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
P25169 UniProt NPD GO	AT1B1_ARTSF	Sodium/potassium-transporting ATPase subunit beta (Sodium/potassium-dependent ATPase beta subunit)	0.05	-	mit	1 *	Membrane; single-pass type II membrane protein				315
P05029 UniProt NPD GO	AT1B1_TORCA	Sodium/potassium-transporting ATPase subunit beta (Sodium/potassium-dependent ATPase beta subunit)	0.05	-	mit	1 *	Membrane; single-pass type II membrane protein				305
Q9BZW2 UniProt NPD GO	S13A1_HUMAN	Solute carrier family 13 member 1 (Renal sodium/sulfate cotransporter) (Na(+)/sulfate cotransporter) ...	0.05	-	end	11 *	Membrane; multi-pass membrane protein		606193		595
P70545 UniProt NPD GO	S13A2_RAT	Solute carrier family 13 member 2 (Intestinal sodium/dicarboxylate cotransporter) (Na(+)/dicarboxyla ...	0.05	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				587
P27674 UniProt NPD GO	GTR1_BOVIN	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.05	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...	integral to plasma membrane [IC]			492
Q8MII5 UniProt NPD GO	S35B1_BOVIN	Solute carrier family 35 member B1 (Endoplasmic reticulum nucleotide sugar transporter 1)	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				322
Q6V7K3 UniProt NPD GO	S35B1_RAT	Solute carrier family 35 member B1 (UDP-galactose transporter-related protein 1) (UGTrel1)	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				322
P97858 UniProt NPD GO	S35B1_MOUSE	Solute carrier family 35 member B1 (UDP-galactose transporter-related protein 1) (UGTrel1) (UDP-gala ...	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				322
P78383 UniProt NPD GO	S35B1_HUMAN	Solute carrier family 35 member B1 (UDP-galactose transporter-related protein 1) (UGTrel1) (hUGTrel1 ...	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	microsome [TAS]			322
Q61LC0 UniProt NPD GO	S35B3_CAEBR	Solute carrier family 35 member B3 homolog	0.05	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				363
Q9NP59 UniProt NPD GO	S40A1_HUMAN	Solute carrier family 40 member 1 (Ferroportin-1) (Iron-regulated transporter 1)	0.05	-	end	10 *	Cell membrane; multi-pass membrane protein. Localized to the basolateral membrane of polarized epith ...	cytoplasm [TAS] integral to plasma membrane [TAS]	606069		571
Q9PRZ6 UniProt NPD GO	SMS1_AMICA	Somatostatin-1 precursor (Somatostatin I) [Contains: Somatostatin-26; Somatostatin-14] (Fragment)	0.05	-	nuc	0	Secreted protein				26
P87219 UniProt NPD GO	SOU1_CANAL	Sorbitol utilization protein SOU1 (EC 1.1.-.-)	0.05	-	cyt	0					281
P22975 UniProt NPD GO	H1L_SPISO	Sperm-specific protein PL-I (PL-I) (Sperm-specific linker histone H1-like protein) (Fragment)	0.05	-	nuc	0	Nucleus				75
Q3SZA5 UniProt NPD GO	SPSY_BOVIN	Spermine synthase (EC 2.5.1.22) (Spermidine aminopropyltransferase) (SPMSY)	0.05	-	mit	0					365
P52788 UniProt NPD GO	SPSY_HUMAN	Spermine synthase (EC 2.5.1.22) (Spermidine aminopropyltransferase) (SPMSY)	0.05	-	mit	0			300105		366
O60906 UniProt NPD GO	NSMA_HUMAN	Sphingomyelin phosphodiesterase 2 (EC 3.1.4.12) (Neutral sphingomyelinase) (nSMase) (N-SMase) (Lyso- ...	0.05	-	mit	3	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603498		423
P83046 UniProt NPD GO	SMA2_LOXIN	Sphingomyelinase P2 precursor (EC 3.1.4.41) (SMase P2)	0.05	-	exc	1 *	Secreted protein				322
Q9DDK4 UniProt NPD GO	EDG1_BRARE	Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate receptor 1) (S1P1)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			362
Q9PUQ8 UniProt NPD GO	EDG3_FUGRU	Sphingosine 1-phosphate receptor Edg-3 (S1P receptor Edg-3) (Sphingosine 1-phosphate receptor 3) (S1 ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				384
P46095 UniProt NPD GO	GPR6_HUMAN	Sphingosine 1-phosphate receptor GPR6 (G-protein coupled receptor 6)	0.05	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600553		362
P51651 UniProt NPD GO	GPR6_RAT	Sphingosine 1-phosphate receptor GPR6 (G-protein coupled receptor 6)	0.05	-	end	7	Membrane; multi-pass membrane protein				363
Q8BFQ3 UniProt NPD GO	SPR1_MOUSE	Sphingosylphosphorylcholine receptor (G-protein coupled receptor 68)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				365
P01251 UniProt NPD GO	THPS_BOVIN	Splenin (Thymopoietin III)	0.05	-	cyt	0					49
Q29350 UniProt NPD GO	U2AF1_PIG	Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor ...	0.05	-	nuc	0	Nucleus (By similarity)				81
P15521 UniProt NPD GO	SPG3_DICDI	Spore germination protein 3 precursor (SPG3)	0.05	-	exc	1 *	Secreted protein (Probable)				127
P13399 UniProt NPD GO	TA4_EIMTE	Sporulated oocyst TA4 antigen precursor (Major sporozoite surface antigen) [Contains: Sporulated ooc ...	0.05	-	exc	0	Surface of sporozoites				253
P41808 UniProt NPD GO	SMK1_YEAST	Sporulation-specific mitogen-activated protein kinase SMK1 (EC 2.7.11.24) (MAP kinase SMK1)	0.05	-	cyt	0		mitochondrion [IDA]			388
Q6BRB7 UniProt NPD GO	ERG6_DEBHA	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.05	-	nuc	0					377
Q9P3R1 UniProt NPD GO	ERG6_NEUCR	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.05	-	cyt	0					379
Q15738 UniProt NPD GO	NSDHL_HUMAN	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating (EC 1.1.1.170) (H105e3 protein)	0.05	-	cyt	1			308050		373
P81662 UniProt NPD GO	ACTP1_STOHE	Sticholysin-1 (Sticholysin I) (Cytolysin St I) (Cytotoxin)	0.05	-	cyt	0	Secreted protein. Found in nematocyst				176
P07845 UniProt NPD GO	ACTP2_STOHE	Sticholysin-2 (Sticholysin II) (Cytolysin St II) (StnII) (Cytolysin III) (Cytotoxin)	0.05	-	cyt	0	Secreted protein. Found in nematocyst			1O72	175
Q8BM72 UniProt NPD GO	STCH_MOUSE	Stress 70 protein chaperone microsome-associated 60 kDa protein precursor (Microsomal stress 70 prot ...	0.05	-	cyt	1 *	Microsome (By similarity)				471
P18417 UniProt NPD GO	STSY_CATRO	Strictosidine synthase precursor (EC 4.3.3.2)	0.05	-	exc	1 *	Vacuole				352
O18495 UniProt NPD GO	STYD_STYCL	Styelin-D precursor	0.05	-	vac	0	Secreted protein				81
O18496 UniProt NPD GO	STYE_STYCL	Styelin-E precursor	0.05	-	vac	0	Secreted protein				81
P28498 UniProt NPD GO	TKNA_GADMO	Substance P	0.05	-		0	Secreted protein				11
Q00711 UniProt NPD GO	DHSA_YEAST	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (FP) ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix	respiratory chain complex II (sensu Eukaryota) [TAS]		1PB4	640
P41955 UniProt NPD GO	C560_CAEBR	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor	0.05	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				184
P36967 UniProt NPD GO	SUCA_DICDI	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.05	-	cyt	0	Mitochondrion				310
P68209 UniProt NPD GO	SUCA1_ARATH	Succinyl-CoA ligase [GDP-forming] subunit alpha-1, mitochondrial precursor (EC 6.2.1.4) (Succinyl-Co ...	0.05	-	mit	0	Mitochondrion				347
Q9D0K2 UniProt NPD GO	SCOT_MOUSE	Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial precursor (EC 2.8.3.5) (Somatic-type ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			520
Q9SBA7 UniProt NPD GO	STP8_ARATH	Sugar transport protein 8 (Hexose transporter 8)	0.05	-	end	12 *	Membrane; multi-pass membrane protein				507
Q9D975 UniProt NPD GO	SRXN1_MOUSE	Sulfiredoxin-1 (EC 1.8.98.2) (Neoplastic progression protein 3)	0.05	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			136
O65198 UniProt NPD GO	SODCP_MEDSA	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.05	-	mit	0	Plastid; chloroplast				202
P41979 UniProt NPD GO	SODM3_MAIZE	Superoxide dismutase [Mn] 3.3, mitochondrial precursor (EC 1.15.1.1)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				233
P41980 UniProt NPD GO	SODM4_MAIZE	Superoxide dismutase [Mn] 3.4, mitochondrial precursor (EC 1.15.1.1)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				233
Q8HXP4 UniProt NPD GO	SODM_MACFU	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198
Q8HXP2 UniProt NPD GO	SODM_MACMU	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198

You are viewing entries 75701 to 75750 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.