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
Q20347 UniProt NPD GO	YR62_CAEEL	Putative serine/threonine-protein kinase F42G10.2 (EC 2.7.12.2)	0.10	-	cyt	0					363
P48458 UniProt NPD GO	YT91_CAEEL	Putative serine/threonine-protein phosphatase C06A1.3 in chromosome II (EC 3.1.3.16)	0.10	-	cyt	0					364
Q10298 UniProt NPD GO	YD44_SCHPO	Putative serine/threonine-protein phosphatase C22H10.04 (EC 3.1.3.16)	0.10	-	cyt	0					307
Q09517 UniProt NPD GO	LE767_CAEEL	Putative steroid dehydrogenase let-767 (EC 1.1.1.-) (Lethal protein 767)	0.10	-	mit	1 *					316
Q9VMQ5 UniProt NPD GO	COQ6_DROME	Putative ubiquinone biosynthesis monooxygenase COQ6 (EC 1.14.13.-)	0.10	-	nuc	0					477
Q9SEH4 UniProt NPD GO	PMT4_TOBAC	Putrescine N-methyltransferase 4 (EC 2.1.1.53) (PMT 4)	0.10	-	cyt	0					419
Q6QWR1 UniProt NPD GO	P2OX_PHACH	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (P2O) (Pyranose oxidase) (PROD) (POD) (POx) (Pyran ...	0.10	-	cyt	0	Hyphal periplasmic space				621
Q6UG02 UniProt NPD GO	P2OX_PHLGI	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.10	-	cyt	0	Hyphal periplasmic space (By similarity)				622
P35486 UniProt NPD GO	ODPA_MOUSE	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			390
P26284 UniProt NPD GO	ODPA_RAT	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix	pyruvate dehydrogenase complex (sensu Eukar... [TAS]			390
P29804 UniProt NPD GO	ODPA_PIG	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.10	-	nuc	0	Mitochondrion; mitochondrial matrix				389
P16387 UniProt NPD GO	ODPA_YEAST	Pyruvate dehydrogenase E1 component subunit alpha, mitochondrial precursor (EC 1.2.4.1) (Pyruvate de ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial nucleoid [IDA] mitochondrion [IDA] pyruvate dehydrogenase complex (sensu Eukar... [TAS]			420
O42582 UniProt NPD GO	RDS2_XENLA	RDS/peripherin-like protein xRDS36	0.10	-	end	3 *	Membrane; multi-pass membrane protein				345
Q568Y3 UniProt NPD GO	RN185_RAT	RING finger protein 185	0.10	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				192
Q9Y225 UniProt NPD GO	RNF24_HUMAN	RING finger protein 24	0.10	-	mit	1 *					148
Q9ZT49 UniProt NPD GO	ATL4L_ARATH	RING-H2 finger protein ATL4L (RING-H2 zinc finger protein RHA3b)	0.10	-	nuc	1 *					200
O77264 UniProt NPD GO	RTC1_DROME	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) (RNA-3'-phosphate cyclase) (RNA cyclase)	0.10	-	mit	0	Nucleus; nucleoplasm (By similarity)				361
Q4WYX0 UniProt NPD GO	TFB5_ASPFU	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.10	-	nuc	0	Nucleus (By similarity)				72
P47926 UniProt NPD GO	RSI1_LYCES	RSI-1 protein precursor (TR132)	0.10	-	nuc	1 *	Secreted protein (Potential)				96
P32864 UniProt NPD GO	RAEP_YEAST	Rab proteins geranylgeranyltransferase component A (Rab escort protein) (REP)	0.10	-	nuc	0		cytoplasm [IDA] membrane [IDA]			603
Q9SSX0 UniProt NPD GO	RAC1_ORYSA	Rac-like GTP-binding protein 1 (OsRac1)	0.10	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with the membrane when activated				214
Q12526 UniProt NPD GO	RAS_EMENI	Ras-like protein	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				212
O93856 UniProt NPD GO	RAS_LACBI	Ras-like protein	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				209
P22125 UniProt NPD GO	RAB1_DISOM	Ras-related protein ORAB-1	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				202
P46638 UniProt NPD GO	RB11B_MOUSE	Ras-related protein Rab-11B	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q9H0U4 UniProt NPD GO	RAB1B_HUMAN	Ras-related protein Rab-1B	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q9D1G1 UniProt NPD GO	RAB1B_MOUSE	Ras-related protein Rab-1B	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
P10536 UniProt NPD GO	RAB1B_RAT	Ras-related protein Rab-1B	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q4LE85 UniProt NPD GO	RB27A_PIG	Ras-related protein Rab-27A	0.10	-	cyt	0	Membrane; lipid-anchor (By similarity)				221
P51157 UniProt NPD GO	RAB28_HUMAN	Ras-related protein Rab-28 (Rab-26)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				221
P51158 UniProt NPD GO	RAB28_RAT	Ras-related protein Rab-28 (Rab-26)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				221
P61105 UniProt NPD GO	RAB2A_CANFA	Ras-related protein Rab-2A	0.10	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				212
P61019 UniProt NPD GO	RAB2A_HUMAN	Ras-related protein Rab-2A	0.10	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...		179509	1Z0A	212
Q15771 UniProt NPD GO	RAB30_HUMAN	Ras-related protein Rab-30	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	Golgi stack [TAS]	605693	2EW1	203
Q923S9 UniProt NPD GO	RAB30_MOUSE	Ras-related protein Rab-30	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q14964 UniProt NPD GO	RB39A_HUMAN	Ras-related protein Rab-39A (Rab-39)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q22782 UniProt NPD GO	RAB6B_CAEEL	Ras-related protein Rab-6.2	0.10	-	cyt	0					205
O04486 UniProt NPD GO	RB11C_ARATH	Ras-related protein Rab11C	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q43463 UniProt NPD GO	RAB7_SOYBN	Ras-related protein Rab7	0.10	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
Q9YH09 UniProt NPD GO	RALBA_XENLA	Ras-related protein ralB-A (XRalB-A)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [NAS]			206
Q9JHJ1 UniProt NPD GO	RAMP2_RAT	Receptor activity-modifying protein 2 precursor	0.10	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				182
Q26721 UniProt NPD GO	CYA4_TRYBB	Receptor-type adenylate cyclase ESAG 4 (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) (Ex ...	0.10	-	end	1	Membrane; multi-pass membrane protein (Potential)				1235
Q99280 UniProt NPD GO	CY43_TRYBB	Receptor-type adenylate cyclase GRESAG 4.3 (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) ...	0.10	-	end	0	Membrane; multi-pass membrane protein (Potential)			1FX4	1229
P41592 UniProt NPD GO	OPSR_ANOCA	Red-sensitive opsin (Red cone photoreceptor pigment)	0.10	-	end	7	Membrane; multi-pass membrane protein				369
P47940 UniProt NPD GO	RES18_RAT	Regulated endocrine-specific protein 18 precursor [Contains: Regulated endocrine-specific protein 18 ...	0.10	-	exc	0	Secreted protein	rough endoplasmic reticulum lumen [IDA]			175
P49807 UniProt NPD GO	RGS11_RAT	Regulator of G-protein signaling 11 (RGS11) (Fragment)	0.10	-	cyt	0					66
P11952 UniProt NPD GO	RELX_RAJER	Relaxin [Contains: Relaxin B chain; Relaxin A chain]	0.10	-	nuc	0	Secreted protein				64
P08012 UniProt NPD GO	PRP1_SOYBN	Repetitive proline-rich cell wall protein 1 precursor	0.10	-	exc	1 *					256
P53033 UniProt NPD GO	RFC2_CHICK	Replication factor C subunit 2 (Replication factor C 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40) ( ...	0.10	-	cyt	0	Nucleus (Probable)				359
O75106 UniProt NPD GO	AOC2_HUMAN	Retina-specific copper amine oxidase precursor (EC 1.4.3.6) (RAO) (Amine oxidase [copper-containing] ...	0.10	-	exc	1 *			602268		756

You are viewing entries 65151 to 65200 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.