analysis of sequence from tem4dkk3
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
MQRLGATLLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEMFREVEELMEDTQHKLRSAVE
EMEAEEAAAKASSEVNLANLPPSYHNETNTDTKVGNNTIHVHREIHKITNNQTGQMVFSETVITSVGDEE
GRRSHECIIDEDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMATRGSNGTICDN
QRDCQPGLCCAFQRGLLFPVCTPLPVEGELCHDPASRLLDLITWELEPDGALDRCPCASGLLCQPHSHSL
VYVCKPTFVGSRDQDGEILLPREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEPAAAAAALLGGEEI
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|6049608|gb|AAF02676.1|AF177396_1
. . . . .
1 MQRLGATLLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEM 50
___HHHHHHHHHHHH_________________________HHHHHHHHHH
. . . . .
51 FREVEELMEDTQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNT 100
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEE_____________
. . . . .
101 DTKVGNNTIHVHREIHKITNNQTGQMVFSETVITSVGDEEGRRSHECIID 150
________EEEHHHHHH_______EEEEEEEEEEE_________EEEEE_
. . . . .
151 EDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMAT 200
________________________EEEE__________EEEEE_EEEEEE
. . . . .
201 RGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGELCHDPASRLLD 250
___________________EEE____EEE________________HHHHH
. . . . .
251 LITWELEPDGALDRCPCASGLLCQPHSHSLVYVCKPTFVGSRDQDGEILL 300
HHHHH______________________EEEEEEE________________
. . . . .
301 PREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEPAAAAAALLGGEEI 350
___________HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 55.4 %
beta-contents : 0.0 %
coil-contents : 44.6 %
class : alpha
method : 2
alpha-contents : 29.8 %
beta-contents : 0.0 %
coil-contents : 70.2 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-0.22 0.00 -0.01 -0.34 0.00 0.00 -24.00 0.00 -0.04 -8.88 -2.61 -12.00 0.00 0.00 0.00 0.00 -48.10
0.12 0.00 0.00 0.00 0.00 0.00 -20.00 -0.14 -0.52 -8.88 -2.61 -12.00 0.00 0.00 0.00 0.00 -44.03
ID: gi|6049608|gb|AAF02676.1|AF177396_1 AC: xxx Len: 280 1:I 268 Sc: -44.03 Pv: 1.642569e-01 NO_GPI_SITE
GPI: learning from protozoa
-12.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.78 -9.43 -12.00 -12.00 -4.00 -12.00 0.00 -64.39
-7.92 0.00 0.00 0.00 0.00 0.00 -24.00 0.00 0.00 -7.59 -9.43 -12.00 0.00 0.00 0.00 0.00 -60.94
ID: gi|6049608|gb|AAF02676.1|AF177396_1 AC: xxx Len: 280 1:I 269 Sc: -60.94 Pv: 2.339264e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|6049608| 0.648 239 Y 0.483 17 Y 0.986 13 Y 0.972 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|6049608| 0.313 40 N 0.446 25 Y 0.992 9 Y 0.905 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|6049608| 0.437 30 Y 0.443 25 Y 0.985 10 Y 0.914 Y
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
1-5 MQRLG
atllclllaaavptapapaptatsap 6-31
32-66 VKPGPALSYPQEEATLNEMFREVEELMEDT
QHKLR
saveemeaeeaaakasse 67-84
85-329 VNLANLPPSYHNETNTDTKVGNNTIHVHRE
IHKITNNQTGQMVFSETVITSVGDEEGRRS
HECIIDEDCGPSMYCQFASFQYTCQPCRGQ
RMLCTRDSECCGDQLCVWGHCTKMATRGSN
GTICDNQRDCQPGLCCAFQRGLLFPVCTPL
PVEGELCHDPASRLLDLITWELEPDGALDR
CPCASGLLCQPHSHSLVYVCKPTFVGSRDQ
DGEILLPREVPDEYEVGSFMEEVRQELEDL
ERSLT
eemalgepaaaaaallggee 330-349
350-350 I
low complexity regions: SEG 25 3.0 3.3
>gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
1-3 MQR
lgatllclllaaavptapapaptatsapvk 4-47
pgpalsypqeeatl
48-66 NEMFREVEELMEDTQHKLR
saveemeaeeaaakasse 67-84
85-306 VNLANLPPSYHNETNTDTKVGNNTIHVHRE
IHKITNNQTGQMVFSETVITSVGDEEGRRS
HECIIDEDCGPSMYCQFASFQYTCQPCRGQ
RMLCTRDSECCGDQLCVWGHCTKMATRGSN
GTICDNQRDCQPGLCCAFQRGLLFPVCTPL
PVEGELCHDPASRLLDLITWELEPDGALDR
CPCASGLLCQPHSHSLVYVCKPTFVGSRDQ
DGEILLPREVPD
eyevgsfmeevrqeledlerslteemalge 307-349
paaaaaallggee
350-350 I
low complexity regions: SEG 45 3.4 3.75
>gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
1-3 MQR
lgatllclllaaavptapapaptatsapvk 4-108
pgpalsypqeeatlnemfreveelmedtqh
klrsaveemeaeeaaakassevnlanlpps
yhnetntdtkvgnnt
109-294 IHVHREIHKITNNQTGQMVFSETVITSVGD
EEGRRSHECIIDEDCGPSMYCQFASFQYTC
QPCRGQRMLCTRDSECCGDQLCVWGHCTKM
ATRGSNGTICDNQRDCQPGLCCAFQRGLLF
PVCTPLPVEGELCHDPASRLLDLITWELEP
DGALDRCPCASGLLCQPHSHSLVYVCKPTF
VGSRDQ
dgeillprevpdeyevgsfmeevrqeledl 295-349
erslteemalgepaaaaaallggee
350-350 I
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|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
MQRLGATLLClllaaavptapapaptatsapVKPGPALSYPQEEATLNEMFREVEELMED
TQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNTDTKVGNNTIHVHREIHKITN
NQTGQMVFSETVITSVGDEEGRRSHECIIDEDCGPSMYCQFASFQYTCQPCRGQRMLCTR
DSECCGDQLCVWGHCTKMATRGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGEL
CHDPASRLLDLITWELEPDGALDRCPCASGLLCQPHSHSLVYVCKPTFVGSRDQDGEILL
PREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEpaaaaaallggeeI
1 - 10 MQRLGATLLC
11 - 31 lllaaavpta papaptatsa p
32 - 336 VKPGPALSY PQEEATLNEM FREVEELMED TQHKLRSAVE EMEAEEAAAK ASSEVNLANL P
PSYHNETNT DTKVGNNTIH VHREIHKITN NQTGQMVFSE TVITSVGDEE GRRSHECIID E
DCGPSMYCQ FASFQYTCQP CRGQRMLCTR DSECCGDQLC VWGHCTKMAT RGSNGTICDN Q
RDCQPGLCC AFQRGLLFPV CTPLPVEGEL CHDPASRLLD LITWELEPDG ALDRCPCASG L
LCQPHSHSL VYVCKPTFVG SRDQDGEILL PREVPDEYEV GSFMEEVRQE LEDLERSLTE E
MALGE
337 - 349 paaa aaallggee
350 - 350 I
low complexity regions: DUST
>gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
MQRLGATLLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEMFREVEELMED
TQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNTDTKVGNNTIHVHREIHKITN
NQTGQMVFSETVITSVGDEEGRRSHECIIDEDCGPSMYCQFASFQYTCQPCRGQRMLCTR
DSECCGDQLCVWGHCTKMATRGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGEL
CHDPASRLLDLITWELEPDGALDRCPCASGLLCQPHSHSLVYVCKPTFVGSRDQDGEILL
PREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEPAAAAAALLGGEEI
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|6049608|gb|AAF02676.1|AF177396_1
sequence: 280 amino acids, 45 residue(s) in coiled coil state
Coil 1 * 39* 84* YPQEEATLNEMFREVEELMEDTQHKLRSAVEEMEAEEAAAKASSEV
. | . | . | . | . | . 60
MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~25 5888889999 9999999999 * 21 M'95 -w border
---------- ---------- ---------- --------ga bcdefgdefg abcdefgabc * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~1135 5555555555 5899999999 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~777999999 9999999999 * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~888999999 9999999999 * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~569999999 9999999888 * 14 M'95 -w local
. | . | . | . | . | . 120
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKITN
9999999999 9999999998 7777333333 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
defgabcdef gabcdefgab cgababcdef ---------- ---------- ---------- * 21 M'95 -w register
9999999999 9998887754 3222~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
9999999999 9999999988 7777311111 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
9999999999 9999999999 999987~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
8888887777 7788888888 88888822~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 180
NQTGQMVFSE TVITSVGDEE GRRSHECIID EDCGPSMYCQ FASFQYTCQP CRGQRMLCTR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
DSECCGDQLC VWGHCTKMAT RGSNGTICDN QRDCQPGLCC AFQRGLLFPV CTPLPVEGEL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . |
CHDPASRLLD LITWELEPDG ALDRCPCASG LLCQPHSHSL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem4dkk3.___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: tem4dkk3.___inter___
(1 sequences)
MQRLGATLLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEM
FREVEELMEDTQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNT
DTKVGNNTIHVHREIHKITNNQTGQMVFSETVITSVGDEEGRRSHECIID
EDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMAT
RGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGELCHDPASRLLD
LITWELEPDGALDRCPCASGLLCQPHSHSLVYVCKPTFVGSRDQDGEILL
PREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEPAAAAAALLGGEEI
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 4 24 1.783 Certain
2 216 236 0.683 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 3 191 114
K+R profile 2.00 +
+
CYT-EXT prof - -0.96
-0.73
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.21
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: undecided
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1
Loop length 3 326
K+R profile 2.00
+
CYT-EXT prof -
-0.98
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: 1.0000
-> Orientation: undecided
CYT-EXT difference: 0.98
-> Orientation: N-out
----------------------------------------------------------------------
"tem4dkk3" 350
4 24 #t 1.78333
216 236 #f 0.683333
************************************
*TOPPREDM with prokaryotic function*
************************************
tem4dkk3.___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: tem4dkk3.___inter___
(1 sequences)
MQRLGATLLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEM
FREVEELMEDTQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNT
DTKVGNNTIHVHREIHKITNNQTGQMVFSETVITSVGDEEGRRSHECIID
EDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMAT
RGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGELCHDPASRLLD
LITWELEPDGALDRCPCASGLLCQPHSHSLVYVCKPTFVGSRDQDGEILL
PREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEPAAAAAALLGGEEI
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 4 24 1.783 Certain
2 216 236 0.683 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 3 191 114
K+R profile 2.00 +
+
CYT-EXT prof - -0.96
-0.73
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.21
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: undecided
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1
Loop length 3 326
K+R profile 2.00
+
CYT-EXT prof -
-0.98
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: 1.0000
-> Orientation: undecided
CYT-EXT difference: 0.98
-> Orientation: N-out
----------------------------------------------------------------------
"tem4dkk3" 350
4 24 #t 1.78333
216 236 #f 0.683333
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem4dkk3.___saps___
SAPS. Version of April 11, 1996.
Date run: Mon Oct 23 15:36:48 2000
File: /people/maria/tem4dkk3.___saps___
ID gi|6049608|gb|AAF02676.1|AF177396_1
DE dickkopf-3 [Homo sapiens]
number of residues: 350; molecular weight: 38.3 kdal
1 MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
61 TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKITN
121 NQTGQMVFSE TVITSVGDEE GRRSHECIID EDCGPSMYCQ FASFQYTCQP CRGQRMLCTR
181 DSECCGDQLC VWGHCTKMAT RGSNGTICDN QRDCQPGLCC AFQRGLLFPV CTPLPVEGEL
241 CHDPASRLLD LITWELEPDG ALDRCPCASG LLCQPHSHSL VYVCKPTFVG SRDQDGEILL
301 PREVPDEYEV GSFMEEVRQE LEDLERSLTE EMALGEPAAA AAALLGGEEI
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 31( 8.9%); C+ : 21( 6.0%); D : 17( 4.9%); E+ : 39(11.1%); F : 8( 2.3%)
G : 23( 6.6%); H : 10( 2.9%); I : 10( 2.9%); K : 7( 2.0%); L : 35(10.0%)
M : 10( 2.9%); N : 11( 3.1%); P : 24( 6.9%); Q : 16( 4.6%); R : 18( 5.1%)
S : 20( 5.7%); T : 23( 6.6%); V : 19( 5.4%); W : 2( 0.6%); Y : 6( 1.7%)
KR : 25 ( 7.1%); ED : 56 ( 16.0%); AGP : 78 ( 22.3%);
KRED : 81 ( 23.1%); KR-ED - : -31 ( -8.9%); FIKMNY- : 52 ( 14.9%);
LVIFM : 82 ( 23.4%); ST : 43 ( 12.3%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 00+0000000 0000000000 0000000000 00+0000000 00--0000-0 0+-0--00--
61 000+0+000- -0-0--000+ 000-000000 000000-000 -0+0000000 00+-00+000
121 000000000- 0000000--- 0++00-000- --00000000 0000000000 0+00+0000+
181 -0-000-000 000000+000 +0000000-0 0+-0000000 000+000000 000000-0-0
241 00-000+00- 0000-0-0-0 00-+000000 0000000000 0000+00000 0+-0-0-000
301 0+-00--0-0 0000--0+0- 0--0-+000- -0000-0000 0000000--0
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 7/30 or 10/45 or 12/60): none
Negative charge clusters (cmin = 12/30 or 17/45 or 20/60): none
Mixed charge clusters (cmin = 16/30 or 21/45 or 26/60): 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 4 | 6 | 7 | 34 | 8 | 11 | 13 | 9 | 13 | 15 | 7 | 9 |
lmin1 5 | 7 | 9 | 41 | 10 | 13 | 15 | 12 | 15 | 18 | 8 | 11 |
lmin2 6 | 8 | 10 | 46 | 11 | 14 | 17 | 13 | 17 | 20 | 10 | 12 |
(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: 0
- runs >= 4: 0
* runs >= 5: 0
0 runs >= 23: 1, at 4;
--------------------------------------------------------------------------------
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: -4.209
M_0.01= 47.75; M_0.05= 39.15; M_0.30= 28.91
1) From 4 to 18: length= 15, score=36.00
4 LGATLLCLLL AAAVP
L: 6(40.0%); A: 4(26.7%);
2. SPACINGS OF C.
H2N-9-C-136-C-5-C-5-C-8-C-2-C-6-C-5-C-C-4-C-4-C-12-C-5-C-4-C-C-10-C-9-C-23-C-1-C-5-C-10-C-66-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-9-C-52-H-31-H-14-H-1-H-3-H-28-H-1-C-5-C-5-C-8-C-2-C-6-C-5-C-C-4-C-3-H-C-12-C-5-C-4-C-C-10-C-9-C-H-22-C-1-C-5-C-2-H-1-H-5-C-66-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alph
abet.
Repeat core block length: 4
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: 27 (Expected range: 7-- 35)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 11 (6-10) 4 (11-20) 7 (>=21) 6
3. Clusters of amino acid multiplets (cmin = 13/30 or 16/45 or 20/60): none
4. Long amino acid multiplets (>= 5; Letter/Length/Position):
A/6/338
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 13 (Expected range: 0-- 19)
1 +plets (f+: 7.1%), 12 -plets (f-: 16.0%)
Total number of charge altplets: 8 (Critical number: 18)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 4 (6-10) 5 (11-20) 2 (>=21) 3
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
6- 37 8 A....... 4 4 0
297- 320 6 E..... 4 4 0
315- 334 5 E.... 4 4 0
338- 343 1 A 6 6 ! 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
295- 336 7 *..0... 6 6 /0/././2/./././
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
10- 147 (1.) C( 137)C 1 of 22 0.0004 large 1. maximal spacing
90- 177 (2.) L( 87)L 1 of 36 0.0009 large maximal spacing
284- 351 (4.) C( 67)C 2 of 22 0.0062 large 2. 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: tem4dkk3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
spectrin Spectrin repeat 5.9 3.5 1
IGFBP Insulin-like growth factor binding prot 3.9 8.8 1
squash Squash family of serine protease inhibi 2.9 3.9 1
Metallothio_5 Metallothionein family 5 -9.8 81 1
UVR UvrB/uvrC motif -9.9 49 1
Plexin_repeat Plexin repeat -11.1 32 1
zf-CXXC CXXC zinc finger -17.1 79 1
Colipase Colipase -21.9 85 1
Keratin_B2 Keratin, high sulfur B2 protein -89.6 23 1
His_binding Tick histamine binding protein -91.1 47 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
spectrin 1/1 47 67 .. 88 108 .] 5.9 3.5
UVR 1/1 55 90 .. 1 36 [] -9.9 49
zf-CXXC 1/1 139 176 .. 1 48 [] -17.1 79
His_binding 1/1 8 186 .. 1 199 [] -91.1 47
Metallothio_5 1/1 157 196 .. 1 41 [] -9.8 81
squash 1/1 169 196 .. 1 30 [] 2.9 3.9
Plexin_repeat 1/1 170 209 .. 1 67 [] -11.1 32
IGFBP 1/1 267 278 .. 66 84 .] 3.9 8.8
Keratin_B2 1/1 119 287 .. 1 177 [] -89.6 23
Colipase 1/1 192 300 .. 1 95 [] -21.9 85
Alignments of top-scoring domains:
spectrin: domain 1 of 1, from 47 to 67: score 5.9, E = 3.5
*->LnerWeaLlelaaeRrqkLee<-*
Lne +++++el+++ ++kL+
gi|6049608 47 LNEMFREVEELMEDTQHKLRS 67
UVR: domain 1 of 1, from 55 to 90: score -9.9, E = 49
*->ekeikeLekeMeeAaenldFEkAAeLRDeIqaLkeq<-*
e++++++ +++ A+e+++ E+AA + L ++
gi|6049608 55 EELMEDTQHKLRSAVEEMEAEEAAAKASSEVNLANL 90
zf-CXXC: domain 1 of 1, from 139 to 176: score -17.1, E = 79
*->kngrkrRrCGvCevCqrpeDCGkCkaCkDkpKFGGsnrkKQaCkkRr
+ gr++ C eDCG C+ F + Q C+ r
gi|6049608 139 EEGRRSH------ECIIDEDCGPSMYCQ----FASFQYTCQPCRGQR 175
C<-*
gi|6049608 176 M 176
His_binding: domain 1 of 1, from 8 to 186: score -91.1, E = 47
*->MKvLlLsLalvLalsQvkankPtWAdEA..anG...shQDAWKsLqk
+L L La++ a Pt A A+ + G+ s+ L +
gi|6049608 8 --LLCLLLAAAVPTA--PAPAPT-ATSApvKPGpalSYPQEEATLNE 49
dvekrYyLvkATyknDpVWGndFTCVgvtAekineDEKkleAtfL...fm
++ L+ T+ ++ +A+ e ++ L++++
gi|6049608 50 MFREVEELMEDTQHKLRSAVEEMEAEEAAAKASSE----VNLANLppsYH 95
NnadTdlqeshEkiTvvKmYgYnkENaikYeTeGtdgQvftDVlaFSDyd
N Td + +i v + + N + gQ ++FS
gi|6049608 96 NETNTDTKVGNNTIHVHREIHKITNN------Q--TGQ-----MVFSE-- 130
NCdVIyvpgedGsdeGDYELWvtdDkydkiPas.ClekfneyAqgqektv
VI g++ E + + d P C + y + +
gi|6049608 131 --TVITSVGDEEGRRS-HECIIDE---DCGPSMyCQFASFQYTCQPCRGQ 174
RdVYT.DSsClp<-*
R T+DS+C
gi|6049608 175 RMLCTrDSECCG 186
Metallothio_5: domain 1 of 1, from 157 to 196: score -9.8, E = 81
*->MvCkGCGsnCkCaaQktkds.CaCnkDCkCvgdkkskdqCse<-*
M C + Q + + + C +D C gd+ + +
gi|6049608 157 MYCQ--FASFQYTCQPCRGQrMLCTRDSECCGDQLCVWGHCT 196
squash: domain 1 of 1, from 169 to 196: score 2.9, E = 3.9
*->riCPrilmeCkrDsDClaeCvCleegeyCG<-*
+ C m C+rDs+C + +C+ +C
gi|6049608 169 QPCRGQRMLCTRDSECCGDQLCVWG--HCT 196
Plexin_repeat: domain 1 of 1, from 170 to 209: score -11.1, E = 32
*->nCsqhRqsCssClsapdpfgCgWCvsrkrCtrreaygpsfpygeCsr
+C+ + +C++++ +C C++ + C+ + +C
gi|6049608 170 PCRGQ---RMLCTRDS---EC--CGD-QLCVW-G---------HCTK 197
gekpedNswlgwsqsseqCp<-*
+ + + + + C
gi|6049608 198 MATRG--------SNGTICD 209
IGFBP: domain 1 of 1, from 267 to 278: score 3.9, E = 8.8
*->CarGaedaakaLrCrpppG<-*
Ca+G L C+p++
gi|6049608 267 CASG-------LLCQPHSH 278
Keratin_B2: domain 1 of 1, from 119 to 287: score -89.6, E = 23
*->qtScCGfptCStlgtrPsCGsscCQPsCCeSCCQpsCcqpSC.....
++ G ++S++ +s + + + C +++
gi|6049608 119 TNNQTGQMVFSETVI-----TSVGDE--------EGRRSHECiided 152
CqPtcsqtscCqPtcfqssCCrPsCcqTSCC..qPtCcqss.sCq.tgCg
C P + Cq+ +fq +C + C++++ C s++C++ C
gi|6049608 153 CGP----SMYCQFASFQY-----TCQP--CRgqRMLCTRDSeCCGdQLCV 191
igGsiGyGQeGsSGAvScrirWCRPdCrv..egtClPpCCvv......sC
g + Gs G ++ r C+P ++ l p+C + + +++ C
gi|6049608 192 WGHCTKMATRGSNGTICDNQRDCQPGLCCafQRGLLFPVCTPlpvegeLC 241
taPTCCqpvsaQa..........sCCRPsCqPyCgqsCCRPaCccsvtCt
+ P ++ + + ++++ + C P+ g + C+P v
gi|6049608 242 HDP-ASRLLDLITwelepdgaldRC--PC---ASG-LLCQPHSHSLV--- 281
rTccePc<-*
c+P+
gi|6049608 282 -YVCKPT 287
Colipase: domain 1 of 1, from 192 to 300: score -21.9, E = 85
*->vPdPRGliinLedGElClnsaqCK.skCCqhdtiLglaRCaskArEn
+ +G +C n C++ CC + +L C++ E
gi|6049608 192 WGHCTKMATRGSNGTICDNQRDCQpGLCCAFQRGLLFPVCTPLPVEG 238
seCs..aktlY..........GiYYkCPCERGLtCeGD.ksivGsitntn
C ++a l + + + +++G +CPC GL C+ ++s+v t
gi|6049608 239 ELCHdpASRLLdlitwelepdGALDRCPCASGLLCQPHsHSLVYVCKPTF 288
fGiChdagrskk<-*
G + g
gi|6049608 289 VGSRDQDGEILL 300
//
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: tem4dkk3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
spectrin Spectrin repeat 5.9 3.5 1
IGFBP Insulin-like growth factor binding pr 3.9 8.8 1
squash Squash family of serine protease inhi 2.9 3.9 1
Cu_bind_like Plastocyanin-like domain 2.9 7.2 1
Fz Fz domain 1.8 11 1
LMWPc Low molecular weight phosphotyrosine 1.3 40 1
Apolipoprotein Apolipoprotein A1/A4/E family 1.0 42 1
Clat_adaptor_s Clathrin adaptor complex small chain 0.9 57 1
Bac_acid_phos_I Class A bacterial acid phosphatase 0.8 39 1
F_actin_cap_B F-actin capping protein, beta subunit -0.9 76 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Clat_adaptor_s 1/1 46 57 .. 110 122 .. 0.9 57
spectrin 1/1 47 67 .. 88 108 .] 5.9 3.5
Apolipoprotein 1/1 52 86 .. 238 277 .] 1.0 42
F_actin_cap_B 1/1 63 90 .. 265 294 .] -0.9 76
squash 1/1 169 196 .. 1 30 [] 2.9 3.9
Cu_bind_like 1/1 207 218 .. 78 89 .] 2.9 7.2
Fz 1/1 228 242 .. 133 149 .] 1.8 11
IGFBP 1/1 267 278 .. 66 84 .] 3.9 8.8
Bac_acid_phos_I 1/1 314 326 .. 239 251 .] 0.8 39
LMWPc 1/1 302 331 .. 132 162 .] 1.3 40
Alignments of top-scoring domains:
Clat_adaptor_s: domain 1 of 1, from 46 to 57: score 0.9, E = 57
*->sLDryFgKNVCEL<-*
+L+++F+ +V+EL
gi|6049608 46 TLNEMFR-EVEEL 57
spectrin: domain 1 of 1, from 47 to 67: score 5.9, E = 3.5
*->LnerWeaLlelaaeRrqkLee<-*
Lne +++++el+++ ++kL+
gi|6049608 47 LNEMFREVEELMEDTQHKLRS 67
Apolipoprotein: domain 1 of 1, from 52 to 86: score 1.0, E = 42
*->ReklapvredlqevltpvlEqaQlklqaeafqeelkkkle<-*
Re ++++ ed q++l +E+ ae +++++++ ++
gi|6049608 52 RE-VEELMEDTQHKLRSAVEE----MEAEEAAAKASSEVN 86
F_actin_cap_B: domain 1 of 1, from 63 to 90: score -0.9, E = 76
*->ngLRsaekaselekqnkdlqreliralqnr<-*
+ LRsa e+e++ + ++ e++ l+n+
gi|6049608 63 HKLRSAVEEMEAEEAAAKASSEVN--LANL 90
squash: domain 1 of 1, from 169 to 196: score 2.9, E = 3.9
*->riCPrilmeCkrDsDClaeCvCleegeyCG<-*
+ C m C+rDs+C + +C+ +C
gi|6049608 169 QPCRGQRMLCTRDSECCGDQLCVWG--HCT 196
Cu_bind_like: domain 1 of 1, from 207 to 218: score 2.9, E = 7.2
*->ICGvpGHCkkGq<-*
IC++++ C+ G+
gi|6049608 207 ICDNQRDCQPGL 218
Fz: domain 1 of 1, from 228 to 242: score 1.8, E = 11
*->fLdCsklPvpedeelCm<-*
f+ C+ lPv+++ lC
gi|6049608 228 FPVCTPLPVEGE--LCH 242
IGFBP: domain 1 of 1, from 267 to 278: score 3.9, E = 8.8
*->CarGaedaakaLrCrpppG<-*
Ca+G L C+p++
gi|6049608 267 CASG-------LLCQPHSH 278
Bac_acid_phos_I: domain 1 of 1, from 314 to 326: score 0.8, E = 39
*->LakareELakkrt<-*
++ +r+EL+++
gi|6049608 314 MEEVRQELEDLER 326
LMWPc: domain 1 of 1, from 302 to 331: score 1.3, E = 40
*->rdidDPyygsedgFeevrdeIeervkkllke<-*
r+++D+ y+ ++ eevr+e+e++ + l +e
gi|6049608 302 REVPDE-YEVGSFMEEVRQELEDLERSLTEE 331
//
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: tem4dkk3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [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: Mon Oct 23 15:41:05 2000
Sequence file: tem4dkk3
----------------------------------------
Sequence gi|6049608|gb|AAF02676.1|AF177396_1 (350 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
96: NETN
106: NNTI
121: NQTG
204: NGTI
Total matches: 4
Matching pattern PS00006 CK2_PHOSPHO_SITE:
46: TLNE
67: SAVE
98: TNTD
135: SVGD
206: TICD
312: SFME
327: SLTE
Total matches: 7
Matching pattern PS00008 MYRISTYL:
202: GSNGTI
217: GLCCAF
Total matches: 2
Matching pattern PS00009 AMIDATION:
140: EGRR
Total matches: 1
Total no of hits in this sequence: 14
========================================
1314 pattern(s) searched in 1 sequence(s), 350 residues.
Total no of hits in all sequences: 14.
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 tem4dkk3
***** 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, 350 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: tem4dkk3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [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: tem4dkk3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [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|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
(350 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
DNASE1 DNASE-1/Sphingomyelinase like domain 24 0.44
DHHC Novel zinc finger domain with DHHC signature 23 0.55
LAMNT Lamin N-terminal domain 23 0.62
CYCL cyclophilin like peptidyl prolyl isomerases 23 0.67
RRM RNA recognition motif domain 23 0.70
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 22 1.2
KIN Protein kinase domain 22 1.4
PAP Papain/bleomycin hydrolase like domain 21 2.1
UBHYD Ubiquitin C-terminal hydrolase domain 21 2.7
S1 S1 RNA binding domain 20 4.4
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 20 4.5
CALC Calcineurin like Phosphoesterase domain 20 4.7
C2 C2 lipid binding signaling domain (Protein Kinase C doma... 20 6.0
POZ Pox virus Zinc finger domain (Also called BTB domain; a... 20 6.6
CHLMY Adenovirus like protease domain 19 9.8
>DNASE1 DNASE-1/Sphingomyelinase like domain
Length = 388
Score = 23.6 bits (50), Expect = 0.44
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 55 EELMEDTQHKLRSAVEEMEAEEAAAKASSEVNLANLPPSYHNETNTD----TKVGNNTIH 110
+EL+E +QH E ++ +E +V L + P H + + + T
Sbjct: 47 QELLEASQHD---QSEPLDPKELL--DECQVALQDRPARLHRDFFSLRSESSSQQPRTFR 101
Query: 111 V 111
V
Sbjct: 102 V 102
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 23.2 bits (49), Expect = 0.55
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 267 CASGLLCQPHS 277
C G+LCQPH+
Sbjct: 200 CLRGVLCQPHA 210
Score = 20.1 bits (41), Expect = 4.6
Identities = 6/31 (19%), Positives = 8/31 (25%), Gaps = 6/31 (19%)
Query: 168 CQPCRGQRMLCTRDSECCG------DQLCVW 192
C C ++ C D C W
Sbjct: 136 CNLCNVDVSARSKHCSACNKCVCGFDHHCKW 166
>LAMNT Lamin N-terminal domain
Length = 256
Score = 23.0 bits (49), Expect = 0.62
Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 10/50 (20%)
Query: 154 GPSMYCQFASFQ-------YTCQPCRGQRMLC-TRDSECCGDQLCVWGHC 195
+YC Y+ Q Q+ + G C GHC
Sbjct: 34 VTEIYCSLTGSTQYTPLNSYSYQDDEQQKSWSQYENPMVRGGHGC--GHC 81
>CYCL cyclophilin like peptidyl prolyl isomerases
Length = 165
Score = 22.8 bits (49), Expect = 0.67
Identities = 7/22 (31%), Positives = 10/22 (44%), Gaps = 1/22 (4%)
Query: 133 ITSVGDEEGRRSHECIIDEDCG 154
+ G G+ S + I DCG
Sbjct: 142 MERFGSRNGKTSKKITI-ADCG 162
>RRM RNA recognition motif domain
Length = 110
Score = 23.0 bits (49), Expect = 0.70
Identities = 7/51 (13%), Positives = 13/51 (24%), Gaps = 7/51 (13%)
Query: 38 LSYPQEEATLNEMFREVEELME-------DTQHKLRSAVEEMEAEEAAAKA 81
+ Y L F + + H A E +E+ +
Sbjct: 28 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 78
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 22.3 bits (47), Expect = 1.2
Identities = 10/62 (16%), Positives = 16/62 (25%), Gaps = 9/62 (14%)
Query: 142 RRSHECIIDEDCGPSMYCQFASFQYTCQPC--RGQRMLCTRDSECCGDQLCVWGHCTKMA 199
RR + + + A Q + C +R+ S G K
Sbjct: 27 RRVEQLLQFSFLPELQFQNAAVKQRIQRLCYREEKRLAV---SSLAK---W-LGQLHKQR 79
Query: 200 TR 201
R
Sbjct: 80 LR 81
>KIN Protein kinase domain
Length = 313
Score = 22.0 bits (46), Expect = 1.4
Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 272 LCQPHSHSLVYVCKPTFVGSRDQDGEILLPREVPDEYEVGSFMEEVRQELEDLERSLTEE 331
+ S+ + KP S++Q ++ + E+ D ++ + + +D + +
Sbjct: 85 FKHENLISIKDILKP---NSKEQFEDVYIVSELMD-TDLHQIITSPQPLSDDHCQYFVYQ 140
Query: 332 MALG 335
M G
Sbjct: 141 MLRG 144
>PAP Papain/bleomycin hydrolase like domain
Length = 376
Score = 21.1 bits (44), Expect = 2.1
Identities = 12/66 (18%), Positives = 14/66 (21%), Gaps = 14/66 (21%)
Query: 8 LLCLLLAAAVPTAPAPAPTATSAPVKPGPALSYPQEEATLNEMFREVEELMEDTQHKLRS 67
LL LL+A P L L E F + S
Sbjct: 10 LLALLVAGLAQGIRGPLRAQ---------DLGPQ--PLELKEAF---KLFQIQFNRSYLS 55
Query: 68 AVEEME 73
E
Sbjct: 56 PEEHAH 61
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 20.7 bits (43), Expect = 2.7
Identities = 5/41 (12%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 297 EILLPREVPDEYEVGSFMEEVRQELEDLERSLTEEMALGEP 337
+ +P+++ + + E ++ E E L ++ +
Sbjct: 315 DHDIPQQLVERLQE-EKRIEAQKRKERQEAHLYMQVQIVAE 354
Score = 19.6 bits (40), Expect = 7.1
Identities = 4/23 (17%), Positives = 12/23 (51%)
Query: 40 YPQEEATLNEMFREVEELMEDTQ 62
YP + + ++ E ++ +E +
Sbjct: 693 YPDKHGCVRDLLEECKKAVELGE 715
>S1 S1 RNA binding domain
Length = 305
Score = 20.2 bits (42), Expect = 4.4
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 33 KPGPALSYPQEEATLNEMFREVEELMED--TQHKLRSAVEEMEA 74
K +LS E E+ + +E+M D + L + + +
Sbjct: 254 KNRISLSTRILETYPGELVEKFDEMMADAPNRLPLVQSKQNLGD 297
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 20.2 bits (42), Expect = 4.5
Identities = 11/30 (36%), Positives = 16/30 (52%)
Query: 56 ELMEDTQHKLRSAVEEMEAEEAAAKASSEV 85
E++ D + KL + E E AK+SS V
Sbjct: 208 EIVRDMKEKLAYVALDYEQELETAKSSSSV 237
>CALC Calcineurin like Phosphoesterase domain
Length = 274
Score = 20.1 bits (41), Expect = 4.7
Identities = 4/23 (17%), Positives = 6/23 (25%), Gaps = 3/23 (13%)
Query: 105 GNNTIHVHREIHKIT---NNQTG 124
G+ V R + G
Sbjct: 251 GSIRTEVKRIQQAEFFPNMQEEG 273
>C2 C2 lipid binding signaling domain (Protein Kinase C domain 2)
Length = 95
Score = 19.7 bits (41), Expect = 6.0
Identities = 8/27 (29%), Positives = 10/27 (36%)
Query: 84 EVNLANLPPSYHNETNTDTKVGNNTIH 110
EV L LP T N+I+
Sbjct: 31 EVELFGLPGDPKRRYRTKLSPSTNSIN 57
>POZ Pox virus Zinc finger domain (Also called BTB domain; a protein-protein interaction domain)
Length = 229
Score = 19.7 bits (40), Expect = 6.6
Identities = 8/51 (15%), Positives = 19/51 (36%), Gaps = 5/51 (9%)
Query: 38 LSYPQEEATLNEMFRE-----VEELMEDTQHKLRSAVEEMEAEEAAAKASS 83
++ PQ + E+ E ++ L+ Q L+ + + +S
Sbjct: 92 ITLPQNRQEIKELMAEAKYYLIQGLVNMCQSALQDKKDSYQPVCNIPIITS 142
>CHLMY Adenovirus like protease domain
Length = 157
Score = 19.0 bits (39), Expect = 9.8
Identities = 6/32 (18%), Positives = 8/32 (24%), Gaps = 3/32 (9%)
Query: 147 CIIDEDCGPSMYCQF--ASFQYTCQPCRGQRM 176
DCG C F + + M
Sbjct: 109 QTNTSDCGVFS-CMFAEYITRNISLTFSQKDM 139
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 15
Number of calls to ALIGN: 17
Length of query: 350
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 5266218.0
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= gi|6049608|gb|AAF02676.1|AF177396_1 dickkopf-3 [Homo sapiens]
(350 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2392378 [1..380] Periplasmic binding protein-like II 27 0.41
gi|1729506 [37..114] DNA-binding 3-helical bundle 25 1.8
gi|1652821 [74..598] Periplasmic binding protein-like II 24 4.5
gi|1827800 [1..380] beta/alpha (TIM)-barrel 24 5.2
gi|1403532 [23..325] Protein kinases (PK), catalytic core 23 5.9
gi|2496858 [21..217] Protein kinases (PK), catalytic core 23 6.1
gi|116200 [2..100] GroES-like 23 7.1
gi|1006595 [10..297] 5' to 3' exonuclease 23 9.1
gi|586059 [74..214] OB-fold 23 9.7
gi|68551 [316..472] Anticodon-binding (C-terminal) domain of... 23 9.7
>gi|2392378 [1..380] Periplasmic binding protein-like II
Length = 380
Score = 27.4 bits (60), Expect = 0.41
Identities = 13/70 (18%), Positives = 26/70 (36%), Gaps = 6/70 (8%)
Query: 21 PAPAPTATSAPVKPGPALSYPQEEATLNEMFREVEELMEDTQHKLRSAVEEM-----EAE 75
A A + + P ++ E A E+ + + M + +R+AV +
Sbjct: 310 GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQ-MSAFWYAVRTAVINAASGRQTVD 368
Query: 76 EAAAKASSEV 85
EA A + +
Sbjct: 369 EALKDAQTRI 378
>gi|1729506 [37..114] DNA-binding 3-helical bundle
Length = 78
Score = 25.1 bits (54), Expect = 1.8
Identities = 6/31 (19%), Positives = 8/31 (25%)
Query: 162 ASFQYTCQPCRGQRMLCTRDSECCGDQLCVW 192
F T P R ++ VW
Sbjct: 22 TLFNETQYPDVFARERVADQIRLQESRIQVW 52
>gi|1652821 [74..598] Periplasmic binding protein-like II
Length = 525
Score = 23.8 bits (51), Expect = 4.5
Identities = 6/37 (16%), Positives = 12/37 (32%)
Query: 73 EAEEAAAKASSEVNLANLPPSYHNETNTDTKVGNNTI 109
S ++ +PP + + + GN I
Sbjct: 214 TDTSLLQFRSGSLDSLGVPPESFSLLKQEEERGNFVI 250
>gi|1827800 [1..380] beta/alpha (TIM)-barrel
Length = 380
Score = 23.7 bits (50), Expect = 5.2
Identities = 2/23 (8%), Positives = 3/23 (12%), Gaps = 2/23 (8%)
Query: 8 LLCLLLAAAVPTAPAPAPTATSA 30
L+ P
Sbjct: 2 YDASLIPNL--QIPQKNIPNNDG 22
>gi|1403532 [23..325] Protein kinases (PK), catalytic core
Length = 303
Score = 23.2 bits (48), Expect = 5.9
Identities = 6/74 (8%), Positives = 15/74 (20%)
Query: 143 RSHECIIDEDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMATRG 202
+EC D G S +Y ++ + +
Sbjct: 146 AENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCLAQAGLQSDTECTSAVDLWS 205
Query: 203 SNGTICDNQRDCQP 216
+ + +
Sbjct: 206 LGIILLEMFSGMKL 219
>gi|2496858 [21..217] Protein kinases (PK), catalytic core
Length = 197
Score = 23.2 bits (48), Expect = 6.1
Identities = 7/104 (6%), Positives = 16/104 (14%)
Query: 141 GRRSHECIIDEDCGPSMYCQFASFQYTCQPCRGQRMLCTRDSECCGDQLCVWGHCTKMAT 200
G S + I+ G F Q + + + ++ +
Sbjct: 26 GDLSVKNILMTHEGVVKLSDFGMANTFEQTRKSKNQSILGTPGFVSVVVFLFEMWKNIVF 85
Query: 201 RGSNGTICDNQRDCQPGLCCAFQRGLLFPVCTPLPVEGELCHDP 244
+ L
Sbjct: 86 IFHQNFDKRTNFKTFVKYYTIAPEIINLQGYDGKADLWGLGILS 129
>gi|116200 [2..100] GroES-like
Length = 99
Score = 23.2 bits (50), Expect = 7.1
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 290 GSRDQDGEILLPREV 304
G D+DGE +P +V
Sbjct: 48 GRWDEDGEKRIPLDV 62
>gi|1006595 [10..297] 5' to 3' exonuclease
Length = 288
Score = 22.9 bits (49), Expect = 9.1
Identities = 7/61 (11%), Positives = 21/61 (33%), Gaps = 4/61 (6%)
Query: 37 ALSYPQEEATLNEMFREVEELMEDTQHKLRSAVEE----MEAEEAAAKASSEVNLANLPP 92
A+ E TL +++ + ++ + +L + ++ V +L
Sbjct: 208 AIKLLAEYETLEKVYENLAQIKGALKTRLDNGKDDAMHSQMLARIVVDVPLPVTWEDLQL 267
Query: 93 S 93
+
Sbjct: 268 T 268
>gi|586059 [74..214] OB-fold
Length = 141
Score = 22.5 bits (48), Expect = 9.7
Identities = 7/39 (17%), Positives = 14/39 (34%), Gaps = 3/39 (7%)
Query: 285 KPTFVGSRDQDGEILL---PREVPDEYEVGSFMEEVRQE 320
K F R + ++ + R E E ++R+
Sbjct: 68 KLIFYDLRGEGVKLQVMANSRNYKSEEEFVRINNKLRRG 106
>gi|68551 [316..472] Anticodon-binding (C-terminal) domain of glutamyl-tRNA synthetase
Length = 157
Score = 22.6 bits (48), Expect = 9.7
Identities = 8/49 (16%), Positives = 16/49 (32%), Gaps = 3/49 (6%)
Query: 41 PQEEATLNEMFREVEELMEDTQHKLRSAVEEMEAEE--AAAKASSEVNL 87
P A + E+ +++ Q L E + +AS +
Sbjct: 69 PAAFAGVKASPEEMLKILNTVQPDLEKI-LEWNKDSIETELRASERMGK 116
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 10
Number of calls to ALIGN: 10
Length of query: 350
Total length of test sequences: 256703
Effective length of test sequences: 209547.0
Effective search space size: 65032980.6
Initial X dropoff for ALIGN: 25.0 bits