UoD Bioinformatics | TREMBL or we'll BLAST you!

VIEWING REQUEST: 15

Submitted On

2002/12/01 05:07:44 PM

Data Directory

/jobs/www-submit/submit_all-20021201_1707_paudley.27728

Raw Sequence

input.sequence

Sequence Type

protein

InfoSeq

USA	Name	Accession	Type	Length	Description
ncbi::stdin:HXD9_HUMAN	HXD9_HUMAN	P28356	P	342	Homeobox protein Hox-D9 (Hox-4C) (Hox-5.2).

InterProScan

Query Sequence swall:HXD9_HUMAN CRC64 Checksum: 731981FE25C5ACD7 Length: 342 aa.

PD000010		sp_P28357_HXD9_MOUSE
PR00024		HOMEOBOX
PR00031		HTHREPRESSR
PF00046		homeobox
PF04617		Hox9_act
SM00389		HOX
PS50071		HOMEOBOX_2
PS50315		GLY_RICH
PS50324		SER_RICH
PS00027		HOMEOBOX_1

Results of
FPrintScan
vs. PRINTS

Results of
HMMSmart
vs. SMART

Results of
HMMPfam
vs. PFAM-A

Results of
HMMTigr
vs. TIGRFAMs

Results of
ScanRegExp
vs. PROSITE

Results of
ProfileScan
vs. PROFILES

Results of
BlastProDom
vs. PRODOM

PR00024
T[297-308]
T[312-322]
T[322-331]

PR00031
T[304-313]
T[313-329]

SM00389
T[275-337]

PF00046
T[276-332]

PF04617
T[1-262]

PS00027
T[308-331]

PS50071
T[273-333]

PS50315
T[115-149]

PS50324
T[165-201]

PD000010
T[276-327]

ACTIONS

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Download: a tar.gz of the results.
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EMBOSS Applications

EMBOSS:antigenic Potentially antigenic regions	Antigenic Regions Report	EMBOSS:charge Protein charge plot	Protein charge plot
EMBOSS:cpgplot CpG rich areas plot	CpG Rich Areas Plot	EMBOSS:dan Calculates DNA RNA/DNA melting temperature	DNA Melting Temp. Graph
EMBOSS:einverted Finds DNA inverted repeats	List of Found Inverted Repeats	EMBOSS:geecee Calculates the fractional GC content of nucleic acid sequences	Calculated GC Content
EMBOSS:hmoment Hydrophobic moment calculation	Plot of Hydrophobic Moment	EMBOSS:iep Calculates the isoelectric point of a protein	Plot of Isoelectric Point
EMBOSS:isochore Plots isochores in large DNA sequences	Plot of Isochores	EMBOSS:marscan Finds MAR/SAR sites in nucleic sequences	Report of MAR/SAR Sites
EMBOSS:newcpgseek CpG rich areas report	CpG Rich Areas Report	EMBOSS:octanol Displays protein hydropathy	Hydrophobicity Plot
EMBOSS:palindrome Looks for inverted repeats in a nucleotide sequence	List of repeats	EMBOSS:pepcoil Predicts coiled coil regions	Predicted coils
EMBOSS:pepinfo Plots simple amino acid properties in parallel	Peptide Plot	EMBOSS:pepnet Displays proteins as a helical net	Helical Net Plot
EMBOSS:pepstats Protein statistics	Statistics Report	EMBOSS:pepwheel Shows protein sequences as helices	Wheel Plot
EMBOSS:pepwindow Displays protein hydropathy	Kyte-Doolittle Plot	EMBOSS:plotorf Plot potential open reading frames	ORF Plot
EMBOSS:remap Display a sequence with restriction cut sites, translation etc	Cut Map	EMBOSS:restrict Restriction Enzyme Sites	Restriction Enzyme Sites
EMBOSS:showfeat Show features of a sequence	Feature Listing	EMBOSS:sigcleave Reports protein signal cleavage sites	Protein Signal Cleavage Report
EMBOSS:syco Synonymous codon usage Gribskov statistic plot	Gribskov Statistic Plot	EMBOSS:wobble Wobble base plot	Wobble Plot

ACTIONS

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Jpred

ACTIONS

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View: PSI-BLAST Output.
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Gotcha

Overall Confidence: 6.1 (high)
Matches to the following GO terms were observed:

GO id	Score	SD	Description
GO:3673	1	0	Gene_Ontology
GO:8150	0.9148	0.1475	biological_process
GO:3674	0.8727	0.1695	molecular_function
GO:5488	0.7734	0.3361	binding
GO:3676	0.7687	0.3441	nucleic acid binding
GO:3677	0.7650	0.3416	DNA binding

ACTIONS

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YinOYang

ACTIONS

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PSort II

PSort Subprogram Results:

PSG:  a new signal peptide prediction method
      N-region:  length 0;  pos.chg 0;  neg.chg 0
      H-region:  length 12;  peak value   5.64
      PSG score:   1.24

GvH:  von Heijne's method for signal seq. recognition
      GvH score (threshold: -2.1):  -6.26
      possible cleavage site: between 59 and 60

>>> Seems to have no N-terminal signal peptide

ALOM: Klein et al's method for TM region allocation
      Init position for calculation: 1
      Tentative number of TMS(s) for the threshold  0.5:   0
      number of TMS(s) .. fixed
      PERIPHERAL  Likelihood =  7.53 (at 56)
      ALOM score:   7.53  (number of TMSs: 0)

MTOP: Prediction of membrane topology (Hartmann et al.)
      Center position for calculation: 6
      Charge difference: -3.5   C(-2.5) - N( 1.0)
      N >= C: N-terminal side will be inside

MITDISC: discrimination of mitochondrial targeting seq
      R content:       0       Hyd Moment(75):  2.44
      Hyd Moment(95):  0.72    G content:       2
      D/E content:     2       S/T content:     6
      Score: -7.33

Gavel: prediction of cleavage sites for mitochondrial preseq
      cleavage site motif not found

NUCDISC: discrimination of nuclear localization signals
      pat4: RKKR (5) at  276
      pat7: none
      bipartite: none
      content of basic residues:  10.5%
      NLS Score: -0.16

KDEL: ER retention motif in the C-terminus: none

ER Membrane Retention Signals:
      KKXX-like motif in the C-terminus: CPKG

SKL: peroxisomal targeting signal in the C-terminus: none

SKL2: 2nd peroxisomal targeting signal:  none

VAC: possible vacuolar targeting motif: none

RNA-binding motif: none

Actinin-type actin-binding motif:
      type 1: none
      type 2: none

NMYR: N-myristoylation pattern : none

Prenylation motif: none

memYQRL: transport motif from cell surface to Golgi: none

Tyrosines in the tail: none

Dileucine motif in the tail: none

checking 63 PROSITE DNA binding motifs:
      'Homeobox' domain signature (PS00027):  *** found ***
         VARILNLTERQVKIWFQNRRMKMK at 308

checking 71 PROSITE ribosomal protein motifs:  none

checking 33 PROSITE prokaryotic DNA binding motifs:  none

NNCN: Reinhardt's method for Cytplasmic/Nuclear discrimination
      Prediction: nuclear
      Reliability: 94.1

COIL: Lupas's algorithm to detect coiled-coil regions
      total: 0 residues

Results of the k-NN Prediction k = 9/23

	 78.3 %: nuclear
	  8.7 %: mitochondrial
	  4.3 %: cytoplasmic
	  4.3 %: vacuolar
	  4.3 %: extracellular, including cell wall

>> prediction for QUERY is nuc (k=23)

ACTIONS

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