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
P20757 UniProt NPD GO	ANGT_SHEEP	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.08	-	mit	0	Secreted protein				476
Q8IV38 UniProt NPD GO	ANKY2_HUMAN	Ankyrin repeat and MYND domain-containing protein 2	0.08	-	nuc	0					441
Q8WXK2 UniProt NPD GO	ASB14_HUMAN	Ankyrin repeat and SOCS box protein 14 (ASB-14)	0.08	-	mit	0					302
Q8VHS7 UniProt NPD GO	ASB14_MOUSE	Ankyrin repeat and SOCS box protein 14 (ASB-14)	0.08	-	mit	0					433
Q8N6D5 UniProt NPD GO	ANR29_HUMAN	Ankyrin repeat domain-containing protein 29	0.08	-	mit	0					301
Q2QL84 UniProt NPD GO	ASZ1_MICMU	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.08	-	nuc	0	Cytoplasm (By similarity)				481
P14950 UniProt NPD GO	ANX11_COLLI	Annexin A1 isoform p35 (Annexin I isoform p35) (Lipocortin I) (Calpactin II) (Chromobindin-9) (Phosp ...	0.08	-	cyt	0					341
Q92411 UniProt NPD GO	TRPG_COCHE	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.08	-	nuc	0					768
P81570 UniProt NPD GO	DEFD3_SPIOL	Antimicrobial peptide D3 (So-D3) (Defensin D3) (Fragment)	0.08	-	mit	0	Cell wall				25
P56771 UniProt NPD GO	CYF_ARATH	Apocytochrome f precursor	0.08	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q8S8W4 UniProt NPD GO	CYF_ATRBE	Apocytochrome f precursor	0.08	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q7YJW0 UniProt NPD GO	CYF_CALFE	Apocytochrome f precursor	0.08	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q8M9X2 UniProt NPD GO	CYF_CHAGL	Apocytochrome f precursor	0.08	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				318
P02653 UniProt NPD GO	APOA2_MACMU	Apolipoprotein A-II (Apo-AII) (ApoA-II)	0.08	-	cyt	0	Secreted protein				77
P02656 UniProt NPD GO	APOC3_HUMAN	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.08	-	exc	0	Secreted protein	extracellular region [NAS]	107720		99
P18659 UniProt NPD GO	APOC3_MACFA	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.08	-	exc	0	Secreted protein				99
P49950 UniProt NPD GO	BCL2_RAT	Apoptosis regulator Bcl-2	0.08	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Nucleus; nuclear membrane ...				236
P80595 UniProt NPD GO	APY_SOLTU	Apyrase precursor (EC 3.6.1.5) (ATP-diphosphatase) (Adenosine diphosphatase) (ADPase) (ATP-diphospho ...	0.08	-	mit	1 *	Membrane; single-pass membrane protein (Probable)				454
P50501 UniProt NPD GO	AQPA_RANES	Aquaporin FA-CHIP	0.08	-	end	6 *	Membrane; multi-pass membrane protein				272
O77750 UniProt NPD GO	AQP4_BOVIN	Aquaporin-4 (AQP-4) (WCH4) (Mercurial-insensitive water channel) (MIWC)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				323
P55064 UniProt NPD GO	AQP5_HUMAN	Aquaporin-5 (AQP-5)	0.08	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600442		265
Q866S3 UniProt NPD GO	AQP5_SHEEP	Aquaporin-5 (AQP-5)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				265
Q42460 UniProt NPD GO	AR5A_PHAVU	Arcelin-5A precursor	0.08	-	exc	0				1IOA	261
Q5SC60 UniProt NPD GO	ANN1_AREMA	Arenicin-1 precursor	0.08	-	vac	0					202
Q5SC59 UniProt NPD GO	ANN2_AREMA	Arenicin-2 precursor	0.08	-	vac	0					202
Q9NH49 UniProt NPD GO	KARG_CALSI	Arginine kinase (EC 2.7.3.3) (AK)	0.08	-	cyt	0					357
Q9U9J4 UniProt NPD GO	KARG_CARMA	Arginine kinase (EC 2.7.3.3) (AK)	0.08	-	cyt	0					357
P51544 UniProt NPD GO	KARG_NORMA	Arginine kinase (EC 2.7.3.3) (AK)	0.08	-	cyt	0					358
P00966 UniProt NPD GO	ASSY_HUMAN	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.08	-	cyt	0		cytoplasm [TAS]	603470		412
P16460 UniProt NPD GO	ASSY_MOUSE	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.08	-	cyt	0		mitochondrion [IDA]			412
P22768 UniProt NPD GO	ASSY_YEAST	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.08	-	cyt	0		cytosol [IDA]			420
Q6P1M9 UniProt NPD GO	ARMX5_HUMAN	Armadillo repeat-containing X-linked protein 5	0.08	-	nuc	0					558
P32122 UniProt NPD GO	ARRH_LOCMI	Arrestin homolog	0.08	-	nuc	0					407
Q9EQP6 UniProt NPD GO	ARRC_MOUSE	Arrestin-C (Cone arrestin) (Retinal cone arrestin-3)	0.08	-	mit	0		synapse [IDA]			381
P17714 UniProt NPD GO	ASNS_MESAU	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.08	-	cyt	0					560
P00507 UniProt NPD GO	AATM_RAT	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix	cell surface [IDA] mitochondrion [IDA]			430
Q6YNY7 UniProt NPD GO	ASP1_ORYSA	Aspartic proteinase Asp1 precursor (EC 3.4.23.-) (OsAsp1) (Nucellin-like protein)	0.08	-	exc	0					410
P69476 UniProt NPD GO	NEP1_NEPDI	Aspartic proteinase nepenthesin-1 (EC 3.4.23.-) (Nepenthesin-I) (Fragments)	0.08	-	cyt	0	Secreted protein				164
P42211 UniProt NPD GO	ASPRX_ORYSA	Aspartic proteinase precursor (EC 3.4.23.-)	0.08	-	exc	1 *					496
P45381 UniProt NPD GO	ACY2_HUMAN	Aspartoacylase (EC 3.5.1.15) (Aminoacylase-2) (ACY-2)	0.08	-	cyt	0			608034		313
P81803 UniProt NPD GO	TTF17_HADVE	Atracotoxin-Hvf17 (AcTx-Hvf17)	0.08	-	nuc	0	Secreted protein				68
Q3T0W7 UniProt NPD GO	ATG12_BOVIN	Autophagy-related protein 12 (APG12-like)	0.08	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			140
Q5KFW2 UniProt NPD GO	ATG22_CRYNE	Autophagy-related protein 22	0.08	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				546
Q4WH97 UniProt NPD GO	AT221_ASPFU	Autophagy-related protein 22-1	0.08	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				609
Q940Y5 UniProt NPD GO	PIN7_ARATH	Auxin efflux carrier component 7 (AtPIN7)	0.08	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				619
Q9CA25 UniProt NPD GO	LAX3_ARATH	Auxin transporter-like protein 3 (AUX1-like protein 3)	0.08	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				470
P32294 UniProt NPD GO	AX22B_PHAAU	Auxin-induced protein 22B (Indole-3-acetic acid-induced protein ARG4)	0.08	-	cyt	0	Nucleus (By similarity)				196
Q5R8H3 UniProt NPD GO	BAP31_PONPY	B-cell receptor-associated protein 31 (BCR-associated protein Bap31)	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				245
P51572 UniProt NPD GO	BAP31_HUMAN	B-cell receptor-associated protein 31 (BCR-associated protein Bap31) (p28 Bap31) (CDM protein) (6C6- ...	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...	integral to plasma membrane [IDA]	300475		245
P32299 UniProt NPD GO	BKRB2_MOUSE	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.08	-	end	7	Membrane; multi-pass membrane protein				392

You are viewing entries 67601 to 67650 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.