	ADAM 18 precursor (A disintegrin and metalloproteinase domain 18) (Transmembrane metalloproteinase-l ...	0.35	-	nuc	1	Membrane; single-pass type I membrane protein	membrane fraction [TAS]			739
Q60718 UniProt NPD GO	ADAM2_MOUSE	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.35	-	end	1	Membrane; single-pass type I membrane protein				735
Q9BZ11 UniProt NPD GO	ADA33_HUMAN	ADAM 33 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 33)	0.35	-	exc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	607114	1R55	813
Q28475 UniProt NPD GO	ADAM7_MACFA	ADAM 7 precursor (A disintegrin and metalloproteinase domain 7) (Epididymal apical protein I) (EAP I ...	0.35	-	nuc	1	Membrane; single-pass type I membrane protein				776
P57110 UniProt NPD GO	ATS8_MOUSE	ADAMTS-8 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 8) ...	0.35	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				905
Q9UP79 UniProt NPD GO	ATS8_HUMAN	ADAMTS-8 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 8) ...	0.35	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		605175		890
Q8N6T3 UniProt NPD GO	ARFG1_HUMAN	ADP-ribosylation factor GTPase-activating protein 1 (ADP-ribosylation factor 1 GTPase-activating pro ...	0.35	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Associates with the Golgi complex (By si ...		608377		406
P06291 UniProt NPD GO	ATPF_MARPO	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.35	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				184
O74479 UniProt NPD GO	ATPO_SCHPO	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.35	-	mit	0	Mitochondrion				216
Q80W57 UniProt NPD GO	ABCG2_RAT	ATP-binding cassette sub-family G member 2 (Breast cancer resistance protein 1 homolog)	0.35	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				657
Q6CIV2 UniProt NPD GO	DBP2_KLULA	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.35	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				554
Q9NUU7 UniProt NPD GO	DD19A_HUMAN	ATP-dependent RNA helicase DDX19A (EC 3.6.1.-) (DEAD box protein 19A) (DDX19-like protein)	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By sim ...				478
Q75B50 UniProt NPD GO	DED1_ASHGO	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.35	-	cyt	0	Cytoplasm (By similarity)				623
Q10055 UniProt NPD GO	FAL1_SCHPO	ATP-dependent RNA helicase tif412 (EC 3.6.1.-)	0.35	-	cyt	0	Nucleus; nucleolus (By similarity)				394
P97998 UniProt NPD GO	MDL1_CANAL	ATP-dependent permease MDL1	0.35	-	nuc	4	Membrane; multi-pass membrane protein (Potential)				685
P37209 UniProt NPD GO	ATIF1_CAEEL	ATPase inhibitor homolog, mitochondrial precursor	0.35	-	nuc	0	Mitochondrion (Potential)				88
P12217 UniProt NPD GO	ACCD_MARPO	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.35	-	cyt	0	Plastid; chloroplast				316
P49158 UniProt NPD GO	ACCD_SOYBN	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.35	-	nuc	0	Plastid; chloroplast				432

You are viewing entries 35551 to 35600 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.