analysis of sequence from tem41
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem41FGENES-M 1.5
MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem41FGENES-M
. . . . .
1 MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG 50
_________EEEEE_______EEEE_________________________
. . . . .
51 HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH 100
EEEEEE___________HHHHHHHHHHHHHH_____EEEE__________
. . . . .
101 SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT 150
___EEE_____EEEEEE__________EEEEEEE___________HHHHH
. . . . .
151 RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN 200
HHH______EEEEEEEEEEE_________EEEEEE______________H
. . .
201 EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV 234
HHHHHH________EEEEE______EEEEEE___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 15.1 %
beta-contents : 40.5 %
coil-contents : 44.4 %
class : mixed
method : 2
alpha-contents : 21.9 %
beta-contents : 33.0 %
coil-contents : 45.1 %
class : mixed
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-23.52 -0.70 -0.96 0.00 -4.00 0.00 0.00 -0.07 -0.30 -4.84 -3.38 -12.00 -12.00 -8.00 -12.00 0.00 -81.78
-15.63 -0.42 -0.04 0.00 -4.00 -4.00 -28.00 0.00 -0.14 -11.10 -3.38 -12.00 0.00 0.00 0.00 0.00 -78.71
ID: tem41FGENES-M AC: xxx Len: 180 1:I 170 Sc: -78.71 Pv: 7.526874e-01 NO_GPI_SITE
GPI: learning from protozoa
-27.59 -6.47 -1.92 -1.49 -4.00 0.00 0.00 -1.02 0.00 -4.14 -11.60 -12.00 -12.00 -8.00 -12.00 0.00 -102.23
-26.38 -6.19 -7.81 -3.11 -4.00 0.00 0.00 0.00 -0.04 -4.49 -11.60 0.00 -12.00 -8.00 -12.00 0.00 -95.61
ID: tem41FGENES-M AC: xxx Len: 180 1:I 154 Sc: -95.61 Pv: 7.959174e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem41FGENES 0.250 173 N 0.206 173 N 0.445 89 N 0.090 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem41FGENES 0.445 170 N 0.439 170 Y 0.858 75 N 0.157 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem41FGENES 0.332 170 N 0.294 91 N 0.851 158 N 0.176 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem41FGENES-M 1.5
1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN
FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYE
DTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKT
RLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDY
NPKERVLYAWDNGHQLTYTLHFVV
low complexity regions: SEG 25 3.0 3.3
>tem41FGENES-M 1.5
1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN
FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYE
DTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKT
RLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDY
NPKERVLYAWDNGHQLTYTLHFVV
low complexity regions: SEG 45 3.4 3.75
>tem41FGENES-M 1.5
1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN
FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYE
DTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKT
RLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDY
NPKERVLYAWDNGHQLTYTLHFVV
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
>tem41FGENES-M 1.5
MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV
1 - 234 MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY
NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD
DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV
AYAFDTHTGT DARPQLPFLN EHAYTTQIDY NPKERVLYAW DNGHQLTYTL HFVV
low complexity regions: DUST
>tem41FGENES-M 1.5
MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY
NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD
DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV
AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem41FGENES-M
sequence: 180 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem41.___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: tem41.___inter___
(1 sequences)
MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG
HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH
SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT
RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN
EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV
(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
1 155 175 0.695 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 154 59
K+R profile +
3.00
CYT-EXT prof 0.85
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -3.00
Tm probability: 0.24
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 6.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 21.0000
POS: 21.0000
-> Orientation: N-in
CYT-EXT difference: 0.85
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment
Loop length 234
K+R profile +
CYT-EXT prof 0.87
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): 0.00
(NEG-POS)/(NEG+POS): 0.0943
NEG: 29.0000
POS: 24.0000
-> Orientation: undecided
CYT-EXT difference: 0.87
-> Orientation: N-out
----------------------------------------------------------------------
"tem41" 234
155 175 #f 0.694792
************************************
*TOPPREDM with prokaryotic function*
************************************
tem41.___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: tem41.___inter___
(1 sequences)
MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG
HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH
SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT
RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN
EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV
(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
1 155 175 0.695 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 154 59
K+R profile +
3.00
CYT-EXT prof 0.85
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -3.00
Tm probability: 0.24
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 6.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 21.0000
POS: 21.0000
-> Orientation: N-in
CYT-EXT difference: 0.85
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment
Loop length 234
K+R profile +
CYT-EXT prof 0.87
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): 0.00
(NEG-POS)/(NEG+POS): 0.0943
NEG: 29.0000
POS: 24.0000
-> Orientation: undecided
CYT-EXT difference: 0.87
-> Orientation: N-out
----------------------------------------------------------------------
"tem41" 234
155 175 #f 0.694792
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem41.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Nov 2 11:56:46 2000
File: /people/maria/tem41.___saps___
ID tem41FGENES-M
DE 1.5
number of residues: 234; molecular weight: 27.6 kdal
1 MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY
61 NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD
121 DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV
181 AYAFDTHTGT DARPQLPFLN EHAYTTQIDY NPKERVLYAW DNGHQLTYTL HFVV
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 15( 6.4%); C : 2( 0.9%); D+ : 19( 8.1%); E : 10( 4.3%); F : 10( 4.3%)
G : 13( 5.6%); H : 7( 3.0%); I : 9( 3.8%); K : 8( 3.4%); L : 18( 7.7%)
M : 2( 0.9%); N : 14( 6.0%); P : 10( 4.3%); Q : 10( 4.3%); R : 16( 6.8%)
S- : 8( 3.4%); T : 16( 6.8%); V : 19( 8.1%); W+ : 8( 3.4%); Y++: 20( 8.5%)
KR : 24 ( 10.3%); ED : 29 ( 12.4%); AGP : 38 ( 16.2%);
KRED : 53 ( 22.6%); KR-ED : -5 ( -2.1%); FIKMNY : 63 ( 26.9%);
LVIFM : 58 ( 24.8%); ST : 24 ( 10.3%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0+-000+--+ 0000000000 000-0+00-0 0+00+00000 +000000000 0000000000
61 0+000+000+ 0-0+0+0000 00000-000- -0000+0+00 0-0-000--0 000000000-
121 -+--000-00 000+0-00-0 000+-000+0 +0++000000 0000000000 -00000-000
181 0000-00000 -0+0000000 -0000000-0 00+-+00000 -000000000 0000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none
Mixed charge clusters (cmin = 15/30 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 | 5 | 7 | 33 | 9 | 9 | 12 | 10 | 11 | 14 | 7 | 8 |
lmin1 6 | 6 | 8 | 40 | 11 | 11 | 15 | 13 | 13 | 17 | 8 | 10 |
lmin2 7 | 7 | 10 | 45 | 12 | 13 | 16 | 14 | 15 | 19 | 9 | 12 |
(Significance level: 0.010000; Minimal displayed length: 6)
(*00) 18(1,0,0); at 25- 43: FRNLENFKQGRWSNMYKLP
(1. quartile) 0+00-00+00+00000+00
Run count statistics:
+ runs >= 3: 0
- runs >= 3: 0
* runs >= 4: 2, at 7; 120;
0 runs >= 22: 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-159-C-3-C-70-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-50-H-48-H-42-H-16-C-3-C-22-H-14-H-21-H-6-H-3-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
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: 15 (Expected range: 2-- 24)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 5 (6-10) 4 (11-20) 1 (>=21) 6
3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 6 (Expected range: 0-- 13)
1 +plets (f+: 10.3%), 5 -plets (f-: 12.4%)
Total number of charge altplets: 6 (Critical number: 15)
2. Histogram of spacin
gs between consecutive charge multiplets:
(1-5) 1 (6-10) 1 (11-20) 2 (>=21) 3
--------------------------------------------------------------------------------
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
There are no periodicities of the prescribed length.
--------------------------------------------------------------------------------
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: tem41
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem41FGENES-M 1.5
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
OLF Olfactomedin-like domain 195.8 6.7e-55 1
TonB_boxC TonB dependent receptor C-terminal region 0.9 73 1
E1_N E1 Protein, N terminal domain 0.4 47 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
E1_N 1/1 18 24 .. 155 161 .] 0.4 47
TonB_boxC 1/1 194 229 .. 1 36 [. 0.9 73
OLF 1/1 1 234 [] 1 293 [] 195.8 6.7e-55
Alignments of top-scoring domains:
E1_N: domain 1 of 1, from 18 to 24: score 0.4, E = 47
*->yGntevE<-*
yGn++vE
tem41FGENE 18 YGNSLVE 24
TonB_boxC: domain 1 of 1, from 194 to 229: score 0.9, E = 73
*->nplsqiPrhtanlgldYdlpegpLegltlgggvryv<-*
+l+++++h+++++ dY++ e L + g +++y+
tem41FGENE 194 PQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYT 229
OLF: domain 1 of 1, from 1 to 234: score 195.8, E = 6.7e-55
*->giLagVskPvllkesekiagksGaWmkDplpnstkTkkrvWvmDgva
mkDp++ +r++v+ +
tem41FGENE 1 -------------------------MKDPAARD----DRIYVTNYY- 17
DGrvlrvvrEYssmsdfldgknkikykLphLiKNKLNNTFalsGTGvVVY
+++ ++ E f +g+ + ykLp+ + GTG VVY
tem41FGENE 18 --YGN-SLVEFRNLENFKQGRWSNMYKLPY----------NWIGTGHVVY 54
nGsLYFnkfeSrsivRyeLeTgvvkkeellpeAgYndrfpYPDHTFEECN
G+ Y+n + +++i++y+L+ + v +llp Y d+ p
tem41FGENE 55 QGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPW--------- 95
ATDRHVWLawgghsDiDLaVDEnGLWvIYAT.....EqnaGkIVisKlnP
w+ghsDiD+aVDE+GLWvIY ++++E+ + IV+s+l+P
tem41FGENE 96 --------KWRGHSDIDFAVDESGLWVIYPAvddrdEAQPEVIVLSRLDP 137
asLev..entWnTeynKrsaanAFiICGvLYvvkSvYEDDDaeslgtkit
L v++e tW T + s +n F +CG+LY v ++ ++
tem41FGENE 138 GDLSVhrETTWKTRLRRNSYGNCFLVCGILYAVDT------YNQQEGQVA 181
YaYdTntgkeklldipfeNkYqyismLdYNPlDrkLYawdNghllkYdvk
Ya+dT tg++ + pf N y + +dYNP++r LYawdNgh+l+Y +
tem41FGENE 182 YAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLH 231
Lee<-*
+
tem41FGENE 232 FVV 234
//
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: tem41
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem41FGENES-M 1.5
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
OLF Olfactomedin-like domain 221.7 1e-62 1
ALA_synthase Aminolevulinic acid synthase domain 1.7 74 1
TonB_boxC TonB dependent receptor C-terminal regio 0.9 73 1
E1_N E1 Protein, N terminal domain 0.4 47 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
E1_N 1/1 18 24 .. 155 161 .] 0.4 47
ALA_synthase 1/1 58 68 .. 1 11 [. 1.7 74
TonB_boxC 1/1 194 229 .. 1 36 [. 0.9 73
OLF 1/1 1 234 [] 26 293 .] 221.7 1e-62
Alignments of top-scoring domains:
E1_N: domain 1 of 1, from 18 to 24: score 0.4, E = 47
*->yGntevE<-*
yGn++vE
tem41FGENE 18 YGNSLVE 24
ALA_synthase: domain 1 of 1, from 58 to 68: score 1.7, E = 74
*->FdYdafFnkel<-*
F+Y+++F+k +
tem41FGENE 58 FYYNRAFTKNI 68
TonB_boxC: domain 1 of 1, from 194 to 229: score 0.9, E = 73
*->nplsqiPrhtanlgldYdlpegpLegltlgggvryv<-*
+l+++++h+++++ dY++ e L + g +++y+
tem41FGENE 194 PQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYT 229
OLF: domain 1 of 1, from 1 to 234: score 221.7, E = 1e-62
*->mkDplpnstkTkkrvWvmDgvaDGrvlrvvrEYssmsdfldgknkik
mkDp++ +r++v+ + +++ ++ E f +g+ +
tem41FGENE 1 MKDPAARD----DRIYVTNYY---YGN-SLVEFRNLENFKQGRWSNM 39
ykLphLiKNKLNNTFalsGTGvVVYnGsLYFnkfeSrsivRyeLeTgvvk
ykLp+ + GTG VVY G+ Y+n + +++i++y+L+ + v
tem41FGENE 40 YKLPY----------NWIGTGHVVYQGAFYYNRAFTKNIIKYDLRQRFVA 79
keellpeAgYndrfpYPDHTFEECNATDRHVWLawgghsDiDLaVDEnGL
+llp Y d+ p w+ghsDiD+aVDE+GL
tem41FGENE 80 SWALLPDVVYEDTTPW-----------------KWRGHSDIDFAVDESGL 112
WvIYAT.....EqnaGkIVisKlnPasLev..entWnTeynKrsaanAFi
WvIY ++++E+ + IV+s+l+P L v++e tW T + s +n F
tem41FGENE 113 WVIYPAvddrdEAQPEVIVLSRLDPGDLSVhrETTWKTRLRRNSYGNCFL 162
ICGvLYvvkSvYEDDDaeslgtkitYaYdTntgkeklldipfeNkYqyis
+CG+LY v ++ ++ Ya+dT tg++ + pf N y +
tem41FGENE 163 VCGILYAVDT------YNQQEGQVAYAFDTHTGTDARPQLPFLNEHAYTT 206
mLdYNPlDrkLYawdNghllkYdvkLee<-*
+dYNP++r LYawdNgh+l+Y + +
tem41FGENE 207 QIDYNPKERVLYAWDNGHQLTYTLHFVV 234
//
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: tem41
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem41FGENES-M 1.5
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 Nov 2 11:58:28 2000
Sequence file: tem41
----------------------------------------
Sequence tem41FGENES-M (234 residues):
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
153: RRNS
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
147: TWK
Total matches: 1
Matching pattern PS00006 CK2_PHOSPHO_SITE:
21: SLVE
101: SDID
133: SRLD
188: TGTD
206: TQID
Total matches: 5
Matching pattern PS00008 MYRISTYL:
165: GILYAV
Total matches: 1
Total no of hits in this sequence: 8
========================================
1314 pattern(s) searched in 1 sequence(s), 234 residues.
Total no of hits in all sequences: 8.
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 tem41
***** 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, 234 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: tem41
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem41FGENES-M 1.5
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: tem41
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem41FGENES-M 1.5
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= tem41FGENES-M 1.5
(234 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
KELCH Kelch repeat- beta propeller like domain 31 0.001
HOG HOG- intein(HINT) like domain 19 6.4
MATH The Meprin associated TRAF homology domain 19 7.4
KH HnRNP K homology domain (A RNA binding domain) 19 8.2
SNARE Alpha helical domains which are involved in vesicle fu... 19 8.8
AP2 A plant specific DNA binding domain (Apetala 2 like) 19 9.5
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 31.2 bits (70), Expect = 0.001
Identities = 10/65 (15%), Positives = 19/65 (28%), Gaps = 7/65 (10%)
Query: 30 NFKQGRWSNMYKLPYNWIGTGHVVYQGAFY----YNRAFTKNIIKYDLRQRFVASWALLP 85
+ + RW+ P W T V + + K++ W +
Sbjct: 196 DQCENRWTVPATCPQPWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETY---QWTKVG 252
Query: 86 DVVYE 90
DV +
Sbjct: 253 DVTAK 257
Score = 24.2 bits (52), Expect = 0.19
Identities = 7/63 (11%), Positives = 13/63 (20%), Gaps = 9/63 (14%)
Query: 30 NFKQGRWSNMYKLPYNWIGTGHVVYQGAFY------YNRAFTKNIIKYDLRQRFVASWAL 83
+ K +P Y +K++ YD W+
Sbjct: 44 DQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWVYDTLHE---EWSK 100
Query: 84 LPD 86
Sbjct: 101 AAP 103
Score = 24.2 bits (52), Expect = 0.19
Identities = 11/49 (22%), Positives = 23/49 (46%)
Query: 5 AARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVV 53
A +++YV Y+G + + + W+++ +PY+ I T V
Sbjct: 264 VASGNKLYVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVS 312
Score = 23.4 bits (50), Expect = 0.32
Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 9/61 (14%)
Query: 8 DDRIYV-------TNYYYGNSLVEFRNLENF--KQGRWSNMYKLPYNWIGTGHVVYQGAF 58
+YV T + V + +E++ +W+ + L V +
Sbjct: 117 KHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPTINKWTMVAPLREGVSNAAVVSAKLKL 176
Query: 59 Y 59
+
Sbjct: 177 F 177
Score = 19.9 bits (41), Expect = 3.2
Identities = 10/95 (10%), Positives = 25/95 (25%), Gaps = 9/95 (9%)
Query: 97 WRGHSDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNS 156
G S+ + L+ + ++ + D + T +
Sbjct: 161 REGVSNAAVVSAKLKLFAFG----GTSVSHDKLPKVQCYDQCENRWTVPAT----CPQPW 212
Query: 157 YGNCFLVC-GILYAVDTYNQQEGQVAYAFDTHTGT 190
V ++ + + AY F++ T
Sbjct: 213 RYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQ 247
>HOG HOG- intein(HINT) like domain
Length = 389
Score = 19.2 bits (39), Expect = 6.4
Identities = 6/21 (28%), Positives = 11/21 (51%), Gaps = 1/21 (4%)
Query: 213 KERVLYAWD-NGHQLTYTLHF 232
+ V +WD + H +LH+
Sbjct: 99 RLLVTESWDEDYHHGQESLHY 119
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 19.0 bits (39), Expect = 7.4
Identities = 4/16 (25%), Positives = 5/16 (31%)
Query: 25 FRNLENFKQGRWSNMY 40
L + G W N
Sbjct: 183 ECRLADELGGLWENSR 198
>KH HnRNP K homology domain (A RNA binding domain)
Length = 92
Score = 18.7 bits (38), Expect = 8.2
Identities = 5/36 (13%), Positives = 14/36 (38%)
Query: 98 RGHSDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLS 133
+ I ++SG +I + Q + + ++
Sbjct: 44 KSGDTIRQLQEKSGCKMILVQDNQSVSDQSKPLRIT 79
>SNARE Alpha helical domains which are involved in vesicle fusion
Length = 254
Score = 18.6 bits (38), Expect = 8.8
Identities = 6/63 (9%), Positives = 15/63 (23%), Gaps = 21/63 (33%)
Query: 163 VCGILYAVDTYNQQEGQVAYAF-----------------DTHTGTDARPQLP-FLNEHAY 204
V ++ + Y +A++F +T + F+
Sbjct: 68 VSYMMLCTENYPN---VLAFSFLDELQKEFITTYNMMKTNTAVRPYCFIEFDNFIQRTKQ 124
Query: 205 TTQ 207
Sbjct: 125 RYN 127
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 18.5 bits (37), Expect = 9.5
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 25 FRNLENFKQGRWSNMYKLP----YNWIGTGHVVYQGAFYYNRAFTK 66
+R + G+W + + P W+GT A ++ A
Sbjct: 36 YRGVRKRNWGKWVSEIREPRKKSRIWLGTFPSPEMAARAHDVAALS 81
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 6
Number of calls to ALIGN: 10
Length of query: 234
Total length of test sequences: 20182
Effective length of test sequences: 17043.0
Effective search space size: 3482620.3
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= tem41FGENES-M 1.5
(234 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1055187 [23..334] Phosphoglycerate mutase-like 25 0.94
gi|136000 [3..610] type I DNA topoisomerase 25 0.94
gi|730933 [142..476] Cysteine proteinases 24 2.0
gi|482303 [240..626] 7-bladed beta-propeller 24 2.8
gi|2408097 [1..121] DNA-binding 3-helical bundle 23 4.7
gi|1827898 [3..132] N-terminal domain of enolase & muconate-... 23 5.8
gi|2114264 [95..597] type I DNA topoisomerase 23 6.1
gi|407037 [59..572] Heme-dependent peroxidases 23 7.6
gi|1360139 [98..407] 7-bladed beta-propeller 22 9.5
gi|549660 [99..278] 7-bladed beta-propeller 22 9.8
>gi|1055187 [23..334] Phosphoglycerate mutase-like
Length = 312
Score = 25.3 bits (55), Expect = 0.94
Identities = 5/47 (10%), Positives = 10/47 (20%), Gaps = 3/47 (6%)
Query: 182 YAFDTHT--GTDARPQLPFLNEHAYT-TQIDYNPKERVLYAWDNGHQ 225
+ NE AY + + V+ +
Sbjct: 125 ENLPALILEKEAGLAVPSWFNEGAYKESLHVFYSALAVMSSVGEYKS 171
>gi|136000 [3..610] type I DNA topoisomerase
Length = 608
Score = 25.3 bits (55), Expect = 0.94
Identities = 15/76 (19%), Positives = 29/76 (37%), Gaps = 14/76 (18%)
Query: 71 YDL-RQRFVASWALLPDVVYEDTT------PWKWRGHSDIDFAVDESGLWVIYPAVDDRD 123
Y+L ++++ PD V+ K+ + + E+G W +RD
Sbjct: 401 YNLIARQYLMQ--FCPDAVFRKCVIELDIAKGKFVAKARF---LAEAG-WRTLLGSKERD 454
Query: 124 EAQPEVIVLSRLDPGD 139
E + + L + GD
Sbjct: 455 E-ENDGTPLPVVAKGD 469
>gi|730933 [142..476] Cysteine proteinases
Length = 335
Score = 24.1 bits (52), Expect = 2.0
Identities = 13/51 (25%), Positives = 20/51 (38%), Gaps = 5/51 (9%)
Query: 2 KDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYK---LPYNWIGT 49
D A R+D YV ++++ + G WS Y P W G+
Sbjct: 64 TDVARRNDPKYVCR--VLSAMINGNDDNGVISGNWSGNYTGGVDPRTWNGS 112
>gi|482303 [240..626] 7-bladed beta-propeller
Length = 387
Score = 23.8 bits (51), Expect = 2.8
Identities = 12/86 (13%), Positives = 23/86 (25%), Gaps = 14/86 (16%)
Query: 8 DDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYN-WIGTGHVVYQGAFYY------ 60
+ +I VT + + W + + + G +
Sbjct: 86 NGQIVVTGGNDAKKTSLY----DSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSWS 141
Query: 61 NRAFTKNIIKYDLRQRFVASWALLPD 86
F KN Y + +W LP+
Sbjct: 142 GGVFEKNGEVYSPSSK---TWTSLPN 164
>gi|2408097 [1..121] DNA-binding 3-helical bundle
Length = 121
Score = 23.0 bits (49), Expect = 4.7
Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 18 YGNSLVEFRNLENFKQGR 35
YG EFR+ ++F+
Sbjct: 95 YGEGAWEFRH-DDFQLHH 111
>gi|1827898 [3..132] N-terminal domain of enolase & muconate-lactonizing enzyme
Length = 130
Score = 22.9 bits (49), Expect = 5.8
Identities = 4/50 (8%), Positives = 6/50 (12%), Gaps = 5/50 (10%)
Query: 59 YYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVD 108
I+ L L +D
Sbjct: 62 QLLDDMAAMIVNEPLAPV-SLEAMLA----KRFCLAGYTGLIRMAAAGID 106
>gi|2114264 [95..597] type I DNA topoisomerase
Length = 503
Score = 22.9 bits (49), Expect = 6.1
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 71 YDL-RQRFVASWALLPDVVYEDTT 93
RQ F+A+ + D Y +T
Sbjct: 300 KGELRQHFIAT--VSHDCKYLQST 321
>gi|407037 [59..572] Heme-dependent peroxidases
Length = 514
Score = 22.5 bits (48), Expect = 7.6
Identities = 6/18 (33%), Positives = 9/18 (49%)
Query: 18 YGNSLVEFRNLENFKQGR 35
YG +L L F+ G+
Sbjct: 162 YGETLDRQHKLRLFQDGK 179
>gi|1360139 [98..407] 7-bladed beta-propeller
Length = 310
Score = 22.2 bits (47), Expect = 9.5
Identities = 10/90 (11%), Positives = 25/90 (27%), Gaps = 20/90 (22%)
Query: 30 NFKQGRWSNMYKLPYNWIGT-------GHVVYQGAFYYNRAFTKNIIKYDLRQRFVASWA 82
+ + + P+N G ++ G + + I ++ + +W
Sbjct: 15 DPLANTLTPIPAPPFNIFCAGHSFLEDGRLLITGGHVDSHVGVPDAIIFNPKSG---AWD 71
Query: 83 LLPD----------VVYEDTTPWKWRGHSD 102
+PD + G +D
Sbjct: 72 NVPDMNDKRWYPNNTTLANGDVLVLSGETD 101
>gi|549660 [99..278] 7-bladed beta-propeller
Length = 180
Score = 22.0 bits (46), Expect = 9.8
Identities = 12/101 (11%), Positives = 30/101 (28%), Gaps = 3/101 (2%)
Query: 92 TTPWKWRGHSD--IDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRE-TTW 148
+ + S A D SGL ++ + + + + ++ +
Sbjct: 46 ISKPQVIIPSLVPNCIAYDPSGLVFALGNPENFEIGLYNLKKIQEGPFLIIKINDATFSQ 105
Query: 149 KTRLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTG 189
+L ++ G LV + ++ GQ +
Sbjct: 106 WNKLEFSNNGKYLLVGSSIGKHLIFDAFTGQQLFELIGTRA 146
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: 234
Total length of test sequences: 256703
Effective length of test sequences: 214185.0
Effective search space size: 42561074.2
Initial X dropoff for ALIGN: 25.0 bits