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
P49282 UniProt NPD GO	NRAM2_MOUSE	Natural resistance-associated macrophage protein 2 (NRAMP 2)	0.00	-	end	9	Membrane; multi-pass membrane protein (Probable)	endomembrane system [IDA] endosome [IDA] endosome membrane [IDA] plasma membrane [IDA]			568
P49281 UniProt NPD GO	NRAM2_HUMAN	Natural resistance-associated macrophage protein 2 (NRAMP 2) (Divalent metal transporter 1) (DMT1)	0.00	-	end	9	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	600523		568
O54902 UniProt NPD GO	NRAM2_RAT	Natural resistance-associated macrophage protein 2 (NRAMP 2) (Metal ion transporter DCT1)	0.00	-	end	9	Membrane; multi-pass membrane protein (Probable)	integral to membrane [IDA]			568
P58522 UniProt NPD GO	NEPH_RAT	Nephritogenoside	0.00	-	cyt	0					21
Q9CQ45 UniProt NPD GO	NENF_MOUSE	Neudesin precursor (Neuron-derived neurotrophic factor) (Secreted protein of unknown function) (SPUF ...	0.00	-	end	1 *	Secreted protein; extracellular space	extracellular space [IDA]			171
O76242 UniProt NPD GO	GLBN_CERLA	Neural hemoglobin (NrHb)	0.00	-	cyt	0				1V07	109
Q8SPU7 UniProt NPD GO	ACHA5_BOVIN	Neuronal acetylcholine receptor protein subunit alpha-5 precursor	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				475
P30532 UniProt NPD GO	ACHA5_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-5 precursor	0.00	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IC]	118505		468
Q5IS51 UniProt NPD GO	ACHA5_PANTR	Neuronal acetylcholine receptor protein subunit alpha-5 precursor	0.00	-	end	4	Membrane; multi-pass membrane protein (By similarity)				468
P20420 UniProt NPD GO	ACHA5_RAT	Neuronal acetylcholine receptor protein subunit alpha-5 precursor	0.00	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]			452
Q13491 UniProt NPD GO	GPM6B_HUMAN	Neuronal membrane glycoprotein M6-b (M6b)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]	300051		265
P10776 UniProt NPD GO	NPAB_LOCMI	Neuroparsin A precursor (NPA) [Contains: Neuroparsin B (NPB)]	0.00	-	mit	0					107
P83435 UniProt NPD GO	SCX4_TITFA	Neurotoxin 4 (Tf4)	0.00	-	nuc	0	Secreted protein				62
P04099 UniProt NPD GO	SCX9_BUTOC	Neurotoxin 9 (Neurotoxin IX) (Fragment)	0.00	-	cyt	0	Secreted protein				33
P58570 UniProt NPD GO	SC18_MESMA	Neurotoxin BmK 18(2) (Fragment)	0.00	-		0	Secreted protein				20
O61705 UniProt NPD GO	SCXA_MESMA	Neurotoxin BmK-X precursor (BmKX) (BmK10) (BmK-M10) (Bmk M10) (Neurotoxin M10) (Alpha-neurotoxin TX9 ...	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			84
Q9N682 UniProt NPD GO	SCXB_MESMA	Neurotoxin BmK-XI precursor (BmK11) (BmK-M11) (Bmk M11) (Alpha-neurotoxin TX14) (BmK M4')	0.00	-	exc	0	Secreted protein				84
P18927 UniProt NPD GO	SCX2_CENLI	Neurotoxin II.22.5 (Fragment)	0.00	-	nuc	0	Secreted protein				30
P01487 UniProt NPD GO	SCX3_LEIQU	Neurotoxin III (Lqq III) (LqqIII) (Lqq3)	0.00	-	nuc	0	Secreted protein			1LQQ	64
P01490 UniProt NPD GO	SCXA_BUTEU	Neurotoxin M10 (BeM10)	0.00	-	cyt	0	Secreted protein				65
P15224 UniProt NPD GO	SCX1_ORTSC	Neurotoxin Os1 (Os-1)	0.00	-	nuc	0	Secreted protein				66
P83909 UniProt NPD GO	TX22_PHORI	Neurotoxin PRTx22C1	0.00	-	nuc	0	Secreted protein				40
O76199 UniProt NPD GO	TX25A_PHONI	Neurotoxin Pn2-5A precursor	0.00	-	exc	0	Secreted protein				82
P83405 UniProt NPD GO	SCBT1_BUTJU	Neurotoxin Tx-1 (BjTx-1)	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			28
P83406 UniProt NPD GO	SCBT2_BUTJU	Neurotoxin Tx-2 (BjTx-2)	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			28
P29425 UniProt NPD GO	TX26_PHONI	Neurotoxin Tx2-6 precursor	0.00	-	exc	0	Secreted protein				82
Q9BLM3 UniProt NPD GO	SCXB_ANDAU	Neurotoxin pcD-985 precursor	0.00	-	nuc	0	Secreted protein				83
P01533 UniProt NPD GO	TXA1_ANESU	Neurotoxin-1 (Toxin ATX-I)	0.00	-	nuc	0	Secreted protein. Found in nematocyst			1ATX	46
Q9W717 UniProt NPD GO	NTX2_NAJAT	Neurotoxin-like protein NTL2 precursor	0.00	-	mit	0	Secreted protein				86
P37357 UniProt NPD GO	EL2A_HORSE	Neutrophil elastase 2A (EC 3.4.21.-) (Proteinase 2A) (Fragments)	0.00	-	cyt	0					85
Q9ZQV4 UniProt NPD GO	NAS5_HORVU	Nicotianamine synthase-like 5 protein (HvNAS5)	0.00	-	mit	0					282
Q01170 UniProt NPD GO	NIA_CHLVU	Nitrate reductase [NADH] (EC 1.7.1.1) (NR) (Fragment)	0.00	-	cyt	0					318
P39882 UniProt NPD GO	NIA_LOTTE	Nitrate reductase [NADH] (EC 1.7.1.1) (NR) (Fragment)	0.00	-	cyt	0					160
Q9TM37 UniProt NPD GO	GLNB_CYACA	Nitrogen regulatory protein P-II	0.00	-	nuc	0	Plastid; chloroplast				113
P51254 UniProt NPD GO	GLNB_PORPU	Nitrogen regulatory protein P-II	0.00	-	cyt	0	Plastid; chloroplast				112
Q94734 UniProt NPD GO	NP4_RHOPR	Nitrophorin-4 precursor (NP4)	0.00	-	exc	1 *	Secreted protein			1YWD	205
P41146 UniProt NPD GO	OPRX_HUMAN	Nociceptin receptor (Orphanin FQ receptor) (Kappa-type 3 opioid receptor) (KOR-3)	0.00	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602548		370
P35377 UniProt NPD GO	OPRX_MOUSE	Nociceptin receptor (Orphanin FQ receptor) (Kappa-type 3 opioid receptor) (KOR-3) (ORGC) (K3 opiate ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				367
P35370 UniProt NPD GO	OPRX_RAT	Nociceptin receptor (Orphanin FQ receptor) (Kappa-type 3 opioid receptor) (KOR-3) (ROR-C) (XOR1)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				367
P47748 UniProt NPD GO	OPRX_CAVPO	Nociceptin receptor (Orphanin FQ receptor) (Kappa-type 3 opioid receptor) (KOR-3) (XOR)	0.00	-	end	7	Membrane; multi-pass membrane protein				370
P08995 UniProt NPD GO	NO26_SOYBN	Nodulin-26 (N-26)	0.00	-	end	6 *	Integral membrane protein. Peribacteroid membrane			1UFD	271
Q8N8Q9 UniProt NPD GO	NIPA2_HUMAN	Non-imprinted in Prader-Willi/Angelman syndrome region protein 2	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)		608146		360
Q9JJC8 UniProt NPD GO	NIPA2_MOUSE	Non-imprinted in Prader-Willi/Angelman syndrome region protein 2 homolog	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				359
Q5R7Q3 UniProt NPD GO	NIPA2_PONPY	Non-imprinted in Prader-Willi/Angelman syndrome region protein 2 homolog	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				360
P07803 UniProt NPD GO	HBL_TRETO	Non-symbiotic hemoglobin (TREto GLB1)	0.00	-	cyt	0					161
O24521 UniProt NPD GO	HBL2_ARATH	Non-symbiotic hemoglobin 2 (Hb2) (ARAth GLB2)	0.00	-	cyt	0					158
Q93Y92 UniProt NPD GO	HBL2_GOSHI	Non-symbiotic hemoglobin 2 (Hb2) (GOShi GLB2)	0.00	-	cyt	0					159
O04985 UniProt NPD GO	HBL2_ORYSA	Non-symbiotic hemoglobin 2 (rHb2) (ORYsa GLB1b)	0.00	-	cyt	0					169
P68168 UniProt NPD GO	HBPL_PARAD	Nonlegume hemoglobin	0.00	-	cyt	0					161
P68169 UniProt NPD GO	HBPL_PARRI	Nonlegume hemoglobin	0.00	-	cyt	0					161

You are viewing entries 96001 to 96050 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.