analysis of sequence from tem8
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]===HEYL human
MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLSTPSSSQMQARKKRRGIIEKRRRDRINSSLSELRRLV
PTAFEKQGSSKLEKAEVLQMTVDHLKMLHATGGTGFFDARALAVDFRSIGFRECLTEVIRYLGVLEGPSS
RADPVRIRLLSHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHSCPGLPALSNQLAILGRVPSPVLPGVSSP
AYPIPALRTAPLRRATGIILPARRNVLPSRGASSTRRARPLERPATPVPVAPSSRAARSSHIAPLLQSSS
PTPPGPTGSAAYVAVPTPNSSSPGPAGRPAGAMLYHSWVSEITEIGAF
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|7657154|ref|NP_055386.1|
. . . . .
1 MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLSTPSSSQMQARKKRRGI 50
_______________________HHHHHH___________HHHHHHHHHH
. . . . .
51 IEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHLKMLHA 100
HHHHH____HHHHHHHHHHHHHH_______HHHHHHHHHHHHHHHHHHHH
. . . . .
101 TGGTGFFDARALAVDFRSIGFRECLTEVIRYLGVLEGPSSRADPVRIRLL 150
______HHHHHHHHHHH____HHHHHHHHHHH______________EEE_
. . . . .
151 SHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHSCPGLPALSNQLAILGRVP 200
___HHHHHH______________________________HHHHHHHH___
. . . . .
201 SPVLPGVSSPAYPIPALRTAPLRRATGIILPARRNVLPSRGASSTRRARP 250
___________________HHHHHHHHHEEE___________________
. . . . .
251 LERPATPVPVAPSSRAARSSHIAPLLQSSSPTPPGPTGSAAYVAVPTPNS 300
_______________________________________EEEEEE_____
. .
301 SSPGPAGRPAGAMLYHSWVSEITEIGAF 328
___________HHHHHH___________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 30.8 %
beta-contents : 0.0 %
coil-contents : 69.2 %
class : alpha
method : 2
alpha-contents : 0.1 %
beta-contents : 3.3 %
coil-contents : 96.6 %
class : irregular
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-3.41 -0.18 -0.33 -0.06 -4.00 -4.00 0.00 0.00 0.00 -2.11 -0.35 -12.00 -12.00 0.00 0.00 -12.00 -50.43
5.71 -0.50 -0.70 0.00 0.00 0.00 -4.00 0.00 -0.02 -1.88 -0.35 -12.00 0.00 0.00 -12.00 -12.00 -37.73
ID: gi|7657154|ref|NP_055386.1| AC: xxx Len: 280 1:I 264 Sc: -37.73 Pv: 1.162592e-01 NO_GPI_SITE
GPI: learning from protozoa
-20.77 0.00 0.00 0.00 -4.00 0.00 0.00 0.00 0.00 -1.19 -2.36 -12.00 -12.00 0.00 0.00 -12.00 -64.32
-10.07 -0.42 -0.73 0.00 -4.00 0.00 -8.00 0.00 0.00 -1.79 -2.36 -12.00 -12.00 0.00 0.00 -12.00 -63.36
ID: gi|7657154|ref|NP_055386.1| AC: xxx Len: 280 1:I 265 Sc: -63.36 Pv: 2.605130e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|7657154| 0.211 143 N 0.130 189 N 0.534 173 N 0.107 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|7657154| 0.614 158 Y 0.309 158 N 0.777 271 N 0.142 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|7657154| 0.599 143 Y 0.365 159 Y 0.953 240 Y 0.257 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
1-43 MKRPKEPSGSDGESDGPIDVGQEGQLSQMA
RPLSTPSSSQMQA
rkkrrgiiekrrrdri 44-59
60-198 NSSLSELRRLVPTAFEKQGSSKLEKAEVLQ
MTVDHLKMLHATGGTGFFDARALAVDFRSI
GFRECLTEVIRYLGVLEGPSSRADPVRIRL
LSHLNSYAAEMEPSPTPTGPLAFPAWPWSF
FHSCPGLPALSNQLAILGR
vpspvlpgvssp 199-210
211-252 AYPIPALRTAPLRRATGIILPARRNVLPSR
GASSTRRARPLE
rpatpvpvapssraarss 253-270
271-277 HIAPLLQ
sssptppgptgs 278-289
290-328 AAYVAVPTPNSSSPGPAGRPAGAMLYHSWV
SEITEIGAF
low complexity regions: SEG 25 3.0 3.3
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
1-43 MKRPKEPSGSDGESDGPIDVGQEGQLSQMA
RPLSTPSSSQMQA
rkkrrgiiekrrrdrinsslselrrl 44-69
70-183 VPTAFEKQGSSKLEKAEVLQMTVDHLKMLH
ATGGTGFFDARALAVDFRSIGFRECLTEVI
RYLGVLEGPSSRADPVRIRLLSHLNSYAAE
MEPSPTPTGPLAFPAWPWSFFHSC
pglpalsnqlailgrvpspvlpgvsspayp 184-312
ipalrtaplrratgiilparrnvlpsrgas
strrarplerpatpvpvapssraarsshia
pllqsssptppgptgsaayvavptpnsssp
gpagrpaga
313-328 MLYHSWVSEITEIGAF
low complexity regions: SEG 45 3.4 3.75
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
mkrpkepsgsdgesdgpidvgqegqlsqma 1-92
rplstpsssqmqarkkrrgiiekrrrdrin
sslselrrlvptafekqgssklekaevlqm
tv
93-161 DHLKMLHATGGTGFFDARALAVDFRSIGFR
ECLTEVIRYLGVLEGPSSRADPVRIRLLSH
LNSYAAEME
psptptgplafpawpwsffhscpglpalsn 162-320
qlailgrvpspvlpgvsspaypipalrtap
lrratgiilparrnvlpsrgasstrrarpl
erpatpvpvapssraarsshiapllqsssp
tppgptgsaayvavptpnssspgpagrpag
amlyhswvs
321-328 EITEIGAF
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
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLstpsssqmqarkkrrgiiekrrrDRIN
SSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHLKMLHATGGTGFFDARALAVDFRSIG
FRECLTEVIRYLGVLEGPSSRADPVRIRLLSHLNSYAAEMEPSPTPTGPLAFPAWPWSFF
HSCPGLPALSNQLAILGRVPSPVLPGVSSPAYPIPALRTAPLRRATGIILPARRNVLPSR
GASSTRRARPLERpatpvpvapssraarsshiapllqsssptppgptgsaayvavptpns
sspgpagrpaGAMLYHSWVSEITEIGAF
1 - 33 MKRPKEPSGS DGESDGPIDV GQEGQLSQMA RPL
34 - 56 stpsssq mqarkkrrgi iekrrr
57 - 253 DRIN SSLSELRRLV PTAFEKQGSS KLEKAEVLQM TVDHLKMLHA TGGTGFFDAR ALAVDF
RSIG FRECLTEVIR YLGVLEGPSS RADPVRIRLL SHLNSYAAEM EPSPTPTGPL AFPAWP
WSFF HSCPGLPALS NQLAILGRVP SPVLPGVSSP AYPIPALRTA PLRRATGIIL PARRNV
LPSR GASSTRRARP LER
254 - 310 patpvpv apssraarss hiapllqsss ptppgptgsa ayvavptpns sspgpagrpa
311 - 328 GAMLYHSWVS EITEIGAF
low complexity regions: DUST
>gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLSTPSSSQMQARKKRRGIIEKRRRDRIN
SSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHLKMLHATGGTGFFDARALAVDFRSIG
FRECLTEVIRYLGVLEGPSSRADPVRIRLLSHLNSYAAEMEPSPTPTGPLAFPAWPWSFF
HSCPGLPALSNQLAILGRVPSPVLPGVSSPAYPIPALRTAPLRRATGIILPARRNVLPSR
GASSTRRARPLERPATPVPVAPSSRAARSSHIAPLLQSSSPTPPGPTGSAAYVAVPTPNS
SSPGPAGRPAGAMLYHSWVSEITEIGAF
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|7657154|ref|NP_055386.1|
sequence: 280 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MKRPKEPSGS DGESDGPIDV GQEGQLSQMA RPLSTPSSSQ MQARKKRRGI IEKRRRDRIN
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~11111111 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~33333333 * 14 M'95 -w local
. | . | . | . | . | . 120
SSLSELRRLV PTAFEKQGSS KLEKAEVLQM TVDHLKMLHA TGGTGFFDAR ALAVDFRSIG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
1111111111 111~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
3333332221 ~~~~~~~~~~ ~~22222222 222222~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 180
FRECLTEVIR YLGVLEGPSS RADPVRIRLL SHLNSYAAEM EPSPTPTGPL AFPAWPWSFF
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
HSCPGLPALS NQLAILGRVP SPVLPGVSSP AYPIPALRTA PLRRATGIIL PARRNVLPSR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . |
GASSTRRARP LERPATPVPV APSSRAARSS HIAPLLQSSS
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem8.___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: tem8.___inter___
(1 sequences)
MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLSTPSSSQMQARKKRRGI
IEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHLKMLHA
TGGTGFFDARALAVDFRSIGFRECLTEVIRYLGVLEGPSSRADPVRIRLL
SHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHSCPGLPALSNQLAILGRVP
SPVLPGVSSPAYPIPALRTAPLRRATGIILPARRNVLPSRGASSTRRARP
LERPATPVPVAPSSRAARSSHIAPLLQSSSPTPPGPTGSAAYVAVPTPNS
SSPGPAGRPAGAMLYHSWVSEITEIGAF
(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 4 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 165 185 1.333 Certain
2 199 219 0.800 Putative
3 278 298 0.862 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 164 13 58 30
K+R profile + 12.00
1.00 1.00
CYT-EXT prof -0.10 -
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 10.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -0.10
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 3
Loop length 164 92 30
K+R profile + 1.00
+
CYT-EXT prof -0.10 -
0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.66
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -0.65
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2
Loop length 164 13 109
K+R profile + +
1.00
CYT-EXT prof -0.10 0.93
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -1.00
Tm probability: 0.50
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: 0.83
-> Orientation: N-out
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1
Loop length 164 143
K+R profile +
+
CYT-EXT prof -0.10
1.03
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem8" 328
165 185 #t 1.33333
199 219 #f 0.8
278 298 #f 0.8625
************************************
*TOPPREDM with prokaryotic function*
************************************
tem8.___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: tem8.___inter___
(1 sequences)
MKRPKEPSGSDGESDGPIDVGQEGQLSQMARPLSTPSSSQMQARKKRRGI
IEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHLKMLHA
TGGTGFFDARALAVDFRSIGFRECLTEVIRYLGVLEGPSSRADPVRIRLL
SHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHSCPGLPALSNQLAILGRVP
SPVLPGVSSPAYPIPALRTAPLRRATGIILPARRNVLPSRGASSTRRARP
LERPATPVPVAPSSRAARSSHIAPLLQSSSPTPPGPTGSAAYVAVPTPNS
SSPGPAGRPAGAMLYHSWVSEITEIGAF
(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 4 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 165 185 1.333 Certain
2 199 219 0.800 Putative
3 278 298 0.862 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 164 13 58 30
K+R profile + 12.00
1.00 1.00
CYT-EXT prof -0.10 -
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 10.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -0.10
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 3
Loop length 164 92 30
K+R profile + 1.00
+
CYT-EXT prof -0.10 -
0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.66
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -0.65
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2
Loop length 164 13 109
K+R profile + +
1.00
CYT-EXT prof -0.10 0.93
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -1.00
Tm probability: 0.50
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: 0.83
-> Orientation: N-out
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1
Loop length 164 143
K+R profile +
+
CYT-EXT prof -0.10
1.03
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): -0.1250
NEG: 21.0000
POS: 27.0000
-> Orientation: N-out
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem8" 328
165 185 #t 1.33333
199 219 #f 0.8
278 298 #f 0.8625
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem8.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 21:38:34 2000
File: /people/maria/tem8.___saps___
ID gi|7657154|ref|NP_055386.1|
DE hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
number of residues: 328; molecular weight: 35.1 kdal
1 MKRPKEPSGS DGESDGPIDV GQEGQLSQMA RPLSTPSSSQ MQARKKRRGI IEKRRRDRIN
61 SSLSELRRLV PTAFEKQGSS KLEKAEVLQM TVDHLKMLHA TGGTGFFDAR ALAVDFRSIG
121 FRECLTEVIR YLGVLEGPSS RADPVRIRLL SHLNSYAAEM EPSPTPTGPL AFPAWPWSFF
181 HSCPGLPALS NQLAILGRVP SPVLPGVSSP AYPIPALRTA PLRRATGIIL PARRNVLPSR
241 GASSTRRARP LERPATPVPV APSSRAARSS HIAPLLQSSS PTPPGPTGSA AYVAVPTPNS
301 SSPGPAGRPA GAMLYHSWVS EITEIGAF
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 34(10.4%); C : 2( 0.6%); D : 8( 2.4%); E : 16( 4.9%); F : 9( 2.7%)
G : 25( 7.6%); H : 6( 1.8%); I : 14( 4.3%); K : 9( 2.7%); L : 30( 9.1%)
M : 7( 2.1%); N- : 5( 1.5%); P+ : 40(12.2%); Q : 9( 2.7%); R+ : 32( 9.8%)
S+ : 41(12.5%); T : 16( 4.9%); V : 17( 5.2%); W : 3( 0.9%); Y : 5( 1.5%)
KR : 41 ( 12.5%); ED : 24 ( 7.3%); AGP + : 99 ( 30.2%);
KRED : 65 ( 19.8%); KR-ED + : 17 ( 5.2%); FIKMNY- : 49 ( 14.9%);
LVIFM : 77 ( 23.5%); ST : 57 ( 17.4%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0++0+-0000 -0-0-000-0 00-0000000 +000000000 000+++++00 0-++++-+00
61 0000-0++00 0000-+0000 +0-+0-0000 00-00+0000 0000000-0+ 0000-0+000
121 0+-000-00+ 00000-0000 +0-00+0+00 00000000-0 -000000000 0000000000
181 0000000000 0000000+00 0000000000 0000000+00 00++000000 00++00000+
241 00000++0+0 0-+0000000 0000+00+00 0000000000 0000000000 0000000000
301 0000000+00 0000000000 -00-0000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 10/30 or 14/45 or 17/60): none
Negative charge clusters (cmin = 7/30 or 10/45 or 12/60): none
Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60):
1) From 44 to 68: RKKRRGIIEKRRRDRINSSLSELRR
+++++000-++++-+000000-0++
quartile: 1; size: 25, +count: 12, -count: 3, 0count: 10; t-value: 5.04 *
S: 3 (12.0%); K: 3 (12.0%); I: 3 (12.0%); R: 9 (36.0%);
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.
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.802 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.198 ( KEDR )
Expected score/letter: -0.784
M_0.01= 47.10; M_0.05= 37.38
1) From 162 to 217: length= 56, score=47.00 *
162 PSPTPTGPLA FPAWPWSFFH SCPGLPALSN QLAILGRVPS PVLPGVSSPA
212 YPIPAL
L: 7(12.5%); A: 6(10.7%); S: 7(12.5%); P: 14(25.0%);
2) From 269 to 320: length= 52, score=43.00 *
269 SSHIAPLLQS SSPTPPGPTG SAAYVAVPTP NSSSPGPAGR PAGAMLYHSW
319 VS
A: 7(13.5%); S: 11(21.2%); P: 10(19.2%);
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 4 | 6 | 40 | 10 | 8 | 12 | 12 | 10 | 14 | 6 | 8 |
lmin1 6 | 5 | 8 | 48 | 12 | 10 | 14 | 14 | 12 | 17 | 8 | 10 |
lmin2 7 | 6 | 9 | 54 | 13 | 11 | 16 | 16 | 14 | 19 | 9 | 11 |
(Significance level: 0.010000; Minimal displayed length: 6)
(*) 7(0,0,0); at 52- 58: EKRRRDR
(1. quartile) -++++-+
(0) 55(1,0,0); at 162- 217: see sequence above
(2. quartile)
L: 7 (12.5%); A: 6 (10.7%); S: 7 (12.5%); P: 14 (25.0%);
LVIFM: 15 (26.8%); ST: 9 (16.1%);
(0) 51(1,0,0); at 269- 320: see sequence above
(4. quartile)
A: 7 (13.5%); S: 11 (21.2%); P: 10 (19.2%); ST: 14 (26.9%);
Run count statistics:
+ runs >= 3: 2, at 44; 53;
- runs >= 3: 0
* runs >= 4: 2, at 44; 52;
0 runs >= 26: 2, at 162; 269;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
There are no high scoring hydrophobic segments.
There are no high scoring transmembrane segments.
2. SPACINGS OF C.
H2N-123-C-58-C-145-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-93-H-4-H-24-C-27-H-28-H-1-C-87-H-44-H-12-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 30- 33] ARPL
[ 248- 251] ARPL
______________________________
[ 138- 142] PSSRA
[ 262- 266] PSSRA
______________________________
[ 163- 169] SPTPTGP
[ 280- 286] SPTPPGP
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: 9-- 38)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 14 (6-10) 6 (11-20) 3 (>=21) 6
3. Clusters of amino acid multiplets (cmin = 14/30 or 17/45 or 21/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 7 (Expected range: 0-- 14)
7 +plets (f+: 12.5%), 0 -plets (f-: 7.3%)
Total number of charge altplets: 7 (Critical number: 15)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 2 (6-10) 1 (11-20) 2 (>=21) 3
3. Long charge multiplets (>= 5; Letter/Length/Position):
+/5/44
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
200- 219 5 P.... 4 4 0
255- 278 6 A..... 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8)
Location Period Element Copies Core Errors
44- 48 1 + 5 5 0
52- 58 1 * 7 7 0
66- 121 8 i....... 7 7 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
5- 45 (1.) K( 40)K 2 of 10 0.9758 small 2. maximal spacing
19- 57 (1.) D( 38)D 2 of 9 0.9872 small 2. maximal spacing
36- 71 (1.) P( 35)P 2 of 41 0.0260 large 2. maximal spacing
71- 138 (2.) P( 67)P 1 of 41 0.0022 large 1. maximal spacing
96- 329 (3.) K( 233)K 1 of 10 0.0001 large 1. maximal spacing
143- 329 (3.) D( 186)D 1 of 9 0.0099 large 1. maximal spacing
161- 198 (3.) *( 37)* 2 of 66 0.0000 large 2. maximal spacing
161- 252 (3.) -( 91)- 1 of 25 0.0073 large 1. maximal spacing
252- 321 (4.) -( 69)- 2 of 25 0.0003 large 2. maximal spacing
268- 308 (4.) *( 40)* 1 of 66 0.0050 large 1. 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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
HLH Helix-loop-helix DNA-binding domain 45.9 9.2e-10 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
HLH 1/1 46 99 .. 1 57 [] 45.9 9.2e-10
Alignments of top-scoring domains:
HLH: domain 1 of 1, from 46 to 99: score 45.9, E = 9.2e-10
*->rRrahNarERrRrkkvNeaFeaLRdliPtlavke.pneKplsKveIL
+Rr + E+rRr+++N+++ +LR+l+Pt a ++ ++K l+K+e+L
gi|7657154 46 KRR--GIIEKRRRDRINSSLSELRRLVPT-AFEKqGSSK-LEKAEVL 88
rkAveYIesLQ<-*
+++v+++ L
gi|7657154 89 QMTVDHLKMLH 99
//
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
HLH Helix-loop-helix DNA-binding domain 44.0 9.6e-13 1
Transposase_17 Transposase IS200 like 2.1 25 1
cytochrome_b_N Cytochrome b(N-terminal)/b6/petB 0.5 32 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Transposase_17 1/1 41 66 .. 1 26 [. 2.1 25
HLH 1/1 46 99 .. 1 57 [] 44.0 9.6e-13
cytochrome_b_N 1/1 94 102 .. 214 222 .] 0.5 32
Alignments of top-scoring domains:
Transposase_17: domain 1 of 1, from 41 to 66: score 2.1, E = 25
*->VfvpKYRrkilygevadelksIlrdl<-*
+ + K Rr i+ ++++d+++s+l +l
gi|7657154 41 MQARKKRRGIIEKRRRDRINSSLSEL 66
HLH: domain 1 of 1, from 46 to 99: score 44.0, E = 9.6e-13
*->rRrahNarERrRrkkvNeaFeaLRdliPtlavke.pneKplsKveIL
+Rr + E+rRr+++N+++ +LR+l+Pt a ++ ++K l+K+e+L
gi|7657154 46 KRR--GIIEKRRRDRINSSLSELRRLVPT-AFEKqGSSK-LEKAEVL 88
rkAveYIesLQ<-*
+++v+++ L
gi|7657154 89 QMTVDHLKMLH 99
cytochrome_b_N: domain 1 of 1, from 94 to 102: score 0.5, E = 32
*->HLlfLHetG<-*
HL +LH tG
gi|7657154 94 HLKMLHATG 102
//
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
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 21:40:18 2000
Sequence file: tem8
----------------------------------------
Sequence gi|7657154|ref|NP_055386.1| (328 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
60: NSSL
299: NSSS
Total matches: 2
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
223: RRAT
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
79: SSK
139: SSR
244: STR
245: TRR
263: SSR
Total matches: 5
Matching pattern PS00006 CK2_PHOSPHO_SITE:
8: SGSD
10: SDGE
62: SLSE
72: TAFE
80: SKLE
140: SRAD
Total matches: 6
Matching pattern PS00008 MYRISTYL:
241: GASSTR
Total matches: 1
Matching pattern PS00038 HELIX_LOOP_HELIX:
83: EKAEVLQMTVDHLKML
Total matches: 1
Total no of hits in this sequence: 16
========================================
1314 pattern(s) searched in 1 sequence(s), 328 residues.
Total no of hits in all sequences: 16.
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 tem8
***** 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, 328 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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related with YRPW motif-like [Homo sapiens]
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= gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related
with YRPW motif-like [Homo sapiens]
(328 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
BHLH basic helix-loop-helix domain 58 2e-11
UBHYD Ubiquitin C-terminal hydrolase domain 25 0.14
PTB Phospho-Tyrosine Binding domain 22 0.88
BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 21 1.5
BZIP Basic Zipper domain (A DNA binding domain) 21 2.1
SAM Sterile alpha Motif domain (A protein-protein interacti... 21 2.2
HOMEO Homeodomain (HTH DNa binding domain) 21 2.2
DHHC Novel zinc finger domain with DHHC signature 21 2.4
PP2C PP2C type phosphatase domain 21 2.9
RASGAP RAS-type GTPase GTP hydrolysis activating protein 20 3.9
RASGEF RAS-type GTPase GDP exchange factor 20 4.7
SCP SCP/PR1 domain (Domain found in plant pathogenesis relat... 19 5.9
PUM Pumilio repeat RNA binding domain 20 6.0
PCNA Proliferating Cell nuclear antigen like domain 19 7.0
VWA Von Willebrand factor A domain 19 7.9
PAP Papain/bleomycin hydrolase like domain 19 7.9
JAB JAB1 associated domain involved in proteolysis 19 8.8
ZZ ZZ domain (A cysteine rich protein-protein interaction do... 19 9.0
S1 S1 RNA binding domain 19 9.7
>BHLH basic helix-loop-helix domain
Length = 103
Score = 57.7 bits (138), Expect = 2e-11
Identities = 18/64 (28%), Positives = 32/64 (49%), Gaps = 6/64 (9%)
Query: 39 SQMQARKKRRG---IIEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQMTVDHL 95
+++ RK RR E+ R +N++L LR +P + Q KL K E L++ +++
Sbjct: 1 AEISKRKVRRVKANGRERARMHGLNNALDMLREYIPITTQHQ---KLSKIETLRLARNYI 57
Query: 96 KMLH 99
L
Sbjct: 58 DALQ 61
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 25.0 bits (54), Expect = 0.14
Identities = 16/80 (20%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 22 QEGQLSQMARPLST---PSSSQMQARKKRRGIIEKRRRDRINSSLSELRRLV-PTAF-EK 76
+E +LS++ + ++ P + ++++R I ++R++R + L ++V F
Sbjct: 302 RESKLSEVLQAVTDHDIPQQLVERLQEEKR-IEAQKRKERQEAHLYMQVQIVAEDQFCGH 360
Query: 77 QGSSKLEKAEVLQMTVDHLK 96
QG+ ++ +V LK
Sbjct: 361 QGNDMYDEEKVKYTVFKVLK 380
>PTB Phospho-Tyrosine Binding domain
Length = 138
Score = 22.5 bits (48), Expect = 0.88
Identities = 11/79 (13%), Positives = 27/79 (33%), Gaps = 13/79 (16%)
Query: 49 GIIE---KRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEV-LQMTVDHLKMLHATGGT 104
G +E D ++ +R +Q + +V +++++D++ +
Sbjct: 13 GCVETPKANGSDVAREAIHAIRFQRDLKRSEQTRETAKLQKVEIRISIDNVIIADI---- 68
Query: 105 GFFDARALAVDF--RSIGF 121
+A F I F
Sbjct: 69 ---KTKAPMYTFPLGRISF 84
Score = 19.0 bits (39), Expect = 8.7
Identities = 7/18 (38%), Positives = 10/18 (54%)
Query: 128 VIRYLGVLEGPSSRADPV 145
V R+LG +E P + V
Sbjct: 8 VARFLGCVETPKANGSDV 25
>BRIGHT BRIGHT domain (Alpha helical DNA binding domain)
Length = 172
Score = 21.5 bits (45), Expect = 1.5
Identities = 6/27 (22%), Positives = 8/27 (29%)
Query: 281 PTPPGPTGSAAYVAVPTPNSSSPGPAG 307
+ G + TP S P G
Sbjct: 134 RSSYGQYEAMHNQMPMTPISRPSLPGG 160
>BZIP Basic Zipper domain (A DNA binding domain)
Length = 89
Score = 21.0 bits (43), Expect = 2.1
Identities = 18/67 (26%), Positives = 29/67 (42%), Gaps = 3/67 (4%)
Query: 32 PLSTPSSSQMQARKK--RRGIIEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQ 89
P+ S +++A +K R I + R R ++ L V T + Q S A +L+
Sbjct: 2 PIDMESQERIKAERKRMRNRIAASKCRKRKLERIARLEEKVKT-LKAQNSELASTANMLR 60
Query: 90 MTVDHLK 96
V LK
Sbjct: 61 EQVAQLK 67
>SAM Sterile alpha Motif domain (A protein-protein interaction domain)
Length = 65
Score = 20.9 bits (44), Expect = 2.2
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 72 TAFEKQGSSKLEKAEVLQMTVDHLKML 98
F + + +E+L + LK L
Sbjct: 22 DIFTRHD---IRGSELLHLERRDLKDL 45
>HOMEO Homeodomain (HTH DNa binding domain)
Length = 65
Score = 20.9 bits (44), Expect = 2.2
Identities = 10/41 (24%), Positives = 19/41 (45%), Gaps = 2/41 (4%)
Query: 52 EKRRRDRINSSLSELRRLVPTAFEKQGS-SKLEKAEVLQMT 91
RR+ R+ S +++ L F++Q S E+ + M
Sbjct: 3 APRRKRRVLFSQAQVYEL-ERRFKQQKYLSAPEREHLASMI 42
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 20.9 bits (43), Expect = 2.4
Identities = 6/15 (40%), Positives = 6/15 (40%)
Query: 166 PTGPLAFPAWPWSFF 180
P PL AW F
Sbjct: 47 PPHPLQIVAWLLYLF 61
>PP2C PP2C type phosphatase domain
Length = 254
Score = 20.6 bits (43), Expect = 2.9
Identities = 4/13 (30%), Positives = 8/13 (60%)
Query: 82 LEKAEVLQMTVDH 94
L ++ ++T DH
Sbjct: 131 LRNQQLERVTEDH 143
>RASGAP RAS-type GTPase GTP hydrolysis activating protein
Length = 292
Score = 20.1 bits (41), Expect = 3.9
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 36 PSSSQMQARKKRRGIIEKRRRDR--INSSLSELRRLVPTAFE 75
P SQ+ A KK I + +DR ++++L L+ V FE
Sbjct: 122 PVLSQIVAEKKPCEIDPSKIKDRSAVDTNLHNLQDYVERVFE 163
>RASGEF RAS-type GTPase GDP exchange factor
Length = 196
Score = 20.1 bits (42), Expect = 4.7
Identities = 7/55 (12%), Positives = 17/55 (30%), Gaps = 11/55 (20%)
Query: 116 FRSIGFRECL--------TEVIRYLGVLEGPSSRADPVR--IRLLSHLNSYAAEM 160
I +++ L +VI +L +L + + I + +
Sbjct: 21 LGEIDWKDLLDLKMKHEGPQVISWLQLLV-RNETLSGIDLAISRFNLTVDWIISE 74
>SCP SCP/PR1 domain (Domain found in plant pathogenesis related proteins and animal trypsin inhibitors)
Length = 159
Score = 19.4 bits (40), Expect = 5.9
Identities = 4/25 (16%), Positives = 8/25 (32%), Gaps = 2/25 (8%)
Query: 300 SSSPGPAGRPAGAMLYHSWVSEITE 324
S+ P + W E+ +
Sbjct: 79 GSTAAKYDDPVKLV--KMWEDEVKD 101
>PUM Pumilio repeat RNA binding domain
Length = 337
Score = 19.8 bits (41), Expect = 6.0
Identities = 6/37 (16%), Positives = 13/37 (34%), Gaps = 2/37 (5%)
Query: 49 GIIEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKA 85
++ + + L L + K S+ +EK
Sbjct: 225 KELDFYLLAELFNRL--SNELCQLSCLKFSSNVVEKF 259
Score = 19.4 bits (40), Expect = 7.7
Identities = 3/51 (5%), Positives = 16/51 (30%), Gaps = 9/51 (17%)
Query: 53 KRRRDRINSSLSELRRLVPTAFEKQGSSKLEKA-------EVLQMTVDHLK 96
++ + ++ + + + G+ L+K + + +
Sbjct: 74 AEQKTLLIQTIYP--NVFQISINQYGTRSLQKIIDTVDNEVQIDLIIKGFS 122
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 19.4 bits (40), Expect = 7.0
Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 88 LQMTVD--HLKMLHATGGTGFFDARALAVDFRSIGFRECLTEVIRYLGVLEGPSSRADPV 145
+++TV+ +A F + S+ FR LT ++ L + +
Sbjct: 49 IKVTVENAKCVQANAFIQADVFQ--EFVIQEESVTFRINLTILLDCLSIFGSSPTPGTLT 106
Query: 146 RIRL 149
+R+
Sbjct: 107 ALRM 110
>VWA Von Willebrand factor A domain
Length = 255
Score = 19.1 bits (39), Expect = 7.9
Identities = 6/45 (13%), Positives = 13/45 (28%)
Query: 85 AEVLQMTVDHLKMLHATGGTGFFDARALAVDFRSIGFRECLTEVI 129
+ + ++ G +A +A C EV+
Sbjct: 119 PQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVL 163
>PAP Papain/bleomycin hydrolase like domain
Length = 376
Score = 19.2 bits (39), Expect = 7.9
Identities = 2/19 (10%), Positives = 3/19 (15%)
Query: 288 GSAAYVAVPTPNSSSPGPA 306
G + P
Sbjct: 353 GITKFPLTARVQKPDMKPR 371
>JAB JAB1 associated domain involved in proteolysis
Length = 136
Score = 19.0 bits (39), Expect = 8.8
Identities = 8/49 (16%), Positives = 16/49 (32%), Gaps = 6/49 (12%)
Query: 179 FFHSCPGLPA--LSNQLAILGRVPSPVL----PGVSSPAYPIPALRTAP 221
++H+ P L ++ + P+ VL P A +
Sbjct: 87 WYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVE 135
>ZZ ZZ domain (A cysteine rich protein-protein interaction domain)
Length = 66
Score = 19.1 bits (39), Expect = 9.0
Identities = 4/17 (23%), Positives = 7/17 (40%)
Query: 159 EMEPSPTPTGPLAFPAW 175
+ T + P+ P W
Sbjct: 50 DYRIIETNSYPILCPDW 66
>S1 S1 RNA binding domain
Length = 305
Score = 19.1 bits (39), Expect = 9.7
Identities = 4/10 (40%), Positives = 6/10 (60%)
Query: 319 VSEITEIGAF 328
V++I G F
Sbjct: 201 VAKIQPYGVF 210
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 19
Number of calls to ALIGN: 21
Length of query: 328
Total length of test sequences: 20182
Effective length of test sequences: 16435.0
Effective search space size: 4814749.7
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= gi|7657154|ref|NP_055386.1| hairy/enhancer-of-split related
with YRPW motif-like [Homo sapiens]
(328 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|8760 [347..417] Helix-loop-helix DNA-binding domain 62 1e-11
gi|1051321 [353..924] P-loop containing nucleotide triphosph... 26 0.94
gi|2493387 [94..456] Cytochrome P450 24 2.6
gi|2621691 [58..315] Class II aaRS and biotin synthetases 25 2.6
gi|155099 [19..420] S-adenosyl-L-methionine-dependent methyl... 24 4.1
gi|1709211 [75..820] P-loop containing nucleotide triphospha... 24 4.1
gi|135944 [3..146] gamma,delta resolvase, large fragment 24 4.8
gi|84873 [335..1022] P-loop containing nucleotide triphospha... 23 5.7
gi|1504014 [3..727] P-loop containing nucleotide triphosphat... 23 6.2
gi|282707 [7..147] gamma,delta resolvase, large fragment 23 7.7
gi|1001633 [151..294] Periplasmic binding protein-like I 23 7.8
>gi|8760 [347..417] Helix-loop-helix DNA-binding domain
Length = 71
Score = 61.9 bits (149), Expect = 1e-11
Identities = 14/68 (20%), Positives = 33/68 (47%), Gaps = 4/68 (5%)
Query: 31 RPLSTPSSSQMQARKKRRGIIEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQM 90
+P T + + ++ + E++R +N + L++++PT S KL K + L++
Sbjct: 4 KPSKTEETDEFSNQRVMANVRERQRTQSLNDAFKSLQQIIPTLP----SDKLSKIQTLKL 59
Query: 91 TVDHLKML 98
++ L
Sbjct: 60 ATRYIDFL 67
>gi|1051321 [353..924] P-loop containing nucleotide triphosphate hydrolases
Length = 572
Score = 26.0 bits (57), Expect = 0.94
Identities = 13/117 (11%), Positives = 31/117 (26%), Gaps = 30/117 (25%)
Query: 48 RGIIEKRRRDRINSSLSEL-----RRLVPTAFEKQGSSKLEKAE-VLQMTVDHL----KM 97
+ + I+ S +L ++ FE G + + Q +
Sbjct: 410 TDFFAR-NKRIISLSAVQLMRNSKNPIIGLLFESYGGNTSDIIVSQAQFVLRGAQDIADK 468
Query: 98 LHATGGTGFF------DARALAVDFRSIGFRECLTEVIRYLGVLEGPSSRADPVRIR 148
++ + F + + F + I+ L + E + R
Sbjct: 469 INVS--HVHFVRCIKSNNERQSTKFDI----PLVNRQIKNLLLAEL-------LSFR 512
>gi|2493387 [94..456] Cytochrome P450
Length = 363
Score = 24.4 bits (52), Expect = 2.6
Identities = 17/129 (13%), Positives = 33/129 (25%), Gaps = 13/129 (10%)
Query: 65 ELRRLVPTAFEKQGSSKLEK--AEVLQMTVDHLKMLHATGGTGFFDARALAVDFRSIGFR 122
R L F L A+ + + + L+ TG +
Sbjct: 7 RWRALFNPGFNPNYLIGLAPLIADEVVVFCEQLRQKARTGTV---------FQLEPL-TL 56
Query: 123 ECLTEVIRYLGVLEGPSSRADPVRIRLLSHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHS 182
+ I + L + + ++S ++ +P P P S
Sbjct: 57 RLTVDTICSV-TLYVVTPVGRWPFLTPDLEIHSSTTKLRTTPLPQRCNGRSNGPRLELPS 115
Query: 183 CPGLPALSN 191
P L+
Sbjct: 116 TPLRRYLTV 124
>gi|2621691 [58..315] Class II aaRS and biotin synthetases
Length = 258
Score = 24.6 bits (53), Expect = 2.6
Identities = 3/28 (10%), Positives = 6/28 (20%)
Query: 116 FRSIGFRECLTEVIRYLGVLEGPSSRAD 143
E L ++ L +
Sbjct: 7 ILDRDHEEVLFPLLVPEDELAKEAIHVK 34
>gi|155099 [19..420] S-adenosyl-L-methionine-dependent methyltransferases
Length = 402
Score = 23.6 bits (50), Expect = 4.1
Identities = 7/78 (8%), Positives = 17/78 (20%), Gaps = 4/78 (5%)
Query: 46 KRRGIIEKRRRDRINSSLSELRRLVPTAFEKQGSSKLEKAEVLQ--MTVDHLKMLHATGG 103
+ + + I R + + + A ++ G
Sbjct: 210 LLWSEKPEWKGEIIRFETGWTREMEASGPPLGSLFHIPFAARSPEFKKHPAVQKEPEPGL 269
Query: 104 TGFFDARALAVDFRSIGF 121
R L + I +
Sbjct: 270 VPVLTGRNLKPGW--IDY 285
>gi|1709211 [75..820] P-loop containing nucleotide triphosphate hydrolases
Length = 746
Score = 23.7 bits (51), Expect = 4.1
Identities = 9/57 (15%), Positives = 11/57 (18%), Gaps = 10/57 (17%)
Query: 129 IRYLGVLEGPS-SRAD-PVRIRLLSHLNSYAAEMEPSPTPTGPLAFPAWPWSFFHSC 183
+R GV+E A P R L Y
Sbjct: 651 LRCGGVMESVRICCAGFPTRRLLSEFYQRYKILY--------VKDINTGSGGGKKGS 699
Score = 23.3 bits (50), Expect = 5.5
Identities = 6/40 (15%), Positives = 15/40 (37%)
Query: 128 VIRYLGVLEGPSSRADPVRIRLLSHLNSYAAEMEPSPTPT 167
+++YL + + + +S + P P+P
Sbjct: 113 LLQYLAAMGNMIKESTSSSSINGINTSSDGIPVTPPPSPM 152
>gi|135944 [3..146] gamma,delta resolvase, large fragment
Length = 144
Score = 23.7 bits (51), Expect = 4.8
Identities = 6/36 (16%), Positives = 13/36 (35%), Gaps = 2/36 (5%)
Query: 41 MQARKKRRGIIEKRRRDRINSSLSELRRLVPTAFEK 76
+ I+ K DR+ + ++R+ V
Sbjct: 56 DRMENGDVLIVTK--LDRLGRNAMDIRKTVEQLASS 89
>gi|84873 [335..1022] P-loop containing nucleotide triphosphate hydrolases
Length = 688
Score = 23.3 bits (50), Expect = 5.7
Identities = 8/43 (18%), Positives = 13/43 (29%), Gaps = 2/43 (4%)
Query: 129 IRYLGVLEGPS-SRAD-PVRIRLLSHLNSYAAEMEPSPTPTGP 169
++ LGVL+ + R+ L Y P
Sbjct: 619 MKALGVLDTVIARQKGFSSRLPFDEFLRRYQFLAFDFDEPVEM 661
>gi|1504014 [3..727] P-loop containing nucleotide triphosphate hydrolases
Length = 725
Score = 23.3 bits (50), Expect = 6.2
Identities = 3/20 (15%), Positives = 8/20 (40%), Gaps = 7/20 (35%)
Query: 129 IRYLGVLEGPSSRADPVRIR 148
+R +L+ +R+
Sbjct: 636 LRGSRLLDA-------MRMY 648
>gi|282707 [7..147] gamma,delta resolvase, large fragment
Length = 141
Score = 22.9 bits (49), Expect = 7.7
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 41 MQARKKRRGIIEKRRRDRINSSLSELRRLVPTAFEK 76
+ + K ++ K DR + + E +L F+K
Sbjct: 57 QKLKDKDLLMVTK--IDRCSRNTLEFLKLQDILFKK 90
>gi|1001633 [151..294] Periplasmic binding protein-like I
Length = 144
Score = 23.0 bits (49), Expect = 7.8
Identities = 4/65 (6%), Positives = 17/65 (26%), Gaps = 5/65 (7%)
Query: 254 PATPVPVAPSSRAARSSHIAPLLQSSSPTPPGPTGSAAYVAVPTPNSSSPGPAGRPAGAM 313
++ + + L+ +++ G T ++ P ++
Sbjct: 53 HNASSATLSAAPTYEAGGL-VLV-NATSDANGITNVGNHIFRVIPQINTSAQT---LVQQ 107
Query: 314 LYHSW 318
+
Sbjct: 108 VGKEV 112
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 11
Number of calls to ALIGN: 12
Length of query: 328
Total length of test sequences: 256703
Effective length of test sequences: 207231.0
Effective search space size: 59359941.3
Initial X dropoff for ALIGN: 25.0 bits