kpsort2

Function

Predicts protein localization for PSORT2

Description

kpsort2 predicts protein localization sites utilizing PSORT II. PSORT II analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals and reports the possiblity for the input protein to be localized at each candidate site with additional information.

kpsort2 utilizes PSORT WWW Server provided by Tokyo University. Original web-service is located at the following URL:

http://psort.ims.u-tokyo.ac.jp/form2.html

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kpsort2 is thus an interface of "runPsort2" method included in KBWS SOAP service.
This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


  Here is a sample session with kpsort2

% kpsort2
prediction of protein localization sets for animal/yeast sequences
Input protein sequence(s): swissprot:FOXP2_HUMAN
Output file [foxp2_human.kpsort2]: 

PSORT II server 
Input Sequence
QUERY (715 aa) 
MMQESATETI SNSSMNQNGM STLSSQLDAG SRDGRSSGDT SSEVSTVELL
HLQQQQALQA ARQLLLQQQT SGLKSPKSSD KQRPLQVPVS VAMMTPQVIT
PQQMQQILQQ QVLSPQQLQA LLQQQQAVML QQQQLQEFYK KQQEQLHLQL
LQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QHPGKQAKEQ
QQQQQQQQQL AAQQLVFQQQ LLQMQQLQQQ QHLLSLQRQG LISIPPGQAA
LPVQSLPQAG LSPAEIQQLW KEVTGVHSME DNGIKHGGLD LTTNNSSSTT
SSNTSKASPP ITHHSIVNGQ SSVLSARRDS SSHEETGASH TLYGHGVCKW
PGCESICEDF GQFLKHLNNE HALDDRSTAQ CRVQMQVVQQ LEIQLSKERE
RLQAMMTHLH MRPSEPKPSP KPLNLVSSVT MSKNMLETSP QSLPQTPTTP
TAPVTPITQG PSVITPASVP NVGAIRRRHS DKYNIPMSSE IAPNYEFYKN
ADVRPPFTYA TLIRQAIMES SDRQLTLNEI YSWFTRTFAY FRRNAATWKN
AVRHNLSLHK CFVRVENVKG AVWTVDEVEY QKRRSQKITG SPTLVKNIPT
SLGYGAALNA SLQAALAESS LPLLSNPGLI NNASSGLLQA VHEDLNGSLD
HIDSNGNSSP GCSPQPHIHS IHVKEEPVIA EDEDCPMSLV TTANHSPELE
DDREIEEEPL SEDLE
Results of Subprograms
PSG:  a new signal peptide prediction method
N-region:  length 8;  pos.chg 0;  neg.chg 2
H-region:  length 19;  peak value   0.00
PSG score:  -4.40
GvH:  von Heijne's method for signal seq. recognition
GvH score (threshold: -2.1):  -6.15
possible cleavage site: between 60 and 61
>>> 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 =  5.41 (at 84)
ALOM score:   5.41  (number of TMSs: 0)
MITDISC: discrimination of mitochondrial targeting seq
R content:       0       Hyd Moment(75): 12.63
Hyd Moment(95): 10.36    G content:       0
D/E content:     2       S/T content:     2
Score: -5.04
Gavel: prediction of cleavage sites for mitochondrial preseq
cleavage site motif not found
NUCDISC: discrimination of nuclear localization signals
pat4: RRRH (3) at  476
pat7: none
bipartite: none
content of basic residues:   7.1%
NLS Score: -0.29
KDEL: ER retention motif in the C-terminus: none
ER Membrane Retention Signals: none
SKL: peroxisomal targeting signal in the C-terminus: none
SKL2: 2nd peroxisomal targeting signal:  found
RLQAMMTHL at 401
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: 
Zinc finger, C2H2 type, domain (PS00028):  *** found ***
CKWPGCESICEDFGQFLKHLNNEH at 348
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
147 L  0.63
148 Q  0.63
149 L  0.63
150 L  0.63
151 Q  0.63
152 Q  0.63
153 Q  0.63
154 Q  0.63
155 Q  0.63
156 Q  0.63
157 Q  0.63
158 Q  0.63
159 Q  0.63
160 Q  0.63
161 Q  0.63
162 Q  0.63
163 Q  0.63
164 Q  0.63
165 Q  0.63
166 Q  0.63
167 Q  0.63
168 Q  0.63
169 Q  0.63
170 Q  0.63
171 Q  0.63
172 Q  0.63
173 Q  0.63
174 Q  0.63
175 Q  0.56
176 Q  0.56
177 Q  0.56
377 T  0.55
378 A  0.55
379 Q  0.55
380 C  0.55
381 R  0.55
382 V  0.55
383 Q  0.55
384 M  0.55
385 Q  0.55
386 V  0.55
387 V  0.55
388 Q  0.55
389 Q  0.55
390 L  0.55
391 E  0.55
392 I  0.55
393 Q  0.55
394 L  0.55
395 S  0.55
396 K  0.55
397 E  0.55
398 R  0.55
399 E  0.55
400 R  0.55
401 L  0.55
402 Q  0.55
403 A  0.55
404 M  0.55
total: 59 residues 
Results of the k-NN Prediction
k = 9/23
65.2 %: nuclear
17.4 %: mitochondrial
8.7 %: cytoplasmic
4.3 %: vesicles of secretory system
4.3 %: endoplasmic reticulum
>> prediction for QUERY is nuc (k=23)

	  

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall Protein sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-outfile]
(Parameter 2)
outfile Standard Psort II output filename Output file <*>.kpsort2
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

kpsort2 can use any amino acid sequence data that seqret can read.

Output file format

The output from kpsort2 is general PSORT II output format.

Data files

None.

Notes

None.

References

      Horton, P., and Nakai, K.,(1997) Better prediction of protein
      cellular localization sites with the k nearest neighbors classifier,
      Proc Int Conf Intell Syst Mol Biol, 12(10), 2360-2366.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
kpsort Predicts protein localization for PSORT
kpsortb Predicts protein localization for PSORT B
kwolfpsort Predicts protein localization for WoLF PSORT
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org)
Institute for Advanced Biosciences, Keio University
252-8520 Japan

History

2009 - Written by Kazuki Oshita
Mar 2013 - Update document by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None.