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
P90900 UniProt NPD GO	IFA4_CAEEL	Intermediate filament protein ifa-4 (Intermediate filament protein A4) (IF-A4) (Cel IF A4)	0.75	-	nuc	0	Cytoplasm (By similarity)				575
Q09501 UniProt NPD GO	IFP1_CAEEL	Intermediate filament protein ifp-1 (Intermediate filament protein E1) (IF-E1) (Cel IF E1)	0.75	-	nuc	0	Cytoplasm (Probable)				776
Q9YGS0 UniProt NPD GO	IRX4_CHICK	Iroquois-class homeodomain protein IRX-4 (Iroquois homeobox protein 4)	0.75	-	nuc	0	Nucleus (By similarity)				485
Q9NX36 UniProt NPD GO	CU055_HUMAN	J domain-containing protein C21orf55	0.75	-	mit	0					388
Q8WXH2 UniProt NPD GO	JPH3_HUMAN	Junctophilin-3 (Junctophilin type 3) (JP-3)	0.75	-	nuc	1	Cell membrane; peripheral membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...	integral to membrane [NAS]	605268		748
P13817 UniProt NPD GO	KNOB_PLAFA	Knob-associated histidine-rich protein precursor (KAHRP) (HRPI) (Fragment)	0.75	+	nuc	0	Host: Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of the membrane ...				473
O14901 UniProt NPD GO	KLF11_HUMAN	Krueppel-like factor 11 (Transforming growth factor-beta-inducible early growth response protein 2) ...	0.75	-	nuc	0	Nucleus	nucleus [TAS]	603301	1PO4	512
O43474 UniProt NPD GO	KLF4_HUMAN	Krueppel-like factor 4 (Epithelial zinc-finger protein EZF) (Gut-enriched krueppel-like factor)	0.75	-	nuc	0	Nucleus	nucleus [ISS]	602253		470
Q9Z0S2 UniProt NPD GO	LHX2_MOUSE	LIM/homeobox protein Lhx2	0.75	-	nuc	0	Nucleus (Probable)				406
P50458 UniProt NPD GO	LHX2_HUMAN	LIM/homeobox protein Lhx2 (Homeobox protein LH-2)	0.75	-	nuc	0	Nucleus (Probable)		603759		406
Q21443 UniProt NPD GO	LMN1_CAEEL	Lamin-1 (CeLam-1) (Ce-lamin)	0.75	+	mit	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side. Remains in the nuclear envelope u ...	nuclear envelope [IDA] nucleoplasm [IDA]			566
P19137 UniProt NPD GO	LAMA1_MOUSE	Laminin alpha-1 chain precursor (Laminin A chain)	0.75	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basal lamina [TAS]			3084
Q13751 UniProt NPD GO	LAMB3_HUMAN	Laminin beta-3 chain precursor (Laminin 5 beta 3) (Laminin B1k chain) (Kalinin B1 chain)	0.75	-	nuc	0	Secreted protein; extracellular space		226700		1172
P14594 UniProt NPD GO	LEGB_PEA	Legumin B [Contains: Legumin B alpha chain (Legumin B acidic chain); Legumin B beta chain (Legumin B ...	0.75	-	nuc	0					338
O75022 UniProt NPD GO	LIRB3_HUMAN	Leukocyte immunoglobulin-like receptor subfamily B member 3 precursor (Leukocyte immunoglobulin-like ...	0.75	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604820		631
P28049 UniProt NPD GO	LAB_XENLA	Lupus La protein homolog B (La ribonucleoprotein B) (La autoantigen homolog B)	0.75	-	nuc	0	Nucleus (Probable)				427
Q60664 UniProt NPD GO	LRMP_MOUSE	Lymphoid-restricted membrane protein (Protein Jaw1)	0.75	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein. Process ...				539
Q69TG5 UniProt NPD GO	MAD55_ORYSA	MADS-box transcription factor 55 (OsMADS55)	0.75	-	nuc	0	Nucleus (Probable)				245
Q3SYZ2 UniProt NPD GO	MAPK3_BOVIN	MAP kinase-activated protein kinase 3 (EC 2.7.11.1) (MAPK-activated protein kinase 3) (MAPKAP kinase ...	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Predominantly located in the nucleus, when activ ...				384
Q99LQ1 UniProt NPD GO	MBIP1_MOUSE	MAP3K12-binding inhibitory protein 1 (MAPK upstream kinase-binding inhibitory protein) (MUK-binding ...	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shows a cytoplasmic localization when co-express ...				341
P53338 UniProt NPD GO	MAL13_YEAST	Maltose fermentation regulatory protein MAL13	0.75	-	nuc	0	Nucleus				473
P32629 UniProt NPD GO	ANP1_YEAST	Mannan polymerase II complex ANP1 subunit (M-Pol II subunit ANP1) (Aminonitrophenyl propanediol resi ...	0.75	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	alpha-1,6-mannosyltransferase complex [TAS]			500
Q92585 UniProt NPD GO	MAML1_HUMAN	Mastermind-like protein 1 (Mam-1)	0.75	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate manner	nucleus [IDA]	605424	2F8X	1016
Q6B2C0 UniProt NPD GO	MTAL2_YEAST	Mating-type protein ALPHA2 (MATalpha2 protein) (Alpha-2 repressor)	0.75	+	nuc	0	Nucleus			1YRN	210
Q9TKD1 UniProt NPD GO	MATK_AGOFL	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
Q8WJ37 UniProt NPD GO	MATK_ANEAN	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
Q717Z2 UniProt NPD GO	MATK_ANNMU	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				507
Q9GF40 UniProt NPD GO	MATK_ARABL	Maturase K (Intron maturase)	0.75	-	mit	0	Plastid; chloroplast				502
Q9GF45 UniProt NPD GO	MATK_ARATU	Maturase K (Intron maturase)	0.75	-	mit	0	Plastid; chloroplast				504
Q8S8Y6 UniProt NPD GO	MATK_ATRBE	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				509
Q8MA72 UniProt NPD GO	MATK_BYBLI	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				513
Q8W7A1 UniProt NPD GO	MATK_CALPE	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				504
Q9TKD7 UniProt NPD GO	MATK_CALPO	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
Q6TND4 UniProt NPD GO	MATK_DALPU	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				509
Q8MEY1 UniProt NPD GO	MATK_DIOSP	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				514
Q8MEY0 UniProt NPD GO	MATK_ENCAL	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				514
Q9TKC0 UniProt NPD GO	MATK_KUNBA	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
O47150 UniProt NPD GO	MATK_PHYEM	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				506
Q6BDH5 UniProt NPD GO	MATK_PICAB	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q6YP18 UniProt NPD GO	MATK_PICEN	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
O63070 UniProt NPD GO	MATK_PICGL	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
O63072 UniProt NPD GO	MATK_PICMA	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q6YP19 UniProt NPD GO	MATK_PICMX	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q7HEK3 UniProt NPD GO	MATK_PICPU	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
O63071 UniProt NPD GO	MATK_PICRU	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q8MC55 UniProt NPD GO	MATK_PICSI	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q8HQQ2 UniProt NPD GO	MATK_PINDE	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q76IH5 UniProt NPD GO	MATK_PINLU	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q76LC1 UniProt NPD GO	MATK_PINMU	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q76IH4 UniProt NPD GO	MATK_PINSY	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515

You are viewing entries 11401 to 11450 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.