analysis of sequence from tem45
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|339944|gb|AAA36771.1| tropomyosin
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEK
LELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEK
MEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIMDQTLKALMAA
EDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLE
LNNM
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|339944|gb|AAA36771.1|
. . . . .
1 MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKL 50
___HHHHHHHHHHHH_HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
. . . . .
51 KGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELD 100
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
. . . . .
101 RAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKE 150
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
. . . . .
151 AKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIM 200
HHHHHHH_HHHHHHHHHHHEEE___HHHHHHHHHHH__HHHHHHHHHHHH
. . . . .
201 DQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLE 250
HHHHHHHHHHHHHH_HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
. . .
251 KSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM 284
HHHHHHHHHHHHHHHH__HHHHHHHHHHHH____
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 100.0 %
beta-contents : 0.0 %
coil-contents : 0.0 %
class : alpha
method : 2
alpha-contents : 100.0 %
beta-contents : 0.0 %
coil-contents : 0.0 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-23.16 -0.62 -0.96 -0.03 -4.00 0.00 0.00 0.00 -0.20 -3.42 -0.22 -12.00 -12.00 -4.00 0.00 0.00 -60.61
-10.11 -1.82 -1.26 -0.07 -4.00 0.00 -16.00 0.00 -1.24 -1.38 -0.22 -12.00 -12.00 0.00 0.00 0.00 -60.10
ID: gi|339944|gb|AAA36771.1| AC: xxx Len: 280 1:I 267 Sc: -60.10 Pv: 3.715427e-01 NO_GPI_SITE
GPI: learning from protozoa
-18.88 -2.05 -2.72 -2.31 -4.00 0.00 -16.00 0.00 -0.43 -1.35 -1.81 -12.00 -12.00 0.00 0.00 0.00 -73.56
-23.62 -0.63 -1.03 -1.98 -4.00 0.00 0.00 0.00 0.00 -3.09 -1.81 -12.00 -12.00 -4.00 0.00 0.00 -64.17
ID: gi|339944|gb|AAA36771.1| AC: xxx Len: 280 1:I 261 Sc: -64.17 Pv: 2.699882e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|339944|g 0.101 264 N 0.041 4 N 0.145 1 N 0.107 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|339944|g 0.516 264 Y 0.188 19 N 0.703 3 N 0.180 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|339944|g 0.405 103 N 0.216 210 N 0.772 4 N 0.074 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|339944|gb|AAA36771.1| tropomyosin
1-19 MDAIKKKMQMLKLDKENAL
draeqaeadkkaaedr 20-35
36-105 SKQLEDELVSLQKKLKGTEDELDKYSEALK
DAQEKLELAEKKATDAEADVASLNRRIQLV
EEELDRAQER
latalqkleeaekaadese 106-124
125-172 RGMKVIESRAQKDEEKMEIQEIQLKEAKHI
AEDADRKYEEVARKLVII
esdleraeeraelse 173-187
188-284 GQVRQLEEQLRIMDQTLKALMAAEDKYSQK
EDRYEEEIKVLSDKLKEAETRAEFAERSVT
KLEKSIDDLEEKVAHAKEENLSMHQMLDQT
LLELNNM
low complexity regions: SEG 25 3.0 3.3
>gi|339944|gb|AAA36771.1| tropomyosin
1-10 MDAIKKKMQM
lkldkenaldraeqaeadkkaaedrskqle 11-125
delvslqkklkgtedeldkysealkdaqek
lelaekkatdaeadvaslnrriqlveeeld
raqerlatalqkleeaekaadeser
126-127 GM
kviesraqkdeekmeiqeiqlkeakhiaed 128-197
adrkyeevarklviiesdleraeeraelse
gqvrqleeql
198-284 RIMDQTLKALMAAEDKYSQKEDRYEEEIKV
LSDKLKEAETRAEFAERSVTKLEKSIDDLE
EKVAHAKEENLSMHQMLDQTLLELNNM
low complexity regions: SEG 45 3.4 3.75
>gi|339944|gb|AAA36771.1| tropomyosin
1-1 M
daikkkmqmlkldkenaldraeqaeadkka 2-281
aedrskqledelvslqkklkgtedeldkys
ealkdaqeklelaekkatdaeadvaslnrr
iqlveeeldraqerlatalqkleeaekaad
esergmkviesraqkdeekmeiqeiqlkea
khiaedadrkyeevarklviiesdleraee
raelsegqvrqleeqlrimdqtlkalmaae
dkysqkedryeeeikvlsdklkeaetraef
aersvtkleksiddleekvahakeenlsmh
qmldqtllel
282-284 NNM
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|339944|gb|AAA36771.1| tropomyosin
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKY
SEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAA
DESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAE
ERAELSEGQVRQLEEQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAE
FAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
1 - 284 MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY
SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEELD RAQERLATAL QKLEEAEKAA
DESERGMKVI ESRAQKDEEK MEIQEIQLKE AKHIAEDADR KYEEVARKLV IIESDLERAE
ERAELSEGQV RQLEEQLRIM DQTLKALMAA EDKYSQKEDR YEEEIKVLSD KLKEAETRAE
FAERSVTKLE KSIDDLEEKV AHAKEENLSM HQMLDQTLLE LNNM
low complexity regions: DUST
>gi|339944|gb|AAA36771.1| tropomyosin
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKY
SEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAA
DESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAE
ERAELSEGQVRQLEEQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAE
FAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|339944|gb|AAA36771.1|
sequence: 280 amino acids, 276 residue(s) in coiled coil state
Coil 1 * 0* 276* MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQT
. | . | . | . | . | . 60
MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY
8889999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 -w border
abcdefgabc defgabcdef gabcdefgab cdefgabcde fgabcdefga bcdefgabcd * 21 M'95 -w register
8888999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 +w polar
8889999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 MTK -w class
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 28 M'95 -w signif.
2224777777 7789999999 9999999999 9999999999 9999999999 9999999999 * 14 M'95 -w local
. | . | . | . | . | . 120
SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEELD RAQERLATAL QKLEEAEKAA
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 -w border
efgabcdefg abcdefgabc defgabcdef gabcdefgab cdefgabcde fgabcdefga * 21 M'95 -w register
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 +w polar
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 MTK -w class
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 28 M'95 -w signif.
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 14 M'95 -w local
. | . | . | . | . | . 180
DESERGMKVI ESRAQKDEEK MEIQEIQLKE AKHIAEDADR KYEEVARKLV IIESDLERAE
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 -w border
bcdefgabcd efgabcdefg abcdefgabc defgabcdef gabcdefgab cdefgabcde * 21 M'95 -w register
9999988877 7555555999 9999999999 9999999999 9999999999 9999999999 * 21 M'95 +w polar
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 21 MTK -w class
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 28 M'95 -w signif.
9999976522 4478888999 9999999999 9966688888 8888888888 9999999999 * 14 M'95 -w local
. | . | . | . | . | . 240
ERAELSEGQV RQLEEQLRIM DQTLKALMAA EDKYSQKEDR YEEEIKVLSD KLKEAETRAE
9999999999 9999999999 9999999999 8999999999 9999999999 9999999999 * 21 M'95 -w border
fgabcdefga bcdefgabcd efgabcdefg ebcdefgabc defgabcdef gabcdefgab * 21 M'95 -w register
9999999999 9999999999 9999999999 8999999999 9999999999 9999999999 * 21 M'95 +w polar
9999999999 9999999999 9999999997 6999999999 9999999999 9999999999 * 21 MTK -w class
9999999999 9999999999 9999999999 9999999999 9999999999 9999999999 * 28 M'95 -w signif.
9999999999 9999999999 9999988689 9999999999 9999999999 9999999999 * 14 M'95 -w local
. | . | . | . |
FAERSVTKLE KSIDDLEEKV AHAKEENLSM HQMLDQTLLE
9999999999 9999999999 9999999999 9999994~~~
cdefgabcde fgabcdefga bcdefgabcd efgabcd---
9999999999 9999999999 9999999999 9999992~~~
9999999999 9999999999 9999999999 8888883~~~
9999999999 9999999999 9999999999 9999999999
9999999999 9999999999 9999999874 ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem45.___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: tem45.___inter___
(1 sequences)
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKL
KGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELD
RAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKE
AKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIM
DQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLE
KSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
(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
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment
Loop length 284
K+R profile +
CYT-EXT prof -1.25
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): -3.00
(NEG-POS)/(NEG+POS): 0.2000
NEG: 78.0000
POS: 52.0000
-> Orientation: N-out
CYT-EXT difference: -1.25
-> Orientation: N-in
----------------------------------------------------------------------
"tem45" 284
************************************
*TOPPREDM with prokaryotic function*
************************************
tem45.___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: tem45.___inter___
(1 sequences)
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKL
KGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELD
RAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKE
AKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIM
DQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLE
KSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
(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
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment
Loop length 284
K+R profile +
CYT-EXT prof -1.25
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): -3.00
(NEG-POS)/(NEG+POS): 0.2000
NEG: 78.0000
POS: 52.0000
-> Orientation: N-out
CYT-EXT difference: -1.25
-> Orientation: N-in
----------------------------------------------------------------------
"tem45" 284
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem45.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Jan 18 20:02:12 2001
File: /people/maria/tem45.___saps___
ID gi|339944|gb|AAA36771.1|
DE tropomyosin
number of residues: 284; molecular weight: 32.9 kdal
1 MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY
61 SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEELD RAQERLATAL QKLEEAEKAA
121 DESERGMKVI ESRAQKDEEK MEIQEIQLKE AKHIAEDADR KYEEVARKLV IIESDLERAE
181 ERAELSEGQV RQLEEQLRIM DQTLKALMAA EDKYSQKEDR YEEEIKVLSD KLKEAETRAE
241 FAERSVTKLE KSIDDLEEKV AHAKEENLSM HQMLDQTLLE LNNM
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 35(12.3%); C : 0( 0.0%); D+ : 24( 8.5%); E++: 54(19.0%); F--: 1( 0.4%)
G--: 3( 1.1%); H : 3( 1.1%); I : 11( 3.9%); K+ : 35(12.3%); L : 34(12.0%)
M : 10( 3.5%); N : 5( 1.8%); P--: 0( 0.0%); Q : 18( 6.3%); R : 17( 6.0%)
S : 13( 4.6%); T- : 7( 2.5%); V : 10( 3.5%); W : 0( 0.0%); Y : 4( 1.4%)
KR + : 52 ( 18.3%); ED ++: 78 ( 27.5%); AGP : 38 ( 13.4%);
KRED ++: 130 ( 45.8%); KR-ED - : -26 ( -9.2%); FIKMNY : 66 ( 23.2%);
LVIFM : 66 ( 23.2%); ST - : 20 ( 7.0%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0-00+++000 0+0-+-000- +0-00-0-++ 00--+0+00- --00000++0 +00---0-+0
61 0-00+-00-+ 0-00-++00- 0-0-00000+ +0000---0- +00-+00000 0+0--0-+00
121 --0-+00+00 -0+00+---+ 0-00-000+- 0+000--0-+ +0--00++00 00-0-0-+0-
181 -+0-00-000 +00--00+00 -000+00000 --+000+--+ 0---0+000- +0+-0-0+0-
241 00-+000+0- +00--0--+0 000+--0000 0000-0000- 0000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 13/30 or 18/45 or 22/60): none
Negative charge clusters (cmin = 18/30 or 24/45 or 30/60): none
Mixed charge clusters (cmin = 24/30 or 33/45 or 42/60): 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 6 | 8 | 12 | 15 | 9 | 11 | 15 | 9 | 11 | 14 | 5 | 7 |
lmin1 8 | 10 | 15 | 19 | 11 | 13 | 18 | 12 | 14 | 17 | 7 | 8 |
lmin2 9 | 11 | 17 | 21 | 13 | 15 | 20 | 13 | 15 | 19 | 8 | 10 |
(Significance level: 0.010000; Minimal displayed length: 6)
There are no charge runs or patterns exceeding the given minimal lengths.
Run count statistics:
+ runs >= 4: 0
- runs >= 5: 0
* runs >= 8: 0
0 runs >= 10: 0
--------------------------------------------------------------------------------
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-284-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-152-H-108-H-8-H-13-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 19- 22] LDRA
[ 99- 102] LDRA
______________________________
[ 25- 28] AEAD
[ 81- 84] AEAD
______________________________
[ 31- 34] AAED
[ 209- 212] AAED
______________________________
[ 40- 43] EDEL
[ 54- 57] EDEL
______________________________
[ 58- 61] DKYS
[ 212- 215] DKYS
______________________________
[ 148- 151] LKEA
[ 232- 235] LKEA
______________________________
[ 177- 180] ERAE
[ 181- 184] ERAE
______________________________
[ 201- 204] DQTL
[ 275- 278] DQTL
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: 21 (Expected range: 10-- 40)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 7 (6-10) 3 (11-20) 8 (>=21) 4
3. Clusters of amino acid multiplets (cmin = 12/30 or 16/45 or 19/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 24 (Expected range: 9-- 38)
7 +plets (f+: 18.3%), 17 -plets (f-: 27.5%)
Total number of charge altplets: 27 (Critical number: 41)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 9 (6-10) 5 (11-20) 9 (>=21) 2
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
43- 77 7 L...... 5 5 ! 0
117- 151 7 E...... 5 5 ! 0
173- 200 7 E...... 4 4 0
236- 263 7 E...... 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 8)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core:11)
Location Period Element Copies Core Errors
7- 118 7 *...0.* 15 8 /1/./././5/./4/
100- 260 7 *..*... 19 10 /4/././6/./././
117- 207 7 -..0..0 11 5 /2/././0/././1/
212- 241 6 -..0.. 5 5 /0/././1/././
218- 241 4 *.*. 6 6 /0/./2/./
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
0- 44 (1.) V( 44)V 1 of 11 0.9904 small maximal spacing
245- 252 (4.) S( 7)S 14 of 14 0.0041 large minimal 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: tem45
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|339944|gb|AAA36771.1| tropomyosin
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Tropomyosin Tropomyosins 523.8 2e-167 2
ACOX Acyl-CoA oxidase 4.7 1.7 1
G-alpha G-protein alpha subunit 2.1 14 1
Hanta_nucleocap Hantavirus nucleocapsid protein 0.1 15 1
hexokinase Hexokinase -1.1 73 1
TS-N TS-N domain -6.7 82 1
OEP Outer membrane efflux protein -41.4 8.1 1
Troponin Troponin -42.2 50 1
UPF0054 Uncharacterized protein family UPF005 -48.5 41 1
KE2 KE2 family protein -59.6 73 1
Fe_dep_repress Iron dependent repressor -70.4 93 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Tropomyosin 1/2 6 46 .. 1 41 [. -6.9 5.6e+03
G-alpha 1/1 26 53 .. 1 28 [. 2.1 14
ACOX 1/1 42 71 .. 490 519 .] 4.7 1.7
KE2 1/1 33 116 .. 1 117 [] -59.6 73
Hanta_nucleocap 1/1 90 119 .. 1 31 [. 0.1 15
TS-N 1/1 145 184 .. 1 40 [] -6.7 82
Fe_dep_repress 1/1 99 205 .. 1 132 [] -70.4 93
hexokinase 1/1 183 209 .. 1 26 [. -1.1 73
OEP 1/1 50 220 .. 1 217 [] -41.4 8.1
UPF0054 1/1 185 280 .. 1 111 [] -48.5 41
Troponin 1/1 135 282 .. 1 190 [] -42.2 50
Tropomyosin 2/2 48 284 .] 1 237 [] 538.5 4e-172
Alignments of top-scoring domains:
Tropomyosin: domain 1 of 2, from 6 to 46: score -6.9, E = 5.6e+03
*->KKiqqteeeldkaeErlekaqreLeeeekkreeAEaEVAsL<-*
KK+q ++ + + a +r+e+a+ +e + ++ E E sL
gi|339944| 6 KKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSL 46
G-alpha: domain 1 of 1, from 26 to 53: score 2.1, E = 14
*->seeekeqakrnkeIekqLkqekkkakre<-*
+++k+++ r+k++e +L +kk k +
gi|339944| 26 EADKKAAEDRSKQLEDELVSLQKKLKGT 53
ACOX: domain 1 of 1, from 42 to 71: score 4.7, E = 1.7
*->ewvkqqsplnetrevkPsYekyLkpmlnra<-*
e v+ q++l +t ++++ Y+++Lk ++++
gi|339944| 42 ELVSLQKKLKGTEDELDKYSEALKDAQEKL 71
KE2: domain 1 of 1, from 33 to 116: score -59.6, E = 73
*->mELPQpqvQaqlaqlQQLQqqLqavivqrQkVEaqLnEnkkAlEELe
+qL+ +v Qk L+ ++ EL+
gi|339944| 33 EDRS---------------KQLEDELVSLQK---KLKGTED---ELD 58
klddDaeVYKlvGnvLVKveKeearkeLeEKlEt.lelRiktlErQeekl
k ++ +K ++e++ eL EK+ t+ e+ + l+r ++ +
gi|339944| 59 KYSEA-----------LKDAQEKL--ELAEKKATdAEADVASLNRRIQLV 95
qekleelqeklqkllkepqag<-*
+e+l qe l+ +l+ +
gi|339944| 96 EEELDRAQERLATALQKLEEA 116
Hanta_nucleocap: domain 1 of 1, from 90 to 119: score 0.1, E = 15
*->msnlkElqeeitaHEqqLviARqKlkdAEka<-*
+++ + ee+ + + L +A qKl +AEka
gi|339944| 90 -RRIQLVEEELDRAQERLATALQKLEEAEKA 119
TS-N: domain 1 of 1, from 145 to 184: score -6.7, E = 82
*->eisaedvklLreqTGagmmdCKKALeeanGDlekAimeLr<-*
ei+ + k + e ++ +++ + L + Dle A+++ +
gi|339944| 145 EIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAE 184
Fe_dep_repress: domain 1 of 1, from 99 to 205: score -70.4, E = 93
*->testEdYLetIYtlsEkekgvvktkdlAerLnVsPssVseMlkkLek
+++++ L t + E+ + + ++ + ++V s +++ +k+e
gi|339944| 99 LDRAQERLATALQKLEEAEKAADESE--RGMKVIESRAQKDEEKMEI 143
mGYVeYkpyrGlvLTdkGrriAraivrrHrLLErFLkdiLGldwEevhke
++ +L + + iA+++ r+++ + r L+ i+ d E++++
gi|339944| 144 QE---------IQLKEA-KHIAEDADRKYEEVARKLV-IIESDLERAEER 182
AcrlEHvlsdelerrLdallrfpeecPhgkpdWIP<-*
A+ ls+ +r+L+ lr + ++
gi|339944| 183 AE-----LSEGQVRQLEEQLRIMD-----QT--LK 205
hexokinase: domain 1 of 1, from 183 to 209: score -1.1, E = 73
*->adllq.aveellddFtvstEtLrevtk<-*
a+l +++v +l++++++ ++tL+++++
gi|339944| 183 AELSEgQVRQLEEQLRIMDQTLKALMA 209
OEP: domain 1 of 1, from 50 to 220: score -41.4, E = 8.1
*->lsellklALknnpdlkaAeaeveaaraqikaaragllPtldlsasys
l++ +++ k ++ lk A++++e a++ ++ a a+ +s++++
gi|339944| 50 LKGTEDELDKYSEALKDAQEKLELAEKKATDAEADV-----ASLNRR 91
rsssssgStatlptragnygdssgfnsnyrsysvglslslPlfdggrnrG
++ +++ + + l +
gi|339944| 92 IQ---------------------LVEEELD------RAQERL----A-T- 108
rvranveaakaqydaakaeyesakleliaeVadaYaqlltaqeklkaake
a ++ +a++ a + e+ ++ e +a ++ ek+++++
gi|339944| 109 ---ALQKLEEAEKAADESERGMKVIESRA---------QKDEEKMEIQEI 146
tleaakeslqlarqrye....aGlgtllDvldAearlysAraeladakyd
+l+ ak + + a + ye+ + ++ + D+ +Ae r ++ + + +++ +
gi|339944| 147 QLKEAKHIAEDADRKYEevarKLVIIESDLERAEERAELSEGQVRQLEEQ 196
leqalaaLaallGggleellklkl<-*
l++ +L+al+ ++++ +k +
gi|339944| 197 LRIMDQTLKALMAAEDKYSQKEDR 220
UPF0054: domain 1 of 1, from 185 to 280: score -48.5, E = 41
*->VsddeIhelNkkfRgkDkPGPTDVLSFPleEldegNLYSkiEiveee
s+ ++l ++R +D L + ++d YS+ E+ +ee
gi|339944| 185 LSEGQVRQLEEQLRIMDQT-----LKALMAAEDK---YSQKEDRYEE 223
epplLGDIV....IcaevaeeqAeeqgHS...lknElalLtiHGvLHLLG
e +L D ++ + ae+ae+ ++++S ++l+ +a+
gi|339944| 224 EIKVLSDKLkeaeTRAEFAERSVTKLEKSiddLEEKVAHAK--------- 264
YDHeeddeeeeMFALqGeslE<-*
ee + +M L +lE
gi|339944| 265 ---EENLSMHQM--LDQTLLE 280
Troponin: domain 1 of 1, from 135 to 282: score -42.2, E = 50
*->KlqlkslmgkekknftvtkkgsqAltfglqkAaeelekeqeekeeEk
++ +++++ ++ +k+a+ + + + +k eE
gi|339944| 135 QKDEEKME---------IQEI-------QLKEAKHIAEDADRKYEEV 165
kraL......aerlieplqlegaeqqaeLqEkckelharidEekleeEkY
r L +++ er e++ + ++ q ++L+E+++ + + ++ + + e+kY
gi|339944| 166 ARKLviiesdLER-AEERAELSEGQVRQLEEQLRIMDQTLKALMAAEDKY 214
DlEkrvekqekeikeLnekvrQvlRnadlrgKfkkpalksekpkvrqsad
++ + e+eik L+ k + a+ r f+ +++ k ++s d
gi|339944| 215 SQKE--DRYEEEIKVLSDKLK----EAETRAEFAERSVT----KLEKSID 254
amlkallgskhkplrrflqidhvsmDkleklraekkekvsLRanlKeVk<
++++ +k+++l+ ++ L++ l e+
gi|339944| 255 DLEEKVAHAKEENLS-------MHQM--------------LDQTLLELN 282
-*
gi|339944| - -
Tropomyosin: domain 2 of 2, from 48 to 284: score 538.5, E = 4e-172
*->KKiqqteeeldkaeErlekaqreLeeeekkreeAEaEVAsLNRRIQL
KK+++te+eldk++E+l++aq++Le++ekk+++AEa+VAsLNRRIQL
gi|339944| 48 KKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQL 94
vEEeLdRAqERLatAlqKLeEAekAADESERgmKViENRAqkDEEKmell
vEEeLdRAqERLatAlqKLeEAekAADESERgmKViE+RAqkDEEKme++
gi|339944| 95 VEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQ 144
EiQLKEAKhiAEEADrKYEEVARKLVivEgDLERAEERAElsEsKivELE
EiQLKEAKhiAE+ADrKYEEVARKLVi+E+DLERAEERAElsE+ +++LE
gi|339944| 145 EIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLE 194
EELrvVgNnLKSLeaseEKysqKEDkYEeeIKvLsdkLKEAEtRAEFAER
E+Lr++++ LK L a+e KysqKED+YEeeIKvLsdkLKEAEtRAEFAER
gi|339944| 195 EQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAER 244
SVqKLeKeiDdLEDeLahaKeeykaiseelDqTLleLnnm<-*
SV+KLeK+iDdLE+++ahaKee+++++++lDqTLleLnnm
gi|339944| 245 SVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM 284
//
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: tem45
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|339944|gb|AAA36771.1| tropomyosin
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Tropomyosin Tropomyosins 523.8 2e-167 2
ACOX Acyl-CoA oxidase 4.7 1.7 1
GA GA module 3.2 18 1
SLH S-layer homology domain containing pr 2.3 46 1
G-alpha G-protein alpha subunit 2.1 14 1
5-FTHF_cyc-lig 5-formyltetrahydrofolate cyclo-ligase 0.4 46 1
Hanta_nucleocap Hantavirus nucleocapsid protein 0.1 15 1
Thymidylate_kin Thymidylate kinase -0.8 70 1
DUF43 Protein of unknown function DUF43 -1.0 70 1
hexokinase Hexokinase -1.1 73 1
FliD Flagellar hook-associated protein 2 -2.1 81 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Tropomyosin 1/2 6 46 .. 1 41 [. -6.9 5.6e+03
G-alpha 1/1 26 53 .. 1 28 [. 2.1 14
ACOX 1/1 42 71 .. 490 519 .] 4.7 1.7
Hanta_nucleocap 1/1 90 119 .. 1 31 [. 0.1 15
5-FTHF_cyc-lig 1/1 90 120 .. 1 31 [. 0.4 46
GA 1/1 137 155 .. 1 19 [. 3.2 18
Thymidylate_kin 1/1 157 169 .. 185 197 .] -0.8 70
hexokinase 1/1 183 209 .. 1 26 [. -1.1 73
FliD 1/1 187 209 .. 704 726 .] -2.1 81
DUF43 1/1 220 239 .. 360 379 .] -1.0 70
SLH 1/1 237 242 .. 38 43 .] 2.3 46
Tropomyosin 2/2 48 284 .] 1 237 [] 538.5 4e-172
Alignments of top-scoring domains:
Tropomyosin: domain 1 of 2, from 6 to 46: score -6.9, E = 5.6e+03
*->KKiqqteeeldkaeErlekaqreLeeeekkreeAEaEVAsL<-*
KK+q ++ + + a +r+e+a+ +e + ++ E E sL
gi|339944| 6 KKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSL 46
G-alpha: domain 1 of 1, from 26 to 53: score 2.1, E = 14
*->seeekeqakrnkeIekqLkqekkkakre<-*
+++k+++ r+k++e +L +kk k +
gi|339944| 26 EADKKAAEDRSKQLEDELVSLQKKLKGT 53
ACOX: domain 1 of 1, from 42 to 71: score 4.7, E = 1.7
*->ewvkqqsplnetrevkPsYekyLkpmlnra<-*
e v+ q++l +t ++++ Y+++Lk ++++
gi|339944| 42 ELVSLQKKLKGTEDELDKYSEALKDAQEKL 71
Hanta_nucleocap: domain 1 of 1, from 90 to 119: score 0.1, E = 15
*->msnlkElqeeitaHEqqLviARqKlkdAEka<-*
+++ + ee+ + + L +A qKl +AEka
gi|339944| 90 -RRIQLVEEELDRAQERLATALQKLEEAEKA 119
5-FTHF_cyc-lig: domain 1 of 1, from 90 to 120: score 0.4, E = 46
*->rRralsreerlqeseelsqllkslpeqqkak<-*
rR +l +ee ++++e+l + l++l e ka+
gi|339944| 90 RRIQLVEEELDRAQERLATALQKLEEAEKAA 120
GA: domain 1 of 1, from 137 to 155: score 3.2, E = 18
*->ekaeatikaaaLaeAKedA<-*
++++ i++++L+eAK A
gi|339944| 137 DEEKMEIQEIQLKEAKHIA 155
Thymidylate_kin: domain 1 of 1, from 157 to 169: score -0.8, E = 70
*->dAsnsieevheeI<-*
dA++++eev +++
gi|339944| 157 DADRKYEEVARKL 169
hexokinase: domain 1 of 1, from 183 to 209: score -1.1, E = 73
*->adllq.aveellddFtvstEtLrevtk<-*
a+l +++v +l++++++ ++tL+++++
gi|339944| 183 AELSEgQVRQLEEQLRIMDQTLKALMA 209
FliD: domain 1 of 1, from 187 to 209: score -2.1, E = 81
*->eqieeRlkkqFtamDdlmgkmnk<-*
e++++ l++q+ +mD++++ + +
gi|339944| 187 EGQVRQLEEQLRIMDQTLKALMA 209
DUF43: domain 1 of 1, from 220 to 239: score -1.0, E = 70
*->rveeEvkkvEdlynDeEgst<-*
r+eeE+k+ d ++++E +
gi|339944| 220 RYEEEIKVLSDKLKEAETRA 239
SLH: domain 1 of 1, from 237 to 242: score 2.3, E = 46
*->TRAEaa<-*
TRAE+a
gi|339944| 237 TRAEFA 242
Tropomyosin: domain 2 of 2, from 48 to 284: score 538.5, E = 4e-172
*->KKiqqteeeldkaeErlekaqreLeeeekkreeAEaEVAsLNRRIQL
KK+++te+eldk++E+l++aq++Le++ekk+++AEa+VAsLNRRIQL
gi|339944| 48 KKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQL 94
vEEeLdRAqERLatAlqKLeEAekAADESERgmKViENRAqkDEEKmell
vEEeLdRAqERLatAlqKLeEAekAADESERgmKViE+RAqkDEEKme++
gi|339944| 95 VEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQ 144
EiQLKEAKhiAEEADrKYEEVARKLVivEgDLERAEERAElsEsKivELE
EiQLKEAKhiAE+ADrKYEEVARKLVi+E+DLERAEERAElsE+ +++LE
gi|339944| 145 EIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLE 194
EELrvVgNnLKSLeaseEKysqKEDkYEeeIKvLsdkLKEAEtRAEFAER
E+Lr++++ LK L a+e KysqKED+YEeeIKvLsdkLKEAEtRAEFAER
gi|339944| 195 EQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAER 244
SVqKLeKeiDdLEDeLahaKeeykaiseelDqTLleLnnm<-*
SV+KLeK+iDdLE+++ahaKee+++++++lDqTLleLnnm
gi|339944| 245 SVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM 284
//
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: tem45
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|339944|gb|AAA36771.1| tropomyosin
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: Thu Jan 18 20:06:12 2001
Sequence file: tem45
----------------------------------------
Sequence gi|339944|gb|AAA36771.1| (284 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
267: NLSM
Total matches: 1
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
76: KKAT
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
123: SER
203: TLK
215: SQK
229: SDK
Total matches: 4
Matching pattern PS00006 CK2_PHOSPHO_SITE:
53: TEDE
79: TDAE
174: SDLE
215: SQKE
237: TRAE
247: TKLE
252: SIDD
277: TLLE
Total matches: 8
Matching pattern PS00029 LEUCINE_ZIPPER:
43: LVSLQKKLKGTEDELDKYSEAL
50: LKGTEDELDKYSEALKDAQEKL
Total matches: 2
Matching pattern PS00326 TROPOMYOSIN:
232: LKEAETRAE
Total matches: 1
Total no of hits in this sequence: 17
========================================
1314 pattern(s) searched in 1 sequence(s), 284 residues.
Total no of hits in all sequences: 17.
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 tem45
***** 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, 284 units
>ER-GOLGI-traffic signal is the MOTIF name
>STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 284 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: tem45
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|339944|gb|AAA36771.1| tropomyosin
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: tem45
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|339944|gb|AAA36771.1| tropomyosin
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|339944|gb|AAA36771.1| tropomyosin
(284 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
INSL Insulinase like Metallo protease domain 25 0.16
UBHYD Ubiquitin C-terminal hydrolase domain 23 0.47
DNASE1 DNASE-1/Sphingomyelinase like domain 22 0.97
SNARE Alpha helical domains which are involved in vesicle fu... 20 3.1
SGTP Small GTPAses 20 3.3
AP2 A plant specific DNA binding domain (Apetala 2 like) 20 4.3
PUM Pumilio repeat RNA binding domain 19 7.1
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 24.5 bits (53), Expect = 0.16
Identities = 13/87 (14%), Positives = 13/87 (14%), Gaps = 3/87 (3%)
Query: 73 LAEKKATDAEADVASLNRRIQ--LVEEELDRAQERLATA-LQKLEEAEKAADESERGMKV 129
Sbjct: 325 FPPENYEKVKKRVFELLKETYENLTDEQVEEAKSRIINSRLFEEERVENDAFDIGYSYTV 384
Query: 130 IESRAQKDEEKMEIQEIQLKEAKHIAE 156
Sbjct: 385 VRDLDFYRFFDKNLSRVRRVDVMRIFE 411
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 23.1 bits (49), Expect = 0.47
Identities = 3/54 (5%), Positives = 3/54 (5%)
Query: 104 ERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAED 157
Sbjct: 307 SEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQEAHLYMQVQIVAEDQFCGH 360
>DNASE1 DNASE-1/Sphingomyelinase like domain
Length = 388
Score = 22.0 bits (46), Expect = 0.97
Identities = 7/43 (16%), Positives = 7/43 (16%), Gaps = 1/43 (2%)
Query: 20 DRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSE 62
Sbjct: 56 DQSEPLDPKELLDECQ-VALQDRPARLHRDFFSLRSESSSQQP 97
Score = 20.9 bits (43), Expect = 1.8
Identities = 3/56 (5%), Positives = 3/56 (5%)
Query: 194 EEQLRIMDQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKL 249
Sbjct: 47 QELLEASQHDQSEPLDPKELLDECQVALQDRPARLHRDFFSLRSESSSQQPRTFRV 102
>SNARE Alpha helical domains which are involved in vesicle fusion
Length = 254
Score = 20.2 bits (42), Expect = 3.1
Identities = 3/103 (2%), Positives = 3/103 (2%), Gaps = 10/103 (9%)
Query: 39 LEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEE 98
Sbjct: 87 LDELQKEFITTYNMMKTNTAVRPYCFIEFDNFIQRTKQRYNNPRSLSTKINL--SDMQME 144
Query: 99 LDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKM 141
Sbjct: 145 IKLR--------PPYQIPMCELGSANGVTSAFSVDCKGAGKIS 179
>SGTP Small GTPAses
Length = 164
Score = 20.1 bits (42), Expect = 3.3
Identities = 9/52 (17%), Positives = 9/52 (17%), Gaps = 4/52 (7%)
Query: 118 KAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKL 169
Sbjct: 114 KKDLDADREVTFLEASRFAQENELMFLETSALTGEDVEE----AFVQCARKI 161
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 19.7 bits (40), Expect = 4.3
Identities = 4/15 (26%), Positives = 4/15 (26%)
Query: 155 AEDADRKYEEVARKL 169
Sbjct: 68 PEMAARAHDVAALSI 82
>PUM Pumilio repeat RNA binding domain
Length = 337
Score = 19.0 bits (39), Expect = 7.1
Identities = 3/18 (16%), Positives = 3/18 (16%)
Query: 84 DVASLNRRIQLVEEELDR 101
Sbjct: 106 DTVDNEVQIDLIIKGFSQ 123
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 7
Number of calls to ALIGN: 8
Length of query: 284
Total length of test sequences: 20182
Effective length of test sequences: 15449.0
Effective search space size: 3677164.0
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|339944|gb|AAA36771.1| tropomyosin
(284 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2494016 [1..267] Single-stranded left-handed beta-helix 28 0.23
gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains 24 2.2
gi|115015 [64..270] Class II aaRS and biotin synthetases 23 4.3
gi|1788726 [121..368] The "swivelling" beta/beta/alpha domain 23 5.0
gi|2147819 [24..211] MHC antigen-recognition domain 23 6.8
gi|2150113 [49..445] Ferritin-like 23 7.2
gi|2209100 [9..467] PLP-dependent transferases 22 7.9
gi|407037 [59..572] Heme-dependent peroxidases 23 8.1
gi|1352423 [103..429] Isocitrate & isopropylmalate dehydroge... 22 8.2
gi|1825699 [8..257] Ribonuclease H-like motif 22 8.6
gi|2804173 [134..260] Biotin carboxylase N-terminal domain-l... 22 8.8
gi|548360 [737..908] Ferredoxin reductase-like, C-terminal N... 22 9.0
gi|1174715 [19..356] Thiamin-binding 22 9.1
>gi|2494016 [1..267] Single-stranded left-handed beta-helix
Length = 267
Score = 27.6 bits (61), Expect = 0.23
Identities = 11/67 (16%), Positives = 11/67 (16%), Gaps = 7/67 (10%)
Query: 190 VRQLEEQLRIM---DQTLKALMAAEDKYSQKEDRYEEEIKVLSDKLKEAETRAE-FAERS 245
Sbjct: 195 YGLNIEGLKRRGFAKEDLHAIRNAYKILYRNGKTLEE---AREEIAQLAADNNNQYVKIF 251
Query: 246 VTKLEKS 252
Sbjct: 252 SDFLENS 258
Score = 22.6 bits (48), Expect = 8.0
Identities = 9/64 (14%), Positives = 9/64 (14%), Gaps = 10/64 (15%)
Query: 90 RRIQLVEEELDRAQ------ERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEI 143
Sbjct: 193 TPYGLNIEGLKRRGFAKEDLHAIRNAYKILYRNGKTLEEAREEIA----QLAADNNNQYV 248
Query: 144 QEIQ 147
Sbjct: 249 KIFS 252
>gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains
Length = 178
Score = 24.2 bits (51), Expect = 2.2
Identities = 5/63 (7%), Positives = 5/63 (7%), Gaps = 4/63 (6%)
Query: 152 KHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIMDQTLKALMAAE 211
Sbjct: 12 GYLTARLAQNPLIN----RVIAVDAIAPSKDMLRRMGRAEFVRADIRNPFIAKVIRNGEV 67
Query: 212 DKY 214
Sbjct: 68 DTV 70
>gi|115015 [64..270] Class II aaRS and biotin synthetases
Length = 207
Score = 23.3 bits (50), Expect = 4.3
Identities = 4/33 (12%), Positives = 4/33 (12%)
Query: 227 VLSDKLKEAETRAEFAERSVTKLEKSIDDLEEK 259
Sbjct: 161 ITLQEAGINLDRNTLAAMLIRELRAALELFEQE 193
>gi|1788726 [121..368] The "swivelling" beta/beta/alpha domain
Length = 248
Score = 23.0 bits (49), Expect = 5.0
Identities = 10/85 (11%), Positives = 10/85 (11%)
Query: 38 QLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEE 97
Sbjct: 13 LLQSDSLDSYRAIPASAQDSTRLEHSLATLAEQLNQQLRERDGESKTILSAHLSLIQDDE 72
Query: 98 ELDRAQERLATALQKLEEAEKAADE 122
Sbjct: 73 FAGNIRRLMTEQHQGLGAAIISNME 97
>gi|2147819 [24..211] MHC antigen-recognition domain
Length = 188
Score = 22.6 bits (48), Expect = 6.8
Identities = 6/50 (12%), Positives = 6/50 (12%), Gaps = 4/50 (8%)
Query: 174 SDLERAEERAELSEGQVRQLEEQLRIM---DQTLKA-LMAAEDKYSQKED 219
Sbjct: 36 SDSMKAEPSVAWLRENPGYFADETQVFTNRMKIFQLSLRNIQQYYNSSGT 85
>gi|2150113 [49..445] Ferritin-like
Length = 397
Score = 22.6 bits (48), Expect = 7.2
Identities = 7/24 (29%), Positives = 7/24 (29%)
Query: 53 TEDELDKYSEALKDAQEKLELAEK 76
Sbjct: 13 VQREKDSGAYSVKAALERSQIYEK 36
>gi|2209100 [9..467] PLP-dependent transferases
Length = 459
Score = 22.5 bits (47), Expect = 7.9
Identities = 4/25 (16%), Positives = 4/25 (16%)
Query: 91 RIQLVEEELDRAQERLATALQKLEE 115
Sbjct: 416 RATYTQTHMDFIIEAFQKVKENAEN 440
>gi|407037 [59..572] Heme-dependent peroxidases
Length = 514
Score = 22.5 bits (48), Expect = 8.1
Identities = 5/17 (29%), Positives = 5/17 (29%), Gaps = 1/17 (5%)
Query: 157 DADRKYEEVARKLVIIE 173
Sbjct: 252 DDERLFQT-SRLILIGE 267
>gi|1352423 [103..429] Isocitrate & isopropylmalate dehydrogenases
Length = 327
Score = 22.5 bits (48), Expect = 8.2
Identities = 10/36 (27%), Positives = 10/36 (27%)
Query: 57 LDKYSEALKDAQEKLELAEKKATDAEADVASLNRRI 92
Sbjct: 2 TQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTI 37
>gi|1825699 [8..257] Ribonuclease H-like motif
Length = 250
Score = 22.4 bits (47), Expect = 8.6
Identities = 8/52 (15%), Positives = 8/52 (15%), Gaps = 5/52 (9%)
Query: 173 ESDLERAEERAELSEGQVRQLEEQ----LRIMDQTLKA-LMAAEDKYSQKED 219
Sbjct: 32 NTIYTTRNDDEVLVEIEPEQLFLQFLRVIKKAYETLPPNAHVDVGLCTQRNS 83
>gi|2804173 [134..260] Biotin carboxylase N-terminal domain-like
Length = 127
Score = 22.1 bits (47), Expect = 8.8
Identities = 7/33 (21%), Positives = 7/33 (21%)
Query: 53 TEDELDKYSEALKDAQEKLELAEKKATDAEADV 85
Sbjct: 42 TPDDLHANSEYIRMADQYVQVPGGTNNNNYANI 74
>gi|548360 [737..908] Ferredoxin reductase-like, C-terminal NADP-linked domain
Length = 172
Score = 22.1 bits (47), Expect = 9.0
Identities = 9/72 (12%), Positives = 9/72 (12%), Gaps = 7/72 (9%)
Query: 62 EALKDAQEKLELAEKKATDAEADV--ASLNRRIQLVEEELDRAQE-----RLATALQKLE 114
Sbjct: 42 AIADEVLDASNPSSPALDPIQIWIVYGNRTEQDILIREELDALSRLKGNLKVWHVLSNCT 101
Query: 115 EAEKAADESERG 126
Sbjct: 102 PENEANWSMGRG 113
>gi|1174715 [19..356] Thiamin-binding
Length = 338
Score = 22.2 bits (47), Expect = 9.1
Identities = 13/77 (16%), Positives = 13/77 (16%), Gaps = 1/77 (1%)
Query: 26 EADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDA-EAD 84
Sbjct: 257 TLINTGKAHGAALGEDEVAATKRILGFDPDKTFAVREDVITHTRGLIARGKEAHERWQLE 316
Query: 85 VASLNRRIQLVEEELDR 101
Sbjct: 317 FEAWAQREPERKALLDR 333
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 13
Number of calls to ALIGN: 14
Length of query: 284
Total length of test sequences: 256703
Effective length of test sequences: 192417.0
Effective search space size: 44127406.3
Initial X dropoff for ALIGN: 25.0 bits
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
calculation of internal repeats with prospero
***** PROSPERO v1.3 Thu Jan 18 20:07:35 2001 *****
Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford
For help see http://www.well.ox.ac.uk/ariadne For usage use -help
using gap penalty 11+1k
using matrix BLOSUM62
printing all alignments with eval < 0.100000
using sequence1 gi|339944|gb|AAA36771.1|
using self-comparison
WARNING: scoring scheme too lax (alpha = 7.380417e-01) for reliable statistics.
Try increasing the gap penalty