analysis of sequence from tem42
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKTQKTSLDEALQWRDSLDKLLQ
NNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITM
KNLVEPSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELIK
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem42gi|3914625|sp|O15539|RGS5_HUMAN
. . . . .
1 MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKT 50
__________HHHHHHHHHHHHHHHEEE______EEEEE___________
. . . . .
51 QKTSLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDY 100
HHHHHHHHHHHHHHHHHHHHHH____HHHHHHHHHHHHHHHHHHHHH___
. . . . .
101 KKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVEPSLSS 150
_______HHHHHHHHHHHHHHHH_____EEEE_________________H
. . .
151 FDMAQKRIHALMEKDSLPRFVRSEFYQELIK 181
HHHHHHHHHHHHHH______HHHHHHHH___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 84.4 %
beta-contents : 0.0 %
coil-contents : 15.6 %
class : alpha
method : 2
alpha-contents : 66.0 %
beta-contents : 0.0 %
coil-contents : 34.0 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-21.13 -0.54 -0.08 -0.16 -4.00 -4.00 -4.00 0.00 -0.37 -10.03 -3.01 -12.00 -12.00 0.00 -12.00 0.00 -83.32
-19.34 -1.08 -0.77 -0.11 -4.00 0.00 0.00 0.00 -0.43 -10.03 -3.01 -12.00 -12.00 0.00 -12.00 0.00 -74.78
ID: tem42gi|3914625|sp|O15539|RGS5_HUMAN AC: xxx Len: 140 1:I 123 Sc: -74.78 Pv: 6.694458e-01 NO_GPI_SITE
GPI: learning from protozoa
-33.03 -0.54 -0.23 0.00 -4.00 -4.00 -4.00 0.00 -0.04 -8.53 -10.55 -12.00 -12.00 0.00 -12.00 0.00 -100.93
-34.69 -1.17 -1.76 -1.62 -4.00 0.00 0.00 0.00 -0.06 -8.53 -10.55 -12.00 -12.00 0.00 -12.00 0.00 -98.38
ID: tem42gi|3914625|sp|O15539|RGS5_HUMAN AC: xxx Len: 140 1:I 123 Sc: -98.38 Pv: 8.400459e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem42gi|391 0.297 174 N 0.112 16 N 0.554 1 N 0.216 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem42gi|391 0.375 17 N 0.339 17 N 0.794 4 N 0.368 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem42gi|391 0.312 113 N 0.169 88 N 0.839 4 N 0.158 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
1-76 MCKGLAALPHSCLERAKEIKIKLGILLQKP
DSVGDLVIPYNEKPEKPAKTQKTSLDEALQ
WRDSLDKLLQNNYGLA
sfksflksefseenlef 77-93
94-181 WIACEDYKKIKSPAKMAEKAKQIYEEFIQT
EAPKEVNIDHFTKDITMKNLVEPSLSSFDM
AQKRIHALMEKDSLPRFVRSEFYQELIK
low complexity regions: SEG 25 3.0 3.3
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
1-181 MCKGLAALPHSCLERAKEIKIKLGILLQKP
DSVGDLVIPYNEKPEKPAKTQKTSLDEALQ
WRDSLDKLLQNNYGLASFKSFLKSEFSEEN
LEFWIACEDYKKIKSPAKMAEKAKQIYEEF
IQTEAPKEVNIDHFTKDITMKNLVEPSLSS
FDMAQKRIHALMEKDSLPRFVRSEFYQELI
K
low complexity regions: SEG 45 3.4 3.75
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
1-181 MCKGLAALPHSCLERAKEIKIKLGILLQKP
DSVGDLVIPYNEKPEKPAKTQKTSLDEALQ
WRDSLDKLLQNNYGLASFKSFLKSEFSEEN
LEFWIACEDYKKIKSPAKMAEKAKQIYEEF
IQTEAPKEVNIDHFTKDITMKNLVEPSLSS
FDMAQKRIHALMEKDSLPRFVRSEFYQELI
K
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
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNekpekpaktqktSLDEALQ
WRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEF
IQTEAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELI
K
1 - 41 MCKGLAALPH SCLERAKEIK IKLGILLQKP DSVGDLVIPY N
42 - 53 ekpekpakt qkt
54 - 181 SLDEALQ WRDSLDKLLQ NNYGLASFKS FLKSEFSEEN LEFWIACEDY KKIKSPAKMA EKA
KQIYEEF IQTEAPKEVN IDHFTKDITM KNLVEPSLSS FDMAQKRIHA LMEKDSLPRF VRS
EFYQELI K
low complexity regions: DUST
>tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKTQKTSLDEALQ
WRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEF
IQTEAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELI
K
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem42gi|3914625|sp|O15539|RGS5_HUMAN
sequence: 140 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MCKGLAALPH SCLERAKEIK IKLGILLQKP DSVGDLVIPY NEKPEKPAKT QKTSLDEALQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
WRDSLDKLLQ NNYGLASFKS FLKSEFSEEN LEFWIACEDY KKIKSPAKMA EKAKQIYEEF
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . |
IQTEAPKEVN IDHFTKDITM
~~~~~~~~~~ ~~~~~~~~~~
---------- ----------
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem42.___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: tem42.___inter___
(1 sequences)
MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKT
QKTSLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDY
KKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVEPSLSS
FDMAQKRIHALMEKDSLPRFVRSEFYQELIK
(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 181
K+R profile +
CYT-EXT prof -0.34
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): -1.00
(NEG-POS)/(NEG+POS): 0.0175
NEG: 29.0000
POS: 28.0000
-> Orientation: N-out
CYT-EXT difference: -0.34
-> Orientation: N-in
----------------------------------------------------------------------
"tem42" 181
************************************
*TOPPREDM with prokaryotic function*
************************************
tem42.___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: tem42.___inter___
(1 sequences)
MCKGLAALPHSCLERAKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKT
QKTSLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDY
KKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVEPSLSS
FDMAQKRIHALMEKDSLPRFVRSEFYQELIK
(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 181
K+R profile +
CYT-EXT prof -0.34
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): -1.00
(NEG-POS)/(NEG+POS): 0.0175
NEG: 29.0000
POS: 28.0000
-> Orientation: N-out
CYT-EXT difference: -0.34
-> Orientation: N-in
----------------------------------------------------------------------
"tem42" 181
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem42.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Nov 2 11:53:55 2000
File: /people/maria/tem42.___saps___
ID tem42gi|3914625|sp|O15539|RGS5_HUMAN
DE REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
number of residues: 181; molecular weight: 20.9 kdal
1 MCKGLAALPH SCLERAKEIK IKLGILLQKP DSVGDLVIPY NEKPEKPAKT QKTSLDEALQ
61 WRDSLDKLLQ NNYGLASFKS FLKSEFSEEN LEFWIACEDY KKIKSPAKMA EKAKQIYEEF
121 IQTEAPKEVN IDHFTKDITM KNLVEPSLSS FDMAQKRIHA LMEKDSLPRF VRSEFYQELI
181 K
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 13( 7.2%); C : 3( 1.7%); D : 10( 5.5%); E : 19(10.5%); F : 9( 5.0%)
G : 4( 2.2%); H : 3( 1.7%); I : 12( 6.6%); K : 24(13.3%); L : 20(11.0%)
M : 5( 2.8%); N : 6( 3.3%); P : 9( 5.0%); Q : 8( 4.4%); R : 5( 2.8%)
S : 14( 7.7%); T : 5( 2.8%); V : 5( 2.8%); W : 2( 1.1%); Y : 5( 2.8%)
KR : 29 ( 16.0%); ED : 29 ( 16.0%); AGP : 26 ( 14.4%);
KRED : 58 ( 32.0%); KR-ED : 0 ( 0.0%); FIKMNY : 61 ( 33.7%);
LVIFM : 51 ( 28.2%); ST : 19 ( 10.5%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 00+0000000 000-+0+-0+ 0+000000+0 -000-00000 0-+0-+00+0 0+000--000
61 0+-00-+000 00000000+0 00+0-00--0 0-00000--0 ++0+000+00 -+0+000--0
121 000-00+-00 0-000+-000 +000-00000 0-000++000 00-+-000+0 0+0-000-00
181 +
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 12/30 or 17/45 or 20/60): none
Negative charge clusters (cmin = 12/30 or 17/45 or 20/60): none
Mixed charge clusters (cmin = 19/30 or 26/45 or 33/60): 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 5 | 5 | 8 | 22 | 9 | 9 | 13 | 10 | 10 | 14 | 6 | 7 |
lmin1 7 | 7 | 10 | 27 | 11 | 11 | 16 | 13 | 13 | 17 | 7 | 9 |
lmin2 8 | 8 | 12 | 30 | 13 | 13 | 18 | 14 | 14 | 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 >= 4: 0
* runs >= 6: 0
0 runs >= 15: 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-1-C-9-C-84-C-84-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-1-C-7-H-1-C-84-C-35-H-25-H-22-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: 8 (Expected range: 1-- 22)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 1 (6-10) 1 (11-20) 4 (>=21) 3
3. Clusters of amino acid multiplets (cmin = 9/30 or 11/45 or 14/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 6 (Expected range: 0-- 17)
2 +plets (f+: 16.0%), 4 -plets (f-: 16.0%)
Total number of charge altplets: 10 (Critical number: 19)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 1 (6-10) 1 (11-20) 1 (>=21) 4
------------------------------
--------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
43- 54 3 K.. 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 7)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9)
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: tem42
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RGS Regulator of G protein signaling domai 169.1 7.3e-47 1
Diphtheria_tox Diphtheria toxin -2.8 91 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Diphtheria_tox 1/1 111 123 .. 266 278 .. -2.8 91
RGS 1/1 64 180 .. 1 143 [] 169.1 7.3e-47
Alignments of top-scoring domains:
Diphtheria_tox: domain 1 of 1, from 111 to 123: score -2.8, E = 91
*->EKAKqYLEEFHqt<-*
EKAKq EEF qt
tem42gi|39 111 EKAKQIYEEFIQT 123
RGS: domain 1 of 1, from 64 to 180: score 169.1, E = 7.3e-47
*->sfeklldkqpiGrllFreFLetefsepkenleFwlaveeyektespa
s++kll ++ +G++ F+ FL++efse enleFw+a+e+y+k +sp
tem42gi|39 64 SLDKLL-QNNYGLASFKSFLKSEFSE--ENLEFWIACEDYKKIKSP- 106
dkrsdkarekesLaaAYGIydeFispeapkfevnldselrestqdnllea
k+ +ka++ Iy+eFi eapk evn+d+ + + t +nl e
tem42gi|39 107 AKMAEKAKQ---------IYEEFIQTEAPK-EVNIDHFTKDITMKNLVE- 145
vededllksLqptkdlFeeaqreiytlMrgDSfprFLeSdyylrfL<-*
p+ F++aq++i+ lM++DS prF +S++y++++
tem42gi|39 146 -----------PSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELI 180
//
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: tem42
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RGS Regulator of G protein signaling domai 169.1 7.3e-47 1
HAT HAT (Half-A-TPR) repeat 1.9 52 1
Diphtheria_tox Diphtheria toxin -2.8 91 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
HAT 1/1 108 121 .. 1 14 [. 1.9 52
Diphtheria_tox 1/1 111 123 .. 266 278 .. -2.8 91
RGS 1/1 64 180 .. 1 143 [] 169.1 7.3e-47
Alignments of top-scoring domains:
HAT: domain 1 of 1, from 108 to 121: score 1.9, E = 52
*->kEidRAReiYeRFv<-*
k ++A++iYe F+
tem42gi|39 108 KMAEKAKQIYEEFI 121
Diphtheria_tox: domain 1 of 1, from 111 to 123: score -2.8, E = 91
*->EKAKqYLEEFHqt<-*
EKAKq EEF qt
tem42gi|39 111 EKAKQIYEEFIQT 123
RGS: domain 1 of 1, from 64 to 180: score 169.1, E = 7.3e-47
*->sfeklldkqpiGrllFreFLetefsepkenleFwlaveeyektespa
s++kll ++ +G++ F+ FL++efse enleFw+a+e+y+k +sp
tem42gi|39 64 SLDKLL-QNNYGLASFKSFLKSEFSE--ENLEFWIACEDYKKIKSP- 106
dkrsdkarekesLaaAYGIydeFispeapkfevnldselrestqdnllea
k+ +ka++ Iy+eFi eapk evn+d+ + + t +nl e
tem42gi|39 107 AKMAEKAKQ---------IYEEFIQTEAPK-EVNIDHFTKDITMKNLVE- 145
vededllksLqptkdlFeeaqreiytlMrgDSfprFLeSdyylrfL<-*
p+ F++aq++i+ lM++DS prF +S++y++++
tem42gi|39 146 -----------PSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELI 180
//
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: tem42
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
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 11:55:30 2000
Sequence file: tem42
----------------------------------------
Sequence tem42gi|3914625|sp|O15539|RGS5_HUMAN (181 residues):
Matching pattern PS00005 PKC_PHOSPHO_SITE:
50: TQK
77: SFK
139: TMK
Total matches: 3
Matching pattern PS00006 CK2_PHOSPHO_SITE:
11: SCLE
32: SVGD
53: TSLD
54: SLDE
149: SSFD
Total matches: 5
Total no of hits in this sequence: 8
========================================
1314 pattern(s) searched in 1 sequence(s), 181 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 tem42
***** 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, 181 units
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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: tem42
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
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: tem42
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN SIGNALING 5 (RGS5)
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]
//
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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= tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN
SIGNALING 5 (RGS5)
(181 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
RGS Regulator of heterotrimeric G protein signalling (G-prot... 143 2e-37
PAS domain (Per-Arnt-Sim Domain (A ligand binding and dimeri... 21 1.1
CYCLIN Cyclin/TFIIB domain 20 1.9
BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 20 3.2
POZ Pox virus Zinc finger domain (Also called BTB domain; a... 19 3.5
FKBP FK506 binding protein (Peptidyl prolyl isomerase) 19 3.8
ANK Ankyrin repeat 19 6.2
14-3-3 14-3-3 protein alpha Helical domain 18 6.7
PDE cyclic NMP phosphodiesterase domain 18 7.4
TBC Probable RAB-type GTPase GTP hydrolysis activating prote... 18 8.6
CATH Cathepsin like protease domain 18 9.8
>RGS Regulator of heterotrimeric G protein signalling (G-protein GTP hydrolysis activating protein)
Length = 117
Score = 143 bits (358), Expect = 2e-37
Identities = 67/117 (57%), Positives = 96/117 (81%)
Query: 64 SLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQT 123
SL+ L+ + GLA+FK+FLKSE+SEEN++FWI+CE+YKKIKSP+K++ KAK+IY EFI
Sbjct: 1 SLENLISHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISV 60
Query: 124 EAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELI 180
+A KEVN+D T++ T +N++EP+++ FD AQK+I LMEKDS RF++S FY +L+
Sbjct: 61 QATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLV 117
>PAS domain (Per-Arnt-Sim Domain (A ligand binding and dimerization domain))
Length = 117
Score = 21.0 bits (44), Expect = 1.1
Identities = 3/27 (11%), Positives = 9/27 (33%)
Query: 111 EKAKQIYEEFIQTEAPKEVNIDHFTKD 137
+ A ++ P + + K+
Sbjct: 47 KAAFADMWFTLKKGEPWSGIVKNRRKN 73
>CYCLIN Cyclin/TFIIB domain
Length = 317
Score = 20.3 bits (42), Expect = 1.9
Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 3/61 (4%)
Query: 99 DYKKIKSPAKMAEKAKQIYEEFIQTE---APKEVNIDHFTKDITMKNLVEPSLSSFDMAQ 155
+ + A++ A + + P + +++T+ E L F
Sbjct: 6 TFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVF 65
Query: 156 K 156
K
Sbjct: 66 K 66
>BRIGHT BRIGHT domain (Alpha helical DNA binding domain)
Length = 172
Score = 19.5 bits (40), Expect = 3.2
Identities = 10/32 (31%), Positives = 16/32 (49%), Gaps = 2/32 (6%)
Query: 150 SFDMAQKRIHALMEKDSLPRFVRSEFYQELIK 181
SF+ K++ L E + P+ R EF +L
Sbjct: 4 SFEEQFKQVRQLYEINDDPK--RKEFLDDLFS 33
>POZ Pox virus Zinc finger domain (Also called BTB domain; a protein-protein interaction domain)
Length = 229
Score = 19.3 bits (39), Expect = 3.5
Identities = 8/66 (12%), Positives = 15/66 (22%), Gaps = 1/66 (1%)
Query: 75 LASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHF 134
L + LK+ FS + + ++ I T I
Sbjct: 46 LTRHDTMLKAMFSGRMEVLTDKEGWILIDRCGKHFGTILNYLRDDTI-TLPQNRQEIKEL 104
Query: 135 TKDITM 140
+
Sbjct: 105 MAEAKY 110
>FKBP FK506 binding protein (Peptidyl prolyl isomerase)
Length = 149
Score = 19.4 bits (40), Expect = 3.8
Identities = 8/51 (15%), Positives = 16/51 (30%)
Query: 89 ENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDIT 139
+L + + ++ P A + +E+N D T D
Sbjct: 76 PDLIQYFSRREFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSITVDFN 126
>ANK Ankyrin repeat
Length = 323
Score = 18.7 bits (38), Expect = 6.2
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 35 DLVIPYNEKPEKPAKTQKTSLDEALQW--RDSLDKLLQN 71
D +I + + +T+ D A+Q R ++ +L
Sbjct: 280 DRLIAAGARTDLKDDADRTAADIAVQLGHRQAIARLAPK 318
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 18.4 bits (37), Expect = 6.7
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 9/89 (10%)
Query: 44 PEKPAKTQKTSLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKI 103
P++ K + DEA+ LD L + +Y S L + +NL W + D +
Sbjct: 190 PDRACYLAKQAFDEAIS---ELDSLSEESYK----DSTLIMQLLRDNLTLWTS--DAEYS 240
Query: 104 KSPAKMAEKAKQIYEEFIQTEAPKEVNID 132
+ A + Q E E D
Sbjct: 241 AAAAGGNTEGAQENAPSNAPEGEAEPKAD 269
>PDE cyclic NMP phosphodiesterase domain
Length = 350
Score = 18.1 bits (36), Expect = 7.4
Identities = 13/41 (31%), Positives = 19/41 (45%), Gaps = 1/41 (2%)
Query: 83 KSEFSEENLEFWIACEDYKKIKSPAKM-AEKAKQIYEEFIQ 122
K E + L F I C D I P + E + ++ +EF Q
Sbjct: 203 KKEDRQMILNFLIKCGDISNIARPWHLNFEWSLRVSDEFFQ 243
>TBC Probable RAB-type GTPase GTP hydrolysis activating protein
Length = 225
Score = 18.2 bits (37), Expect = 8.6
Identities = 4/25 (16%), Positives = 6/25 (24%)
Query: 114 KQIYEEFIQTEAPKEVNIDHFTKDI 138
Q Y ++ P D
Sbjct: 26 TQRYLALLKLGPPSTTIYQKIKNDT 50
>CATH Cathepsin like protease domain
Length = 371
Score = 17.9 bits (36), Expect = 9.8
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 129 VNIDHFTKDITMKNLVEPSLSSFDM 153
V+ ++T D T N+ + M
Sbjct: 208 VDPQYYTGDFTWVNVTRKAYWQIHM 232
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 11
Number of calls to ALIGN: 11
Length of query: 181
Total length of test sequences: 20182
Effective length of test sequences: 16536.0
Effective search space size: 2414358.4
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= tem42gi|3914625|sp|O15539|RGS5_HUMAN REGULATOR OF G-PROTEIN
SIGNALING 5 (RGS5)
(181 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2688670 [455..688] beta-Lactamase/D-ala carboxypeptidase 24 1.4
gi|585004 [165..410] Creatinase/methionine aminopeptidase 24 1.7
gi|475909 [133..273] beta/alpha (TIM)-barrel 23 2.7
gi|2497339 [24..179] 4-helical cytokines 23 3.8
gi|1651961 [243..399] S-adenosylmethionine synthetase. MAT 23 4.0
gi|2407311 [3..100] MHC antigen-recognition domain 22 6.6
gi|2493481 [6..259] Ribonuclease H-like motif 22 6.7
gi|2648434 [141..374] beta/alpha (TIM)-barrel 22 7.1
gi|1351184 [55..290] ATP pyrophoshatases 22 8.0
gi|1420859 [36..611] Periplasmic binding protein-like II 22 8.1
gi|2494278 [153..355] Elongation factor Ts (EF-Ts), dimerisa... 22 8.9
gi|153548 [125..455] beta-Lactamase/D-ala carboxypeptidase 21 9.6
gi|1787711 [41..320] Periplasmic binding protein-like II 22 9.9
>gi|2688670 [455..688] beta-Lactamase/D-ala carboxypeptidase
Length = 234
Score = 24.1 bits (52), Expect = 1.4
Identities = 15/112 (13%), Positives = 31/112 (27%), Gaps = 18/112 (16%)
Query: 37 VIPYNEKPEKPAKTQKTSLDEALQWRDSL--DKLLQNNYGLASFKSFLKS--------EF 86
Y +AL ++ ++L G S S+ E
Sbjct: 42 GEVYAPGNYGGKWRGNVLTRQALALSLNIPALRILD-RLGFDSAISYSSKLLGITDPKEI 100
Query: 87 SE-ENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKD 137
+ + +A SP +MA + + + + E + +D
Sbjct: 101 EKTFPKVYPLALGVIS--VSPIQMA----RAFAILGNSGSEIEPYGIRYIED 146
>gi|585004 [165..410] Creatinase/methionine aminopeptidase
Length = 246
Score = 24.1 bits (52), Expect = 1.7
Identities = 8/77 (10%), Positives = 21/77 (26%), Gaps = 1/77 (1%)
Query: 98 EDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKR 157
E+ IK+ A++A+ E I+ E + + ++ + +
Sbjct: 6 EEIDLIKNGARIADIGGAAVVEAIREGV-PEYEVALHGTEAMVREIARTYPHAELRDTWI 64
Query: 158 IHALMEKDSLPRFVRSE 174
+
Sbjct: 65 WFQSGINTDGAHNWATS 81
>gi|475909 [133..273] beta/alpha (TIM)-barrel
Length = 141
Score = 23.2 bits (50), Expect = 2.7
Identities = 12/84 (14%), Positives = 25/84 (29%), Gaps = 17/84 (20%)
Query: 16 AKEIKIKLGILLQKPDSVGDLVIPYNEKPEKPAK-----TQKTSLDEALQWRDSLDKLLQ 70
K+K+G LQ + Q+ + EA++W L K
Sbjct: 2 WTRFKVKVGADLQD---DMRRCQIIRDMIGPEKTLMMDANQRWDVPEAVEWMSKLAK--- 55
Query: 71 NNYGLASFKSFLKSEFSEENLEFW 94
+ ++ S +++
Sbjct: 56 --FKPLW----IEEPTSPDDILGH 73
>gi|2497339 [24..179] 4-helical cytokines
Length = 156
Score = 23.0 bits (48), Expect = 3.8
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 60 QWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWI 95
Q +D LD +L + L FK +L + E ++F++
Sbjct: 33 QMKDQLDNMLLDGSLLEDFKGYLGCQALSEMIQFYL 68
>gi|1651961 [243..399] S-adenosylmethionine synthetase. MAT
Length = 157
Score = 22.9 bits (49), Expect = 4.0
Identities = 16/62 (25%), Positives = 28/62 (44%), Gaps = 7/62 (11%)
Query: 121 IQTEAPKEVNIDHF-TKDITMKNLVEPSLSSFDMAQKRIHALMEKDSLPRFVR---SEFY 176
I P V ID F T + + L+E L++F++ R +++ +L FY
Sbjct: 71 IGVARPVSVLIDTFGTGKVDEEKLLEVVLANFEL---RPAGIIQSLNLRNLPAERGGRFY 127
Query: 177 QE 178
Q+
Sbjct: 128 QD 129
>gi|2407311 [3..100] MHC antigen-recognition domain
Length = 98
Score = 22.0 bits (47), Expect = 6.6
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 40 YNEKPE-KPAKTQKTSLDEALQWRDSLDKLLQNNYGL 75
Y E+PE +P +QK L+ R ++D ++NYG+
Sbjct: 58 YLEQPEGRPWNSQKDILE---DERAAVDTYCRHNYGV 91
>gi|2493481 [6..259] Ribonuclease H-like motif
Length = 254
Score = 22.1 bits (47), Expect = 6.7
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 12/60 (20%)
Query: 10 HSCLERAKEIKIKLGILLQKPDSVG-----DLVIPYNEKPEKPAKTQKTSLDEALQWRDS 64
L + K K I +VG + ++ +N++ P + A+ W+D
Sbjct: 51 SVQLATMQSAKNKAQIKSNNIAAVGITNQRETIVLWNKENGLP-------VYNAIVWQDQ 103
>gi|2648434 [141..374] beta/alpha (TIM)-barrel
Length = 234
Score = 22.1 bits (47), Expect = 7.1
Identities = 12/100 (12%), Positives = 30/100 (30%), Gaps = 15/100 (15%)
Query: 1 MCKGLAALPHSCLERAK------EIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKTQKTS 54
K + ++ K I L +L D+ I + S
Sbjct: 3 TVKMVEKYAELGIDVVKLRFRRERINEDLEVLKAVAREFSDVKISVDANQAWSYTPPYWS 62
Query: 55 LDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFW 94
+A++ L+ + + L+ ++++E +
Sbjct: 63 RKKAMKVAKELEN-----FEVLW----LEEPLWKDDVEGY 93
>gi|1351184 [55..290] ATP pyrophoshatases
Length = 236
Score = 21.7 bits (46), Expect = 8.0
Identities = 6/67 (8%), Positives = 16/67 (22%), Gaps = 9/67 (13%)
Query: 33 VGDLVIPYNEKPEKPAKTQKTSLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLE 92
+G + + + D S+ + L + F K+
Sbjct: 70 IGGATGKVGDPSGRKTERDVMENDIRQSNVASISQQL---------QRFFKNGLEYYRNR 120
Query: 93 FWIACED 99
+ +
Sbjct: 121 CALTEDV 127
>gi|1420859 [36..611] Periplasmic binding protein-like II
Length = 576
Score = 21.8 bits (46), Expect = 8.1
Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 11/105 (10%)
Query: 67 KLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKM------AEKAKQIYEEF 120
K L+N +F + +S+F E + D K + A EKAK +
Sbjct: 327 KALRNMLVPPTFVTIGESDFGSEVEKEMAKLGDEWKDVNLADAQDGFYNPEKAKAEFA-- 384
Query: 121 IQTEAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKRIHALMEKD 165
+A + + + T + + V+ + ++ + +E
Sbjct: 385 ---KAKEALTAEGVTFPVQLDYPVDQANAATVQEAQSFKQSVEAS 426
>gi|2494278 [153..355] Elongation factor Ts (EF-Ts), dimerisation domain
Length = 203
Score = 21.8 bits (46), Expect = 8.9
Identities = 10/92 (10%), Positives = 35/92 (37%), Gaps = 18/92 (19%)
Query: 101 KKIKSPAKMAEKAKQIYEEFIQTEA-PKEV-------NIDHFTKDITMKN---------- 142
+I+ ++ K+ +E+ ++ + P+++ ++ F D T+ +
Sbjct: 91 SRIELSDEVLAHQKKAFEDELKAQGKPEKIWDKIVPGKMERFIADNTLIDQRLTLLGQFY 150
Query: 143 LVEPSLSSFDMAQKRIHALMEKDSLPRFVRSE 174
+++ + + + + +VR E
Sbjct: 151 VMDDKKTIAQVVADCSKEWNDDLKITEYVRFE 182
>gi|153548 [125..455] beta-Lactamase/D-ala carboxypeptidase
Length = 331
Score = 21.4 bits (45), Expect = 9.6
Identities = 7/67 (10%), Positives = 22/67 (32%), Gaps = 2/67 (2%)
Query: 18 EIKIKLGILLQKPDSVGDLVIPYNEKPEKPAKTQKT--SLDEALQWRDSLDKLLQNNYGL 75
+++ I+ + + + +P + K S + ++ GL
Sbjct: 221 GVRVAPRIVEGIYGNNDKGGLGDLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGL 280
Query: 76 ASFKSFL 82
+ ++F
Sbjct: 281 TTGRAFS 287
>gi|1787711 [41..320] Periplasmic binding protein-like II
Length = 280
Score = 21.5 bits (45), Expect = 9.9
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 1/41 (2%)
Query: 105 SPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVE 145
+K +F + E VN+ M +L+
Sbjct: 5 IERGQTDKQYDWVTQF-EKETGCAVNVKTAATSDEMVSLMT 44
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 13
Number of calls to ALIGN: 13
Length of query: 181
Total length of test sequences: 256703
Effective length of test sequences: 207231.0
Effective search space size: 28848035.5
Initial X dropoff for ALIGN: 25.0 bits