analysis of sequence from tem44
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLGPVAPTREGVENACFSSEEHE
THFQNPGNTRLGSSPSPPGGVSSLPRSQRDDLSLHSEEGPALEPVSRPVDYGFVSALVFLVSGILLVVTA
YAIPREARVNPDTVTAREMERLEMYYARLGSHLDRCIIAGLGLLTVGGMLLSVLLMVSLCKGELYRRRTF
VPGKGSRKTYGSINLRMRQLNGDGGQALVENEVVQVSETSHTLQRS
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|8922927|ref|NP_060824.1|
. . . . .
1 MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLG 50
____HHHHHHHH___________________EEEE_______________
. . . . .
51 PVAPTREGVENACFSSEEHETHFQNPGNTRLGSSPSPPGGVSSLPRSQRD 100
_______HHHHHHH____________________________________
. . . . .
101 DLSLHSEEGPALEPVSRPVDYGFVSALVFLVSGILLVVTAYAIPREARVN 150
______________________HHHHH__HHHHHEEEE_EEE________
. . . . .
151 PDTVTAREMERLEMYYARLGSHLDRCIIAGLGLLTVGGMLLSVLLMVSLC 200
__HHHHHHHHHHHHHHHHH_____HHHHH_________HHHHHHHHHHHH
. . . . .
201 KGELYRRRTFVPGKGSRKTYGSINLRMRQLNGDGGQALVENEVVQVSETS 250
_____________________HHHHHHHHH______EEEE___EEEE___
251 HTLQRS 256
______
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 18.4 %
beta-contents : 15.8 %
coil-contents : 65.8 %
class : mixed
method : 2
alpha-contents : 0.0 %
beta-contents : 15.3 %
coil-contents : 84.7 %
class : beta
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-8.05 0.00 0.00 0.00 0.00 0.00 0.00 -0.54 0.00 -6.13 -2.27 -12.00 -12.00 0.00 -12.00 0.00 -52.99
-4.54 0.00 0.00 0.00 0.00 0.00 0.00 -0.04 -0.06 -5.36 -2.27 -12.00 -12.00 0.00 -12.00 0.00 -48.27
ID: gi|8922927|ref|NP_060824.1| AC: xxx Len: 256 1:I 233 Sc: -48.27 Pv: 2.059361e-01 NO_GPI_SITE
GPI: learning from protozoa
-29.03 0.00 0.00 0.00 -4.00 0.00 0.00 -0.15 0.00 -4.71 -8.43 -12.00 -12.00 0.00 -12.00 0.00 -82.32
-20.14 0.00 0.00 0.00 -4.00 0.00 0.00 -0.55 -0.02 -6.88 -8.43 -12.00 -12.00 0.00 -12.00 0.00 -76.04
ID: gi|8922927|ref|NP_060824.1| AC: xxx Len: 256 1:I 235 Sc: -76.04 Pv: 4.399766e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|8922927| 0.942 143 Y 0.829 143 Y 0.975 187 Y 0.161 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|8922927| 0.446 143 N 0.556 143 Y 0.980 132 Y 0.197 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|8922927| 0.875 143 Y 0.705 143 Y 0.976 131 Y 0.213 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
1-79 MPPAQGYEFAAAKGPRDELGPSFPMASPPG
LELKTLSNGPQAPRRSAPLGPVAPTREGVE
NACFSSEEHETHFQNPGNT
rlgsspsppggvsslprs 80-97
98-179 QRDDLSLHSEEGPALEPVSRPVDYGFVSAL
VFLVSGILLVVTAYAIPREARVNPDTVTAR
EMERLEMYYARLGSHLDRCIIA
glglltvggmllsvllmvsl 180-199
200-256 CKGELYRRRTFVPGKGSRKTYGSINLRMRQ
LNGDGGQALVENEVVQVSETSHTLQRS
low complexity regions: SEG 25 3.0 3.3
>gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
1-80 MPPAQGYEFAAAKGPRDELGPSFPMASPPG
LELKTLSNGPQAPRRSAPLGPVAPTREGVE
NACFSSEEHETHFQNPGNTR
lgsspsppggvsslprsqrddlslhseegp 81-120
alepvsrpvd
121-179 YGFVSALVFLVSGILLVVTAYAIPREARVN
PDTVTAREMERLEMYYARLGSHLDRCIIA
glglltvggmllsvllmvsl 180-199
200-256 CKGELYRRRTFVPGKGSRKTYGSINLRMRQ
LNGDGGQALVENEVVQVSETSHTLQRS
low complexity regions: SEG 45 3.4 3.75
>gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
1-38 MPPAQGYEFAAAKGPRDELGPSFPMASPPG
LELKTLSN
gpqaprrsaplgpvaptregvenacfssee 39-171
hethfqnpgntrlgsspsppggvsslprsq
rddlslhseegpalepvsrpvdygfvsalv
flvsgillvvtayaiprearvnpdtvtare
merlemyyarlgs
172-256 HLDRCIIAGLGLLTVGGMLLSVLLMVSLCK
GELYRRRTFVPGKGSRKTYGSINLRMRQLN
GDGGQALVENEVVQVSETSHTLQRS
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|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLGPVAPTREGVE
NACFSSEEHETHFQNPGNTRLGSSPSPPGGVSSLPRSQRDDLSLHSEEGPALEPVSRPVD
YGFVSALVFLVSGILLVVTAYAIPREARVNPDTVTAREMERLEMYYARLGSHLDRCIIAG
LGLLTVGGMLLSVLLMVSLCKGELYRRRTFVPGKGSRKTYGSINLRMRQLNGDGGQALVE
NEVVQVSETSHTLQRS
1 - 256 MPPAQGYEFA AAKGPRDELG PSFPMASPPG LELKTLSNGP QAPRRSAPLG PVAPTREGVE
NACFSSEEHE THFQNPGNTR LGSSPSPPGG VSSLPRSQRD DLSLHSEEGP ALEPVSRPVD
YGFVSALVFL VSGILLVVTA YAIPREARVN PDTVTAREME RLEMYYARLG SHLDRCIIAG
LGLLTVGGML LSVLLMVSLC KGELYRRRTF VPGKGSRKTY GSINLRMRQL NGDGGQALVE
NEVVQVSETS HTLQRS
low complexity regions: DUST
>gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo sapiens]
MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLGPVAPTREGVE
NACFSSEEHETHFQNPGNTRLGSSPSPPGGVSSLPRSQRDDLSLHSEEGPALEPVSRPVD
YGFVSALVFLVSGILLVVTAYAIPREARVNPDTVTAREMERLEMYYARLGSHLDRCIIAG
LGLLTVGGMLLSVLLMVSLCKGELYRRRTFVPGKGSRKTYGSINLRMRQLNGDGGQALVE
NEVVQVSETSHTLQRS
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|8922927|ref|NP_060824.1|
sequence: 256 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MPPAQGYEFA AAKGPRDELG PSFPMASPPG LELKTLSNGP QAPRRSAPLG PVAPTREGVE
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
NACFSSEEHE THFQNPGNTR LGSSPSPPGG VSSLPRSQRD DLSLHSEEGP ALEPVSRPVD
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 180
YGFVSALVFL VSGILLVVTA YAIPREARVN PDTVTAREME RLEMYYARLG SHLDRCIIAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~1333333 3333333333 3333311~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~33333 333333333~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
LGLLTVGGML LSVLLMVSLC KGELYRRRTF VPGKGSRKTY GSINLRMRQL NGDGGQALVE
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | .
NEVVQVSETS HTLQRS
~~~~~~~~~~ ~~~~~~
---------- ------
~~~~~~~~~~ ~~~~~~
~~~~~~~~~~ ~~~~~~
~~~~~~~~~~ ~~~~~~
~~~~~~~~~~ ~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem44.___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: tem44.___inter___
(1 sequences)
MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLG
PVAPTREGVENACFSSEEHETHFQNPGNTRLGSSPSPPGGVSSLPRSQRD
DLSLHSEEGPALEPVSRPVDYGFVSALVFLVSGILLVVTAYAIPREARVN
PDTVTAREMERLEMYYARLGSHLDRCIIAGLGLLTVGGMLLSVLLMVSLC
KGELYRRRTFVPGKGSRKTYGSINLRMRQLNGDGGQALVENEVVQVSETS
HTLQRS
(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
1 122 142 2.242 Certain
2 180 200 2.221 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 121 37 56
K+R profile + 10.00
6.00
CYT-EXT prof 0.82 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -3.00
(NEG-POS)/(NEG+POS): 0.2000
NEG: 15.0000
POS: 10.0000
-> Orientation: N-out
CYT-EXT difference: 0.82
-> Orientation: N-out
----------------------------------------------------------------------
"tem44" 256
122 142 #t 2.24167
180 200 #t 2.22083
************************************
*TOPPREDM with prokaryotic function*
************************************
tem44.___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: tem44.___inter___
(1 sequences)
MPPAQGYEFAAAKGPRDELGPSFPMASPPGLELKTLSNGPQAPRRSAPLG
PVAPTREGVENACFSSEEHETHFQNPGNTRLGSSPSPPGGVSSLPRSQRD
DLSLHSEEGPALEPVSRPVDYGFVSALVFLVSGILLVVTAYAIPREARVN
PDTVTAREMERLEMYYARLGSHLDRCIIAGLGLLTVGGMLLSVLLMVSLC
KGELYRRRTFVPGKGSRKTYGSINLRMRQLNGDGGQALVENEVVQVSETS
HTLQRS
(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
1 122 142 2.242 Certain
2 180 200 2.221 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 121 37 56
K+R profile + 10.00
6.00
CYT-EXT prof 0.82 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -3.00
(NEG-POS)/(NEG+POS): 0.2000
NEG: 15.0000
POS: 10.0000
-> Orientation: N-out
CYT-EXT difference: 0.82
-> Orientation: N-out
----------------------------------------------------------------------
"tem44" 256
122 142 #t 2.24167
180 200 #t 2.22083
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem44.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 18:38:45 2000
File: /people/maria/tem44.___saps___
ID gi|8922927|ref|NP_060824.1|
DE hypothetical protein FLJ11190 [Homo sapiens]
number of residues: 256; molecular weight: 27.6 kdal
1 MPPAQGYEFA AAKGPRDELG PSFPMASPPG LELKTLSNGP QAPRRSAPLG PVAPTREGVE
61 NACFSSEEHE THFQNPGNTR LGSSPSPPGG VSSLPRSQRD DLSLHSEEGP ALEPVSRPVD
121 YGFVSALVFL VSGILLVVTA YAIPREARVN PDTVTAREME RLEMYYARLG SHLDRCIIAG
181 LGLLTVGGML LSVLLMVSLC KGELYRRRTF VPGKGSRKTY GSINLRMRQL NGDGGQALVE
241 NEVVQVSETS HTLQRS
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 18( 7.0%); C : 3( 1.2%); D : 7( 2.7%); E : 19( 7.4%); F : 7( 2.7%)
G : 26(10.2%); H : 5( 2.0%); I- : 5( 2.0%); K : 5( 2.0%); L : 30(11.7%)
M : 7( 2.7%); N : 8( 3.1%); P : 23( 9.0%); Q : 8( 3.1%); R : 21( 8.2%)
S : 25( 9.8%); T : 12( 4.7%); V : 20( 7.8%); W : 0( 0.0%); Y : 7( 2.7%)
KR : 26 ( 10.2%); ED : 26 ( 10.2%); AGP : 67 ( 26.2%);
KRED : 52 ( 20.3%); KR-ED : 0 ( 0.0%); FIKMNY- : 39 ( 15.2%);
LVIFM : 69 ( 27.0%); ST : 37 ( 14.5%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0000000-00 00+00+--00 0000000000 0-0+000000 000++00000 00000+-00-
61 000000--0- 000000000+ 0000000000 00000+00+- -00000--00 00-000+00-
121 0000000000 0000000000 0000+-0+00 0-0000+-0- +0-0000+00 000-+00000
181 0000000000 0000000000 +0-00+++00 000+00++00 00000+0+00 00-000000-
241 0-00000-00 0000+0
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Negative charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): 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 | 4 | 6 | 38 | 9 | 9 | 12 | 11 | 11 | 14 | 6 | 8 |
lmin1 6 | 6 | 8 | 46 | 11 | 11 | 14 | 13 | 13 | 17 | 8 | 9 |
lmin2 7 | 7 | 9 | 51 | 12 | 12 | 16 | 15 | 15 | 19 | 9 | 11 |
(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: 1, at 206;
- runs >= 3: 0
* runs >= 4: 0
0 runs >= 25: 1, at 176;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
__________________________________
High scoring hydrophobic segments:
2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ)
-8.00 (KEDR)
Expected score/letter: -1.922
M_0.01= 22.86; M_0.05= 18.66
1) From 121 to 143: length= 23, score=21.00 *
121 YGFVSALVFL VSGILLVVTA YAI
L: 4(17.4%); A: 3(13.0%); V: 5(21.7%);
2) From 176 to 197: length= 22, score=26.00 **
176 CIIAGLGLLT VGGMLLSVLL MV
L: 7(31.8%); G: 4(18.2%); V: 3(13.6%);
____________________________________
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: -3.391
M_0.01= 56.08; M_0.05= 45.35; M_0.30= 32.58
1) From 122 to 143: length= 22, score=68.00 **
122 GFVSALVFLV SGILLVVTAY AI
L: 4(18.2%); A: 3(13.6%); V: 5(22.7%);
2) From 177 to 199: length= 23, score=73.00 **
177 IIAGLGLLTV GGMLLSVLLM VSL
L: 8(34.8%); G: 4(17.4%); V: 3(13.0%);
2. SPACINGS OF C.
H2N-62-C-112-C-23-C-56-COOH
2*. SPACINGS OF C and H. (additiona
l deluxe function for ALEX)
H2N-62-C-5-H-2-H-32-H-66-H-3-C-23-C-50-H-5-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 27- 30] SPPG
[ 86- 89] SPPG
______________________________
[ 80- 83] RLGS
[ 168- 171] RLGS
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: 23 (Expected range: 5-- 30)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 10 (6-10) 4 (11-20) 7 (>=21) 3
3. Clusters of amino acid multiplets (cmin = 14/30 or 18/45 or 22/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 7 (Expected range: 0-- 12)
3 +plets (f+: 10.2%), 4 -plets (f-: 10.2%)
Total number of charge altplets: 7 (Critical number: 14)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 2 (11-20) 1 (>=21) 5
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
There are no periodicities of the prescribed length.
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
115- 138 4 i... 6 6 0
189- 200 2 i. 6 6 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
There are no unusual spacings.
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
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: tem44
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [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 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: tem44
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [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 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: tem44
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [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 18:41:49 2000
Sequence file: tem44
----------------------------------------
Sequence gi|8922927|ref|NP_060824.1| (256 residues):
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
206: RRRT
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
97: SQR
155: TAR
216: SRK
Total matches: 3
Matching pattern PS00006 CK2_PHOSPHO_SITE:
65: SSEE
97: SQRD
155: TARE
171: SHLD
Total matches: 4
Matching pattern PS00008 MYRISTYL:
58: GVENAC
89: GGVSSL
188: GMLLSV
215: GSRKTY
Total matches: 4
Total no of hits in this sequence: 12
========================================
1314 pattern(s) searched in 1 sequence(s), 256 residues.
Total no of hits in all sequences: 12.
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 tem44
***** 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, 256 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: tem44
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [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: tem44
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [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|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo
sapiens]
(256 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
INSL Insulinase like Metallo protease domain 20 3.4
JAB JAB1 associated domain involved in proteolysis 19 5.2
RASGAP RAS-type GTPase GTP hydrolysis activating protein 19 5.2
DHHC Novel zinc finger domain with DHHC signature 19 5.5
DNASE1 DNASE-1/Sphingomyelinase like domain 19 7.6
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 19 7.7
LRR Leucine rich repeats 19 8.9
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 19.9 bits (41), Expect = 3.4
Identities = 4/30 (13%), Positives = 10/30 (33%)
Query: 24 PMASPPGLELKTLSNGPQAPRRSAPLGPVA 53
+ + L ++ L NG + +
Sbjct: 14 QVLTAQELYIRDLPNGAKLIVKPRDDTEAV 43
>JAB JAB1 associated domain involved in proteolysis
Length = 136
Score = 19.4 bits (40), Expect = 5.2
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 133 GILLVVTAYAIPREARVNPDTVTAREMERLEMYYARL 169
+L V ++A+P + D+V + + LE Y
Sbjct: 39 KVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGMF 75
>RASGAP RAS-type GTPase GTP hydrolysis activating protein
Length = 292
Score = 19.3 bits (39), Expect = 5.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 114 PVSRPVDYGFVSALVFL 130
P +R V Y VS +FL
Sbjct: 192 PSNREVRYSVVSGFIFL 208
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 19.3 bits (39), Expect = 5.5
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 83 SSPSPPGGVSSLPRSQRDDLSLHSEEGPALEPVSRPVDYGFVSALVFLVSGILLVVTAYA 142
++P+ P G S + QR S P ++ L F V G ++V
Sbjct: 22 TAPAQPSGPSPELQGQR------SRRNGWSWPPHPLQIVAWLLYLFFAVIGFGILVPLLP 75
Query: 143 I 143
Sbjct: 76 H 76
>DNASE1 DNASE-1/Sphingomyelinase like domain
Length = 388
Score = 18.9 bits (38), Expect = 7.6
Identities = 9/93 (9%), Positives = 19/93 (19%), Gaps = 5/93 (5%)
Query: 89 GGVSSLPRSQRDDLSLHSEEGPALEPVSRPVDYGFVSALVFLVSG-ILLVVTAYAIPREA 147
G + R L ++ + + L +G L + R
Sbjct: 191 DGCALFFLQDRFQLVNSAKIRLSARTLKT-NQVAIAETLQCCETGRQLCFAVTHLKARTG 249
Query: 148 RVNPDTVTAREMERLEMYYARLGSHLDRCIIAG 180
+ L + +I
Sbjct: 250 WER---FRLAQGSDLLDNLESITQGATVPLIIC 279
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 19.0 bits (39), Expect = 7.7
Identities = 8/23 (34%), Positives = 10/23 (42%)
Query: 32 ELKTLSNGPQAPRRSAPLGPVAP 54
EL+ +S P APL P
Sbjct: 95 ELRVVSEEPXVLSXEAPLNPKVN 117
>LRR Leucine rich repeats
Length = 339
Score = 18.8 bits (38), Expect = 8.9
Identities = 8/32 (25%), Positives = 9/32 (28%), Gaps = 1/32 (3%)
Query: 77 GNTRLGSSPSPPGGVSSLPRSQRDDLSLHSEE 108
N L P P L D SL +
Sbjct: 301 ENENLVMPPKPNDARKKL-AFYNIDFSLEHQR 331
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 7
Number of calls to ALIGN: 7
Length of query: 256
Total length of test sequences: 20182
Effective length of test sequences: 16536.0
Effective search space size: 3664766.2
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|8922927|ref|NP_060824.1| hypothetical protein FLJ11190 [Homo
sapiens]
(256 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|129541 [240..563] N-terminal nucleophile aminohydrolases ... 23 3.8
gi|2384758 [390..431] FAD/NAD(P)-binding domain 23 6.5
>gi|129541 [240..563] N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Length = 324
Score = 23.4 bits (50), Expect = 3.8
Identities = 7/26 (26%), Positives = 9/26 (33%)
Query: 229 QLNGDGGQALVENEVVQVSETSHTLQ 254
Q DG A NE V+ +
Sbjct: 82 QFAEDGRTARFGNEFEPVAWRRDRIA 107
>gi|2384758 [390..431] FAD/NAD(P)-binding domain
Length = 42
Score = 22.6 bits (48), Expect = 6.5
Identities = 8/23 (34%), Positives = 12/23 (51%), Gaps = 2/23 (8%)
Query: 54 PTREGVENACFSSEEHE--THFQ 74
P E + CF S ++ THF+
Sbjct: 1 PVNEPSLDNCFVSTSYDATTHFE 23
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 2
Number of calls to ALIGN: 2
Length of query: 256
Total length of test sequences: 256703
Effective length of test sequences: 208388.0
Effective search space size: 44829786.3
Initial X dropoff for ALIGN: 25.0 bits