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
Q8INB9 UniProt NPD GO	AKT1_DROME	RAC serine/threonine-protein kinase (EC 2.7.11.1) (DRAC-PK) (Akt) (Dakt1) (Protein kinase B) (PKB)	0.36	-	mit	0	Cytoplasm; cytosol. Cell membrane. Recruited to plasma membrane upon activation	plasma membrane [NAS]			611
Q9GPS0 UniProt NPD GO	RACG_DICDI	RAS-related protein racG	0.36	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q6NML0 UniProt NPD GO	ATL1J_ARATH	RING-H2 finger protein ATL1J	0.36	-	nuc	1					225
Q06213 UniProt NPD GO	MED10_YEAST	RNA polymerase II mediator complex subunit 10 (Negative regulator of URS2 protein 2)	0.36	-	nuc	0	Nucleus	mediator complex [IDA]			157
Q02427 UniProt NPD GO	RBP1_DROME	RNA-binding protein 1	0.36	-	nuc	0	Nucleus	nucleus [IDA]			144
Q8C7Q4 UniProt NPD GO	RBM4_MOUSE	RNA-binding protein 4 (RNA-binding motif protein 4) (RNA-binding motif protein 4a) (Lark homolog) (m ...	0.36	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). May undergo ...				361
O60518 UniProt NPD GO	RNBP6_HUMAN	Ran-binding protein 6 (RanBP6)	0.36	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1105
Q7TT45 UniProt NPD GO	RRAGD_MOUSE	Ras-related GTP-binding protein D (Rag D)	0.36	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic. May shuttle between the cytoplasm and nucleus, depend ...	cytoplasm [ISS] nucleus [ISS]			449
P93267 UniProt NPD GO	RAB7_MESCR	Ras-related protein Rab7A	0.36	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q09777 UniProt NPD GO	RGS1_SCHPO	Regulator of G-protein signaling protein 1	0.36	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			481
Q23696 UniProt NPD GO	RFA1_CRIFA	Replication factor A 51 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 1) (Single-stranded ...	0.36	-	cyt	0	Nucleus				467
O14003 UniProt NPD GO	RFC3_SCHPO	Replication factor C subunit 3 (Replication factor C3)	0.36	-	nuc	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS] DNA replication factor C complex [TAS] Elg1 RFC-like complex [IDA] Rad17 RFC-like complex [TAS]			342
Q8N3C7 UniProt NPD GO	RSNL2_HUMAN	Restin-like protein 2	0.36	-	nuc	0					705
O75679 UniProt NPD GO	RFPL3_HUMAN	Ret finger protein-like 3	0.36	-	exc	0			605970		317
Q4TUC0 UniProt NPD GO	RTBDN_CANFA	Retbindin precursor	0.36	-	mit	1 *	Secreted protein (Potential)				223
O08604 UniProt NPD GO	RAE1C_MOUSE	Retinoic acid early inducible protein 1 gamma precursor (RAE-1gamma)	0.36	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA]			253
Q9DAK3 UniProt NPD GO	RHBT1_MOUSE	Rho-related BTB domain-containing protein 1	0.36	-	nuc	0					695
Q695T8 UniProt NPD GO	RHBL4_TOXGO	Rhomboid-like protease 4 (EC 3.4.21.105)	0.36	-	end	6	Membrane; multi-pass membrane protein. Uniformly distributed at the surface of intracellular and ext ...				641
Q5B3K6 UniProt NPD GO	RNY1_EMENI	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.36	-	nuc	0	Secreted protein (By similarity)				417
Q8SQ09 UniProt NPD GO	RNAS1_PAPHA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.36	-	nuc	1 *	Secreted protein				152
Q4R741 UniProt NPD GO	RIR2B_MACFA	Ribonucleoside-diphosphate reductase M2 subunit B (EC 1.17.4.1)	0.36	-	cyt	1	Cytoplasm. Translocates from cytoplasm to nucleus in response to DNA damage (By similarity)				351
P35178 UniProt NPD GO	RRP1_YEAST	Ribosomal RNA-processing protein 1	0.36	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			278
P30397 UniProt NPD GO	ROAA_EUGGR	Ribosomal operon-associated A protein (RoaA)	0.36	-	end	4	Plastid; chloroplast				516
Q8R0F9 UniProt NPD GO	S14L4_MOUSE	SEC14-like protein 4	0.36	-	cyt	0					403
Q8NB12 UniProt NPD GO	SMYD1_HUMAN	SET and MYND domain-containing protein 1	0.36	+	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)		606846		490
P40635 UniProt NPD GO	ADW4_ALLMI	SRY-related protein ADW4 (Fragment)	0.36	-	nuc	0	Nucleus (Potential)				72
Q5BER4 UniProt NPD GO	SWC5_EMENI	SWR1-complex protein 5	0.36	-	nuc	0	Nucleus (By similarity)				256
P02810 UniProt NPD GO	PRPC_HUMAN	Salivary acidic proline-rich phosphoprotein 1/2 precursor (PRP-1/PRP-2) (Parotid proline-rich protei ...	0.36	-	exc	0	Secreted protein	extracellular space [TAS]	168790		166
Q9JLJ1 UniProt NPD GO	SELK_MOUSE	Selenoprotein K	0.36	-	nuc	1 *					94
Q9BVL4 UniProt NPD GO	SELO_HUMAN	Selenoprotein O	0.36	-	mit	0			607917		669
Q98SV1 UniProt NPD GO	SELPA_BRARE	Selenoprotein Pa precursor (zSelPa)	0.36	-	exc	0	Secreted protein	extracellular region [IDA]			367
P59797 UniProt NPD GO	SELV_HUMAN	Selenoprotein V	0.36	-	mit	0			607919		346
Q99719 UniProt NPD GO	SEPT5_HUMAN	Septin-5 (Peanut-like protein 1) (Cell division control-related protein 1) (CDCrel-1)	0.36	-	nuc	0		plasma membrane [IDA] synaptic vesicle [IDA]	602724		369
Q758F0 UniProt NPD GO	GLYM_ASHGO	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.36	+	mit	0	Mitochondrion				497
P57760 UniProt NPD GO	STK16_RAT	Serine/threonine-protein kinase 16 (EC 2.7.11.1) (Protein kinase PKL12) (Myristoylated and palmitoyl ...	0.36	-	cyt	0	Membrane; lipid-anchor (By similarity)				304
Q99KH8 UniProt NPD GO	STK24_MOUSE	Serine/threonine-protein kinase 24 (EC 2.7.11.1)	0.36	-	nuc	0	Cytoplasm (By similarity)				431
Q8AYC9 UniProt NPD GO	CHK1_CHICK	Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)	0.36	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear export is mediated at least in part by X ...				476
O14757 UniProt NPD GO	CHK1_HUMAN	Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)	0.36	+	cyt	0	Nucleus. Cytoplasm. Nuclear export is mediated at least in part by XPO1/CRM1. Also localizes to the ...	condensed nuclear chromosome [TAS]	603078	2CGX	476
Q96QS6 UniProt NPD GO	KPSH2_HUMAN	Serine/threonine-protein kinase H2 (EC 2.7.11.1) (PSK-H2)	0.36	-	mit	0					385
Q8TDX7 UniProt NPD GO	NEK7_HUMAN	Serine/threonine-protein kinase Nek7 (EC 2.7.11.1) (NimA-related protein kinase 7)	0.36	-	cyt	0	Cytoplasm (By similarity)		606848		302
Q5R495 UniProt NPD GO	OXSR1_PONPY	Serine/threonine-protein kinase OSR1 (EC 2.7.11.1) (Oxidative stress-responsive 1 protein)	0.36	-	cyt	0					527
P36874 UniProt NPD GO	PP1G_XENLA	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G)	0.36	-	cyt	0	Cytoplasm				323
O17821 UniProt NPD GO	SRD41_CAEEL	Serpentine receptor class delta-41 (Protein srd-41)	0.36	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				324
P08759 UniProt NPD GO	ALBUA_XENLA	Serum albumin A precursor (68 kDa serum albumin)	0.36	-	exc	0	Secreted protein				606
P58003 UniProt NPD GO	SESN1_XENLA	Sestrin-1 (p53-regulated protein PA26) (XPA26)	0.36	-	nuc	0	Nucleus				481
P70390 UniProt NPD GO	SHOX2_MOUSE	Short stature homeobox protein 2 (Homeobox protein Og12X) (OG-12) (Paired family homeodomain protein ...	0.36	+	nuc	0	Nucleus				331
Q9Y3R4 UniProt NPD GO	NEUR2_HUMAN	Sialidase-2 (EC 3.2.1.18) (Cytosolic sialidase) (N-acetyl-alpha-neuraminidase 2)	0.36	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	605528	1VCU	380
Q9JMH7 UniProt NPD GO	NEUR3_MOUSE	Sialidase-3 (EC 3.2.1.18) (Membrane sialidase) (Ganglioside sialidase) (N-acetyl-alpha-neuraminidase ...	0.36	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				418
Q9BZZ2 UniProt NPD GO	SN_HUMAN	Sialoadhesin precursor (Sialic acid-binding Ig-like lectin-1) (Siglec-1) (CD169 antigen)	0.36	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to membrane [NAS]	600751		1709
P06625 UniProt NPD GO	SRPR_CANFA	Signal recognition particle receptor subunit alpha (SR-alpha) (Docking protein alpha) (DP-alpha)	0.36	+	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Thought to be an ...				638

You are viewing entries 35351 to 35400 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.