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
Q8N1B4 UniProt NPD GO	VPS52_HUMAN	Vacuolar protein sorting protein 52 (SAC2 suppressor of actin mutations 2-like protein)	0.37	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...		603443		723
P93736 UniProt NPD GO	SYV_ARATH	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.37	+	mit	0					1108
Q04462 UniProt NPD GO	SYV_RAT	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.37	-	cyt	0					1264
P29534 UniProt NPD GO	VCAM1_RAT	Vascular cell adhesion protein 1 precursor (V-CAM 1)	0.37	+	end	1 *	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			739
P25385 UniProt NPD GO	BOS1_YEAST	Vesicular transport protein BOS1	0.37	-	nuc	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein. Secretory pathway vesicl ...	endoplasmic reticulum membrane [IDA]			244
Q08761 UniProt NPD GO	PROS_MOUSE	Vitamin K-dependent protein S precursor	0.37	-	end	0	Secreted protein				675
Q9Y698 UniProt NPD GO	CCG2_HUMAN	Voltage-dependent calcium channel gamma-2 subunit (Neuronal voltage-gated calcium channel gamma-2 su ...	0.37	-	end	4 *	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	602911		323
Q62850 UniProt NPD GO	VN1A1_RAT	Vomeronasal type-1 receptor A1 (Vomeronasal receptor 1) (Pheromone receptor VN1)	0.37	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				311
Q5J3L6 UniProt NPD GO	V1A12_RAT	Vomeronasal type-1 receptor A12 (Vomeronasal receptor 3) (Pheromone receptor VN3)	0.37	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				326
Q8VBS7 UniProt NPD GO	VN1A6_MOUSE	Vomeronasal type-1 receptor A6 (Vomeronasal type-1 receptor A3) (Vomeronasal type-1 receptor A1) (Vo ...	0.37	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				329
Q9HC57 UniProt NPD GO	WFDC1_HUMAN	WAP four-disulfide core domain protein 1 precursor (Prostate stromal protein ps20) (ps20 growth inhi ...	0.37	-	exc	0	Secreted protein (Potential)	extracellular space [NAS]	605322		220
Q8IWB7 UniProt NPD GO	WDFY1_HUMAN	WD repeat and FYVE domain-containing protein 1 (WD40- and FYVE domain-containing protein 1) (Phospho ...	0.37	-	mit	0	Endosome; early endosome	cytosol [IDA] early endosome [IDA] nucleus [IDA]			410
Q9GZL7 UniProt NPD GO	WDR12_HUMAN	WD repeat protein 12 (YTM1 homolog)	0.37	-	nuc	0	Nucleus; nucleolus				423
Q96S15 UniProt NPD GO	WDR24_HUMAN	WD repeat protein 24	0.37	-	nuc	0					920
Q3MJ13 UniProt NPD GO	WDR72_HUMAN	WD repeat protein 72	0.37	-	mit	0					1102
P36130 UniProt NPD GO	YK16_YEAST	WD repeat protein YKR036C	0.37	-	nuc	0		CCR4-NOT complex [IPI] mitochondrion [IDA]			659
Q8RXN0 UniProt NPD GO	WBC11_ARATH	White-brown complex homolog protein 11	0.37	+	end	6	Membrane; multi-pass membrane protein (By similarity)				703
P59824 UniProt NPD GO	IRPL1_RAT	X-linked interleukin-1 receptor accessory protein-like 1 precursor (IL1RAPL-1)	0.37	-	nuc	0	Membrane; single-pass type I membrane protein				696
Q5GH73 UniProt NPD GO	XKR6_HUMAN	XK-related protein 6	0.37	-	end	6	Membrane; multi-pass membrane protein (Potential)				641
Q12553 UniProt NPD GO	XDH_EMENI	Xanthine dehydrogenase (EC 1.17.1.4) (Purine hydroxylase I)	0.37	-	cyt	0	Peroxisome				1363
Q8H038 UniProt NPD GO	KATAM_ORYSA	Xyloglucan galactosyltransferase KATAMARI1 homolog (EC 2.4.1.-)	0.37	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				588
Q5QQ50 UniProt NPD GO	XYLT2_CANFA	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (Peptide O-xylosyltransferase 2)	0.37	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				865
Q9EPI0 UniProt NPD GO	XYLT2_RAT	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (Peptide O-xylosyltransferase 2)	0.37	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				864
Q9QY24 UniProt NPD GO	ZBP1_MOUSE	Z-DNA-binding protein 1 (Tumor stroma and activated macrophage protein DLM-1)	0.37	-	nuc	0				1J75	411
P04702 UniProt NPD GO	ZEA6_MAIZE	Zein-alpha M6 precursor (19 kDa zein M6)	0.37	-	exc	0					240
Q8GXX7 UniProt NPD GO	ZFN1_ARATH	Zinc finger CCCH domain-containing protein ZFN1	0.37	-	nuc	0	Nucleus (By similarity)				397
Q14589 UniProt NPD GO	ZN160_HUMAN	Zinc finger protein 160 (Zinc finger protein HZF5) (Fragment)	0.37	-	nuc	0	Nucleus (Probable)		600398		169
Q9DAI4 UniProt NPD GO	Z297B_MOUSE	Zinc finger protein 297B	0.37	-	nuc	0	Nucleus (Probable)				467
Q4R6C2 UniProt NPD GO	ZN383_MACFA	Zinc finger protein 383	0.37	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttling between the nucleus and cytoplasm may ...				475
Q9BUY5 UniProt NPD GO	ZN426_HUMAN	Zinc finger protein 426	0.37	-	nuc	0	Nucleus (Potential)				554
Q9H7X3 UniProt NPD GO	ZN696_HUMAN	Zinc finger protein 696	0.37	-	nuc	0	Nucleus (Potential)				374
Q15935 UniProt NPD GO	ZNF77_HUMAN	Zinc finger protein 77 (ZNFpT1)	0.37	-	nuc	0	Nucleus (Potential)		194551		545
O08954 UniProt NPD GO	SLUG_RAT	Zinc finger protein SLUG (Neural crest transcription factor Slug) (Snail homolog 2)	0.37	-	nuc	0	Nucleus (Probable)				268
Q9XTD6 UniProt NPD GO	NAS12_CAEEL	Zinc metalloproteinase nas-12 precursor (EC 3.4.24.21) (Nematode astacin 12)	0.37	-	cyt	0	Secreted protein (Potential)				384
Q62005 UniProt NPD GO	ZP1_MOUSE	Zona pellucida sperm-binding protein 1 precursor (Zona pellucida glycoprotein 1) (Zp-1)	0.37	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				623
Q6CPK7 UniProt NPD GO	KAPR_KLULA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.37	-	nuc	0					466
P31323 UniProt NPD GO	KAP3_HUMAN	cAMP-dependent protein kinase type II-beta regulatory subunit	0.37	-	cyt	0			176912		417
P12369 UniProt NPD GO	KAP3_RAT	cAMP-dependent protein kinase type II-beta regulatory subunit	0.37	-	cyt	0				1CX4	415
Q28279 UniProt NPD GO	CNGA1_CANFA	cGMP-gated cation channel alpha 1 (CNG channel alpha 1) (CNG-1) (CNG1) (Cyclic nucleotide-gated chan ...	0.37	+	end	4	Membrane; multi-pass membrane protein				691
Q39761 UniProt NPD GO	DCS1_GOSAR	(+)-delta-cadinene synthase isozyme XC1 (EC 4.2.3.13) (D-cadinene synthase)	0.36	-	cyt	0					554
P46514 UniProt NPD GO	LE10_HELAN	10 kDa late embryogenesis abundant protein (DS10)	0.36	-	nuc	0					92
P43686 UniProt NPD GO	PRS6B_HUMAN	26S protease regulatory subunit 6B (MIP224) (MB67-interacting protein) (TAT-binding protein 7) (TBP- ...	0.36	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	602707		418
Q63570 UniProt NPD GO	PRS6B_RAT	26S protease regulatory subunit 6B (TAT-binding protein 7) (TBP-7)	0.36	-	cyt	0	Cytoplasm. Nucleus				418
P35998 UniProt NPD GO	PRS7_HUMAN	26S protease regulatory subunit 7 (Protein MSS1)	0.36	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] proteasome complex (sensu Eukaryota) [TAS]	154365		432
Q63347 UniProt NPD GO	PRS7_RAT	26S protease regulatory subunit 7 (Protein MSS1)	0.36	-	nuc	0	Cytoplasm. Nucleus				432
P46472 UniProt NPD GO	PRS7_XENLA	26S protease regulatory subunit 7 (Protein MSS1)	0.36	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				433
P15457 UniProt NPD GO	2SS1_ARATH	2S seed storage protein 1 precursor (2S albumin storage protein) (NWMU2-2S albumin 1) [Contains: 2S ...	0.36	-	nuc	1 *					164
P15458 UniProt NPD GO	2SS2_ARATH	2S seed storage protein 2 precursor (2S albumin storage protein) (NWMU2-2S albumin 2) [Contains: 2S ...	0.36	-	exc	1 *					170
P15459 UniProt NPD GO	2SS3_ARATH	2S seed storage protein 3 precursor (2S albumin storage protein) (NWMU2-2S albumin 3) [Contains: 2S ...	0.36	-	exc	1 *					164
Q6BMB3 UniProt NPD GO	RT10_DEBHA	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.36	-	mit	0	Mitochondrion (By similarity)				267

You are viewing entries 34651 to 34700 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.