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
P58396 UniProt NPD GO	KLPS_SCARA	Kinin-like peptide-S (Fragment)	0.02	-		0					14
P84881 UniProt NPD GO	IELK1_BAURF	Kunitz-type elastase inhibitor BrEI	0.02	-	cyt	0					144
P10280 UniProt NPD GO	IP52_ANESU	Kunitz-type protease inhibitor 5 II (SA5 II)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				62
P81547 UniProt NPD GO	AXP1_ANTAF	Kunitz-type proteinase inhibitor AXPI-I	0.02	-	nuc	0	Secreted protein. Found in nematocyst				58
P83605 UniProt NPD GO	BMTI4_BOOMI	Kunitz-type serine protease inhibitor BmTI-4 (Fragment)	0.02	-	cyt	0	Secreted protein				25
P16344 UniProt NPD GO	ITR4_RADMA	Kunitz-type trypsin inhibitor IV	0.02	-	nuc	0	Secreted protein. Found in nematocyst				56
Q6FV34 UniProt NPD GO	LYS5_CANGA	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (AASD-PPT)	0.02	-	cyt	0					258
P93404 UniProt NPD GO	APX1_ORYSA	L-ascorbate peroxidase 1, cytosolic (EC 1.11.1.11) (APXa)	0.02	-	nuc	0	Cytoplasm				249
P30364 UniProt NPD GO	ASPG_LUPAN	L-asparaginase precursor (EC 3.5.1.1) (L-asparagine amidohydrolase) [Contains: L-asparaginase subuni ...	0.02	-	cyt	0					325
P58710 UniProt NPD GO	GGLO_MOUSE	L-gulonolactone oxidase (EC 1.1.3.8) (LGO) (L-gulono-gamma-lactone oxidase) (GLO)	0.02	-	mit	0	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				439
Q27888 UniProt NPD GO	LDH_CAEEL	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.02	-	cyt	0	Cytoplasm (By similarity)				333
Q27743 UniProt NPD GO	LDH_PLAFD	L-lactate dehydrogenase (EC 1.1.1.27) (LDH-P)	0.02	-	end	1 *				2A94	316
O13276 UniProt NPD GO	LDHA_SPHAG	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.02	-	cyt	0	Cytoplasm (By similarity)				331
Q9BE24 UniProt NPD GO	LDHA_MACFA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm (By similarity)				331
Q9XT87 UniProt NPD GO	LDHA_MONDO	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm (By similarity)				331
P06151 UniProt NPD GO	LDHA_MOUSE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm				331
Q5R1W9 UniProt NPD GO	LDHA_PANTR	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm (By similarity)				331
Q5R5F0 UniProt NPD GO	LDHA_PONPY	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm (By similarity)				331
P04642 UniProt NPD GO	LDHA_RAT	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.02	-	cyt	0	Cytoplasm				332
Q6ZMR3 UniProt NPD GO	LDH6A_HUMAN	L-lactate dehydrogenase A-like 6A (EC 1.1.1.27)	0.02	-	mit	0					332
P22989 UniProt NPD GO	LDHB_HORVU	L-lactate dehydrogenase B (EC 1.1.1.27) (LDH-B) (Fragment)	0.02	-	cyt	0					344
Q9PW04 UniProt NPD GO	LDHB_COLLI	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH testis subunit) (LDH-C)	0.02	-	cyt	0	Cytoplasm (By similarity)				332
Q06176 UniProt NPD GO	LDHC_FUNHE	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C)	0.02	-	mit	0	Cytoplasm (By similarity)				333
P42121 UniProt NPD GO	LDHC_XENLA	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C)	0.02	-	cyt	0	Cytoplasm (By similarity)				333
Q9TSX5 UniProt NPD GO	LDHC_PIG	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C) (LDH testis subunit) (LDH-X)	0.02	-	mit	0	Cytoplasm (By similarity)				331
Q9PSI9 UniProt NPD GO	MYCL1_BRARE	L-myc 1 protein (zL-Myc) (Fragment)	0.02	-	cyt	0	Nucleus (Potential)	nucleus [NAS]			77
P20132 UniProt NPD GO	SDHL_HUMAN	L-serine dehydratase (EC 4.3.1.17) (L-serine deaminase)	0.02	-	mit	0	Cytoplasm		182128	1P5J	328
Q99046 UniProt NPD GO	LAC2_TRAVI	Laccase 2 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.02	-	vac	0	Secreted protein				519
Q02497 UniProt NPD GO	LAC1_TRAHI	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Ligninolytic ...	0.02	-	exc	0	Secreted protein				520
Q90WJ8 UniProt NPD GO	AJL2_ANGJA	Lactose-binding lectin l-2 precursor (Ajl-2)	0.02	-	vac	0	Secreted protein	extracellular region [IDA]			166
O49818 UniProt NPD GO	LGUL_CICAR	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.02	-	cyt	0					186
Q2KHK3 UniProt NPD GO	LAEVR_MOUSE	Laeverin (EC 3.4.-.-)	0.02	-	vac	1 *	Membrane; single-pass type II membrane protein (Potential)				558
P58807 UniProt NPD GO	CXL1_CONMR	Lambda-conotoxin CMrVIA	0.02	-		0	Secreted protein				11
P58810 UniProt NPD GO	CXL4_CONMR	Lambda/chi-conotoxin MrIB (Chi-MrIB)	0.02	-		0	Secreted protein			1IEO	13
O02443 UniProt NPD GO	CULP1_HELAM	Larval cuticle protein 1 precursor	0.02	-	exc	0					109
P80681 UniProt NPD GO	CUA1A_TENMO	Larval cuticle protein A1A (TM-A1A) (TM-LCP A1A)	0.02	-	cyt	0					174
P80682 UniProt NPD GO	CUA2B_TENMO	Larval cuticle protein A2B (TM-A2B) (TM-LCP A2B)	0.02	-	cyt	0					117
Q08738 UniProt NPD GO	CU30_BOMMO	Larval cuticle protein LCP-30 precursor	0.02	-	exc	0					239
P09618 UniProt NPD GO	THN6_HORVU	Leaf-specific thionin BTH6 precursor [Contains: Leaf-specific thionin BTH6; Acidic protein]	0.02	-	nuc	0	Secreted protein (Potential)				137
P08772 UniProt NPD GO	THN3_HORVU	Leaf-specific thionin DB4 precursor [Contains: Leaf-specific thionin DB4; Acidic protein]	0.02	-	nuc	0	Secreted protein (Potential)				137
P84037 UniProt NPD GO	LEBCB_VIPLE	Lebecetin subunit beta (Fragment)	0.02	-	cyt	0	Secreted protein				43
P02875 UniProt NPD GO	LEC_DOLAX	Lectin (Fragment)	0.02	-	nuc	0					32
P58909 UniProt NPD GO	LECA_DIOVO	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma chain] (Fragments)	0.02	-	nuc	0					49
P84871 UniProt NPD GO	LEC1_HYPMC	Lectin-1 (HCA) [Contains: Lectin-1 N-terminal subunit; Lectin-1 C-terminal subunit]	0.02	-	nuc	0					90
P28586 UniProt NPD GO	LEC1_AXIDI	Lectin-1 (Lectin I)	0.02	-	cyt	0	Stored in spherulous cells in the sponge tissue				144
P24146 UniProt NPD GO	LEC4_GRISI	Lectin-4 (Lectin IV) (GS4)	0.02	-	cyt	0				1LED	243
P80424 UniProt NPD GO	LDTI_HIRME	Leech-derived tryptase inhibitor C (LDTI-C) [Contains: Leech-derived tryptase inhibitor B (LDTI-B); ...	0.02	-	nuc	0				1LDT	46
P23223 UniProt NPD GO	GP63_LEIDO	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.02	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor				590
Q9WVB7 UniProt NPD GO	LENEP_RAT	Lens epithelial cell protein LEP503	0.02	-	cyt	0					61
P28238 UniProt NPD GO	MIP_CHICK	Lens fiber major intrinsic protein (Aquaporin-0) (AQP0) (MIP26) (MP26)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				262

You are viewing entries 84151 to 84200 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.