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
P12001 UniProt NPD GO	RL18_RAT	60S ribosomal protein L18	0.51	-	nuc	0	Cytoplasm				187
Q95342 UniProt NPD GO	RL18_PIG	60S ribosomal protein L18 (Fragment)	0.51	-	nuc	0					103
P13732 UniProt NPD GO	RL22_TRIGR	60S ribosomal protein L22 (Development-specific protein 217)	0.51	-	nuc	0					130
O01868 UniProt NPD GO	RL24_CAEEL	60S ribosomal protein L24	0.51	-	nuc	0					159
P49149 UniProt NPD GO	RL3_TOXCA	60S ribosomal protein L3	0.51	-	mit	0	Cytoplasm				401
P22738 UniProt NPD GO	RL32_ARATH	60S ribosomal protein L3-2	0.51	-	mit	0	Cytoplasm				389
O42935 UniProt NPD GO	RL32B_SCHPO	60S ribosomal protein L32-B	0.51	-	nuc	0					127
Q7ZWJ7 UniProt NPD GO	RL34_BRARE	60S ribosomal protein L34	0.51	-	mit	0					116
P36532 UniProt NPD GO	RM37_YEAST	60S ribosomal protein L37, mitochondrial precursor (YmL37)	0.51	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			105
P31866 UniProt NPD GO	RL44_PICGU	60S ribosomal protein L44 (60S ribosomal protein L41)	0.51	-	nuc	0					102
P27074 UniProt NPD GO	RL44Q_CANMA	60S ribosomal protein L44 Q (L41) (L41 Q-type)	0.51	-	nuc	0					105
Q6UNT2 UniProt NPD GO	RL5_CUCSA	60S ribosomal protein L5	0.51	-	mit	0					302
P15126 UniProt NPD GO	RL5B_XENLA	60S ribosomal protein L5-B	0.51	-	mit	0	Cytoplasm				295
Q13443 UniProt NPD GO	ADAM9_HUMAN	ADAM 9 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 9) (Metalloprotease/disin ...	0.51	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS]	602713	1M1V	819
Q9H324 UniProt NPD GO	ATS10_HUMAN	ADAMTS-10 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 10 ...	0.51	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		608990		1077
Q9UM73 UniProt NPD GO	ALK_HUMAN	ALK tyrosine kinase receptor precursor (EC 2.7.10.1) (Anaplastic lymphoma kinase) (CD246 antigen)	0.51	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	105590		1620
Q9XIR4 UniProt NPD GO	APO1_ARATH	APO protein 1, chloroplast precursor (Accumulation of photosystem I protein 1) (Protein ACCUMULATION ...	0.51	-	mit	0	Plastid; chloroplast				436
Q9JHS4 UniProt NPD GO	CLPX_MOUSE	ATP-dependent Clp protease ATP-binding subunit ClpX-like, mitochondrial precursor	0.51	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			634
P13010 UniProt NPD GO	KU86_HUMAN	ATP-dependent DNA helicase 2 subunit 2 (EC 3.6.1.-) (ATP-dependent DNA helicase II 80 kDa subunit) ( ...	0.51	-	cyt	0	Nucleus	nucleus [TAS]	194364	1RW2	731
Q28141 UniProt NPD GO	DHX9_BOVIN	ATP-dependent RNA helicase A (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II) (DEAH box protein 9)	0.51	+	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Can shuttle between nucleus and cytop ...				1287
Q6CWQ5 UniProt NPD GO	MRH4_KLULA	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.51	-	mit	0	Mitochondrion (By similarity)				584
P32580 UniProt NPD GO	SUV3_YEAST	ATP-dependent RNA helicase SUV3, mitochondrial precursor (EC 3.6.1.-)	0.51	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			737
Q04182 UniProt NPD GO	PDR15_YEAST	ATP-dependent permease PDR15	0.51	-	end	12	Membrane; multi-pass membrane protein (Potential)				1529
Q31796 UniProt NPD GO	ACCD_ANTFO	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.51	-	cyt	0	Plastid; chloroplast				313
Q9MTL3 UniProt NPD GO	ACCD_OENHO	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.51	-	nuc	0	Plastid; chloroplast				438
P78704 UniProt NPD GO	ACR2_NEUCR	Acriflavine sensitivity control protein acr-2	0.51	-	mit	0	Nucleus (By similarity)				595
Q5AC48 UniProt NPD GO	ARP4_CANAL	Actin-like protein ARP4	0.51	-	nuc	0	Nucleus (By similarity)				469
Q9H9F9 UniProt NPD GO	ARP5_HUMAN	Actin-related protein 5 (hARP5) (Sarcoma antigen NY-SAR-16)	0.51	-	cyt	0					607
P97490 UniProt NPD GO	ADCY8_MOUSE	Adenylate cyclase type 8 (EC 4.6.1.1) (Adenylate cyclase type VIII) (ATP pyrophosphate-lyase 8) (Ca( ...	0.51	-	end	10	Membrane; multi-pass membrane protein				1249
Q9FPN7 UniProt NPD GO	AGL31_ARATH	Agamous-like MADS-box protein AGL31 (Protein MADS AFFECTING FLOWERING 2)	0.51	-	nuc	0	Nucleus (By similarity)				196
P12764 UniProt NPD GO	ALLS_DIPPU	Allatostatins precursor [Contains: Allatostatin-1 (AST1); Allatostatin-2 (AST2) (ASB2) (ASA5); Allat ...	0.51	-	exc	0	Secreted protein				370
P35221 UniProt NPD GO	CTN1_HUMAN	Alpha-1 catenin (Cadherin-associated protein) (Alpha E-catenin) (NY-REN-13 antigen)	0.51	+	nuc	0	Cell membrane; cell-cell junction. Cell membrane; cell-matrix junction. Found at cell-cell boundarie ...		116805	1L7C	906
P22086 UniProt NPD GO	ADA2C_RAT	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor) (Alpha-2 adrenergic r ...	0.51	+	end	7	Membrane; multi-pass membrane protein	axon [IDA]			458
Q9XZC0 UniProt NPD GO	LCTA_LATMA	Alpha-latrocrustotoxin (Alpha-LCT) (Crusta1)	0.51	-	nuc	1	Secreted protein				1395
Q9WU38 UniProt NPD GO	SCNNB_MOUSE	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.51	-	mit	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...	integral to membrane [IDA]			638
O70248 UniProt NPD GO	APBA3_RAT	Amyloid beta A4 precursor protein-binding family A member 3 (Neuron-specific X11L2 protein) (Neurona ...	0.51	-	nuc	0					569
Q3TY65 UniProt NPD GO	AL2SE_MOUSE	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 15 protein homolog (Ica69-related ...	0.51	-	nuc	0					431
Q9Y679 UniProt NPD GO	AUP1_HUMAN	Ancient ubiquitous protein 1 precursor	0.51	-	end	2 *			602434		476
Q9VLJ6 UniProt NPD GO	ACER_DROME	Angiotensin-converting enzyme-related protein precursor (EC 3.4.15.1)	0.51	-	cyt	0	Secreted protein; extracellular space	extracellular region [IDA]			630
P04920 UniProt NPD GO	B3A2_HUMAN	Anion exchange protein 2 (Non-erythroid band 3-like protein) (AE2 anion exchanger) (Solute carrier f ...	0.51	-	end	11	Membrane; multi-pass membrane protein	membrane fraction [TAS]	109280		1241
Q9Z1P7 UniProt NPD GO	ANR47_MOUSE	Ankyrin repeat domain-containing protein 47	0.51	-	nuc	0					791
P15358 UniProt NPD GO	ANTA_HAEOF	Antistasin precursor (ATS) (Blood coagulation factor Xa/proclotting enzyme inhibitor)	0.51	-	exc	0	Secreted protein			1SKZ	136
P37880 UniProt NPD GO	SYR_CRILO	Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.51	-	nuc	0	Cytoplasm				661
Q28056 UniProt NPD GO	ASPH_BOVIN	Aspartyl/asparaginyl beta-hydroxylase (EC 1.14.11.16) (Aspartate beta-hydroxylase) (ASP beta-hydroxy ...	0.51	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				754
Q75B79 UniProt NPD GO	ATG11_ASHGO	Autophagy-related protein 11	0.51	-	mit	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1072
Q524W4 UniProt NPD GO	ATG18_MAGGR	Autophagy-related protein 18	0.51	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				469
Q5VRR0 UniProt NPD GO	IAA20_ORYSA	Auxin-responsive protein IAA20 (Indoleacetic acid-induced protein 20)	0.51	+	cyt	0	Nucleus (By similarity)				183
P20273 UniProt NPD GO	CD22_HUMAN	B-cell receptor CD22 precursor (Leu-14) (B-lymphocyte cell adhesion molecule) (BL-CAM) (Siglec-2)	0.51	-	end	1	Membrane; single-pass type I membrane protein		107266		847
Q91YN9 UniProt NPD GO	BAG2_MOUSE	BAG family molecular chaperone regulator 2 (BCL2-associated athanogene 2) (BAG-2)	0.51	-	nuc	0					210
Q9JLV1 UniProt NPD GO	BAG3_MOUSE	BAG family molecular chaperone regulator 3 (BCL-2-binding athanogene-3) (BAG-3) (Bcl-2-binding prote ...	0.51	-	nuc	0				1UK5	577

You are viewing entries 24151 to 24200 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.