analysis of sequence from tem39
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPTVMTHVPYQVL
ALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVE
KNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVRE
WLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLIL
MMIPPHRLDNPGQGGQRKKRALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY
LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
Info> Identical 7-residue fragments found in:
Info> 1tfg.brk -
> Tem39_gi|135684|sp|P10600|TGF3_HUMAN
. . . . .
1 MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK 50
___HHHHHHHHHHHH__HHHHH_____________HHHHHHHHHHHHHHH
. . . . .
51 LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY 100
HH________EEEE__EEEEEE___HHHHHHHHHHHH________HHHHH
. . . . .
101 YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE 150
HHHHHH_HHHHHHHHH__EEEEE______EEEEEEEE______HHHHHHH
. . . . .
151 FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL 200
HEEEE_________HHHHHHHHH________________________EEE
. . . . .
201 SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF 250
E____HHHHHHHHHHH_____EEEEE__________HHHHHHHHHHHHHH
. . . . .
251 KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR 300
______________HHHHH________EEEEE______________HHHH
. . . . .
301 ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY 350
HHH______________E__EEEHHHH___EEEE_____EEEE_______
. . . . .
351 LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ 400
___________________________EE_EEEEEEEEEEEE________
.
401 LSNMVVKSCKCS 412
___EEEEEEEE_
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 30.8 %
beta-contents : 25.6 %
coil-contents : 43.6 %
class : mixed
method : 2
alpha-contents : 22.9 %
beta-contents : 14.3 %
coil-contents : 62.8 %
class : mixed
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-30.78 -3.09 -1.36 -0.50 -4.00 -4.00 -4.00 0.00 -0.25 -10.30 -3.10 -12.00 -12.00 0.00 -12.00 0.00 -97.39
-24.56 -0.96 -0.72 0.00 -4.00 0.00 0.00 0.00 -4.95 -9.96 -3.10 -12.00 -12.00 0.00 -12.00 0.00 -84.25
ID: Tem39_gi|135684|sp|P10600|TGF3_HUMAN AC: xxx Len: 350 1:I 327 Sc: -84.25 Pv: 8.562063e-01 NO_GPI_SITE
GPI: learning from protozoa
-44.43 -4.38 -0.16 0.00 -4.00 0.00 0.00 0.00 -0.83 -7.88 -10.82 -12.00 -12.00 0.00 -12.00 0.00 -108.50
-23.66 -3.19 -0.32 0.00 -4.00 0.00 -16.00 0.00 0.00 -8.75 -10.82 -12.00 -12.00 0.00 -12.00 0.00 -102.74
ID: Tem39_gi|135684|sp|P10600|TGF3_HUMAN AC: xxx Len: 350 1:I 337 Sc: -102.74 Pv: 8.991142e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem39_gi|13 0.464 24 Y 0.588 24 Y 0.981 12 Y 0.947 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem39_gi|13 0.548 375 Y 0.310 25 N 0.975 9 Y 0.869 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem39_gi|13 0.524 375 Y 0.475 375 Y 0.989 10 Y 0.197 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
1-20 MKMHLQRALVVLALLNFATV
slslstcttl 21-30
31-76 DFGHIKKKRVEAIRGQILSKLRLTSPPEPT
VMTHVPYQVLALYNST
relleemhgereeg 77-90
91-412 CTQENTESEYYAKEIHKFDMIQGLAEHNEL
AVCPKGITSKVFRFNVSSVEKNRTNLFRAE
FRVLRVPNPSSKRNEQRIELFQILRPDEHI
AKQRYIGGKNLPTRGTAEWLSFDVTDTVRE
WLLRRESNLGLEISIHCPCHTFQPNGDILE
NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQ
KDHHNPHLILMMIPPHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGW
KWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILY
YVGRTPKVEQLSNMVVKSCKCS
low complexity regions: SEG 25 3.0 3.3
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
1-7 MKMHLQR
alvvlallnfatvslslstcttl 8-30
31-73 DFGHIKKKRVEAIRGQILSKLRLTSPPEPT
VMTHVPYQVLALY
nstrelleemhgereegctqentese 74-99
100-412 YYAKEIHKFDMIQGLAEHNELAVCPKGITS
KVFRFNVSSVEKNRTNLFRAEFRVLRVPNP
SSKRNEQRIELFQILRPDEHIAKQRYIGGK
NLPTRGTAEWLSFDVTDTVREWLLRRESNL
GLEISIHCPCHTFQPNGDILENIHEVMEIK
FKGVDNEDDHGRGDLGRLKKQKDHHNPHLI
LMMIPPHRLDNPGQGGQRKKRALDTNYCFR
NLEENCCVRPLYIDFRQDLGWKWVHEPKGY
YANFCSGPCPYLRSADTTHSTVLGLYNTLN
PEASASPCCVPQDLEPLTILYYVGRTPKVE
QLSNMVVKSCKCS
low complexity regions: SEG 45 3.4 3.75
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
1-412 MKMHLQRALVVLALLNFATVSLSLSTCTTL
DFGHIKKKRVEAIRGQILSKLRLTSPPEPT
VMTHVPYQVLALYNSTRELLEEMHGEREEG
CTQENTESEYYAKEIHKFDMIQGLAEHNEL
AVCPKGITSKVFRFNVSSVEKNRTNLFRAE
FRVLRVPNPSSKRNEQRIELFQILRPDEHI
AKQRYIGGKNLPTRGTAEWLSFDVTDTVRE
WLLRRESNLGLEISIHCPCHTFQPNGDILE
NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQ
KDHHNPHLILMMIPPHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGW
KWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILY
YVGRTPKVEQLSNMVVKSCKCS
low complexity regions: XNU
# Score cutoff = 21, Search from offsets 1 to 4
# both members of each repeat flagged
# lambda = 0.347, K = 0.200, H = 0.664
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT
VMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNEL
AVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHI
AKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILE
NIHEVMEIKFKGVDNEDDHGRGDLGRLkkqkdhhnphlilmmippHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS
1 - 267 MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT
VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL
AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI
AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE
NIHEVMEIKF KGVDNEDDHG RGDLGRL
268 - 285 kkq kdhhnphlil mmipp
286 - 412 HRLDN PGQGGQRKKR ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCS
GPCPY LRSADTTHST VLGLYNTLNP EASASPCCVP QDLEPLTILY YVGRTPKVEQ LSNMV
VKSCK CS
low complexity regions: DUST
>Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT
VMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNEL
AVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHI
AKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILE
NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for Tem39_gi|135684|sp|P10600|TGF3_HUMAN
sequence: 350 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 120
VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~22222 222222222~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 180
AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 300
NIHEVMEIKF KGVDNEDDHG RGDLGRLKKQ KDHHNPHLIL MMIPPHRLDN PGQGGQRKKR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . |
ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCSGPCPY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem39.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem39.___inter___
(1 sequences)
MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK
LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY
YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE
FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL
SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF
KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY
LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ
LSNMVVKSCKCS
(p)rokaryotic or (e)ukaryotic: e
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 8 28 1.642 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 7 384
K+R profile 3.00
+
CYT-EXT prof -
-0.13
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 2.0000
-> Orientation: undecided
CYT-EXT difference: 0.13
-> Orientation: N-out
----------------------------------------------------------------------
"tem39" 412
8 28 #t 1.64167
************************************
*TOPPREDM with prokaryotic function*
************************************
tem39.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem39.___inter___
(1 sequences)
MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK
LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY
YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE
FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL
SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF
KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY
LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ
LSNMVVKSCKCS
(p)rokaryotic or (e)ukaryotic: p
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 8 28 1.642 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 7 384
K+R profile 2.00
+
CYT-EXT prof -
-0.13
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 2.0000
-> Orientation: undecided
CYT-EXT difference: 0.13
-> Orientation: N-out
----------------------------------------------------------------------
"tem39" 412
8 28 #t 1.64167
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem39.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 18:36:10 2000
File: /people/maria/tem39.___saps___
ID Tem39_gi|135684|sp|P10600|TGF3_HUMAN
DE TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
number of residues: 412; molecular weight: 47.3 kdal
1 MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT
61 VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL
121 AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI
181 AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE
241 NIHEVMEIKF KGVDNEDDHG RGDLGRLKKQ KDHHNPHLIL MMIPPHRLDN PGQGGQRKKR
301 ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCSGPCPY LRSADTTHST
361 VLGLYNTLNP EASASPCCVP QDLEPLTILY YVGRTPKVEQ LSNMVVKSCK CS
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 16( 3.9%); C : 14( 3.4%); D : 17( 4.1%); E : 33( 8.0%); F : 14( 3.4%)
G : 23( 5.6%); H : 17( 4.1%); I : 19( 4.6%); K : 25( 6.1%); L : 45(10.9%)
M : 9( 2.2%); N : 23( 5.6%); P : 24( 5.8%); Q : 15( 3.6%); R : 29( 7.0%)
S : 23( 5.6%); T : 24( 5.8%); V : 25( 6.1%); W : 4( 1.0%); Y : 13( 3.2%)
KR : 54 ( 13.1%); ED : 50 ( 12.1%); AGP : 63 ( 15.3%);
KRED : 104 ( 25.2%); KR-ED : 4 ( 1.0%); FIKMNY : 103 ( 25.0%);
LVIFM : 112 ( 27.2%); ST : 47 ( 11.4%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0+0000+000 0000000000 0000000000 -0000++++0 -00+00000+ 0+00000-00
61 0000000000 000000+-00 --000-+--0 000-00-0-0 00+-00+0-0 00000-00-0
121 0000+0000+ 00+000000- +0+0000+0- 0+00+00000 0++0-0+0-0 0000+0--00
181 0+0+0000+0 000+000-00 00-00-00+- 000++-0000 0-00000000 000000-00-
241 000-00-0+0 +00-0---00 +0-00+0++0 +-00000000 000000+0-0 000000++++
301 00-00000+0 0--0000+00 00-0+0-000 +000-0+000 0000000000 0+00-00000
361 0000000000 -000000000 0-0-000000 000+00+0-0 000000+00+ 00
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 11/30 or 14/45 or 18/60): none
Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none
Mixed charge clusters (cmin = 17/30 or 23/45 or 28/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
There are no high scoring negative charge segments.
There are no high scoring mixed charge segments.
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 8 | 32 | 10 | 10 | 13 | 11 | 11 | 15 | 8 | 10 |
lmin1 7 | 6 | 9 | 38 | 12 | 12 | 16 | 14 | 14 | 18 | 9 | 12 |
lmin2 8 | 8 | 11 | 43 | 13 | 13 | 18 | 16 | 15 | 21 | 10 | 13 |
(Significance level: 0.010000; Minimal displayed length: 6)
There are no charge runs or patterns exceeding the given minimal lengths.
Run count statistics:
+ runs >= 3: 2, at 36; 297;
- runs >= 3: 1, at 256;
* runs >= 5: 0
0 runs >= 21: 1, at 8;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
There are no high scoring hydrophobic segments.
____________________________________
High scoring transmembrane segments:
5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST)
-6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED)
Expected score/letter: -4.583
M_0.01= 49.71; M_0.05= 40.98; M_0.30= 30.59
1) From 8 to 24: length= 17, score=40.00
(pocket at 16 to 16: length= 1, score=-10.00)
8 ALVVLALL |N| F ATVSLSL
L: 6(35.3%); A: 3(17.6%); S: 2(11.8%); V: 3(17.6%);
2. SPACINGS OF C.
H2N-26-C-63-C-31-C-103-C-1-C-77-C-7-C-C-27-C-3-C-28-C-C-30-C-1-C-1-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-3-H-22-C-6
-H-29-H-19-H-6-C-14-H-10-H-5-C-55-H-46-H-C-1-C-H-12-H-15-H-13-H-H-2-H-8-H-20-C-7-C-C-17-H-9-C-3-C-9-H-18-C-C-30-C-1-C-1-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 11- 14] VLAL
[ 69- 72] VLAL
B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet.
(i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C)
Repeat core block length: 8
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 28 (Expected range: 8-- 37)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 7 (6-10) 7 (11-20) 8 (>=21) 7
3. Clusters of amino acid multiplets (cmin = 12/30 or 15/45 or 18/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 10 (Expected range: 1-- 22)
5 +plets (f+: 13.1%), 5 -plets (f-: 12.1%)
Total number of charge altplets: 7 (Critical number: 25)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 2 (11-20) 2 (>=21) 7
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
89- 108 5 E.... 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 7)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9)
Location Period Element Copies Core Errors
89- 113 5 -00.0 5 5 /0/0/0/./1/
278- 283 1 i 6 6 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
224- 345 (3.) S( 121)S 1 of 24 0.0062 large maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem39
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
TGFb_propeptide TGF-beta propeptide 242.4 6.5e-69 1
TGF-beta Transforming growth factor beta like 175.7 1.4e-56 1
cyclin Cyclin 0.6 35 1
DUF25 Domain of unknown function DUF25 0.5 86 1
enolase Enol-ase -1.4 62 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
DUF25 1/1 139 155 .. 1 17 [. 0.5 86
enolase 1/1 172 195 .. 417 440 .] -1.4 62
TGFb_propeptide 1/1 27 255 .. 1 250 [] 242.4 6.5e-69
cyclin 1/1 309 331 .. 31 54 .. 0.6 35
TGF-beta 1/1 315 412 .] 1 109 [] 175.7 1.4e-56
Alignments of top-scoring domains:
DUF25: domain 1 of 1, from 139 to 155: score 0.5, E = 86
*->deewkavLspeqyrVlr<-*
e+++ +L + ++rVlr
Tem39_gi|1 139 VEKNRTNLFRAEFRVLR 155
enolase: domain 1 of 1, from 172 to 195: score -1.4, E = 62
*->qLLRIEEelgsaavyagknfrkak<-*
q+LR E ++++ + +gkn+ +
Tem39_gi|1 172 QILRPDEHIAKQRYIGGKNLPTRG 195
TGFb_propeptide: domain 1 of 1, from 27 to 255: score 242.4, E = 6.5e-69
*->crpldlrrrqkqkrleaiegeiLskLgLkrrPrpskeknphpkepas
c++ld + +k kr+eai+g+iLskL+L+++P+p+ + +
Tem39_gi|1 27 CTTLDFGHIKK-KRVEAIRGQILSKLRLTSPPEPT--------VMTH 64
vPefmldLYnalseleegk............eisdydgreasrantvrsf
vP ++l+LYn+++el+e+++++++++ ++++ +s+y+++e++++++++
Tem39_gi|1 65 VPYQVLALYNSTRELLEEMhgereegctqenTESEYYAKEIHKFDMIQGL 114
sheesldreesteeshrkrfvFnlSsiPegetltalLarAELRlyrqdpl
+++l ++ + ++k f+Fn+Ss++++ t+ L+rAE+R++r +p+
Tem39_gi|1 115 AEHNELAVCPKG--ITSKVFRFNVSSVEKNRTN---LFRAEFRVLR-VPN 158
anrfpawsraeqrveiYqvlkpgsdgsrdekGdpstrlLdsrlvdasnsg
+ + +r eqr+e++q+l+p+ + + +r+++ ++++++ +
Tem39_gi|1 159 PSS----KRNEQRIELFQILRPDEHIAK-------QRYIGGKNLPTRGTA 197
ggWlsFDVTpavnrWlsnpqsnlGlqleveclcgdkapgrhvrpsragli
+WlsFDVT++v++Wl +++snlGl+++++c+c+ +++p +++l
Tem39_gi|1 198 -EWLSFDVTDTVREWLLRRESNLGLEISIHCPCH------TFQPNGDIL- 239
ge.gpqqkqPllvtff<-*
++ ++ ++ ++ +++
Tem39_gi|1 240 ENiHEVMEIKFKGVDN 255
cyclin: domain 1 of 1, from 309 to 331: score 0.6, E = 35
*->relEektlpnpdymdqQpseinps<-*
r lEe ++++p y+d++ ++ ++
Tem39_gi|1 309 RNLEENCCVRPLYIDFRQ-DLGWK 331
TGF-beta: domain 1 of 1, from 315 to 412: score 175.7, E = 1.4e-56
*->CrrreLyVdFkdiGWddWIiaPkGYhAnYChGeCpfplagvgdslna
C++r+Ly+dF+ +++++W+++PkGY+An+C+G Cp+ + +
Tem39_gi|1 315 CCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRS------AD 355
tnhaivqtLvhslnPgtaapkPCCVPtkGtLsplsvLYyddnGdnvvlkq
t+h++v+ L+++lnP+ a+++PCCVP++ L+pl++LYy ++ +++++q
Tem39_gi|1 356 TTHSTVLGLYNTLNPE-ASASPCCVPQD--LEPLTILYYVGR--TPKVEQ 400
ypNMvVeeCGCr<-*
++NMvV++C+C+
Tem39_gi|1 401 LSNMVVKSCKCS 412
//
Start with PfamFrag (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/PfamFrag
Sequence file: tem39
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
TGFb_propeptide TGF-beta propeptide 240.5 2.4e-68 1
TGF-beta Transforming growth factor beta like 175.7 1.4e-56 1
HTH_5 Bacterial regulatory protein, arsR fa 4.3 8.7 1
Bac_globin Protozoan/cyanobacterial globin 1.1 63 1
cyclin Cyclin 0.6 35 1
DUF25 Domain of unknown function DUF25 0.5 86 1
7tm_2 7 transmembrane receptor (Secretin fa -0.2 40 1
enolase Enol-ase -1.4 62 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Bac_globin 1/1 38 50 .. 106 118 .] 1.1 63
HTH_5 1/1 99 117 .. 62 82 .] 4.3 8.7
DUF25 1/1 139 155 .. 1 17 [. 0.5 86
enolase 1/1 172 195 .. 417 440 .] -1.4 62
TGFb_propeptide 1/1 27 255 .. 1 250 [] 240.5 2.4e-68
cyclin 1/1 309 331 .. 31 54 .. 0.6 35
7tm_2 1/1 383 393 .. 1 11 [. -0.2 40
TGF-beta 1/1 315 412 .] 1 109 [] 175.7 1.4e-56
Alignments of top-scoring domains:
Bac_globin: domain 1 of 1, from 38 to 50: score 1.1, E = 63
*->aVvestrgdvlnk<-*
++ve +rg +l+k
Tem39_gi|1 38 KRVEAIRGQILSK 50
HTH_5: domain 1 of 1, from 99 to 117: score 4.3, E = 8.7
*->yYslseldelvvdiielllel<-*
+Y+ + +++++d+i+ l+e+
Tem39_gi|1 99 EYYAK--EIHKFDMIQGLAEH 117
DUF25: domain 1 of 1, from 139 to 155: score 0.5, E = 86
*->deewkavLspeqyrVlr<-*
e+++ +L + ++rVlr
Tem39_gi|1 139 VEKNRTNLFRAEFRVLR 155
enolase: domain 1 of 1, from 172 to 195: score -1.4, E = 62
*->qLLRIEEelgsaavyagknfrkak<-*
q+LR E ++++ + +gkn+ +
Tem39_gi|1 172 QILRPDEHIAKQRYIGGKNLPTRG 195
TGFb_propeptide: domain 1 of 1, from 27 to 255: score 240.5, E = 2.4e-68
*->crpldlrrrqkqkrleaiegeiLskLgLkrrPrpskeknphpkepas
c++ld + +k kr+eai+g+iLskL+L+++P+p+ + +
Tem39_gi|1 27 CTTLDFGHIKK-KRVEAIRGQILSKLRLTSPPEPT--------VMTH 64
vPefmldLYnalseleegk............eisdydgreasrantvrsf
vP ++l+LYn+++el+e+++++++++ ++++ +s+y+++e++++++++
Tem39_gi|1 65 VPYQVLALYNSTRELLEEMhgereegctqenTESEYYAKEIHKFDMIQGL 114
sheesldreesteeshrkrfvFnlSsiPegetltalLarAELRlyrqdpl
+++l ++ + ++k f+Fn+Ss++++ t+ L+rAE+R++r +p+
Tem39_gi|1 115 AEHNELAVCPKG--ITSKVFRFNVSSVEKNRTN---LFRAEFRVLR-VPN 158
anrfpawsraeqrveiYqvlkpgsdgsrdekGdpstrlLdsrlvdasnsg
+ + +r eqr+e++q+l+p+ + + +r+++ ++++++ +
Tem39_gi|1 159 PSS----KRNEQRIELFQILRPDEHIAK-------QRYIGGKNLPTRGTA 197
ggWlsFDVTpavnrWlsnpqsnlGlqleveclcgdkapgrhvrpsragli
+WlsFDVT++v++Wl +++snlGl+++++c+c+ +++p +++l
Tem39_gi|1 198 -EWLSFDVTDTVREWLLRRESNLGLEISIHCPCH------TFQPNGDIL- 239
ge.gpqqkqPllvtff<-*
++ ++ ++ ++ +++
Tem39_gi|1 240 ENiHEVMEIKFKGVDN 255
cyclin: domain 1 of 1, from 309 to 331: score 0.6, E = 35
*->relEektlpnpdymdqQpseinps<-*
r lEe ++++p y+d++ ++ ++
Tem39_gi|1 309 RNLEENCCVRPLYIDFRQ-DLGWK 331
7tm_2: domain 1 of 1, from 383 to 393: score -0.2, E = 40
*->allLkviytVG<-*
++ L+++y+VG
Tem39_gi|1 383 LEPLTILYYVG 393
TGF-beta: domain 1 of 1, from 315 to 412: score 175.7, E = 1.4e-56
*->CrrreLyVdFkdiGWddWIiaPkGYhAnYChGeCpfplagvgdslna
C++r+Ly+dF+ +++++W+++PkGY+An+C+G Cp+ + +
Tem39_gi|1 315 CCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRS------AD 355
tnhaivqtLvhslnPgtaapkPCCVPtkGtLsplsvLYyddnGdnvvlkq
t+h++v+ L+++lnP+ a+++PCCVP++ L+pl++LYy ++ +++++q
Tem39_gi|1 356 TTHSTVLGLYNTLNPE-ASASPCCVPQD--LEPLTILYYVGR--TPKVEQ 400
ypNMvVeeCGCr<-*
++NMvV++C+C+
Tem39_gi|1 401 LSNMVVKSCKCS 412
//
Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib
Sequence file: tem39
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Tue Oct 31 18:39:44 2000
Sequence file: tem39
----------------------------------------
Sequence Tem39_gi|135684|sp|P10600|TGF3_HUMAN (412 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
74: NSTR
135: NVSS
142: NRTN
Total matches: 3
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
214: RRES
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
75: STR
128: TSK
160: SSK
161: SKR
207: TVR
395: TPK
408: SCK
Total matches: 7
Matching pattern PS00006 CK2_PHOSPHO_SITE:
28: TTLD
55: SPPE
75: STRE
96: TESE
137: SSVE
207: TVRE
Total matches: 6
Matching pattern PS00007 TYR_PHOSPHO_SITE:
331: KWVHEPKGY
Total matches: 1
Matching pattern PS00008 MYRISTYL:
45: GQILSK
220: GLEISI
363: GLYNTL
Total matches: 3
Matching pattern PS00016 RGD:
261: RGD
Total matches: 1
Matching pattern PS00250 TGF_BETA:
333: VHEPKGYYANFCSGPC
Total matches: 1
Total no of hits in this sequence: 23
========================================
1314 pattern(s) searched in 1 sequence(s), 412 residues.
Total no of hits in all sequences: 23.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
argv[1]=P
argv[2]=-m /data/patterns/own/motif.fa
argv[4]=-seq tem39
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
SeqTyp=2 : PROTEIN search;
>APC D-Box is the MOTIF name
>STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 412 units
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~
Start with HMM-search search against own library
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm.lib
Sequence file: tem39
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem39
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR
BETA 3 PRECURSOR (TGF-BETA 3)
(412 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
PDE cyclic NMP phosphodiesterase domain 26 0.079
ARM Armadillo repeat 22 1.4
AAA AAA+ ATPase Module 21 2.0
BHLH basic helix-loop-helix domain 21 4.1
UBHYD Ubiquitin C-terminal hydrolase domain 20 5.9
SH2 Src Homology domain 2 20 7.1
HISDAC Histone deacetylase domain 20 7.6
SEC7 Sec7 like GDP exchange factor for ARF like GTPases 20 7.6
PTB Phospho-Tyrosine Binding domain 19 8.8
GAF GAF domain (Predicted Small-ligand binding domain) 19 9.9
>PDE cyclic NMP phosphodiesterase domain
Length = 350
Score = 26.3 bits (57), Expect = 0.079
Identities = 46/200 (23%), Positives = 76/200 (38%), Gaps = 41/200 (20%)
Query: 201 SFDVTDTVREWLLRRESNLGL------EISIHCPCH---------TFQPNG--------- 236
+FDVT TV +L + L + I C CH TFQ N
Sbjct: 72 AFDVTQTVYTFLTSFNAAQYLTHLDIFALLISCMCHDLNHPGFNNTFQVNAQTELSLEYN 131
Query: 237 --DILENIHEVMEIK---------FKGVDNEDDHG--RGDLGRLKKQKDHHNPHLILMMI 283
+LEN H ++ K +G+ NED + R + +L D N H
Sbjct: 132 DISVLENHHAMLTFKILRNSECNILEGL-NEDQYKELRRSVVQLILATDMQN-HFEHTNK 189
Query: 284 PPHRLDN-PGQGGQRKKRALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYAN 342
H L+N P +++ R + N+ + + + RP +++F L + +Y
Sbjct: 190 FQHHLNNLPFDRNKKEDRQMILNFLIKCGDISNIARPWHLNFEWSLRVSDEFFQQSHYET 249
Query: 343 FCSGP-CPYLRSADTTHSTV 361
C P P++ TT + +
Sbjct: 250 ICGYPVTPFMDKTKTTRARI 269
>ARM Armadillo repeat
Length = 532
Score = 22.2 bits (47), Expect = 1.4
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 143 RTNLFRAEFRVLRVPNPSS-KRNEQRIELFQILRPDEHIAKQRYIG 187
+T + R ++V +R + +E+ + R +E + K+R G
Sbjct: 8 KTEVRRNRYKVAVDAEEGRRRREDNMVEIRKSKR-EESLMKKRREG 52
>AAA AAA+ ATPase Module
Length = 298
Score = 21.4 bits (44), Expect = 2.0
Identities = 21/168 (12%), Positives = 49/168 (28%), Gaps = 26/168 (15%)
Query: 78 ELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEH---------------NELAV 122
EL+++ GE + + +A I D I + EL
Sbjct: 115 ELVQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSRLEGGSGGDSEVQRTMLELLN 174
Query: 123 CPKGITSKVFRFNV---SSVEKNRTNLFRAE--FRVLRVPNPSSKRNEQRIELFQILRPD 177
G + + + ++ + L R R + P P+ E R+++ +I
Sbjct: 175 QLDGFEATKNIKVIMATNRIDILDSALLRPGRIDRKIEFPPPN---EEARLDILKIHSRK 231
Query: 178 EHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISI 225
++ + + +V E + + ++
Sbjct: 232 MNLTRGINL---RKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQ 276
>BHLH basic helix-loop-helix domain
Length = 103
Score = 20.7 bits (43), Expect = 4.1
Identities = 11/46 (23%), Positives = 21/46 (44%), Gaps = 1/46 (2%)
Query: 130 KVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILR 175
KV R + E+ R + +LR P + ++ Q++ + LR
Sbjct: 7 KVRRVKANGRERARMHGLNNALDMLREYIPITTQH-QKLSKIETLR 51
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 19.9 bits (41), Expect = 5.9
Identities = 9/48 (18%), Positives = 17/48 (34%), Gaps = 2/48 (4%)
Query: 65 VPYQVLALYNSTRELLEEMHGEREEG--CTQENTESEYYAKEIHKFDM 110
+P Q++ + + + ER+E Q +E DM
Sbjct: 318 IPQQLVERLQEEKRIEAQKRKERQEAHLYMQVQIVAEDQFCGHQGNDM 365
>SH2 Src Homology domain 2
Length = 119
Score = 19.8 bits (41), Expect = 7.1
Identities = 6/37 (16%), Positives = 11/37 (29%), Gaps = 3/37 (8%)
Query: 93 QENTESEYYAKEIHKFDMIQGLAEH---NELAVCPKG 126
+ YY F I + +H +C +
Sbjct: 64 RSLDNGGYYISPRITFPCISDMIKHYQKQSDGLCRRL 100
>HISDAC Histone deacetylase domain
Length = 433
Score = 19.8 bits (41), Expect = 7.6
Identities = 14/119 (11%), Positives = 34/119 (27%), Gaps = 11/119 (9%)
Query: 75 STRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRF 134
L+ ++ + ++ + H + I L+ + + +F
Sbjct: 47 MAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDN--LEMFKRESVKF 104
Query: 135 NVSSVEKNRTNLFRAEFRVLRVPNPSS-----KRNEQRIELFQILRPDEHIAKQRYIGG 188
NV +F + + S + N + ++ H AK+ G
Sbjct: 105 NVGD----DCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASG 159
>SEC7 Sec7 like GDP exchange factor for ARF like GTPases
Length = 192
Score = 19.8 bits (41), Expect = 7.6
Identities = 7/40 (17%), Positives = 16/40 (39%), Gaps = 5/40 (12%)
Query: 99 EYYAKEIHKFDM-----IQGLAEHNELAVCPKGITSKVFR 133
+Y ++ F+ +Q L E + P G+ + +
Sbjct: 6 RHYRIGLNLFNKKPEKGVQYLIERGFVPDTPVGVAHFLLQ 45
>PTB Phospho-Tyrosine Binding domain
Length = 138
Score = 19.4 bits (40), Expect = 8.8
Identities = 7/26 (26%), Positives = 11/26 (41%), Gaps = 3/26 (11%)
Query: 229 CHTFQPNG---DILENIHEVMEIKFK 251
C+ F DI I E ++ +K
Sbjct: 110 CYAFTSEKLAEDITLTIGEAFDLAYK 135
>GAF GAF domain (Predicted Small-ligand binding domain)
Length = 160
Score = 19.4 bits (40), Expect = 9.9
Identities = 9/44 (20%), Positives = 16/44 (35%), Gaps = 3/44 (6%)
Query: 74 NSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEH 117
N EL + ++ +E + EI F + G+ H
Sbjct: 31 NGIAELATRLFNVHKDAVLEECLVAP--DSEIV-FPLDMGVVGH 71
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 10
Number of calls to ALIGN: 10
Length of query: 412
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 6303507.0
Initial X dropoff for ALIGN: 25.0 bits
Y. Wolf's SCOP PSSM
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR
BETA 3 PRECURSOR (TGF-BETA 3)
(412 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1504014 [3..727] P-loop containing nucleotide triphosphat... 26 1.6
gi|584960 [16..180] EF Hand-like 26 1.6
gi|121286 [210..431] Double-stranded beta-helix 24 4.4
gi|2150113 [49..445] Ferritin-like 23 6.7
gi|136297 [237..503] beta/alpha (TIM)-barrel 24 6.7
gi|1051321 [353..924] P-loop containing nucleotide triphosph... 23 6.8
gi|730692 [7..211] beta/alpha (TIM)-barrel 23 6.9
gi|1354131 [16..303] Protein kinases (PK), catalytic core 24 6.9
gi|2308977 [178..600] P-loop containing nucleotide triphosph... 23 7.2
gi|544221 [55..339] beta/alpha (TIM)-barrel 23 9.1
gi|1709211 [75..820] P-loop containing nucleotide triphospha... 23 9.5
>gi|1504014 [3..727] P-loop containing nucleotide triphosphate hydrolases
Length = 725
Score = 25.7 bits (56), Expect = 1.6
Identities = 20/84 (23%), Positives = 33/84 (38%), Gaps = 6/84 (7%)
Query: 5 LQRALVVLALLNFATVSLSLST----CTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT 60
++ A N T+ +T +LDF + +I+ +L KLR+ P
Sbjct: 73 QALYTLLEAFGNSPTIINGNATRFSQILSLDFDQAGQVASASIQTMLLEKLRVARRPASE 132
Query: 61 VMTHVPYQVLALYNSTRELLEEMH 84
+V Y +LA L E+H
Sbjct: 133 ATFNVFYYLLA--CGDGTLRTELH 154
>gi|584960 [16..180] EF Hand-like
Length = 165
Score = 25.5 bits (55), Expect = 1.6
Identities = 7/95 (7%), Positives = 17/95 (17%), Gaps = 4/95 (4%)
Query: 202 FDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDH-- 259
F + + + + + F D +
Sbjct: 60 FKKIGMDYGKEVEFPAFVDGWKELANYDLKLWSQNKKSLIRDWGEAV-FDIFDKDGSGSI 118
Query: 260 GRGDLGR-LKKQKDHHNPHLILMMIPPHRLDNPGQ 293
+ + + LDN G+
Sbjct: 119 SLDEWKAYGRISGICSSDEDAEKTFKHCDLDNSGK 153
>gi|121286 [210..431] Double-stranded beta-helix
Length = 222
Score = 24.1 bits (52), Expect = 4.4
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 59 PTVMTHVPYQVLAL-YNSTRELLEEMHGEREEG 90
+ + +L Y++ E + ++ REEG
Sbjct: 157 QSYLQGFSKNILEASYDTKFEEINKVLFGREEG 189
>gi|2150113 [49..445] Ferritin-like
Length = 397
Score = 23.4 bits (50), Expect = 6.7
Identities = 25/117 (21%), Positives = 36/117 (30%), Gaps = 32/117 (27%)
Query: 264 LGRLKKQKD--HHNPHLILMMIPPHRLDNPGQGGQRKKRA-LDTNY---------CFRNL 311
+Q D HH HL + P NP G +R L+ Y C+ +
Sbjct: 270 WDTFLQQLDQQHHGMHLGVWFWRPTVWWNPAAGVTPAERDWLEEKYPGWNSTWGQCWDVI 329
Query: 312 EEN-----------------CCVRPLYIDFRQDLGWK---WVHEPKGYYANFCSGPC 348
EN C + L I++ W + E G +F S P
Sbjct: 330 IENLVDGNVAQTYPETLPIVCNMSQLPINYTPGDAWAVKDYQLEYNGRLYHFGSEPD 386
>gi|136297 [237..503] beta/alpha (TIM)-barrel
Length = 267
Score = 23.6 bits (50), Expect = 6.7
Identities = 12/121 (9%), Positives = 31/121 (24%), Gaps = 18/121 (14%)
Query: 162 KRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGL 221
K E + L ++ + G T V
Sbjct: 48 KAAEVKPALMAEVKRASPSKGPIAMNGNAAQQALTYALAGASV----------------- 90
Query: 222 EISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281
IS+ F+ + + + ++ D ++ + + H ++L+
Sbjct: 91 -ISVLTEPTWFKGSLLDMRLARQAIDNLPHRPAILRKDFIIDEYQIDEARLHGADTVLLI 149
Query: 282 M 282
+
Sbjct: 150 V 150
>gi|1051321 [353..924] P-loop containing nucleotide triphosphate hydrolases
Length = 572
Score = 23.3 bits (50), Expect = 6.8
Identities = 7/55 (12%), Positives = 16/55 (28%), Gaps = 2/55 (3%)
Query: 30 LDFGHIKKKRVEAIRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84
L + + L R+ S ++ Y+V + E+ +
Sbjct: 75 LLYKRNVLTGLNLKYTVPLEVPRVISQKPGERNFNIFYEVYH--GLSDEMKAKFG 127
>gi|730692 [7..211] beta/alpha (TIM)-barrel
Length = 205
Score = 23.3 bits (50), Expect = 6.9
Identities = 4/37 (10%), Positives = 13/37 (34%)
Query: 245 VMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281
KF + + + + KK+ + + ++
Sbjct: 38 STNGKFIPYWDTEKVTPEVIKKFKKKYEPTALRVKVL 74
>gi|1354131 [16..303] Protein kinases (PK), catalytic core
Length = 288
Score = 23.6 bits (49), Expect = 6.9
Identities = 7/84 (8%), Positives = 14/84 (16%), Gaps = 5/84 (5%)
Query: 279 ILMMIPPHRLDNPGQGGQRKKRALDTNYCFRNLEENCCV-----RPLYIDFRQDLGWKWV 333
+ + P +N EN R D + +
Sbjct: 200 LEFFVTPFDGSPMKIIRGSYDLPKPIEDTEKNWLENTLEIDQNKRWNSQDLFNAVKTNSI 259
Query: 334 HEPKGYYANFCSGPCPYLRSADTT 357
+ + T
Sbjct: 260 VPKQHLKEQITITEKQVSKQPSDT 283
>gi|2308977 [178..600] P-loop containing nucleotide triphosphate hydrolases
Length = 423
Score = 23.3 bits (50), Expect = 7.2
Identities = 10/42 (23%), Positives = 16/42 (37%), Gaps = 2/42 (4%)
Query: 43 IRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84
I L + R+ S P HV Y +LA ++ +
Sbjct: 1 IIDHRLERSRIASVPTGERSFHVLYYLLA--GTSAAEKAHLG 40
>gi|544221 [55..339] beta/alpha (TIM)-barrel
Length = 285
Score = 23.0 bits (49), Expect = 9.1
Identities = 5/34 (14%), Positives = 10/34 (28%)
Query: 248 IKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281
V N + R K K + + ++
Sbjct: 51 NDKVFVSNNPNVQHLLTNRAKYLKPLQDKGIKVI 84
>gi|1709211 [75..820] P-loop containing nucleotide triphosphate hydrolases
Length = 746
Score = 22.9 bits (49), Expect = 9.5
Identities = 10/42 (23%), Positives = 20/42 (46%), Gaps = 2/42 (4%)
Query: 43 IRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84
I +L K + H+ YQ+L+ ++ EL E+++
Sbjct: 208 ILAYLLEKSGIVRQVYNERNYHIFYQLLS--GASEELKEKLN 247
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 11
Number of calls to ALIGN: 11
Length of query: 412
Total length of test sequences: 256703
Effective length of test sequences: 209547.0
Effective search space size: 78128845.0
Initial X dropoff for ALIGN: 25.0 bits