analysis of sequence from tem6
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
MAPAAWLRSAAARALLPPMLLLLLQPPPLLARALPPDVHHLHAERRGPQPWHAALPSSPAPAPATQEAPR
PASSLRPPRCGVPDPSDGLSARNRQKRFVLSGGRWEKTDLTYRILRFPWQLVQEQVRQTMAEALKVWSDV
TPLTFTEVHEGRADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGDDQGTDLL
QVAAHEFGHVLGLQHTTAAKALMSAFYTFRYPLSLSPDDCRGVQHLYGQPWPTVTSRTPALGPQAGIDTN
EIAPLEPDAPPDACEASFDAVSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDA
QGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDS
PVPRRATDWRGVPSEIDAAFQDADGYAYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGCAEPANTFL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem6gi|456257|emb|CAA40918.1|
. . . . .
1 MAPAAWLRSAAARALLPPMLLLLLQPPPLLARALPPDVHHLHAERRGPQP 50
___HHHHHHHHHHHHH__HHHHH___________________________
. . . . .
51 WHAALPSSPAPAPATQEAPRPASSLRPPRCGVPDPSDGLSARNRQKRFVL 100
_____________________________________________EEEEE
. . . . .
101 SGGRWEKTDLTYRILRFPWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHE 150
________________HHHHHHHHHHHHHHHHHHHHHH____EEEE____
. . . . .
151 GRADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWT 200
____EEEEHHHHH___________________________EEE_____EE
. . . . .
201 IGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYTFRYPLSLSPDDC 250
E_____HHHHHHHHHHH__EEE_HHHHHHHHHHHHHHHH___________
. . . . .
251 RGVQHLYGQPWPTVTSRTPALGPQAGIDTNEIAPLEPDAPPDACEASFDA 300
__________________________________________HHHHHHHH
. . . . .
301 VSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDA 350
_______EEEE____EEEE___________HHHHHHH_____________
. . . . .
351 QGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKI 400
___EEE____EEEEE______________EEEEEHHHHHHHH______EE
. . . . .
401 YFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGYAYFL 450
EEE___EEEEE______________________HHHHHHHHH____EEEE
. . .
451 RGRLYWKFDPVKVKALEGFPRLVGPDFFGCAEPANTFL 488
E__EEE_____EEEE_______________________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 43.7 %
beta-contents : 0.0 %
coil-contents : 56.3 %
class : alpha
method : 2
alpha-contents : 17.9 %
beta-contents : 0.0 %
coil-contents : 82.1 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-26.83 -0.62 -0.01 -0.03 -4.00 0.00 -4.00 -0.08 -0.41 -11.23 -3.34 -12.00 -12.00 -4.00 -12.00 0.00 -90.55
-14.80 -1.18 -1.71 -2.96 -4.00 0.00 0.00 0.00 -0.46 -10.92 -3.34 -12.00 -12.00 -4.00 -12.00 0.00 -79.36
ID: tem6gi|456257|emb|CAA40918.1| AC: xxx Len: 420 1:I 389 Sc: -79.36 Pv: 7.658634e-01 NO_GPI_SITE
GPI: learning from protozoa
-18.22 -3.81 -3.55 -7.98 -4.00 0.00 -8.00 0.00 -3.29 -9.30 -11.47 -12.00 -12.00 0.00 -12.00 0.00 -105.62
-25.17 -4.03 -0.65 0.00 -4.00 0.00 -12.00 0.00 -1.25 -9.30 -11.47 -12.00 -12.00 0.00 -12.00 0.00 -103.87
ID: tem6gi|456257|emb|CAA40918.1| AC: xxx Len: 420 1:I 406 Sc: -103.87 Pv: 9.120710e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem6gi|4562 0.895 32 Y 0.791 32 Y 0.979 11 Y 0.865 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem6gi|4562 0.656 32 Y 0.630 32 Y 0.987 9 Y 0.754 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem6gi|4562 0.563 34 Y 0.571 32 Y 0.967 10 Y 0.878 Y
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
1-1 M
apaawlrsaaarallppmlllllqppplla 2-36
ralpp
37-49 DVHHLHAERRGPQ
pwhaalpsspapapatqeaprpasslrppr 50-79
80-488 CGVPDPSDGLSARNRQKRFVLSGGRWEKTD
LTYRILRFPWQLVQEQVRQTMAEALKVWSD
VTPLTFTEVHEGRADIMIDFARYWHGDDLP
FDGPGGILAHAFFPKTHREGDVHFDYDETW
TIGDDQGTDLLQVAAHEFGHVLGLQHTTAA
KALMSAFYTFRYPLSLSPDDCRGVQHLYGQ
PWPTVTSRTPALGPQAGIDTNEIAPLEPDA
PPDACEASFDAVSTIRGELFFFKAGFVWRL
RGGQLQPGYPALASRHWQGLPSPVDAAFED
AQGHIWFFQGAQYWVYDGEKPVLGPAPLTE
LGLVRFPVHAALVWGPEKNKIYFFRGRDYW
RFHPSTRRVDSPVPRRATDWRGVPSEIDAA
FQDADGYAYFLRGRLYWKFDPVKVKALEGF
PRLVGPDFFGCAEPANTFL
low complexity regions: SEG 25 3.0 3.3
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
1-1 M
apaawlrsaaarallppmlllllqppplla 2-92
ralppdvhhlhaerrgpqpwhaalpsspap
apatqeaprpasslrpprcgvpdpsdglsa
r
93-488 NRQKRFVLSGGRWEKTDLTYRILRFPWQLV
QEQVRQTMAEALKVWSDVTPLTFTEVHEGR
ADIMIDFARYWHGDDLPFDGPGGILAHAFF
PKTHREGDVHFDYDETWTIGDDQGTDLLQV
AAHEFGHVLGLQHTTAAKALMSAFYTFRYP
LSLSPDDCRGVQHLYGQPWPTVTSRTPALG
PQAGIDTNEIAPLEPDAPPDACEASFDAVS
TIRGELFFFKAGFVWRLRGGQLQPGYPALA
SRHWQGLPSPVDAAFEDAQGHIWFFQGAQY
WVYDGEKPVLGPAPLTELGLVRFPVHAALV
WGPEKNKIYFFRGRDYWRFHPSTRRVDSPV
PRRATDWRGVPSEIDAAFQDADGYAYFLRG
RLYWKFDPVKVKALEGFPRLVGPDFFGCAE
PANTFL
low complexity regions: SEG 45 3.4 3.75
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
1-1 M
apaawlrsaaarallppmlllllqppplla 2-92
ralppdvhhlhaerrgpqpwhaalpsspap
apatqeaprpasslrpprcgvpdpsdglsa
r
93-488 NRQKRFVLSGGRWEKTDLTYRILRFPWQLV
QEQVRQTMAEALKVWSDVTPLTFTEVHEGR
ADIMIDFARYWHGDDLPFDGPGGILAHAFF
PKTHREGDVHFDYDETWTIGDDQGTDLLQV
AAHEFGHVLGLQHTTAAKALMSAFYTFRYP
LSLSPDDCRGVQHLYGQPWPTVTSRTPALG
PQAGIDTNEIAPLEPDAPPDACEASFDAVS
TIRGELFFFKAGFVWRLRGGQLQPGYPALA
SRHWQGLPSPVDAAFEDAQGHIWFFQGAQY
WVYDGEKPVLGPAPLTELGLVRFPVHAALV
WGPEKNKIYFFRGRDYWRFHPSTRRVDSPV
PRRATDWRGVPSEIDAAFQDADGYAYFLRG
RLYWKFDPVKVKALEGFPRLVGPDFFGCAE
PANTFL
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
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
MAPAAWLRSAAARAllppmlllllqpppllARALPPDVHHLHAERRGPQPWHAALpsspa
papaTQEAPRPASSLRPPRCGVPDPSDGLSARNRQKRFVLSGGRWEKTDLTYRILRFPWQ
LVQEQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFARYWHGDDLPFDGPGGILAHA
FFPKTHREGDVHFDYDETWTIGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYTFR
YPLSLSPDDCRGVQHLYGQPWPTVTSRTPALGPQAGIDTNEIAPLEPDAPPDACEASFDA
VSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDAQGHIWFFQGA
QYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDS
PVPRRATDWRGVPSEIDAAFQDADGYAYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC
AEPANTFL
1 - 14 MAPAAWLRSA AARA
15 - 30 llppml llllqpppll
31 - 55 ARALPPDVHH LHAERRGPQP WHAAL
56 - 64 psspa papa
65 - 488 TQEAPR PASSLRPPRC GVPDPSDGLS ARNRQKRFVL SGGRWEKTDL TYRILRFPWQ LVQE
QVRQTM AEALKVWSDV TPLTFTEVHE GRADIMIDFA RYWHGDDLPF DGPGGILAHA FFPK
THREGD VHFDYDETWT IGDDQGTDLL QVAAHEFGHV LGLQHTTAAK ALMSAFYTFR YPLS
LSPDDC RGVQHLYGQP WPTVTSRTPA LGPQAGIDTN EIAPLEPDAP PDACEASFDA VSTI
RGELFF FKAGFVWRLR GGQLQPGYPA LASRHWQGLP SPVDAAFEDA QGHIWFFQGA QYWV
YDGEKP VLGPAPLTEL GLVRFPVHAA LVWGPEKNKI YFFRGRDYWR FHPSTRRVDS PVPR
RATDWR GVPSEIDAAF QDADGYAYFL RGRLYWKFDP VKVKALEGFP RLVGPDFFGC AEPA
NTFL
low complexity regions: DUST
>tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
MAPAAWLRSAAARALLPPMLLLLLQPPPLLARALPPDVHHLHAERRGPQPWHAALPSSPA
PAPATQEAPRPASSLRPPRCGVPDPSDGLSARNRQKRFVLSGGRWEKTDLTYRILRFPWQ
LVQEQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFARYWHGDDLPFDGPGGILAHA
FFPKTHREGDVHFDYDETWTIGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYTFR
YPLSLSPDDCRGVQHLYGQPWPTVTSRTPALGPQAGIDTNEIAPLEPDAPPDACEASFDA
VSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDAQGHIWFFQGA
QYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDS
PVPRRATDWRGVPSEIDAAFQDADGYAYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC
AEPANTFL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem6gi|456257|emb|CAA40918.1|
sequence: 420 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MAPAAWLRSA AARALLPPML LLLLQPPPLL ARALPPDVHH LHAERRGPQP WHAALPSSPA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PAPATQEAPR PASSLRPPRC GVPDPSDGLS ARNRQKRFVL SGGRWEKTDL TYRILRFPWQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~1 * 14 M'95 -w local
. | . | . | . | . | . 180
LVQEQVRQTM AEALKVWSDV TPLTFTEVHE GRADIMIDFA RYWHGDDLPF DGPGGILAHA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
1111111111 111~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
FFPKTHREGD VHFDYDETWT IGDDQGTDLL QVAAHEFGHV LGLQHTTAAK ALMSAFYTFR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 300
YPLSLSPDDC RGVQHLYGQP WPTVTSRTPA LGPQAGIDTN EIAPLEPDAP PDACEASFDA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 360
VSTIRGELFF FKAGFVWRLR GGQLQPGYPA LASRHWQGLP SPVDAAFEDA QGHIWFFQGA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 420
QYWVYDGEKP VLGPAPLTEL GLVRFPVHAA LVWGPEKNKI YFFRGRDYWR FHPSTRRVDS
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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*
***********************************
tem6.___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: tem6.___inter___
(1 sequences)
MAPAAWLRSAAARALLPPMLLLLLQPPPLLARALPPDVHHLHAERRGPQP
WHAALPSSPAPAPATQEAPRPASSLRPPRCGVPDPSDGLSARNRQKRFVL
SGGRWEKTDLTYRILRFPWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHE
GRADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWT
IGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYTFRYPLSLSPDDC
RGVQHLYGQPWPTVTSRTPALGPQAGIDTNEIAPLEPDAPPDACEASFDA
VSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDA
QGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKI
YFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGYAYFL
RGRLYWKFDPVKVKALEGFPRLVGPDFFGCAEPANTFL
(p)rokaryotic or (e)ukaryotic: e
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 14 34 1.003 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 13 454
K+R profile 3.00
+
CYT-EXT prof -
0.52
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.52
-> Orientation: N-in
----------------------------------------------------------------------
"tem6" 488
14 34 #t 1.00313
************************************
*TOPPREDM with prokaryotic function*
************************************
tem6.___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: tem6.___inter___
(1 sequences)
MAPAAWLRSAAARALLPPMLLLLLQPPPLLARALPPDVHHLHAERRGPQP
WHAALPSSPAPAPATQEAPRPASSLRPPRCGVPDPSDGLSARNRQKRFVL
SGGRWEKTDLTYRILRFPWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHE
GRADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWT
IGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYTFRYPLSLSPDDC
RGVQHLYGQPWPTVTSRTPALGPQAGIDTNEIAPLEPDAPPDACEASFDA
VSTIRGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDA
QGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKI
YFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGYAYFL
RGRLYWKFDPVKVKALEGFPRLVGPDFFGCAEPANTFL
(p)rokaryotic or (e)ukaryotic: p
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 14 34 1.003 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 13 454
K+R profile 3.00
+
CYT-EXT prof -
0.52
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.52
-> Orientation: N-in
----------------------------------------------------------------------
"tem6" 488
14 34 #t 1.00313
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem6.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 14:05:16 2000
File: /people/maria/tem6.___saps___
ID tem6gi|456257|emb|CAA40918.1|
DE stromelysin-3 precursor [Homo sapiens]
number of residues: 488; molecular weight: 54.6 kdal
1 MAPAAWLRSA AARALLPPML LLLLQPPPLL ARALPPDVHH LHAERRGPQP WHAALPSSPA
61 PAPATQEAPR PASSLRPPRC GVPDPSDGLS ARNRQKRFVL SGGRWEKTDL TYRILRFPWQ
121 LVQEQVRQTM AEALKVWSDV TPLTFTEVHE GRADIMIDFA RYWHGDDLPF DGPGGILAHA
181 FFPKTHREGD VHFDYDETWT IGDDQGTDLL QVAAHEFGHV LGLQHTTAAK ALMSAFYTFR
241 YPLSLSPDDC RGVQHLYGQP WPTVTSRTPA LGPQAGIDTN EIAPLEPDAP PDACEASFDA
301 VSTIRGELFF FKAGFVWRLR GGQLQPGYPA LASRHWQGLP SPVDAAFEDA QGHIWFFQGA
361 QYWVYDGEKP VLGPAPLTEL GLVRFPVHAA LVWGPEKNKI YFFRGRDYWR FHPSTRRVDS
421 PVPRRATDWR GVPSEIDAAF QDADGYAYFL RGRLYWKFDP VKVKALEGFP RLVGPDFFGC
481 AEPANTFL
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 55(11.3%); C : 4( 0.8%); D : 33( 6.8%); E : 21( 4.3%); F : 30( 6.1%)
G : 38( 7.8%); H : 17( 3.5%); I : 11( 2.3%); K : 12( 2.5%); L : 48( 9.8%)
M : 5( 1.0%); N- : 4( 0.8%); P+ : 52(10.7%); Q : 21( 4.3%); R : 37( 7.6%)
S : 20( 4.1%); T : 23( 4.7%); V : 27( 5.5%); W+ : 16( 3.3%); Y : 14( 2.9%)
KR : 49 ( 10.0%); ED : 54 ( 11.1%); AGP + : 145 ( 29.7%);
KRED : 103 ( 21.1%); KR-ED : -5 ( -1.0%); FIKMNY- : 76 ( 15.6%);
LVIFM : 121 ( 24.8%); ST : 43 ( 8.8%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0000000+00 00+0000000 0000000000 0+0000-000 000-++0000 0000000000
61 000000-00+ 00000+00+0 000-00-000 0+0+0++000 000+0-+0-0 00+00+0000
121 000-00+000 0-00+000-0 000000-00- 0+0-000-00 +0000--000 -000000000
181 000+00+-0- 000-0--000 00--000-00 00000-0000 000000000+ 000000000+
241 0000000--0 +000000000 000000+000 0000000-00 -0000-0-00 0-00-000-0
301 0000+0-000 0+00000+0+ 0000000000 000+000000 000-000--0 0000000000
361 00000-0-+0 00000000-0 000+000000 00000-+0+0 000+0+-00+ 00000++0-0
421 000++00-0+ 0000-0-000 0-0-000000 +0+000+0-0 0+0+00-000 +0000-0000
481 0-000000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Mixed charge clusters (cmin = 15/30 or 20/45 or 25/60): 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 | 7 | 39 | 9 | 10 | 13 | 11 | 12 | 15 | 7 | 9 |
lmin1 6 | 6 | 9 | 47 | 11 | 12 | 15 | 14 | 14 | 18 | 9 | 11 |
lmin2 7 | 7 | 10 | 52 | 13 | 13 | 17 | 15 | 16 | 20 | 10 | 13 |
(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 >= 5: 0
0 runs >= 26: 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-79-C-169-C-43-C-185-C-8-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-38-H-H-1-H-9-H-27-C-68-H-14-H-14-H-6-H-5-H-22-H-3-H-5-H-24-C-4-H-38-C-40-H-17-H-34-H-23-H-67-C-8-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[
12- 18] ARALLPP
[ 31- 36] ARA_LPP
______________________________
[ 52- 55] HAAL
[ 388- 391] HAAL
______________________________
[ 340- 350] PSPVDAAFEDA
[ 433- 443] PSEIDAAFQDA
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: 35 (Expected range: 14-- 48)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 15 (6-10) 6 (11-20) 8 (>=21) 7
3. Clusters of amino acid multiplets (cmin = 12/30 or 16/45 or 19/60): none
4. Long amino acid multiplets (>= 5; Letter/Length/Position):
L/5/20
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 9 (Expected range: 0-- 20)
4 +plets (f+: 10.0%), 5 -plets (f-: 11.1%)
Total number of charge altplets: 6 (Critical number: 23)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 2 (11-20) 0 (>=21) 8
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
20- 24 1 L 5 5 ! 0
60- 75 4 A... 4 4 0
61- 92 8 P....... 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9)
Location Period Element Copies Core Errors
19- 24 1 i 6 6 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
There are no unusual spacings.
~~~~~ ~~~~~ ~~~~~ ~~~hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washmmpfam - 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: tem6
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
hemopexin Hemopexin 207.8 1.6e-58 4
Peptidase_M10 Matrixin 121.9 1.2e-32 1
Peptidase_M7 Streptomyces extracellular neutral prot -29.4 21 1
Frataxin_Cyay Frataxin-like domain -48.1 74 1
Astacin Astacin (Peptidase family M12A) -119.3 7.4 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Peptidase_M10 1/1 23 200 .. 1 171 [] 121.9 1.2e-32
Frataxin_Cyay 1/1 140 224 .. 1 117 [] -48.1 74
Peptidase_M7 1/1 107 260 .. 1 133 [] -29.4 21
Astacin 1/1 103 261 .. 1 200 [] -119.3 7.4
hemopexin 1/4 298 341 .. 1 50 [] 60.4 3.8e-14
hemopexin 2/4 343 384 .. 1 50 [] 50.4 3.9e-11
hemopexin 3/4 387 434 .. 1 50 [] 56.1 7.7e-13
hemopexin 4/4 436 480 .. 1 50 [] 55.2 1.4e-12
Alignments of top-scoring domains:
Peptidase_M10: domain 1 of 1, from 23 to 200: score 121.9, E = 1.2e-32
*->YLekfYylpksnfrqstrkkasnslveKlkeMQ.kFfGLpvTGkLDs
L +++ l ++ ++ l + + Q+ + Lp +
tem6gi|456 23 LLQPPPLLA-RALP-----PDVHHLHAERRGPQpWHAALPSSPAPAP 63
nTlev......MkkPRCGVPD..........VgefrtfPgspkWsknnll
+T e++++ ++++ PRCGVPD++++ + +++ +f+++ +W+k+ l
tem6gi|456 64 ATQEAprpassLRPPRCGVPDpsdglsarnrQKRFVLS--GGRWEKTD-L 110
TYrIvNYTpDLpredVDdairrAFqvWsdVtPLtFtrvsdgeADImIsFa
TYrI+ +L++e V + + A++vWsdVtPLtFt+v++g ADImI Fa
tem6gi|456 111 TYRILRFPWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFA 160
rgeHGDfypFDGkgGlLAHAFaPGpGigIGDAHFDddEtWT<-*
r+ HGD +pFDG+gG+LAHAF P + GD HFD dEtWT
tem6gi|456 161 RYWHGDDLPFDGPGGILAHAFFPKTHRE-GDVHFDYDETWT 200
Frataxin_Cyay: domain 1 of 1, from 140 to 224: score -48.1, E = 74
*->lndsEFHrlAdqlldkieEtLedldgevGdPYtfaDiDvetngGVlT
+ ++F + + d ++ + g d D gG+l
tem6gi|456 140 VTPLTFTEVHEGRADIMIDFARYWHG---D-----DLPFDGPGGILA 178
ltfGengskiVINkQePlhQvWLaskvgGPyHFdykgksgeWvssRdGet
f + + G HFdy + +W d +t
tem6gi|456 179 HAF------------------FPKTHREGDVHFDYDE---TWTIGDDQGT 207
fwdlLaqaltkaageevsFk<-*
dlL a+ +g + ++
tem6gi|456 208 --DLLQVAAH-EFGHVLGLQ 224
Peptidase_M7: domain 1 of 1, from 107 to 260: score -29.4, E = 21
*->avtvtYdasnAP......sFrsqiarsaqiWnssvsnvrLqegssg.
tY P + ++ r+ +a++ ++W s v e +g+
tem6gi|456 107 KTDLTYRILRFPwqlvqeQVRQTMAEALKVW-SDVTPLTFTEVHEGr 152
....aDFt.YrEGnD.....sRGsYAst...dgHGrGYiFLDYrq.....
+ +DF++Y G D + +++ G A + H G + DY + + +
tem6gi|456 153 adimIDFArYWHGDDlpfdgPGGILAHAffpKTHREGDVHFDYDEtwtig 202
.nqqYdstRvtaHEtGHvLGLPDhYsGPCseLmsGGGPGPsCtnayPnsa
+ q d v aHE GHvLGL + Lms t yP s
tem6gi|456 203 dDQGTDLLQVAAHEFGHVLGL--QHTTAAKALMSA-----FYTFRYPLSL 245
..ERsR.vnqLWAnG<-*
+++ R+v+ L+ +
tem6gi|456 246 spDDCRgVQHLYGQP 260
Astacin: domain 1 of 1, from 103 to 261: score -119.3, E = 7.4
*->rrWpngsGiVvIPYvi.....sssysgrersliraAmrewenkTCir
rW+++ + Y+i + + + +++ ++ ++++A + w++ T ++
tem6gi|456 103 GRWEKT----DLTYRIlrfpwQLVQEQVRQ-TMAEALKVWSDVTPLT 144
FvprtsagendylrffsgdGCwSyVGrrggGkeQevSlganGCi......
F + +g+ d++ f + G ++ + +G i +
tem6gi|456 145 FTEVH-EGRADIMIDFARY---------WHGD--DLPFDGPGGIlahaff 182
..........................yfGiivHElmHALGFwHEQsRpDR
++++++++ + + +++ + +++++++ + +++HE +H+LG+ H
tem6gi|456 183 pkthregdvhfdydetwtigddqgtdLLQVAAHEFGHVLGLQH------- 225
DdyVsInwqNIdpgqeynFdKydpdqvdslGvpYDYgSiMHYgpyaFSkn
++ +k
tem6gi|456 226 --------------------------------------------TTAAKA 231
gskpTIvpkdnkvyqatiGQReglSflDikkiNklYnCpe<-*
+ + + + ++ lS+ D + + lY+ p
tem6gi|456 232 L----MSAFYT--FRYPL----SLSPDDCRGVQHLYGQPW 261
hemopexin: domain 1 of 4, from 298 to 341: score 60.4, E = 3.8e-14
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DA+ ++r g+++FFk ++Wr+++ + ++pgyP l s++w+ g
tem6gi|456 298 FDAVSTIR--GELFFFKAGFVWRLRGGQ---LQPGYPALASRHWQ-G 338
lpc<-*
lp+
tem6gi|456 339 LPS 341
hemopexin: domain 2 of 4, from 343 to 384: score 50.4, E = 3.9e-11
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DAAfed + g+++FF+G +YW++d+e+ + g P ++++l g
tem6gi|456 343 VDAAFEDAQ-GHIWFFQGAQYWVYDGEK---PVLG-PAPLTEL---G 381
lpc<-*
l
tem6gi|456 382 LVR 384
hemopexin: domain 3 of 4, from 387 to 434: score 56.1, E = 7.7e-13
*->iDAAfedrd.rgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpd
++AA+ ++++++k+YFF+G+ YWrf+p ++rvd+ P++ +d++
tem6gi|456 387 VHAALVWGPeKNKIYFFRGRDYWRFHPS-TRRVDSPVPRRATDWR-- 430
glpc<-*
g+p+
tem6gi|456 431 GVPS 434
hemopexin: domain 4 of 4, from 436 to 480: score 55.2, E = 1.4e-12
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
iDAAf+d d g++YF +G+ YW+fdp + + g+P+l+ + +
tem6gi|456 436 IDAAFQDAD-GYAYFLRGRLYWKFDPV-KVKALEGFPRLVGPD---F 477
lpc<-*
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washmmpfam - 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: tem6
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
hemopexin Hemopexin 200.4 2.5e-59 4
Peptidase_M10 Matrixin 157.6 1.2e-44 1
Fragilysin Fragilysin metallopeptidase (M10C) ente 11.4 0.019 1
Astacin Astacin (Peptidase family M12A) 5.0 1.4 1
Peptidase_M7 Streptomyces extracellular neutral prot 3.8 5.4 1
DUF2 Domain of unknown function 2 2.9 11 1
Reprolysin Reprolysin (M12B) family zinc metallopr 2.5 22 1
Gemini_mov Geminivirus putative movement protein 2.5 18 1
vATP-synt_E ATP synthase (E/31 kDa) subunit -0.4 65 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
DUF2 1/1 29 38 .. 255 264 .] 2.9 11
Gemini_mov 1/1 47 63 .. 85 101 .] 2.5 18
Peptidase_M10 1/1 75 200 .. 52 171 .] 157.6 1.2e-44
Peptidase_M7 1/1 212 223 .. 81 92 .. 3.8 5.4
Reprolysin 1/1 214 225 .. 137 148 .. 2.5 22
Astacin 1/1 212 226 .. 90 104 .. 5.0 1.4
Fragilysin 1/1 212 238 .. 334 360 .. 11.4 0.019
vATP-synt_E 1/1 299 309 .. 198 208 .] -0.4 65
hemopexin 1/4 298 341 .. 1 50 [] 58.6 3.4e-16
hemopexin 2/4 343 384 .. 1 50 [] 48.6 3.6e-13
hemopexin 3/4 387 434 .. 1 50 [] 54.2 7.3e-15
hemopexin 4/4 436 480 .. 1 50 [] 53.4 1.3e-14
Alignments of top-scoring domains:
DUF2: domain 1 of 1, from 29 to 38: score 2.9, E = 11
*->lFaralPgdv<-*
l+aralP+dv
tem6gi|456 29 LLARALPPDV 38
Gemini_mov: domain 1 of 1, from 47 to 63: score 2.5, E = 18
*->GptearSALArsgavpp<-*
Gp++ ++AL +s+a++p
tem6gi|456 47 GPQPWHAALPSSPAPAP 63
Peptidase_M10: domain 1 of 1, from 75 to 200: score 157.6, E = 1.2e-44
*->MkkPRCGVPD..........VgefrtfPgspkWsknnllTYrIvNYT
++ PRCGVPD++++ + +++ +f+++ +W+k+ lTYrI+
tem6gi|456 75 LRPPRCGVPDpsdglsarnrQKRFVLS--GGRWEKTD-LTYRILRFP 118
pDLpredVDdairrAFqvWsdVtPLtFtrvsdgeADImIsFargeHGDfy
+L++e V + + A++vWsdVtPLtFt+v++g ADImI Far+ HGD +
tem6gi|456 119 WQLVQEQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFARYWHGDDL 168
pFDGkgGlLAHAFaPGpGigIGDAHFDddEtWT<-*
pFDG+gG+LAHAF P + GD HFD dEtWT
tem6gi|456 169 PFDGPGGILAHAFFPKTHRE-GDVHFDYDETWT 200
Peptidase_M7: domain 1 of 1, from 212 to 223: score 3.8, E = 5.4
*->vtaHEtGHvLGL<-*
v aHE GHvLGL
tem6gi|456 212 VAAHEFGHVLGL 223
Reprolysin: domain 1 of 1, from 214 to 225: score 2.5, E = 22
*->AHELGHNLGmtH<-*
AHE GH LG++H
tem6gi|456 214 AHEFGHVLGLQH 225
Astacin: domain 1 of 1, from 212 to 226: score 5.0, E = 1.4
*->iivHElmHALGFwHE<-*
+++HE +H+LG+ H+
tem6gi|456 212 VAAHEFGHVLGLQHT 226
Fragilysin: domain 1 of 1, from 212 to 238: score 11.4, E = 0.019
*->vlAHElGHlLGAeHvDnekDLMYtwYt<-*
v AHE GH+LG +H+ k LM + Yt
tem6gi|456 212 VAAHEFGHVLGLQHTTAAKALMSAFYT 238
vATP-synt_E: domain 1 of 1, from 299 to 309: score -0.4, E = 65
*->qllpeIrkaLF<-*
++ ++Ir +LF
tem6gi|456 299 DAVSTIRGELF 309
hemopexin: domain 1 of 4, from 298 to 341: score 58.6, E = 3.4e-16
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DA+ ++r g+++FFk ++Wr+++ + ++pgyP l s++w+ g
tem6gi|456 298 FDAVSTIR--GELFFFKAGFVWRLRGGQ---LQPGYPALASRHWQ-G 338
lpc<-*
lp+
tem6gi|456 339 LPS 341
hemopexin: domain 2 of 4, from 343 to 384: score 48.6, E = 3.6e-13
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DAAfed + g+++FF+G +YW++d+e+ + g P ++++l g
tem6gi|456 343 VDAAFEDAQ-GHIWFFQGAQYWVYDGEK---PVLG-PAPLTEL---G 381
lpc<-*
l
tem6gi|456 382 LVR 384
hemopexin: domain 3 of 4, from 387 to 434: score 54.2, E = 7.3e-15
*->iDAAfedrd.rgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpd
++AA+ ++++++k+YFF+G+ YWrf+p ++rvd+ P++ +d++
tem6gi|456 387 VHAALVWGPeKNKIYFFRGRDYWRFHPS-TRRVDSPVPRRATDWR-- 430
glpc<-*
g+p+
tem6gi|456 431 GVPS 434
hemopexin: domain 4 of 4, from 436 to 480: score 53.4, E = 1.3e-14
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
iDAAf+d d g++YF +G+ YW+fdp + + g+P+l+ + +
tem6gi|456 436 IDAAFQDAD-GYAYFLRGRLYWKFDPV-KVKALEGFPRLVGPD---F 477
lpc<-*
++c
tem6gi|456 478 FGC 480
//
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: tem6
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Tue Oct 31 14:14:03 2000
Sequence file: tem6
----------------------------------------
Sequence tem6gi|456257|emb|CAA40918.1| (488 residues):
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
424: RRAT
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
74: SLR
90: SAR
111: TYR
185: THR
238: TFR
265: TSR
303: TIR
414: STR
415: TRR
Total matches: 9
Matching pattern PS00006 CK2_PHOSPHO_SITE:
129: TMAE
144: TFTE
185: THRE
200: TIGD
246: SPDD
341: SPVD
434: SEID
Total matches: 7
Matching pattern PS00008 MYRISTYL:
174: GGILAH
222: GLQHTT
276: GIDTNE
Total matches: 3
Matching pattern PS00024 HEMOPEXIN:
332: ASRHWQGLPSPVDAAF
Total matches: 1
Matching pattern PS00142 ZINC_PROTEASE:
212: VAAHEFGHVL
Total matches: 1
Matching pattern PS00546 CYSTEINE_SWITCH:
78: PRCGVPDP
Total matches: 1
Total no of hits in this sequence: 23
========================================
1314 pattern(s) searched in 1 sequence(s), 488 residues.
Total no of hits in all sequences: 23.
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 tem6
***** 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, 488 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: tem6
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem6
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= tem6gi|456257|emb|CAA40918.1| stromelysin-3 precursor [Homo
sapiens]
(488 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
KELCH Kelch repeat- beta propeller like domain 25 0.27
CHLMY Adenovirus like protease domain 23 1.3
RASGEF RAS-type GTPase GDP exchange factor 22 1.6
CATH Cathepsin like protease domain 22 1.7
ARR Arrestin domain 21 4.7
SPRY SPRY domain 21 4.9
RGS Regulator of heterotrimeric G protein signalling (G-prot... 20 8.3
BRCT BRCA C-terminal domain 20 8.6
SGTP Small GTPAses 20 9.0
SH2 Src Homology domain 2 19 9.8
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 25.0 bits (54), Expect = 0.27
Identities = 14/105 (13%), Positives = 30/105 (28%), Gaps = 27/105 (25%)
Query: 351 QGHIWFFQGAQ------YWVYDGEKPVLGPAPLTELGLVRFPVHAALVWGPEKNKIYFFR 404
I+ G + ++ E + ++ R A+ G NK+Y
Sbjct: 221 GNQIFIMGGDTEFSACSAYKFNSET--YQWTKVGDVTAKRM-SCHAVASG---NKLYVVG 274
Query: 405 GRDY-------WRFHPST---RRVDSPVPRRA-----TDWRGVPS 434
G + P+ + + + W+ +PS
Sbjct: 275 GYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS 319
Score = 21.1 bits (44), Expect = 3.9
Identities = 9/49 (18%), Positives = 12/49 (24%), Gaps = 15/49 (30%)
Query: 388 HAALVWGPEKNKIYFFRGRDY--------WRFHPSTRR----VDSPVPR 424
+A G K+Y GR W + V R
Sbjct: 63 FSACAIG---CKVYITGGRGSENGVSKDVWVYDTLHEEWSKAAPMLVAR 108
Score = 20.3 bits (42), Expect = 5.5
Identities = 8/50 (16%), Positives = 12/50 (24%), Gaps = 15/50 (30%)
Query: 388 HAALVWGPEKNKIYFFRGRDY--------WRFHPSTRRV----DSPVPRR 425
A + K++ F G + R P P R
Sbjct: 167 AAVVSAK---LKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQPWR 213
>CHLMY Adenovirus like protease domain
Length = 157
Score = 22.5 bits (48), Expect = 1.3
Identities = 6/25 (24%), Positives = 9/25 (36%), Gaps = 6/25 (24%)
Query: 385 FPVH------AALVWGPEKNKIYFF 403
PVH + KN I ++
Sbjct: 38 VPVHVDNVHWCMAIIDMSKNMISYY 62
>RASGEF RAS-type GTPase GDP exchange factor
Length = 196
Score = 22.1 bits (47), Expect = 1.6
Identities = 4/25 (16%), Positives = 10/25 (40%)
Query: 418 VDSPVPRRATDWRGVPSEIDAAFQD 442
+ S V + WR + +++
Sbjct: 114 LSSSVVKFTDAWRLIEPGDLLTWEE 138
>CATH Cathepsin like protease domain
Length = 371
Score = 22.2 bits (47), Expect = 1.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 357 FQGAQYWVYDGEKPVLGPAP 376
F G+ Y V+D + +G A
Sbjct: 347 FIGSYYTVFDRDNDAVGFAK 366
Score = 20.6 bits (43), Expect = 5.5
Identities = 5/16 (31%), Positives = 6/16 (37%)
Query: 188 EGDVHFDYDETWTIGD 203
DV W +GD
Sbjct: 330 GLDVPPPAGPLWILGD 345
>ARR Arrestin domain
Length = 454
Score = 20.6 bits (43), Expect = 4.7
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 8/42 (19%)
Query: 71 PASSLRPPRCGVPDPSDGLSARNRQKR-FVLSGGRWEKTDLT 111
P +L P L + N+ KR L G K + T
Sbjct: 297 PGGTLSKVFAVCP-----LLSNNKDKRGLALDG--QLKHEDT 331
>SPRY SPRY domain
Length = 122
Score = 20.5 bits (43), Expect = 4.9
Identities = 6/54 (11%), Positives = 16/54 (29%), Gaps = 13/54 (24%)
Query: 150 EGRADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGD 203
+ ++ + +G + G G + Y +++ GD
Sbjct: 26 DHPIEVYPGNYQGSYG----YSGDGKCYFG---------TNEGRVYGPSFSSGD 66
>RGS Regulator of heterotrimeric G protein signalling (G-protein GTP hydrolysis activating protein)
Length = 117
Score = 19.7 bits (41), Expect = 8.3
Identities = 5/21 (23%), Positives = 10/21 (46%)
Query: 337 QGLPSPVDAAFEDAQGHIWFF 357
+ + P F++AQ I+
Sbjct: 78 RNMLEPTITCFDEAQKKIFNL 98
>BRCT BRCA C-terminal domain
Length = 138
Score = 19.8 bits (41), Expect = 8.6
Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 5/39 (12%)
Query: 96 KRFVLSG-----GRWEKTDLTYRILRFPWQLVQEQVRQT 129
V SG + E+TD+ +F +V +
Sbjct: 10 CVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDV 48
>SGTP Small GTPAses
Length = 164
Score = 19.7 bits (41), Expect = 9.0
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 192 HFDYDETWTIGDDQGTDLLQV 212
F D TIG + G+ ++ V
Sbjct: 24 KFKDDSNHTIGVEFGSKIINV 44
>SH2 Src Homology domain 2
Length = 119
Score = 19.4 bits (40), Expect = 9.8
Identities = 2/12 (16%), Positives = 4/12 (32%)
Query: 114 ILRFPWQLVQEQ 125
+ PW +
Sbjct: 108 KPQKPWDKDAWE 119
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 10
Number of calls to ALIGN: 13
Length of query: 488
Total length of test sequences: 20182
Effective length of test sequences: 16941.0
Effective search space size: 7754284.3
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 Collectio............................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|116871 [267..480] 4-bladedone
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|116871 [267..480] 4-bladed beta-propeller 277 3e-76
gi|2829864 [79..325] Metzincin-like 228 2e-61
gi|1070649 [50..283] 4-bladed beta-propeller 193 8e-51
gi|1616941 [10..247] Metzincin-like 188 2e-49
gi|1731806 [90..289] Metzincin-like 123 9e-30
gi|1815643 [227..431] Metzincin-like 33 0.014
gi|1360139 [98..407] 7-bladed beta-propeller 32 0.016
gi|2809057 [242..451] Metzincin-like 30 0.072
gi|118558 [166..782] 7-bladed beta-propeller 26 1.6
gi|1478030 [251..542] beta/alpha (TIM)-barrel 26 1.6
gi|2622786 [14..221] beta/alpha (TIM)-barrel 26 1.6
gi|121769 [3..207] Class I glutamine amidotransferases 25 3.1
gi|2688435 [36..228] Sugar phosphatases 25 4.4
gi|1778568 [354..541] Heat shock protein 70kD (HSP70), C-ter... 24 5.8
gi|1495469 [3..289] P-loop containing nucleotide triphosphat... 23 8.1
gi|2500207 [212..776] R1 subunit of ribonucleotide reductase... 23 9.6
gi|482303 [240..626] 7-bladed beta-propeller 23 9.9
>gi|116871 [267..480] 4-bladed beta-propeller
Length = 214
Score = 277 bits (703), Expect = 3e-76
Identities = 214/214 (100%), Positives = 214/214 (100%)
Query: 267 RTPALGPQAGIDTNEIAPLEPDAPPDACEASFDAVSTIRGELFFFKAGFVWRLRGGQLQP 326
RTPALGPQAGIDTNEIAPLEPDAPPDACEASFDAVSTIRGELFFFKAGFVWRLRGGQLQP
Sbjct: 1 RTPALGPQAGIDTNEIAPLEPDAPPDACEASFDAVSTIRGELFFFKAGFVWRLRGGQLQP 60
Query: 327 GYPALASRHWQGLPSPVDAAFEDAQGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFP 386
GYPALASRHWQGLPSPVDAAFEDAQGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFP
Sbjct: 61 GYPALASRHWQGLPSPVDAAFEDAQGHIWFFQGAQYWVYDGEKPVLGPAPLTELGLVRFP 120
Query: 387 VHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGY 446
VHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGY
Sbjct: 121 VHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGY 180
Query: 447 AYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC 480
AYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC
Sbjct: 181 AYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC 214
>gi|2829864 [79..325] Metzincin-like
Length = 247
Score = 228 bits (576), Expect = 2e-61
Identities = 72/237 (30%), Positives = 98/237 (40%), Gaps = 40/237 (16%)
Query: 55 LPSSPAPAPATQEAPRPASSLRPPRCGVPD---PSDGLSARNRQKRFVLSGG-------- 103
L + T + + PRCG PD + + + + +G
Sbjct: 19 LNVTGVLDELTLKH------VVIPRCGNPDVVNGTSTMHSGRKTFEVSFAGRGQRFHAVK 72
Query: 104 ---------RWEKTDLTYRILRFPWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHE-GRA 153
RW + P + E+V+ + A W +VTPLTFT V +
Sbjct: 73 HYSFFPGEPRWPRNRRDLTYAFDPRNALTEEVKSVFSRAFTRWEEVTPLTFTRVERFSTS 132
Query: 154 DIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGD---------D 204
DI I F HGD PFDGP LAHAF P T G H D +E W +
Sbjct: 133 DISIGFYSGEHGDGEPFDGPMRTLAHAFSPPT---GHFHLDGEENWIVSGEGGDGFISVS 189
Query: 205 QGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFY-TFRYPLSLSPDDCRGVQHLYGQP 260
+ DL VA HE GH+LGL H++ ++M T R + L+ DD GVQ+LYG
Sbjct: 190 EAVDLESVAVHEIGHLLGLGHSSVEGSIMYPTIRTGRRKVDLTTDDVEGVQYLYGAN 246
>gi|1070649 [50..283] 4-bladed beta-propeller
Length = 234
Score = 193 bits (486), Expect = 8e-51
Identities = 50/196 (25%), Positives = 73/196 (36%), Gaps = 22/196 (11%)
Query: 297 SFDAVSTI-RGELFFFKAGFVWRLRGGQLQPGYPALASRHWQGLPSPVDAAFEDAQGHIW 355
SFDA + G + FFK FVW+ G L S W+ PVDA ++
Sbjct: 8 SFDATTLDDNGTMLFFKDEFVWKSH-----RGIRELISERWKNFIGPVDAFRHG-HTSVY 61
Query: 356 FFQGAQYWVYDGEKPVLGPAPLTELGLVRFP--VHAALVWGP---EKNKIYFFRGRDYWR 410
+G + WVY +K G L + P + AA+ + I FF+G W
Sbjct: 62 LIKGDKGWVYPPDKKDKGYPKLLQDEFPLIPFPLDAAVECHRGECQDEGILFFQGNRKWF 121
Query: 411 FHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGYAYFLRGRLYWKFDPVKVKALEGFP 470
+ +T W V + A G Y +G + +F+PV + G+P
Sbjct: 122 WDLTTGTKK------ERSWPAVGNCTSALRW--LGRYYCFQGNQFLRFNPVSGEVPPGYP 173
Query: 471 RLVGPDFFGCAEPANT 486
V F C P
Sbjct: 174 LDVRDYFLSC--PGRG 187
Score = 38.8 bits (90), Expect = 2e-04
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 429 WRGVPSEIDAAF-QDADGYAYFLRGRLYWKFD 459
R P + +A D G Y G YW+ D
Sbjct: 203 TRCDPDLVLSAMVSDNHGATYVFSGSHYWRLD 234
Score = 35.7 bits (82), Expect = 0.002
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 335 HWQGLPSPVDAAF-EDAQGHIWFFQGAQYWVYD 366
+ P V +A D G + F G+ YW D
Sbjct: 202 STRCDPDLVLSAMVSDNHGATYVFSGSHYWRLD 234
Score = 29.9 bits (67), Expect = 0.086
Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 4/38 (10%)
Query: 378 TELGLVRFP----VHAALVWGPEKNKIYFFRGRDYWRF 411
T+ G + + + Y F G YWR
Sbjct: 196 TQHGHESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRL 233
>gi|1616941 [10..247] Metzincin-like
Length = 238
Score = 188 bits (473), Expect = 2e-49
Identities = 40/208 (19%), Positives = 57/208 (27%), Gaps = 23/208 (11%)
Query: 75 LRPPRCGVPDPSDG---LSARNRQKRFVLSGGRWEKTDLTYRILRFPWQLVQEQVRQTMA 131
LR P D LS K W+ Y + +F Q +
Sbjct: 40 LREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFS--AQQQAQAK 97
Query: 132 EALKVWSDVTPLTFTEVHEGR-ADIMIDFARYWHGDDLPFDGPGGILAHAFFPKTHRE-- 188
+L+ WSDVT + F + +G D+ F G A AF P
Sbjct: 98 LSLQSWSDVTNIHFVDAGQGHQGDLTFGN----------FSSSVGGAAFAFLPDVPDALK 147
Query: 189 GDVHFDYDETWT--IGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMSAFYT-FRYPLSL 245
G + + +++ + Q HE GH LGL Y Y
Sbjct: 148 GQSWYLINSSYSANVNPANANYGRQTLTHEIGHTLGLSTPDYNAGEGDPTYADATYAEDT 207
Query: 246 SPDDCRGVQHLYGQP--WPTVTSRTPAL 271
+ S P L
Sbjct: 208 RAYSVMSYWEEQNTGQDFKGAYSSAPLL 235
>gi|1731806 [90..289] Metzincin-like
Length = 200
Score = 123 bits (306), Expect = 9e-30
Identities = 19/164 (11%), Positives = 38/164 (22%), Gaps = 33/164 (20%)
Query: 104 RWEKTDLTYRILRFPWQLVQEQV-RQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFARY 162
W K+ + + +A++ + +T + F + I
Sbjct: 9 LWPKSADGIVPVPYNLSYSYNADQLALFKKAIQEFEALTCVRFVPWTTEVNFLNIMS--- 65
Query: 163 WHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGDDQGTDLLQVAAHEFGHVLG 222
+G G G G + + HE H LG
Sbjct: 66 -NGGCGSLIGKNGGAQRLELDA--------------------NGCMNMGIIQHELNHALG 104
Query: 223 LQHTTAAK------ALMSAFY--TFRYPLSLSPDDCRGVQHLYG 258
H + + F + G+++ Y
Sbjct: 105 FYHEQNRSDRDDYVIIHTENIIPDFLKMFEKYNTNNLGIEYDYA 148
>gi|1815643 [227..431] Metzincin-like
Length = 205
Score = 32.7 bits (74), Expect = 0.014
Identities = 8/31 (25%), Positives = 12/31 (37%), Gaps = 3/31 (9%)
Query: 200 TIGDDQGTDLLQVA---AHEFGHVLGLQHTT 227
+ + A GH+LGL+H T
Sbjct: 119 IVKGVEQFATHWNGELLAQSIGHLLGLEHDT 149
>gi|1360139 [98..407] 7-bladed beta-propeller
Length = 310
Score = 32.4 bits (73), Expect = 0.016
Identities = 30/234 (12%), Positives = 42/234 (17%), Gaps = 50/234 (21%)
Query: 277 IDTNEIAPLEPDAPPDACEASFDAVSTIRGELFFFKAGFVWRLRGGQLQPGYPA------ 330
N + P+ C G L GG +
Sbjct: 16 PLANTLTPIPAPPFNIFCAGHSFLED---GRLLIT---------GGHVDSHVGVPDAIIF 63
Query: 331 -LASRHWQGLPSPVD-----AAFEDAQGHIWFFQGA---------QYWVYDGEKPVLGPA 375
S W +P D A G + G Y
Sbjct: 64 NPKSGAWDNVPDMNDKRWYPNNTTLANGDVLVLSGETDGEGLFNELPQRYVAATNSWQNL 123
Query: 376 PLTELGLVRFPVHAALVWGPEKNKIYFFRG-RDYWRFHPSTRRVDSPVPRRATDWRGVPS 434
+ + +P H L NK++F R P P R
Sbjct: 124 TTAQRKIPYYP-HMFLAPN---NKLFFSGPWRSSQWLDPDGTGTWFEAPYSHFGGRS--- 176
Query: 435 EIDAAFQDADGYAYFLRGRL-------YWKFDPVKVKALEGFPRLVGPDFFGCA 481
DG + G + P V
Sbjct: 177 --YGGHVYFDGKVLPVGGGNPPTETVELIDLNLPLPTWAYQTPMSVARRQHNTT 228
>gi|2809057 [242..451] Metzincin-like
Length = 210
Score = 30.3 bits (68), Expect = 0.072
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 212 VAAHEFGHVLGLQHTTAAK 230
AHE GHV + H A
Sbjct: 141 TTAHELGHVFNMPHDDAKH 159
>gi|118558 [166..782] 7-bladed beta-propeller
Length = 617
Score = 25.7 bits (56), Expect = 1.6
Identities = 12/81 (14%), Positives = 18/81 (21%), Gaps = 16/81 (19%)
Query: 395 PEKNKIYFFR---GRDYWRFHPSTRRVDSPVPRRATD-------WRGVPSE-IDAAFQ-- 441
P + W+ T R P + G S + F
Sbjct: 509 PAWGYVAGVDLKTHEVVWKKRIGTIRDSLPNLFQLPAVKIGVPGLGGSISTAGNVMFVGA 568
Query: 442 DADGYAYFLR---GRLYWKFD 459
D Y G+ W+
Sbjct: 569 TQDNYLRAFNVTNGKKLWEAR 589
Score = 23.8 bits (51), Expect = 7.0
Identities = 12/73 (16%), Positives = 22/73 (29%), Gaps = 4/73 (5%)
Query: 405 GRDYWRFHPSTRRVDSPVPRRATDWRGVPSEIDAAFQDADGYAYFL---RGRLYWKFDPV 461
+ W + D+ + + A + G+ W+FDP
Sbjct: 27 LKVAWTLRTGDLKTDNDSGETTNQVTPIKIGNNMFICTAHQQLIAIDPATGKEKWRFDP- 85
Query: 462 KVKALEGFPRLVG 474
K+K + F L
Sbjct: 86 KLKTDKSFQHLTC 98
>gi|1478030 [251..542] beta/alpha (TIM)-barrel
Length = 292
Score = 25.9 bits (56), Expect = 1.6
Identities = 12/86 (13%), Positives = 25/86 (28%), Gaps = 14/86 (16%)
Query: 124 EQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFAR-YWHGDDLPFDGPGGILAHAFF 182
Q +A+A K W G + +D + +H + + F+
Sbjct: 114 SPAYQAIADAAKGWIAR----------GVDGLRLDAVKHIYHSETSEENPR---FLKMFY 160
Query: 183 PKTHREGDVHFDYDETWTIGDDQGTD 208
+ D+ + IG+
Sbjct: 161 EDMNAYYKQKGHTDDFYMIGEVLSEY 186
>gi|2622786 [14..221] beta/alpha (TIM)-barrel
Length = 208
Score = 26.0 bits (57), Expect = 1.6
Identities = 13/75 (17%), Positives = 15/75 (19%), Gaps = 11/75 (14%)
Query: 418 VDSPVPRR------ATDWRGVPSEIDAAFQDADGYAYFLRGRLYWKFDPVKV-KALEGFP 470
+DS R + L G L P V E
Sbjct: 125 LDSSSGGRTGGTGRMIPPELALGMLRLIRSHESAPEVALAGGL----GPSTVRLNPEYLL 180
Query: 471 RLVGPDFFGCAEPAN 485
DF E A
Sbjct: 181 EFDCLDFNSGIEAAP 195
>gi|121769 [3..207] Class I glutamine amidotransferases
Length = 205
Score = 25.0 bits (54), Expect = 3.1
Identities = 16/99 (16%), Positives = 25/99 (25%), Gaps = 15/99 (15%)
Query: 147 EVHEGRADIMIDFA---RYWHGDDLPFDGPGGILAHAFFPKTHREGDVHFDYDETWTIGD 203
E G A + + D L DG GD +
Sbjct: 103 EREFGYAQVEVVNDSALVRGIEDALTADGKPL------LDVWMSHGDKVTAIPSDFITVA 156
Query: 204 DQGTDLLQVAAHEFGHVLGLQ------HTTAAKALMSAF 236
+ + A+E G+Q HT ++ F
Sbjct: 157 STESCPFAIMANEEKRFYGVQFHPEVTHTRQGMRMLERF 195
>gi|2688435 [36..228] Sugar phosphatases
Length = 193
Score = 24.6 bits (53), Expect = 4.4
Identities = 4/21 (19%), Positives = 7/21 (33%)
Query: 143 LTFTEVHEGRADIMIDFARYW 163
+F ++ G F W
Sbjct: 158 YSFAKLFTGSYKAYFSFVGLW 178
>gi|1778568 [354..541] Heat shock protein 70kD (HSP70), C-terminal, substrate-binding fragment
Length = 188
Score = 24.1 bits (52), Expect = 5.8
Identities = 6/17 (35%), Positives = 7/17 (40%), Gaps = 1/17 (5%)
Query: 430 RGVPSEIDAAFQ-DADG 445
G ID F D +G
Sbjct: 80 TGAYQSIDIRFSYDING 96
>gi|1495469 [3..289] P-loop containing nucleotide triphosphate hydrolases
Length = 287
Score = 23.5 bits (49), Expect = 8.1
Identities = 10/117 (8%), Positives = 27/117 (22%), Gaps = 1/117 (0%)
Query: 118 PWQLVQEQVRQTMAEALKVWSDVTPLTFTEVHEGRADIMIDFARYWHGDDLPFDGPGGIL 177
++ + + T+ V L +V + + + G G I
Sbjct: 45 TRLILHAKAQDTILSLAADAGSVEDLELEDVMKIGYQNIRCVESGGPEPGVGCAGRGVIT 104
Query: 178 AHAFFPKTHREGDVHFDYDETWTIGDDQGTDLLQVAAHEFGHVLGLQHTTAAKALMS 234
+ F + D + + G + + + +
Sbjct: 105 SINFLEEEGAYDDTDYVSYDVLGDVVCGGFAMPIRENK-AQEIYIVMSGEMMAMYAA 160
>gi|2500207 [212..776] R1 subunit of ribonucleotide reductase, C-terminal domain
Length = 565
Score = 23.3 bits (50), Expect = 9.6
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 246 SPDDCRGVQHLYGQP 260
P +C+ + LYGQ
Sbjct: 137 DPYECKDLTELYGQD 151
>gi|482303 [240..626] 7-bladed beta-propeller
Length = 387
Score = 23.0 bits (49), Expect = 9.9
Identities = 7/58 (12%), Positives = 21/58 (36%), Gaps = 12/58 (20%)
Query: 376 PLTELGLVRFPVHAALVWGPEKNKIYFFRG--------RDYWRFHPSTRR-VDSPVPR 424
P ++ + R +A + +++ G ++ + PS++ P +
Sbjct: 112 PGPDMQVARGYQSSATMSD---GRVFTIGGSWSGGVFEKNGEVYSPSSKTWTSLPNAK 166
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 17
Number of calls to ALIGN: 21
Length of query: 488
Total length of test sequences: 256703
Effective length of test sequences: 214185.0
Effective search space size: 96870993.0
Initial X dropoff for ALIGN: 25.0 bits