analysis of sequence from tem13
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY
EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG
TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL
SLLQATDFMSL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> sp|P04216|THY1_HUMAN
. . . . .
1 MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY 50
___HHHHHHHHHHHHH_____EEE__HHHHHHHHHHHHH_________HH
. . . . .
51 EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG 100
HHHHHHHH___EEE__________________HHHHHHHHHEEE______
. . . . .
101 TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL 150
_EEEEEE_____________HHHHHHH______EEE____HHHHHHHHHH
.
151 SLLQATDFMSL 161
HHHHHHH____
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 24.9 %
beta-contents : 53.1 %
coil-contents : 22.1 %
class : mixed
method : 2
alpha-contents : 15.9 %
beta-contents : 54.8 %
coil-contents : 29.4 %
class : mixed
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-5.17 -0.80 -0.02 -0.02 -4.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -10.01
13.72 -0.80 -0.65 -0.06 0.00 0.00 0.00 -4.55 -0.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.51
ID: sp|P04216|THY1_HUMAN AC: xxx Len: 150 1:D 130 Sc: 7.51 Pv: 8.453277e-03 2:N 133 Sc: -10.01 Pv: 2.366370e-02
GPI: learning from protozoa
-14.43 -0.72 0.00 0.00 -4.00 0.00 0.00 -2.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -21.64
-9.81 -0.83 -0.01 0.00 -4.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -14.65
ID: sp|P04216|THY1_HUMAN AC: xxx Len: 150 1:N 133 Sc: -14.65 Pv: 2.426271e-02 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
sp|P04216|T 1.000 20 Y 0.852 20 Y 0.982 151 Y 0.874 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
sp|P04216|T 0.399 156 N 0.469 156 Y 0.964 2 Y 0.319 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
sp|P04216|T 0.517 156 Y 0.496 156 Y 0.971 151 Y 0.347 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
1-133 MNLAISIALLLTVLQVSRGQKVTSLTACLV
DQSLRLDCRHENTSSSPIQYEFSLTRETKK
HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY
LSAFTSKDEGTYTCALHHSGHSPPISSQNV
TVLRDKLVKCEGI
sllaqntswllllllslsll 134-153
154-161 QATDFMSL
low complexity regions: SEG 25 3.0 3.3
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
1-133 MNLAISIALLLTVLQVSRGQKVTSLTACLV
DQSLRLDCRHENTSSSPIQYEFSLTRETKK
HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY
LSAFTSKDEGTYTCALHHSGHSPPISSQNV
TVLRDKLVKCEGI
sllaqntswllllllslsll 134-153
154-161 QATDFMSL
low complexity regions: SEG 45 3.4 3.75
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
1-161 MNLAISIALLLTVLQVSRGQKVTSLTACLV
DQSLRLDCRHENTSSSPIQYEFSLTRETKK
HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY
LSAFTSKDEGTYTCALHHSGHSPPISSQNV
TVLRDKLVKCEGISLLAQNTSWLLLLLLSL
SLLQATDFMSL
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
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQYEFSLTRETKK
HVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNV
TVLRDKLVKCEGISLLAQNTSWllllllslslLQATDFMSL
1 - 142 MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK
HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV
TVLRDKLVKC EGISLLAQNT SW
143 - 152 llllllsl sl
153 - 161 LQATDFMS L
low complexity regions: DUST
>sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQYEFSLTRETKK
HVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNV
TVLRDKLVKCEGISLLAQNTSWLLLLLLSLSLLQATDFMSL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for sp|P04216|THY1_HUMAN
sequence: 150 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . |
TVLRDKLVKC EGISLLAQNT SWLLLLLLSL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem13.___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: tem13.___inter___
(1 sequences)
MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY
EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG
TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL
SLLQATDFMSL
(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 1 21 0.799 Putative
2 136 156 1.433 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 0 114 5
K+R profile 1.00 0.00
+
CYT-EXT prof - -
0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.50
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): 1007125513474669412352.0000
NEG: 0.0000
POS: 0.0000
-> Orientation: N-out
CYT-EXT difference: -0.55
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2
Loop length 135 5
K+R profile +
0.00
CYT-EXT prof 0.57
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): -0.2000
NEG: 10.0000
POS: 15.0000
-> Orientation: N-in
CYT-EXT difference: 0.57
-> Orientation: N-out
----------------------------------------------------------------------
"tem13" 161
1 21 #f 0.798958
136 156 #t 1.43333
************************************
*TOPPREDM with prokaryotic function*
************************************
tem13.___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: tem13.___inter___
(1 sequences)
MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY
EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG
TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL
SLLQATDFMSL
(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 1 21 0.799 Putative
2 136 156 1.433 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 0 114 5
K+R profile 1.00 0.00
+
CYT-EXT prof - -
0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.50
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -2.00
(NEG-POS)/(NEG+POS): 1007125513474669412352.0000
NEG: 0.0000
POS: 0.0000
-> Orientation: N-out
CYT-EXT difference: -0.55
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2
Loop length 135 5
K+R profile +
0.00
CYT-EXT prof 0.57
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): -0.2000
NEG: 10.0000
POS: 15.0000
-> Orientation: N-in
CYT-EXT difference: 0.57
-> Orientation: N-out
----------------------------------------------------------------------
"tem13" 161
1 21 #f 0.798958
136 156 #t 1.43333
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem13.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 14:32:39 2000
File: /people/maria/tem13.___saps___
ID sp|P04216|THY1_HUMAN
DE THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
number of residues: 161; molecular weight: 18.0 kdal
1 MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK
61 HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV
121 TVLRDKLVKC EGISLLAQNT SWLLLLLLSL SLLQATDFMS L
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 7( 4.3%); C : 4( 2.5%); D : 5( 3.1%); E : 6( 3.7%); F : 5( 3.1%)
G : 6( 3.7%); H : 7( 4.3%); I : 5( 3.1%); K : 8( 5.0%); L : 28(17.4%)
M : 3( 1.9%); N : 5( 3.1%); P : 4( 2.5%); Q : 7( 4.3%); R : 7( 4.3%)
S : 21(13.0%); T : 16( 9.9%); V : 11( 6.8%); W : 1( 0.6%); Y : 5( 3.1%)
KR : 15 ( 9.3%); ED : 11 ( 6.8%); AGP : 17 ( 10.6%);
KRED : 26 ( 16.1%); KR-ED : 4 ( 2.5%); FIKMNY : 31 ( 19.3%);
LVIFM : 52 ( 32.3%); ST : 37 ( 23.0%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0000000000 0000000+00 +000000000 -000+0-0+0 -000000000 -0000+-0++
61 0000000000 -000+0+000 00+000+000 000000+--0 0000000000 0000000000
121 000+-+00+0 -000000000 0000000000 000000-000 0
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 11/45 or 14/60): none
Negative charge clusters (cmin = 7/30 or 9/45 or 11/60): none
Mixed charge clusters (cmin = 12/30 or 17/45 or 21/60): 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 | 5 | 45 | 8 | 8 | 10 | 10 | 9 | 13 | 7 | 9 |
lmin1 5 | 5 | 7 | 54 | 10 | 9 | 13 | 13 | 11 | 15 | 9 | 11 |
lmin2 6 | 6 | 8 | 60 | 12 | 11 | 14 | 14 | 13 | 17 | 10 | 12 |
(Significance level: 0.010000; Minimal displayed length: 6)
There are no charge runs or patterns exceeding the given minimal lengths.
Run count statistics:
+ runs >= 3: 0
- runs >= 3: 0
* runs >= 3: 2, at 97; 124;
0 runs >= 30: 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-27-C-9-C-65-C-25-C-31-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-27-C-9-C-1-H-20-H-10-H-12-H-18-C-2-H-H-2-H-18-C-31-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 80- 83] FTSK
[ 94- 97] FTSK
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: 9 (Expected range: 1-- 22)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 3 (6-10) 3 (11-20) 2 (>=21) 2
3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 16/60): none
4. Long amino acid multiplets (>= 5; Letter/Length/Position):
L/6/143
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 2 (Expected range: 0-- 7)
1 +plets (f+: 9.3%), 1 -plets (f-: 6.8%)
Total number of charge altplets: 3 (Critica
l number: 8)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 0 (11-20) 0 (>=21) 3
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
143- 148 1 L 6 6 ! 0
144- 153 2 L. 5 5 ! 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 5)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8)
Location Period Element Copies Core Errors
1- 14 2 i0 7 7 /0/2/
143- 148 1 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: tem13
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ig Immunoglobulin domain 26.8 9.5e-07 1
Ribosomal_S19 Ribosomal protein S19 6.8 1.4 1
phytochrome Phytochrome region -1.4 83 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Ribosomal_S19 1/1 51 61 .. 71 81 .] 6.8 1.4
ig 1/1 31 106 .. 1 45 [] 26.8 9.5e-07
phytochrome 1/1 127 144 .. 30 47 .. -1.4 83
Alignments of top-scoring domains:
Ribosomal_S19: domain 1 of 1, from 51 to 61: score 6.8, E = 1.4
*->EFapTRkfrgH<-*
EF++TR +++H
sp|P04216| 51 EFSLTRETKKH 61
ig: domain 1 of 1, from 31 to 106: score 26.8, E = 9.5e-07
*->GesvtLtCsvs..gfgpp.p.vtWlrngk..................
+s++L C+ +++++p +++++++r+ k++ ++ + ++++ +++
sp|P04216| 31 DQSLRLDCRHEntSSSPIqYeFSLTRETKkhvlfgtvgvpehtyrsr 77
.........lslti.svtpeDsgGtYtCvv<-*
++ +++ + +l ++ +t+ D+ GtYtC+
sp|P04216| 78 tnftskyhmKVLYLsAFTSKDE-GTYTCAL 106
phytochrome: domain 1 of 1, from 127 to 144: score -1.4, E = 83
*->LvkCDGAALyYkkkvwrl<-*
LvkC+G L+ ++ w+l
sp|P04216| 127 LVKCEGISLLAQNTSWLL 144
//
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: tem13
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ig Immunoglobulin domain 26.8 9.5e-07 1
Ribosomal_S19 Ribosomal protein S19 6.8 1.4 1
DUF138 Domain of unknown function DUF138 0.2 73 1
phytochrome Phytochrome region -1.4 83 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Ribosomal_S19 1/1 51 61 .. 71 81 .] 6.8 1.4
DUF138 1/1 74 99 .. 1 29 [. 0.2 73
ig 1/1 31 106 .. 1 45 [] 26.8 9.5e-07
phytochrome 1/1 127 144 .. 30 47 .. -1.4 83
Alignments of top-scoring domains:
Ribosomal_S19: domain 1 of 1, from 51 to 61: score 6.8, E = 1.4
*->EFapTRkfrgH<-*
EF++TR +++H
sp|P04216| 51 EFSLTRETKKH 61
DUF138: domain 1 of 1, from 74 to 99: score 0.2, E = 73
*->wskklkski.erylyheevslLaAYvyedq<-*
+ s+++++++yh +v L+A+ ++d+
sp|P04216| 74 YR----SRTnFTSKYHMKVLYLSAFTSKDE 99
ig: domain 1 of 1, from 31 to 106: score 26.8, E = 9.5e-07
*->GesvtLtCsvs..gfgpp.p.vtWlrngk..................
+s++L C+ +++++p +++++++r+ k++ ++ + ++++ +++
sp|P04216| 31 DQSLRLDCRHEntSSSPIqYeFSLTRETKkhvlfgtvgvpehtyrsr 77
.........lslti.svtpeDsgGtYtCvv<-*
++ +++ + +l ++ +t+ D+ GtYtC+
sp|P04216| 78 tnftskyhmKVLYLsAFTSKDE-GTYTCAL 106
phytochrome: domain 1 of 1, from 127 to 144: score -1.4, E = 83
*->LvkCDGAALyYkkkvwrl<-*
LvkC+G L+ ++ w+l
sp|P04216| 127 LVKCEGISLLAQNTSWLL 144
//
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: tem13
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
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 14:34:32 2000
Sequence file: tem13
----------------------------------------
Sequence sp|P04216|THY1_HUMAN (161 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
42: NTSS
79: NFTS
119: NVTV
139: NTSW
Total matches: 4
Matching pattern PS00005 PKC_PHOSPHO_SITE:
33: SLR
58: TKK
73: TYR
81: TSK
95: TSK
Total matches: 5
Matching pattern PS00006 CK2_PHOSPHO_SITE:
95: TSKD
96: SKDE
Total matches: 2
Matching pattern PS00008 MYRISTYL:
19: GQKVTS
100: GTYTCA
Total matches: 2
Total no of hits in this sequence: 13
========================================
1314 pattern(s) searched in 1 sequence(s), 161 residues.
Total no of hits in all sequences: 13.
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 tem13
***** 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, 161 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: tem13
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
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: tem13
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
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= sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR
(THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
(161 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
MATH The Meprin associated TRAF homology domain 22 0.55
CYCL cyclophilin like peptidyl prolyl isomerases 22 0.68
HISDAC Histone deacetylase domain 21 1.2
DHHC Novel zinc finger domain with DHHC signature 19 5.3
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 19 5.4
PAP Papain/bleomycin hydrolase like domain 18 5.6
PBD Rho binding domain 19 5.8
INSL Insulinase like Metallo protease domain 18 7.2
UBHYD Ubiquitin C-terminal hydrolase domain 18 7.6
ARR Arrestin domain 18 8.6
UBC Ubiquitin Conjugating enzyme domain 18 9.0
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 18 9.1
HOMEO Homeodomain (HTH DNa binding domain) 18 10.0
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 21.8 bits (46), Expect = 0.55
Identities = 4/23 (17%), Positives = 9/23 (38%)
Query: 33 SLRLDCRHENTSSSPIQYEFSLT 55
L L + S ++ +F +
Sbjct: 83 YLSLYLLLVSCPKSEVRAKFKFS 105
>CYCL cyclophilin like peptidyl prolyl isomerases
Length = 165
Score = 21.7 bits (46), Expect = 0.68
Identities = 13/30 (43%), Positives = 18/30 (59%), Gaps = 7/30 (23%)
Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67
NT+ S Q+ F T +T+ KHV+FG V
Sbjct: 106 NTNGS--QF-FICTAKTEWLDGKHVVFGKV 132
>HISDAC Histone deacetylase domain
Length = 433
Score = 20.6 bits (43), Expect = 1.2
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 12/43 (27%)
Query: 83 KYHMKVLYL-----------SAFTSKDEGTYTCALHHSGHSPP 114
+YH +VLY+ AF + D TC+ H G P
Sbjct: 175 RYHPRVLYIDIDVHHGDGVEEAFYTTDR-VMTCSFHKYGEFFP 216
Score = 18.7 bits (38), Expect = 4.6
Identities = 5/40 (12%), Positives = 14/40 (34%), Gaps = 6/40 (15%)
Query: 64 FGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYT 103
G + + + N+ + + ++ + G YT
Sbjct: 281 LGCFNLSMEGHANCVNYVKSFGIPMMVVG------GGGYT 314
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 18.5 bits (37), Expect = 5.3
Identities = 7/24 (29%), Positives = 12/24 (49%)
Query: 95 TSKDEGTYTCALHHSGHSPPISSQ 118
T+ ++ +T SG SP + Q
Sbjct: 14 TAPEKSVWTAPAQPSGPSPELQGQ 37
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 18.6 bits (38), Expect = 5.4
Identities = 9/34 (26%), Positives = 12/34 (34%), Gaps = 3/34 (8%)
Query: 79 NFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHS 112
N + Y LS + S G T + SG
Sbjct: 129 NVPAMYVAIQAVLSLYAS---GRTTGIVLDSGDG 159
>PAP Papain/bleomycin hydrolase like domain
Length = 376
Score = 18.4 bits (37), Expect = 5.6
Identities = 3/22 (13%), Positives = 9/22 (40%)
Query: 100 GTYTCALHHSGHSPPISSQNVT 121
G+ TC + + + ++
Sbjct: 348 GSNTCGITKFPLTARVQKPDMK 369
>PBD Rho binding domain
Length = 61
Score = 18.6 bits (37), Expect = 5.8
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 76 SRTNFTSKYHM 86
S TNFT K H+
Sbjct: 3 SPTNFTHKVHV 13
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 18.3 bits (37), Expect = 7.2
Identities = 6/14 (42%), Positives = 8/14 (56%)
Query: 91 LSAFTSKDEGTYTC 104
++A TSKD Y
Sbjct: 94 INAGTSKDYTYYHV 107
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 18.0 bits (36), Expect = 7.6
Identities = 21/64 (32%), Positives = 33/64 (50%), Gaps = 12/64 (18%)
Query: 83 KYHMKVLYLSAFTSKDEGTYTCALHHSGH-SPPISSQNVTVLRDKL-VKCEGISLLAQNT 140
K H +L+L + K T +L++ GH PIS + +RD L V C+ + Q+T
Sbjct: 463 KDHDVMLFLKMYDPK-----TRSLNYCGHIYTPISCK----IRDLLPVMCDRAGFI-QDT 512
Query: 141 SWLL 144
S +L
Sbjct: 513 SLIL 516
>ARR Arrestin domain
Length = 454
Score = 17.9 bits (36), Expect = 8.6
Identities = 6/14 (42%), Positives = 8/14 (56%)
Query: 44 SSSPIQYEFSLTRE 57
SS + E SL +E
Sbjct: 224 SSGLLHMEVSLDKE 237
>UBC Ubiquitin Conjugating enzyme domain
Length = 144
Score = 17.8 bits (36), Expect = 9.0
Identities = 4/28 (14%), Positives = 8/28 (28%), Gaps = 2/28 (7%)
Query: 62 VLFGTVGVPEH--TYRSRTNFTSKYHMK 87
+ G G P +R + +
Sbjct: 33 TIEGPEGTPYAGGLFRMKLLLGKDFPAS 60
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 18.0 bits (36), Expect = 9.1
Identities = 4/46 (8%), Positives = 9/46 (18%), Gaps = 1/46 (2%)
Query: 20 QKVTSLTACLV-DQSLRLDCRHENTSSSPIQYEFSLTRETKKHVLF 64
V L + RL + + + +
Sbjct: 46 AAVKQRIQRLCYREEKRLAVSSLAKWLGQLHKQRLRAPKNPPVAIC 91
>HOMEO Homeodomain (HTH DNa binding domain)
Length = 65
Score = 17.8 bits (36), Expect = 10.0
Identities = 2/9 (22%), Positives = 4/9 (44%)
Query: 75 RSRTNFTSK 83
+ R F+
Sbjct: 7 KRRVLFSQA 15
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 13
Number of calls to ALIGN: 14
Length of query: 161
Total length of test sequences: 20182
Effective length of test sequences: 16536.0
Effective search space size: 2086753.0
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= sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR
(THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human).
(161 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1515350 [4..198] Cyclophilin 23 2.5
gi|1070649 [50..283] 4-bladed beta-propeller 23 3.1
gi|1166598 [22..183] alpha/beta-Hydrolases 23 3.3
gi|1083654 [20..356] 6-bladed beta-propeller 22 5.5
gi|2088814 [406..557] Cyclophilin 22 6.2
gi|435746 [11..204] 4-helical cytokines 22 7.5
gi|2136468 [19..195] Lipocalins 21 8.6
gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains 22 9.2
gi|1223762 [9..227] Galactose-binding domain-like 21 9.7
gi|1780973 [457..589] Ribonuclease H-like motif 21 9.8
>gi|1515350 [4..198] Cyclophilin
Length = 195
Score = 23.3 bits (50), Expect = 2.5
Identities = 11/30 (36%), Positives = 15/30 (49%), Gaps = 7/30 (23%)
Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67
NT++S Q+ F T KH +FG V
Sbjct: 135 NTNNS--QF-FITTYAAPHLNGKHSIFGQV 161
>gi|1070649 [50..283] 4-bladed beta-propeller
Length = 234
Score = 22.9 bits (49), Expect = 3.1
Identities = 17/72 (23%), Positives = 23/72 (31%), Gaps = 12/72 (16%)
Query: 49 QYEFS-----LTRETKKHVLFGTVGVPEHTYRSR-TNFTSKYHMKV-----LYLSAFTSK 97
F+ + V + P +RS N T H L LSA S
Sbjct: 158 FLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRSSHRNSTQHGHESTRCDPDLVLSAMVSD 217
Query: 98 DEG-TYTCALHH 108
+ G TY + H
Sbjct: 218 NHGATYVFSGSH 229
>gi|1166598 [22..183] alpha/beta-Hydrolases
Length = 162
Score = 22.9 bits (49), Expect = 3.3
Identities = 7/76 (9%), Positives = 20/76 (26%), Gaps = 8/76 (10%)
Query: 62 VLFGTVGVPEHTYRSRTNFTSKYHMKVL----YLSAFTSKDEGTYTCALHHSGHSPPISS 117
+ + T+ +++ ++ F + T A H++
Sbjct: 67 YAWSGPRSGDETFVKMLKEHVFEQYRIVRDGDFVPDFPLRISQTLPAAHHNTFEIYYPK- 125
Query: 118 QNVTVLRDKLVKCEGI 133
+ D C+
Sbjct: 126 ---HMTTDNYRICDQA 138
>gi|1083654 [20..356] 6-bladed beta-propeller
Length = 337
Score = 22.2 bits (47), Expect = 5.5
Identities = 11/46 (23%), Positives = 15/46 (31%), Gaps = 4/46 (8%)
Query: 55 TRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG 100
++TK LF R + + V L TS D G
Sbjct: 73 DKQTKTLFLFFIA----VPGRVSEQHQLQTRVNVTRLCRVTSTDYG 114
>gi|2088814 [406..557] Cyclophilin
Length = 152
Score = 22.1 bits (47), Expect = 6.2
Identities = 5/30 (16%), Positives = 9/30 (29%), Gaps = 7/30 (23%)
Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67
SS + + L ++ G V
Sbjct: 93 TVFSS--LF-YVLLDKSGPSVVDGCPIGDV 119
>gi|435746 [11..204] 4-helical cytokines
Length = 194
Score = 21.8 bits (46), Expect = 7.5
Identities = 7/22 (31%), Positives = 10/22 (44%)
Query: 137 AQNTSWLLLLLLSLSLLQATDF 158
A LL L +SLL++
Sbjct: 60 ALTLQQEQLLSLIMSLLRSWTP 81
>gi|2136468 [19..195] Lipocalins
Length = 177
Score = 21.5 bits (45), Expect = 8.6
Identities = 3/53 (5%), Positives = 14/53 (25%), Gaps = 3/53 (5%)
Query: 73 TYRSRTNFTSKYHMKVLYLSAFTSKDE--GTYTCALHHSGHSPPISSQNVTVL 123
T + R + + + + + E + + + ++
Sbjct: 56 TAKGRVRLLNNWDVCA-DMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWII 107
>gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains
Length = 196
Score = 21.5 bits (44), Expect = 9.2
Identities = 5/73 (6%), Positives = 14/73 (18%)
Query: 36 LDCRHENTSSSPIQYEFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFT 95
L C ++ ++ + + S + V ++
Sbjct: 30 LACLPDDPRREDAAAAMKQAGARSVELIDFDALDTDSHPKMIEAAFSGGDVDVAIVAFGL 89
Query: 96 SKDEGTYTCALHH 108
D
Sbjct: 90 LGDAEELWQNQRK 102
>gi|1223762 [9..227] Galactose-binding domain-like
Length = 219
Score = 21.3 bits (44), Expect = 9.7
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 13/64 (20%)
Query: 72 HTYRSRTNFTS--KYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNVTVLRDKLVK 129
H YR TS K H L F+ D LHH +P + +Q V +++
Sbjct: 95 HYYRRPAFSTSDDKQH-----LGMFSEADYNPVGSYLHHFDLTPALRNQRV------IIR 143
Query: 130 CEGI 133
EG+
Sbjct: 144 FEGV 147
>gi|1780973 [457..589] Ribonuclease H-like motif
Length = 133
Score = 21.4 bits (45), Expect = 9.8
Identities = 6/26 (23%), Positives = 10/26 (38%), Gaps = 3/26 (11%)
Query: 108 HSGHSPPISSQNVTVLRDKLVKCEGI 133
H+ P++ N D LV +
Sbjct: 111 HTNLPGPLTKANEQA--DLLVS-SAL 133
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: 161
Total length of test sequences: 256703
Effective length of test sequences: 207231.0
Effective search space size: 24736309.4
Initial X dropoff for ALIGN: 25.0 bits