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
Q58CW6 UniProt NPD GO	AL2S8_BOVIN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein homolog	0.64	-	nuc	0	Nucleus (Potential)				703
O00192 UniProt NPD GO	ARVC_HUMAN	Armadillo repeat protein deleted in velo-cardio-facial syndrome	0.64	-	nuc	0		intracellular [TAS]	602269		962
Q6BIA1 UniProt NPD GO	ATG21_DEBHA	Autophagy-related protein 21	0.64	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				532
Q6C2F5 UniProt NPD GO	ATG9_YARLI	Autophagy-related protein 9	0.64	-	end	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				788
Q4R3K5 UniProt NPD GO	IDLC_MACFA	Axonemal dynein light intermediate polypeptide 1 (Inner dynein arm light chain, axonemal)	0.64	-	nuc	0					258
O14645 UniProt NPD GO	IDLC_HUMAN	Axonemal dynein light intermediate polypeptide 1 (Inner dynein arm light chain, axonemal) (hp28)	0.64	-	nuc	0		axonemal dynein complex [TAS] axoneme [TAS]	602135		258
Q13873 UniProt NPD GO	BMPR2_HUMAN	Bone morphogenetic protein receptor type-2 precursor (EC 2.7.11.30) (Bone morphogenetic protein rece ...	0.64	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600799		1038
O35607 UniProt NPD GO	BMPR2_MOUSE	Bone morphogenetic protein receptor type-2 precursor (EC 2.7.11.30) (Bone morphogenetic protein rece ...	0.64	-	exc	1	Membrane; single-pass type I membrane protein	cell surface [IDA]			1038
Q3KR97 UniProt NPD GO	BI2L1_RAT	Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 (BAI1-associated protein ...	0.64	-	nuc	0					516
Q9JI08 UniProt NPD GO	BIN3_MOUSE	Bridging integrator 3	0.64	-	nuc	0					253
Q68FW8 UniProt NPD GO	BIN3_RAT	Bridging integrator 3	0.64	-	nuc	0					253
P27637 UniProt NPD GO	BUD14_YEAST	Bud site selection protein BUD14	0.64	-	nuc	0		bud neck [IDA] bud tip [IDA] incipient bud site [IDA]			707
P10157 UniProt NPD GO	ETS2_CHICK	C-ETS-2 protein	0.64	-	nuc	0	Nucleus				479
O95628 UniProt NPD GO	CNOT4_HUMAN	CCR4-NOT transcription complex subunit 4 (EC 6.3.2.-) (E3 ubiquitin protein ligase CNOT4) (CCR4-asso ...	0.64	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)		604911	1UR6	575
Q8BT14 UniProt NPD GO	CNOT4_MOUSE	CCR4-NOT transcription complex subunit 4 (EC 6.3.2.-) (E3 ubiquitin protein ligase CNOT4) (CCR4-asso ...	0.64	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)			2CPI	575
Q9Y5K6 UniProt NPD GO	CD2AP_HUMAN	CD2-associated protein (Cas ligand with multiple SH3 domains) (Adapter protein CMS)	0.64	-	nuc	0	Cytoplasm (By similarity). Colocalizes with F-actin and BCAR1/p130Cas in membrane ruffles. Located a ...	actin cytoskeleton [TAS] cytoplasm [TAS] filamentous actin [IDA] ruffle [IDA]	607832		639
P97834 UniProt NPD GO	CSN1_RAT	COP9 signalosome complex subunit 1 (Signalosome subunit 1) (SGN1) (JAB1-containing signalosome subun ...	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				471
Q99LD4 UniProt NPD GO	CSN1_MOUSE	COP9 signalosome complex subunit 1 (Signalosome subunit 1) (SGN1) (JAB1-containing signalosome subun ...	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	signalosome complex [IDA]			471
Q13098 UniProt NPD GO	CSN1_HUMAN	COP9 signalosome complex subunit 1 (Signalosome subunit 1) (SGN1) (JAB1-containing signalosome subun ...	0.64	-	nuc	0	Cytoplasm. Nucleus		601934		471
Q9NYQ7 UniProt NPD GO	CELR3_HUMAN	Cadherin EGF LAG seven-pass G-type receptor 3 precursor (Flamingo homolog 1) (hFmi1) (Multiple epide ...	0.64	+	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]	604264		3312
Q6RET7 UniProt NPD GO	CCAMK_MEDTR	Calcium and calcium/calmodulin-dependent serine/threonine-protein kinase DMI-3 (EC 2.7.11.17) (Does ...	0.64	+	nuc	0					523
Q923T9 UniProt NPD GO	KCC2G_MOUSE	Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.11.17) (CaM-kinase II gamma ...	0.64	-	mit	0					529
Q64691 UniProt NPD GO	CAN3_MOUSE	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.64	-	cyt	0	Cytoplasm				821
Q8TCG5 UniProt NPD GO	CPT1C_HUMAN	Carnitine O-palmitoyltransferase I, brain isoform (EC 2.3.1.21) (Carnitine palmitoyltransferase 1C) ...	0.64	-	nuc	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)		608846		803
P25792 UniProt NPD GO	CYSP_SCHMA	Cathepsin B-like cysteine proteinase precursor (EC 3.4.22.-) (Antigen Sm31)	0.64	+	exc	0				1MGU	340
Q9H3Q1 UniProt NPD GO	BORG4_HUMAN	Cdc42 effector protein 4 (Binder of Rho GTPases 4)	0.64	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein		605468		356
P30665 UniProt NPD GO	CDC54_YEAST	Cell division control protein 54	0.64	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] MCM complex [IDA] nucleus [IDA] pre-replicative complex [IDA]			933
Q8SPZ3 UniProt NPD GO	P53_DELLE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			387
Q3U3S3 UniProt NPD GO	CENPL_MOUSE	Centromere protein L (CENP-L)	0.64	-	cyt	0					329
Q3ZAU7 UniProt NPD GO	CENPL_RAT	Centromere protein L (CENP-L)	0.64	+	cyt	0					345
Q5XGW6 UniProt NPD GO	CHM4B_XENLA	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b)	0.64	-	nuc	0	Cytoplasm (By similarity)				222
Q9NZA1 UniProt NPD GO	CLIC5_HUMAN	Chloride intracellular channel protein 5	0.64	-	nuc	0	Isoform 2: Golgi apparatus	actin cytoskeleton [IDA] insoluble fraction [IDA] microvillus [IDA]	607293		410
Q9MTJ2 UniProt NPD GO	RR11_OENHO	Chloroplast 30S ribosomal protein S11	0.64	-	nuc	0	Plastid; chloroplast				144
Q6YXP6 UniProt NPD GO	RR15_PHYPA	Chloroplast 30S ribosomal protein S15	0.64	+	nuc	0	Plastid; chloroplast				88
Q8M9Y7 UniProt NPD GO	RR18_CHAGL	Chloroplast 30S ribosomal protein S18	0.64	-	nuc	0	Plastid; chloroplast				79
Q85V01 UniProt NPD GO	RR18_LARDC	Chloroplast 30S ribosomal protein S18	0.64	-	mit	0	Plastid; chloroplast				86
Q85UZ8 UniProt NPD GO	RR18_LARLA	Chloroplast 30S ribosomal protein S18	0.64	-	mit	0	Plastid; chloroplast				86
Q85UZ5 UniProt NPD GO	RR18_LAROX	Chloroplast 30S ribosomal protein S18	0.64	-	mit	0	Plastid; chloroplast				86
P69631 UniProt NPD GO	RR4_ANDIS	Chloroplast 30S ribosomal protein S4 (Fragment)	0.64	-	mit	0	Plastid; chloroplast				196
P69650 UniProt NPD GO	RR4_SETVI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.64	-	mit	0	Plastid; chloroplast				196
P69653 UniProt NPD GO	RR4_TRIDA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.64	-	mit	0	Plastid; chloroplast				196
P69654 UniProt NPD GO	RR4_TRIRO	Chloroplast 30S ribosomal protein S4 (Fragment)	0.64	-	mit	0	Plastid; chloroplast				196
Q71L39 UniProt NPD GO	RR7_BOWSE	Chloroplast 30S ribosomal protein S7	0.64	-	nuc	0	Plastid; chloroplast				156
Q71L24 UniProt NPD GO	RR7_METGY	Chloroplast 30S ribosomal protein S7	0.64	-	nuc	0	Plastid; chloroplast				155
P41652 UniProt NPD GO	RR7_PINTH	Chloroplast 30S ribosomal protein S7	0.64	-	nuc	0	Plastid; chloroplast				155
Q9MSQ3 UniProt NPD GO	RR7_ZAMFU	Chloroplast 30S ribosomal protein S7	0.64	-	nuc	0	Plastid; chloroplast				156
Q8WHY1 UniProt NPD GO	RK2_PSINU	Chloroplast 50S ribosomal protein L2	0.64	+	nuc	0	Plastid; chloroplast				277
Q5QA76 UniProt NPD GO	RK20_ACOGR	Chloroplast 50S ribosomal protein L20	0.64	-	mit	0	Plastid; chloroplast				117
Q6YXJ7 UniProt NPD GO	RK36_PHYPA	Chloroplast 50S ribosomal protein L36	0.64	-	nuc	0	Plastid; chloroplast				37
Q9VEG6 UniProt NPD GO	PERC_DROME	Chorion peroxidase precursor (EC 1.11.1.7) (Peroxinectin-related protein) (Dpxt) [Contains: Chorion ...	0.64	-	exc	0	Secreted protein. In the chorion layer of the mature eggs (By similarity)	extracellular region [ISS]			831

You are viewing entries 16751 to 16800 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.