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
Q95Y83 UniProt NPD GO	RM19_CAEEL	Probable 39S ribosomal protein L19, mitochondrial precursor	0.53	-	mit	0	Mitochondrion (By similarity)				288
Q21454 UniProt NPD GO	RM35_CAEEL	Probable 39S ribosomal protein L35, mitochondrial precursor (L35mt)	0.53	-	nuc	0	Mitochondrion (By similarity)				158
Q5W5U4 UniProt NPD GO	DDX4_BOVIN	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4)	0.53	-	nuc	0	Cytoplasm (By similarity)				729
Q8K0Z9 UniProt NPD GO	GP153_MOUSE	Probable G-protein coupled receptor 153 (G-protein coupled receptor PGR1)	0.53	-	end	7 *	Membrane; multi-pass membrane protein				631
Q9QYC6 UniProt NPD GO	GPR37_RAT	Probable G-protein coupled receptor 37 precursor (G-protein coupled receptor CNS1)	0.53	-	end	7	Membrane; multi-pass membrane protein				603
Q9LP56 UniProt NPD GO	WRK65_ARATH	Probable WRKY transcription factor 65 (WRKY DNA-binding protein 65)	0.53	-	nuc	0	Nucleus (Potential)				259
Q9VRB3 UniProt NPD GO	CP6V1_DROME	Probable cytochrome P450 6v1 (EC 1.14.-.-) (CYPVIV1)	0.53	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				520
Q8W3K0 UniProt NPD GO	DRL9_ARATH	Probable disease resistance protein At1g58602	0.53	-	nuc	0					1138
Q9Y7Y8 UniProt NPD GO	SYQ_SCHPO	Probable glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.53	-	nuc	0					811
O82333 UniProt NPD GO	GH31_ARATH	Probable indole-3-acetic acid-amido synthetase GH3.1 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.53	-	cyt	0					590
P31396 UniProt NPD GO	HR3_DROME	Probable nuclear hormone receptor HR3 (dHR3)	0.53	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			487
Q07949 UniProt NPD GO	PSR2_YEAST	Probable phosphatase PSR2 (EC 3.1.3.-) (Plasma membrane sodium response protein 2)	0.53	-	nuc	0	Cell membrane (By similarity)	plasma membrane [ISS]			397
O60423 UniProt NPD GO	AT8B3_HUMAN	Probable phospholipid-transporting ATPase IK (EC 3.6.3.1) (ATPase class I type 8B member 3)	0.53	-	end	7	Membrane; multi-pass membrane protein		605866		1310
P53170 UniProt NPD GO	YGF9_YEAST	Probable protein kinase YGL059W (EC 2.7.11.-)	0.53	-	nuc	0	Mitochondrion	mitochondrion [IDA]			491
Q09958 UniProt NPD GO	EBP2_CAEEL	Probable rRNA-processing protein EBP2 homolog	0.53	+	mit	0	Nucleus; nucleolus (By similarity)				340
P46579 UniProt NPD GO	SYWM_CAEEL	Probable tryptophanyl-tRNA synthetase, mitochondrial (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.53	-	nuc	0	Mitochondrion; mitochondrial matrix (Potential)				650
Q95336 UniProt NPD GO	GON2_TUPGB	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.53	-	exc	0	Secreted protein				114
P32240 UniProt NPD GO	PE2R4_MOUSE	Prostaglandin E2 receptor, EP4 subtype (Prostanoid EP4 receptor) (PGE receptor, EP4 subtype)	0.53	-	end	6 *	Membrane; multi-pass membrane protein				513
Q5ZJV4 UniProt NPD GO	CJ119_CHICK	Protein C10orf119 homolog	0.53	-	nuc	0					634
Q9D131 UniProt NPD GO	CK001_MOUSE	Protein C11orf1 homolog	0.53	-	nuc	0	Nucleus (By similarity)				166
O43822 UniProt NPD GO	CU002_HUMAN	Protein C21orf2 (C21orf-HUMF09G8.5) (YF5/A2)	0.53	-	mit	0			603191		256
Q9JJG9 UniProt NPD GO	CD014_MOUSE	Protein C4orf14 homolog	0.53	+	mit	0		mitochondrial inner membrane [IDA]			693
Q5FW52 UniProt NPD GO	CF142_MOUSE	Protein C6orf142 homolog	0.53	-	nuc	0					269
Q96N11 UniProt NPD GO	CG026_HUMAN	Protein C7orf26	0.53	-	mit	0					449
Q96KS9 UniProt NPD GO	CH013_HUMAN	Protein C8orf13	0.53	-	nuc	0					214
Q4FZH1 UniProt NPD GO	CI061_MOUSE	Protein C9orf61 ortholog (Protein Gm967)	0.53	-	nuc	0					290
Q9CQY2 UniProt NPD GO	F103A_MOUSE	Protein FAM103A1	0.53	-	nuc	0					119
Q9NP50 UniProt NPD GO	FA60A_HUMAN	Protein FAM60A (Tera protein homolog)	0.53	+	nuc	0					221
Q8C8M1 UniProt NPD GO	FA60A_MOUSE	Protein FAM60A (Tera protein)	0.53	+	nuc	0					221
Q8K2F8 UniProt NPD GO	FA61A_MOUSE	Protein FAM61A	0.53	+	nuc	0					462
Q3U7R1 UniProt NPD GO	FA62A_MOUSE	Protein FAM62A (Membrane-bound C2 domain-containing protein)	0.53	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				1092
P32334 UniProt NPD GO	MSB2_YEAST	Protein MSB2 (Multicopy suppressor of bud emergence 2)	0.53	-	exc	1		integral to plasma membrane [IMP] site of polarized growth [IDA]			1306
Q64299 UniProt NPD GO	NOV_MOUSE	Protein NOV homolog precursor (NovH) (Nephroblastoma overexpressed gene protein homolog)	0.53	-	exc	0	Secreted protein				354
O55125 UniProt NPD GO	NIPS1_MOUSE	Protein NipSnap1	0.53	-	mit	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			284
P43299 UniProt NPD GO	PROL_ARATH	Protein PROLIFERA	0.53	-	cyt	0	Nucleus				716
Q03446 UniProt NPD GO	RCR2_YEAST	Protein RCR2 (Protein SSH5)	0.53	-	nuc	1 *		cytoplasm [IDA] vacuole (sensu Fungi) [IDA]			210
Q99909 UniProt NPD GO	SSX3_HUMAN	Protein SSX3	0.53	-	nuc	0			300325		188
Q9SKT0 UniProt NPD GO	THF1_ARATH	Protein THYLAKOID FORMATION1, chloroplast precursor	0.53	-	exc	0	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein. Plastid; chloroplast ...	chloroplast [IDA] thylakoid membrane (sensu Viridiplantae) [IDA]			300
P32630 UniProt NPD GO	UTR5_YEAST	Protein UTR5 (Unknown transcript 5 protein)	0.53	-	nuc	0					166
P34641 UniProt NPD GO	CED11_CAEEL	Protein ced-11 (Cell death protein 11)	0.53	-	end	6	Membrane; multi-pass membrane protein (Potential)				1418
Q8R3P2 UniProt NPD GO	DTX2_MOUSE	Protein deltex-2 (Deltex-2) (Deltex2) (mDTX2)	0.53	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)			1V87	619
Q9UKS6 UniProt NPD GO	PACN3_HUMAN	Protein kinase C and casein kinase substrate in neurons protein 3 (SH3 domain-containing protein 651 ...	0.53	-	cyt	0	Cytoplasm. Cell membrane; cytoplasmic side. Detected at the inner aspect of the plasma membrane in c ...	cytoplasm [ISS]	606513		424
P10830 UniProt NPD GO	KPCE_RABIT	Protein kinase C epsilon type (EC 2.7.11.13) (nPKC-epsilon)	0.53	-	cyt	0					736
P09216 UniProt NPD GO	KPCE_RAT	Protein kinase C epsilon type (EC 2.7.11.13) (nPKC-epsilon)	0.53	-	cyt	0				1GMI	737
P25724 UniProt NPD GO	NANOS_DROME	Protein nanos	0.53	-	nuc	0		pole plasm [TAS]			401
Q96FA3 UniProt NPD GO	PELI1_HUMAN	Protein pellino homolog 1 (Pellino-1) (Pellino-related intracellular signaling molecule)	0.53	-	nuc	0					418
Q8BG95 UniProt NPD GO	MYPT2_MOUSE	Protein phosphatase 1 regulatory subunit 12B (Myosin phosphatase-targeting subunit 2) (Fragment)	0.53	-	nuc	0	Cytoplasm (By similarity). Along actomyosin filaments and stress fibers (By similarity)				484
P41000 UniProt NPD GO	SCP3_SCHPO	Protein scp3	0.53	-	nuc	0					583
Q8TGG5 UniProt NPD GO	SEY1_ASPFU	Protein sey1	0.53	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				864
Q9C5P7 UniProt NPD GO	SEC1A_ARATH	Protein transport Sec1a (AtSec1a)	0.53	-	nuc	0					611

You are viewing entries 23301 to 23350 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.