analysis of sequence from tem7
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELAVQYLNTFYGCPKESCNLFVL
KDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETV
DDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDD
ELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEALF
TMGGNAEGQPCKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCV
FPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPDIDLGTGPTPTLGPVTPEICKQDIVFDGIAQIRGEIFFFKD
RFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLERGYPKPLTSLG
LPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDPGFPKLIADAWNAIPDNLDAVVDLQGGGHSY
FFKGAYYLKLENQSLKSVKFGSIKSDWLGC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem7gi|116856|sp|P08253|COG2_HUMAN
. . . . .
1 MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELA 50
___HHHHH_____HHHHHHH_HHHHHHH______________HHHHHHHH
. . . . .
51 VQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKP 100
HHHHHH__________EEEHHHHHHHHHHHH___________HHHHH___
. . . . .
101 RCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQV 150
______________________EEEEEEE____________HHHHHHHHH
. . . . .
151 WSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTG 200
H_______EEE______EEEEEE__________________EEE______
. . . . .
201 VGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDT 250
__________EEEE____EEEEEEE__________________EEEE___
. . . . .
251 GRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGT 300
____________________________EEE___________________
. . . . .
301 SYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCV 350
_____________EEE__________________________________
. . . . .
351 FPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLV 400
_______________________EEEE___________________HHHH
. . . . .
401 AAHEFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD 450
HHHHHH_________________EEEE__________HHHHHHHH_____
. . . . .
451 IDLGTGPTPTLGPVTPEICKQDIVFDGIAQIRGEIFFFKDRFIWRTVTPR 500
_____________________EEEE___HHHHH_______EEEEEE____
. . . . .
501 DKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLER 550
_______EEEEE______HHHHHH_____HHHHH____EEEEEE______
. . . . .
551 GYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDP 600
________________HHHHHHH_____EEEEEE_____HHHHHHHH___
. . . . .
601 GFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKF 650
___HHHHHHHH________EEEE____________HHHHHH____EEE__
.
651 GSIKSDWLGC 660
__________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 14.7 %
beta-contents : 6.8 %
coil-contents : 78.5 %
class : irregular
method : 2
alpha-contents : 4.7 %
beta-contents : 17.8 %
coil-contents : 77.5 %
class : beta
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-18.82 -0.50 -0.30 -0.04 0.00 0.00 0.00 -0.64 -0.93 -3.89 -1.10 0.00 -12.00 -4.00 -12.00 -12.00 -66.22
-14.63 -0.36 -0.60 -0.35 -4.00 0.00 0.00 0.00 -0.33 -2.36 -1.10 0.00 -12.00 0.00 -12.00 -12.00 -59.73
ID: tem7gi|116856|sp|P08253|COG2_HUMAN AC: xxx Len: 630 1:I 607 Sc: -59.73 Pv: 3.650661e-01 NO_GPI_SITE
GPI: learning from protozoa
-12.31 -2.26 -0.52 -0.40 0.00 0.00 -8.00 -2.85 0.00 -3.87 -4.92 -12.00 -12.00 0.00 -12.00 -12.00 -83.12
-28.01 -0.34 -0.61 -1.30 0.00 0.00 0.00 0.00 -0.03 -2.19 -4.92 0.00 -12.00 0.00 -12.00 -12.00 -73.40
ID: tem7gi|116856|sp|P08253|COG2_HUMAN AC: xxx Len: 630 1:I 607 Sc: -73.40 Pv: 3.972112e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem7gi|1168 0.918 30 Y 0.865 30 Y 0.970 11 Y 0.866 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem7gi|1168 0.610 28 Y 0.580 28 Y 0.964 24 Y 0.632 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem7gi|1168 0.669 30 Y 0.674 30 Y 0.981 23 Y 0.776 Y
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
1-13 MEALMARGALTGP
lralcllgcllshaaaa 14-30
31-452 PSPIIKFPGDVAPKTDKELAVQYLNTFYGC
PKESCNLFVLKDTLKKMQKFFGLPQTGDLD
QNTIETMRKPRCGNPDVANYNFFPRKPKWD
KNQITYRIIGYTPDLDPETVDDAFARAFQV
WSDVTPLRFSRIHDGEADIMINFGRWEHGD
GYPFDGKDGLLAHAFAPGTGVGGDSHFDDD
ELWTLGEGQVVRVKYGNADGEYCKFPFLFN
GKEYNSCTDTGRSDGFLWCSTTYNFEKDGK
YGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYG
FCPETAMSTVGGNSEGAPCVFPFTFLGNKY
ESCTSAGRSDGKMWCATTANYDDDRKWGFC
PDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPD
ID
lgtgptptlgpvtp 453-466
467-660 EICKQDIVFDGIAQIRGEIFFFKDRFIWRT
VTPRDKPMGPLLVATFWPELPEKIDAVYEA
PQEEKAVFFAGNEYWIYSASTLERGYPKPL
TSLGLPPDVQRVDAAFNWSKNKKTYIFAGD
KFWRYNEVKKKMDPGFPKLIADAWNAIPDN
LDAVVDLQGGGHSYFFKGAYYLKLENQSLK
SVKFGSIKSDWLGC
low complexity regions: SEG 25 3.0 3.3
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
1-2 ME
almargaltgplralcllgcllshaaaaps 3-32
33-298 PIIKFPGDVAPKTDKELAVQYLNTFYGCPK
ESCNLFVLKDTLKKMQKFFGLPQTGDLDQN
TIETMRKPRCGNPDVANYNFFPRKPKWDKN
QITYRIIGYTPDLDPETVDDAFARAFQVWS
DVTPLRFSRIHDGEADIMINFGRWEHGDGY
PFDGKDGLLAHAFAPGTGVGGDSHFDDDEL
WTLGEGQVVRVKYGNADGEYCKFPFLFNGK
EYNSCTDTGRSDGFLWCSTTYNFEKDGKYG
FCPHEALFTMGGNAEGQPCKFPFRFQ
gtsydscttegrtdgyrwcgttedydrdkk 299-330
yg
331-660 FCPETAMSTVGGNSEGAPCVFPFTFLGNKY
ESCTSAGRSDGKMWCATTANYDDDRKWGFC
PDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPD
IDLGTGPTPTLGPVTPEICKQDIVFDGIAQ
IRGEIFFFKDRFIWRTVTPRDKPMGPLLVA
TFWPELPEKIDAVYEAPQEEKAVFFAGNEY
WIYSASTLERGYPKPLTSLGLPPDVQRVDA
AFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSY
FFKGAYYLKLENQSLKSVKFGSIKSDWLGC
low complexity regions: SEG 45 3.4 3.75
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
1-660 MEALMARGALTGPLRALCLLGCLLSHAAAA
PSPIIKFPGDVAPKTDKELAVQYLNTFYGC
PKESCNLFVLKDTLKKMQKFFGLPQTGDLD
QNTIETMRKPRCGNPDVANYNFFPRKPKWD
KNQITYRIIGYTPDLDPETVDDAFARAFQV
WSDVTPLRFSRIHDGEADIMINFGRWEHGD
GYPFDGKDGLLAHAFAPGTGVGGDSHFDDD
ELWTLGEGQVVRVKYGNADGEYCKFPFLFN
GKEYNSCTDTGRSDGFLWCSTTYNFEKDGK
YGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYG
FCPETAMSTVGGNSEGAPCVFPFTFLGNKY
ESCTSAGRSDGKMWCATTANYDDDRKWGFC
PDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPD
IDLGTGPTPTLGPVTPEICKQDIVFDGIAQ
IRGEIFFFKDRFIWRTVTPRDKPMGPLLVA
TFWPELPEKIDAVYEAPQEEKAVFFAGNEY
WIYSASTLERGYPKPLTSLGLPPDVQRVDA
AFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSY
FFKGAYYLKLENQSLKSVKFGSIKSDWLGC
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
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELAVQYLNTFYGC
PKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKPKWD
KNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGD
GYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFN
GKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCVFPFTFLGNKY
ESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPDIDLGTGPTPTLGPVTPEICKQDIVFDGIAQ
IRGEIFFFKDRFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEY
WIYSASTLERGYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKFGSIKSDWLGC
1 - 660 MEALMARGAL TGPLRALCLL GCLLSHAAAA PSPIIKFPGD VAPKTDKELA VQYLNTFYGC
PKESCNLFVL KDTLKKMQKF FGLPQTGDLD QNTIETMRKP RCGNPDVANY NFFPRKPKWD
KNQITYRIIG YTPDLDPETV DDAFARAFQV WSDVTPLRFS RIHDGEADIM INFGRWEHGD
GYPFDGKDGL LAHAFAPGTG VGGDSHFDDD ELWTLGEGQV VRVKYGNADG EYCKFPFLFN
GKEYNSCTDT GRSDGFLWCS TTYNFEKDGK YGFCPHEALF TMGGNAEGQP CKFPFRFQGT
SYDSCTTEGR TDGYRWCGTT EDYDRDKKYG FCPETAMSTV GGNSEGAPCV FPFTFLGNKY
ESCTSAGRSD GKMWCATTAN YDDDRKWGFC PDQGYSLFLV AAHEFGHAMG LEHSQDPGAL
MAPIYTYTKN FRLSQDDIKG IQELYGASPD IDLGTGPTPT LGPVTPEICK QDIVFDGIAQ
IRGEIFFFKD RFIWRTVTPR DKPMGPLLVA TFWPELPEKI DAVYEAPQEE KAVFFAGNEY
WIYSASTLER GYPKPLTSLG LPPDVQRVDA AFNWSKNKKT YIFAGDKFWR YNEVKKKMDP
GFPKLIADAW NAIPDNLDAV VDLQGGGHSY FFKGAYYLKL ENQSLKSVKF GSIKSDWLGC
low complexity regions: DUST
>tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELAVQYLNTFYGC
PKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKPKWD
KNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGD
GYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFN
GKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCVFPFTFLGNKY
ESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLVAAHEFGHAMGLEHSQDPGAL
MAPIYTYTKNFRLSQDDIKGIQELYGASPDIDLGTGPTPTLGPVTPEICKQDIVFDGIAQ
IRGEIFFFKDRFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEY
WIYSASTLERGYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKFGSIKSDWLGC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem7gi|116856|sp|P08253|COG2_HUMAN
sequence: 630 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MEALMARGAL TGPLRALCLL GCLLSHAAAA PSPIIKFPGD VAPKTDKELA VQYLNTFYGC
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PKESCNLFVL KDTLKKMQKF FGLPQTGDLD QNTIETMRKP RCGNPDVANY NFFPRKPKWD
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 180
KNQITYRIIG YTPDLDPETV DDAFARAFQV WSDVTPLRFS RIHDGEADIM INFGRWEHGD
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 240
GYPFDGKDGL LAHAFAPGTG VGGDSHFDDD ELWTLGEGQV VRVKYGNADG EYCKFPFLFN
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GKEYNSCTDT GRSDGFLWCS TTYNFEKDGK YGFCPHEALF TMGGNAEGQP CKFPFRFQGT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
SYDSCTTEGR TDGYRWCGTT EDYDRDKKYG FCPETAMSTV GGNSEGAPCV FPFTFLGNKY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
ESCTSAGRSD GKMWCATTAN YDDDRKWGFC PDQGYSLFLV AAHEFGHAMG LEHSQDPGAL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 480
MAPIYTYTKN FRLSQDDIKG IQELYGASPD IDLGTGPTPT LGPVTPEICK QDIVFDGIAQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 540
IRGEIFFFKD RFIWRTVTPR DKPMGPLLVA TFWPELPEKI DAVYEAPQEE KAVFFAGNEY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 600
WIYSASTLER GYPKPLTSLG LPPDVQRVDA AFNWSKNKKT YIFAGDKFWR YNEVKKKMDP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . |
GFPKLIADAW NAIPDNLDAV VDLQGGGHSY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem7.___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: tem7.___inter___
(1 sequences)
MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELA
VQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKP
RCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQV
WSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTG
VGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDT
GRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCV
FPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLV
AAHEFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD
IDLGTGPTPTLGPVTPEICKQDIVFDGIAQIRGEIFFFKDRFIWRTVTPR
DKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLER
GYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKF
GSIKSDWLGC
(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 15 35 1.290 Certain
2 337 357 0.617 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 14 301 303
K+R profile 3.00 +
+
CYT-EXT prof - 0.59
-0.09
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 0.04
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -0.3333
NEG: 1.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: 0.67
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1
Loop length 14 625
K+R profile 3.00
+
CYT-EXT prof -
0.28
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): -0.3333
NEG: 1.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
"tem7" 660
15 35 #t 1.28958
337 357 #f 0.616667
************************************
*TOPPREDM with prokaryotic function*
************************************
tem7.___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: tem7.___inter___
(1 sequences)
MEALMARGALTGPLRALCLLGCLLSHAAAAPSPIIKFPGDVAPKTDKELA
VQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKP
RCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQV
WSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTG
VGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDT
GRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGT
SYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCV
FPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLV
AAHEFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPD
IDLGTGPTPTLGPVTPEICKQDIVFDGIAQIRGEIFFFKDRFIWRTVTPR
DKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLER
GYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDP
GFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKF
GSIKSDWLGC
(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 15 35 1.290 Certain
2 337 357 0.617 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 14 301 303
K+R profile 3.00 +
+
CYT-EXT prof - 0.59
-0.09
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 0.04
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -0.3333
NEG: 1.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: 0.67
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1
Loop length 14 625
K+R profile 3.00
+
CYT-EXT prof -
0.28
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): -0.3333
NEG: 1.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
"tem7" 660
15 35 #t 1.28958
337 357 #f 0.616667
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem7.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 14:06:27 2000
File: /people/maria/tem7.___saps___
ID tem7gi|116856|sp|P08253|COG2_HUMAN
DE 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
number of residues: 660; molecular weight: 73.9 kdal
1 MEALMARGAL TGPLRALCLL GCLLSHAAAA PSPIIKFPGD VAPKTDKELA VQYLNTFYGC
61 PKESCNLFVL KDTLKKMQKF FGLPQTGDLD QNTIETMRKP RCGNPDVANY NFFPRKPKWD
121 KNQITYRIIG YTPDLDPETV DDAFARAFQV WSDVTPLRFS RIHDGEADIM INFGRWEHGD
181 GYPFDGKDGL LAHAFAPGTG VGGDSHFDDD ELWTLGEGQV VRVKYGNADG EYCKFPFLFN
241 GKEYNSCTDT GRSDGFLWCS TTYNFEKDGK YGFCPHEALF TMGGNAEGQP CKFPFRFQGT
301 SYDSCTTEGR TDGYRWCGTT EDYDRDKKYG FCPETAMSTV GGNSEGAPCV FPFTFLGNKY
361 ESCTSAGRSD GKMWCATTAN YDDDRKWGFC PDQGYSLFLV AAHEFGHAMG LEHSQDPGAL
421 MAPIYTYTKN FRLSQDDIKG IQELYGASPD IDLGTGPTPT LGPVTPEICK QDIVFDGIAQ
481 IRGEIFFFKD RFIWRTVTPR DKPMGPLLVA TFWPELPEKI DAVYEAPQEE KAVFFAGNEY
541 WIYSASTLER GYPKPLTSLG LPPDVQRVDA AFNWSKNKKT YIFAGDKFWR YNEVKKKMDP
601 GFPKLIADAW NAIPDNLDAV VDLQGGGHSY FFKGAYYLKL ENQSLKSVKF GSIKSDWLGC
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 47( 7.1%); C : 19( 2.9%); D+ : 54( 8.2%); E : 33( 5.0%); F+ : 47( 7.1%)
G : 66(10.0%); H : 10( 1.5%); I : 25( 3.8%); K : 45( 6.8%); L : 47( 7.1%)
M : 12( 1.8%); N : 24( 3.6%); P : 44( 6.7%); Q : 19( 2.9%); R : 26( 3.9%)
S : 29( 4.4%); T : 42( 6.4%); V : 26( 3.9%); W : 15( 2.3%); Y : 30( 4.5%)
KR : 71 ( 10.8%); ED : 87 ( 13.2%); AGP : 157 ( 23.8%);
KRED : 158 ( 23.9%); KR-ED : -16 ( -2.4%); FIKMNY : 183 ( 27.7%);
LVIFM : 157 ( 23.8%); ST : 71 ( 10.8%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0-0000+000 0000+00000 0000000000 00000+000- 000+0-+-00 0000000000
61 0+-0000000 +-00++00+0 0000000-0- 0000-00++0 +0000-0000 0000++0+0-
121 +00000+000 000-0-0-00 --000+0000 00-0000+00 +00-0-0-00 0000+0-00-
181 0000-0+-00 0000000000 000-000--- -00000-000 0+0+0000-0 -00+000000
241 0+-00000-0 0+0-000000 00000-+-0+ 000000-000 000000-000 0+000+0000
301 00-0000-0+ 0-00+00000 --0-+-++00 000-000000 0000-00000 00000000+0
361 -000000+0- 0+00000000 0---++0000 0-00000000 000-000000 0-000-0000
421 00000000+0 0+000--0+0 00-000000- 0-00000000 000000-00+ 0-000-0000
481 0+0-0000+- +000+0000+ -+00000000 0000-00-+0 -000-000-- +0000000-0
541 00000000-+ 000+000000 000-00+0-0 00000+0++0 00000-+00+ 00-0+++0-0
601 000+000-00 0000-00-00 0-00000000 00+00000+0 -0000+00+0 000+0-0000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Negative charge clusters (cmin = 11/30 or 15/45 or 18/60): none
Mixed charge clusters (cmin = 16/30 or 22/45 or 27/60): 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 | 35 | 10 | 10 | 13 | 11 | 12 | 16 | 6 | 8 |
lmin1 6 | 7 | 9 | 43 | 12 | 12 | 16 | 14 | 15 | 19 | 8 | 10 |
lmin2 7 | 8 | 11 | 47 | 13 | 14 | 18 | 16 | 17 | 21 | 9 | 11 |
(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: 1, at 595;
- runs >= 4: 1, at 208;
* runs >= 5: 2, at 324; 382;
0 runs >= 24: 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-17-C-3-C-37-C-4-C-36-C-130-C-13-C-11-C-14-C-16-C-13-C-11-C-14-C-16-C-13-C-11-C-14-C-78-C-190-C-0-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-17-C-3-C-3-H-33-C-4-C-36-C-60-H-14-H-14-H-12-H-26-C-13-C-11-C-14-C-1-H-14-C-13-C-11-C-14-C-16-C-13-C-11-C-14-C-12-H-3-H-5-H-55-C-158-H-31-C-0-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
Aligned matching blocks:
[ 227- 228]-( 4)-[ 233- 237]-( 8)-[ 246- 262]-( 7)-[ 270- 275]
[ 285- 286]-( 4)-[ 291- 295]--------[ ]--------[ 328- 333]
[ ]--------[ ]--------[ 362- 378]-( 7)-[ 386- 391]
[ 233- 237] CKFPF
[ 291- 295] CKFPF
[ 246- 262] SCTDTGRSDGFLWCSTT
[ 362- 378] SCTSAGRSDGKMWCATT
[ 270- 275] KYGFCP
[ 328- 333] KYGFCP
[ 386- 391] KWGFCP
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: 9
Aligned matching blocks:
[ 302- 334] a-ocoo-s+o-sa+acsoo--a-+-++asicp-
[ 360- 392] a-ocooss+o-s+macsoosna---++asicp-
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 35 (Expected range: 19-- 55)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 10 (6-10) 4 (11-20) 9 (>=21) 13
3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 15/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 13 (Expected range: 4-- 29)
7 +plets (f+: 10.8%), 6 -plets (f-: 13.2%)
Total number of charge altplets: 15 (Critical number: 33)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 2 (6-10) 0 (11-20) 2 (>=21) 10
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
14- 25 3 L.. 4 4 0
27- 30 1 A 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
411- 470 10 i...00000. 6 6 /0/./././0/2/2/2/2/./
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
171- 424 (2.) I( 253)I 1 of 26 0.0001 large maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Peptidase_M10 Matrixin 402.5 4.1e-117 1
fn2 Fibronectin type II domain 272.3 3.9e-103 3
hemopexin Hemopexin 203.3 3.7e-57 4
PG_binding_1 Putative peptidoglycan binding domain -17.1 17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PG_binding_1 1/1 44 101 .. 1 67 [] -17.1 17
Peptidase_M10 1/1 53 214 .. 1 171 [] 402.5 4.1e-117
fn2 1/3 233 274 .. 1 42 [] 92.4 4e-34
fn2 2/3 291 332 .. 1 42 [] 91.9 6.5e-34
fn2 3/3 349 390 .. 1 42 [] 104.0 1.5e-38
hemopexin 1/4 475 518 .. 1 50 [] 44.3 2.7e-09
hemopexin 2/4 520 563 .. 1 50 [] 56.1 7.6e-13
hemopexin 3/4 568 615 .. 1 50 [] 75.0 1.6e-18
hemopexin 4/4 617 660 .] 1 50 [] 33.7 4.2e-06
Alignments of top-scoring domains:
PG_binding_1: domain 1 of 1, from 44 to 101: score -17.1, E = 17
*->sGeaVkqlQsaLaalgfyPDkgakkggvDGvfGpkTkaAVkaFQkam
+ ++ +++Q+ L+ + P k ++ v +k+ +k++Qk++
tem7gi|116 44 KTDKELAVQY-LNTFYGCP-KESCNLFV-------LKDTLKKMQKFF 81
GLtaDGivGpaTkkaLkals<-*
GL+++G + +T+ + +
tem7gi|116 82 GLPQTGDLDQNTIETMRKPR 101
Peptidase_M10: domain 1 of 1, from 53 to 214: score 402.5, E = 4.1e-117
*->YLekfYylpksnfrqstrkkasnslveKlkeMQkFfGLpvTGkLDsn
YL++fY++pk++++ ++l+++lk+MQkFfGLp+TG+LD+n
tem7gi|116 53 YLNTFYGCPKESCN-------LFVLKDTLKKMQKFFGLPQTGDLDQN 92
TlevMkkPRCGVPDVgefrtfPgspkWsknnllTYrIvNYTpDLpredVD
T+e+M+kPRCG+PDV+++++fP++pkW+kn+ +TYrI++YTpDL++e+VD
tem7gi|116 93 TIETMRKPRCGNPDVANYNFFPRKPKWDKNQ-ITYRIIGYTPDLDPETVD 141
dairrAFqvWsdVtPLtFtrvsdgeADImIsFargeHGDfypFDGkgGlL
da++rAFqvWsdVtPL+F+r++dgeADImI+F+r+eHGD+ypFDGk+GlL
tem7gi|116 142 DAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLL 191
AHAFaPGpGigIGDAHFDddEtWT<-*
AHAFaPG+G+g GD+HFDddE+WT
tem7gi|116 192 AHAFAPGTGVG-GDSHFDDDELWT 214
fn2: domain 1 of 3, from 233 to 274: score 92.4, E = 4e-34
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
C+FPF++nGk+Y+sCT++GRsdg+lWCsTT+N+++D+k+GFC
tem7gi|116 233 CKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFC 274
fn2: domain 2 of 3, from 291 to 332: score 91.9, E = 6.5e-34
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
C+FPF+++G sY+sCT+eGR+dg++WC+TT++YDrDkk+GFC
tem7gi|116 291 CKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFC 332
fn2: domain 3 of 3, from 349 to 390: score 104.0, E = 1.5e-38
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
CvFPF++ G++YesCTs+GRsdg++WC+TTaNYD+D+kwGFC
tem7gi|116 349 CVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFC 390
hemopexin: domain 1 of 4, from 475 to 518: score 44.3, E = 2.7e-09
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+D + ++r g+++FFk+++ Wr + p+ P l++++wp
tem7gi|116 475 FDGIAQIR--GEIFFFKDRFIWRTVTPR---DKPMGPLLVATFWP-E 515
lpc<-*
lp
tem7gi|116 516 LPE 518
hemopexin: domain 2 of 4, from 520 to 563: score 56.1, E = 7.6e-13
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
iDA++e ++++k+ FF G+ YW ++ t +++gyPk++++l g
tem7gi|116 520 IDAVYEAPQEEKAVFFAGNEYWIYSAST---LERGYPKPLTSL---G 560
lpc<-*
lp+
tem7gi|116 561 LPP 563
hemopexin: domain 3 of 4, from 568 to 615: score 75.0, E = 1.6e-18
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DAAf ++ ++ktY+F Gdk+Wr+++ ++++dpg+Pkli+d w+
tem7gi|116 568 VDAAFNWSKNKKTYIFAGDKFWRYNEV-KKKMDPGFPKLIADAWN-A 612
lpc<-*
+p
tem7gi|116 613 IPD 615
hemopexin: domain 4 of 4, from 617 to 660: score 33.7, E = 4.2e-06
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DA++ + +g+ YFFkG +Y ++ ++ + ++ ++ d+
tem7gi|116 617 LDAVVDLQGGGHSYFFKGAYYLKLENQ----SLKSVKFGSIKS--DW 657
lpc<-*
l+c
tem7gi|116 658 LGC 660
//
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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Peptidase_M10 Matrixin 400.5 1.6e-116 1
fn2 Fibronectin type II domain 272.3 3.9e-103 3
hemopexin Hemopexin 195.8 6e-58 4
Fragilysin Fragilysin metallopeptidase (M10C) ent 6.8 0.39 1
PG_binding_1 Putative peptidoglycan binding domain 5.8 5 1
wap WAP-type (Whey Acidic Protein) 'four-d 3.9 20 1
chitin_binding Chitin recognition protein 2.7 26 1
CX CX module 0.0 99 1
DUF144 Domain of unknown function DUF144 -0.1 69 1
Peptidase_M7 Streptomyces extracellular neutral pro -0.3 80 1
T2SP_N Bacterial type II secretion system pro -1.3 79 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PG_binding_1 1/1 74 101 .. 40 67 .] 5.8 5
Peptidase_M10 1/1 53 214 .. 1 171 [] 400.5 1.6e-116
fn2 1/3 233 274 .. 1 42 [] 92.4 4e-34
T2SP_N 1/1 293 301 .. 252 260 .] -1.3 79
fn2 2/3 291 332 .. 1 42 [] 91.9 6.5e-34
chitin_binding 1/1 316 332 .. 24 40 .] 2.7 26
wap 1/1 328 350 .. 1 23 [. 3.9 20
fn2 3/3 349 390 .. 1 42 [] 104.0 1.5e-38
Peptidase_M7 1/1 393 411 .. 74 92 .. -0.3 80
Fragilysin 1/1 400 447 .. 334 382 .] 6.8 0.39
DUF144 1/1 513 518 .. 140 145 .] -0.1 69
hemopexin 1/4 475 518 .. 1 50 [] 42.4 2.7e-11
hemopexin 2/4 520 563 .. 1 50 [] 54.3 6.9e-15
hemopexin 3/4 568 615 .. 1 50 [] 73.1 1.3e-20
CX 1/1 630 644 .. 1 18 [. 0.0 99
hemopexin 4/4 617 660 .] 1 50 [] 31.9 4.5e-08
Alignments of top-scoring domains:
PG_binding_1: domain 1 of 1, from 74 to 101: score 5.8, E = 5
*->VkaFQkamGLtaDGivGpaTkkaLkals<-*
+k++Qk++GL+++G + +T+ + +
tem7gi|116 74 LKKMQKFFGLPQTGDLDQNTIETMRKPR 101
Peptidase_M10: domain 1 of 1, from 53 to 214: score 400.5, E = 1.6e-116
*->YLekfYylpksnfrqstrkkasnslveKlkeMQkFfGLpvTGkLDsn
YL++fY++pk++++ ++l+++lk+MQkFfGLp+TG+LD+n
tem7gi|116 53 YLNTFYGCPKESCN-------LFVLKDTLKKMQKFFGLPQTGDLDQN 92
TlevMkkPRCGVPDVgefrtfPgspkWsknnllTYrIvNYTpDLpredVD
T+e+M+kPRCG+PDV+++++fP++pkW+kn+ +TYrI++YTpDL++e+VD
tem7gi|116 93 TIETMRKPRCGNPDVANYNFFPRKPKWDKNQ-ITYRIIGYTPDLDPETVD 141
dairrAFqvWsdVtPLtFtrvsdgeADImIsFargeHGDfypFDGkgGlL
da++rAFqvWsdVtPL+F+r++dgeADImI+F+r+eHGD+ypFDGk+GlL
tem7gi|116 142 DAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLL 191
AHAFaPGpGigIGDAHFDddEtWT<-*
AHAFaPG+G+g GD+HFDddE+WT
tem7gi|116 192 AHAFAPGTGVG-GDSHFDDDELWT 214
fn2: domain 1 of 3, from 233 to 274: score 92.4, E = 4e-34
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
C+FPF++nGk+Y+sCT++GRsdg+lWCsTT+N+++D+k+GFC
tem7gi|116 233 CKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFC 274
T2SP_N: domain 1 of 1, from 293 to 301: score -1.3, E = 79
*->fPlrfQGrl<-*
fP+rfQG
tem7gi|116 293 FPFRFQGTS 301
fn2: domain 2 of 3, from 291 to 332: score 91.9, E = 6.5e-34
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
C+FPF+++G sY+sCT+eGR+dg++WC+TT++YDrDkk+GFC
tem7gi|116 291 CKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFC 332
chitin_binding: domain 1 of 1, from 316 to 332: score 2.7, E = 26
*->yCGstedYCgkgCqsqC<-*
+CG+tedY + + C
tem7gi|116 316 WCGTTEDYDRDKKYGFC 332
wap: domain 1 of 1, from 328 to 350: score 3.9, E = 20
*->KpGvCPwvsipeiaalifagqCl<-*
K G+CP++ +++ ++++C+
tem7gi|116 328 KYGFCPETAMSTVGGNSEGAPCV 350
fn2: domain 3 of 3, from 349 to 390: score 104.0, E = 1.5e-38
*->CvFPFiynGksYesCTseGRsdgrlWCsTTaNYDrDkkwGFC<-*
CvFPF++ G++YesCTs+GRsdg++WC+TTaNYD+D+kwGFC
tem7gi|116 349 CVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFC 390
Peptidase_M7: domain 1 of 1, from 393 to 411: score -0.3, E = 80
*->qqYdstRvtaHEtGHvLGL<-*
q Y v aHE GH +GL
tem7gi|116 393 QGYSLFLVAAHEFGHAMGL 411
Fragilysin: domain 1 of 1, from 400 to 447: score 6.8, E = 0.39
*->vlAHElGHlLGAeHvDnekDLMYtwYtgyltPnHLSedNmvrilknl
v AHE GH +G eH ++ LM Yt y LS d i +
tem7gi|116 400 VAAHEFGHAMGLEHSQDPGALMAPIYT-YTKNFRLSQDDIKGIQELY 445
gk<-*
g
tem7gi|116 446 GA 447
DUF144: domain 1 of 1, from 513 to 518: score -0.1, E = 69
*->WPekPe<-*
WPe+Pe
tem7gi|116 513 WPELPE 518
hemopexin: domain 1 of 4, from 475 to 518: score 42.4, E = 2.7e-11
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+D + ++r g+++FFk+++ Wr + p+ P l++++wp
tem7gi|116 475 FDGIAQIR--GEIFFFKDRFIWRTVTPR---DKPMGPLLVATFWP-E 515
lpc<-*
lp
tem7gi|116 516 LPE 518
hemopexin: domain 2 of 4, from 520 to 563: score 54.3, E = 6.9e-15
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
iDA++e ++++k+ FF G+ YW ++ t +++gyPk++++l g
tem7gi|116 520 IDAVYEAPQEEKAVFFAGNEYWIYSAST---LERGYPKPLTSL---G 560
lpc<-*
lp+
tem7gi|116 561 LPP 563
hemopexin: domain 3 of 4, from 568 to 615: score 73.1, E = 1.3e-20
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DAAf ++ ++ktY+F Gdk+Wr+++ ++++dpg+Pkli+d w+
tem7gi|116 568 VDAAFNWSKNKKTYIFAGDKFWRYNEV-KKKMDPGFPKLIADAWN-A 612
lpc<-*
+p
tem7gi|116 613 IPD 615
CX: domain 1 of 1, from 630 to 644: score 0.0, E = 99
*->YYWsgkdkhYvsdtennt<-*
Y+ g +Y+++ en +
tem7gi|116 630 YFFKG---AYYLKLENQS 644
hemopexin: domain 4 of 4, from 617 to 660: score 31.9, E = 4.5e-08
*->iDAAfedrdrgktYFFkGdkYWrfdpetrqrvdpgyPklisdlwpdg
+DA++ + +g+ YFFkG +Y ++ ++ + ++ ++ d+
tem7gi|116 617 LDAVVDLQGGGHSYFFKGAYYLKLENQ----SLKSVKFGSIKS--DW 657
lpc<-*
l+c
tem7gi|116 658 LGC 660
//
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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
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 14:16:14 2000
Sequence file: tem7
----------------------------------------
Sequence tem7gi|116856|sp|P08253|COG2_HUMAN (660 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
573: NWSK
642: NQSL
Total matches: 2
Matching pattern PS00005 PKC_PHOSPHO_SITE:
45: TDK
73: TLK
96: TMR
125: TYR
250: TGR
498: TPR
644: SLK
647: SVK
652: SIK
Total matches: 9
Matching pattern PS00006 CK2_PHOSPHO_SITE:
45: TDKE
139: TVDD
205: SHFD
214: TLGE
246: SCTD
300: TSYD
319: TTED
434: SQDD
498: TPRD
546: STLE
Total matches: 10
Matching pattern PS00008 MYRISTYL:
21: GCLLSH
82: GLPQTG
198: GTGVGG
226: GNADGE
284: GNAEGQ
342: GNSEGA
410: GLEHSQ
625: GGGHSY
651: GSIKSD
Total matches: 9
Matching pattern PS00343 GRAM_POS_ANCHORING:
83: LPQTGD
Total matches: 1
Matching pattern PS00023 FIBRONECTIN_2:
233: CKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFC
291: CKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFC
349: CVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFC
Total matches: 3
Matching pattern PS00024 HEMOPEXIN:
606: IADAWNAIPDNLDAVV
Total matches: 1
Matching pattern PS00142 ZINC_PROTEASE:
400: VAAHEFGHAM
Total matches: 1
Matching pattern PS00546 CYSTEINE_SWITCH:
100: PRCGNPDV
Total matches: 1
Total no of hits in this sequence: 37
========================================
1314 pattern(s) searched in 1 sequence(s), 660 residues.
Total no of hits in all sequences: 37.
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 tem7
***** 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, 660 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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2) (GELATINASE A) (TBE-1)
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= tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE
PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2)
(GELATINASE A) (TBE-1)
(660 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
MATH The Meprin associated TRAF homology domain 23 2.0
KELCH Kelch repeat- beta propeller like domain 22 3.0
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 21 3.7
CALC Calcineurin like Phosphoesterase domain 21 4.3
UB Ubiquitin domain 21 5.4
SGTP Small GTPAses 21 5.4
UBHYD Ubiquitin C-terminal hydrolase domain 21 5.9
PCNA Proliferating Cell nuclear antigen like domain 21 7.0
CATH Cathepsin like protease domain 21 7.1
KR Kringle domain (Adhesion module) 20 8.1
HECT A ubiquitin conjugating enzyme domain 20 8.2
AP2 A plant specific DNA binding domain (Apetala 2 like) 20 8.3
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 22.5 bits (48), Expect = 2.0
Identities = 7/50 (14%), Positives = 14/50 (28%), Gaps = 5/50 (10%)
Query: 574 WSKNKKTYIFAGDKFWRYNEVKKKMDPGFPKLIADAWNAIPD-NLDAVVD 622
+ + + + D GF K I + + D + D
Sbjct: 107 LNAKGEETKAMESQRAYRFV--QGKDWGFKKFI--RRDFLLDEANGLLPD 152
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 21.9 bits (46), Expect = 3.0
Identities = 22/92 (23%), Positives = 25/92 (26%), Gaps = 6/92 (6%)
Query: 317 CGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCVFPFTFLGNK-YESCTSAGRSDGKMWC 375
G ++ Y F ET T G+ GNK Y G G C
Sbjct: 227 MGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKLY----VVGGYFGIQRC 282
Query: 376 ATTANYD-DDRKWGFCPDQGYSLFLVAAHEFG 406
T YD W YSL A
Sbjct: 283 KTLDCYDPTLDVWNSITTVPYSLIPTAFVSTW 314
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 21.5 bits (45), Expect = 3.7
Identities = 1/33 (3%), Positives = 7/33 (21%)
Query: 55 NTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTG 87
++ + + + + G
Sbjct: 66 SSLAKWLGQLHKQRLRAPKNPPVAICWINSYVG 98
>CALC Calcineurin like Phosphoesterase domain
Length = 274
Score = 21.3 bits (44), Expect = 4.3
Identities = 3/31 (9%), Positives = 6/31 (18%)
Query: 560 GLPPDVQRVDAAFNWSKNKKTYIFAGDKFWR 590
Q + + + GD
Sbjct: 37 TQASFAQVLKEIQQENNEFDVILATGDLVQD 67
>UB Ubiquitin domain
Length = 128
Score = 20.9 bits (44), Expect = 5.4
Identities = 12/62 (19%), Positives = 16/62 (25%), Gaps = 12/62 (19%)
Query: 46 DKELAVQYLNTFYGCPKESCNLFVLKDTLKKMQK---FFGLPQTGDLDQNTIETMRKPRC 102
V L G + S K K + LP RK +C
Sbjct: 65 STLHLVLRLRG--GIIEPSLKALASKYNCDKSVCRKCYARLPPRATNC-------RKRKC 115
Query: 103 GN 104
G+
Sbjct: 116 GH 117
>SGTP Small GTPAses
Length = 164
Score = 20.8 bits (44), Expect = 5.4
Identities = 14/60 (23%), Positives = 20/60 (33%), Gaps = 12/60 (20%)
Query: 204 DSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTY 263
+ F DD T+G K N G+Y K DT + F + +Y
Sbjct: 22 EKKFKDDSNHTIGVE--FGSKIINVGGKYVKL----------QIWDTAGQERFRSVTRSY 69
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 20.7 bits (43), Expect = 5.9
Identities = 7/27 (25%), Positives = 12/27 (43%)
Query: 206 HFDDDELWTLGEGQVVRVKYGNADGEY 232
FDDD + + + + YG D +
Sbjct: 261 KFDDDVVSRCTKEEAIEHNYGGHDDDL 287
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 20.6 bits (43), Expect = 7.0
Identities = 11/83 (13%), Positives = 19/83 (22%), Gaps = 9/83 (10%)
Query: 58 YGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKP 117
+ +ES + L FG T T+ +R G F +
Sbjct: 73 FVIQEESVTFRINLTILLDCLSIFGSSPTPG----TLTALRMCYQGYGH--PLMLFLEEG 126
Query: 118 KWDKNQITYRIIGYTPDLDPETV 140
P+ +
Sbjct: 127 GVVT-VCKITT--QEPEETLDFD 146
>CATH Cathepsin like protease domain
Length = 371
Score = 20.6 bits (43), Expect = 7.1
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 426 TYTKNFRLSQDDIKGIQELYGASPDID 452
T T D+IK +Q+ GA P I
Sbjct: 254 TGTSLITGPTDEIKQLQKAIGAKPIIK 280
>KR Kringle domain (Adhesion module)
Length = 86
Score = 20.3 bits (42), Expect = 8.1
Identities = 6/22 (27%), Positives = 9/22 (40%), Gaps = 2/22 (9%)
Query: 369 SDGKMWCATTANYDDDRKWGFC 390
+D + WC D W +C
Sbjct: 60 NDERPWCYVVK--DSALSWEYC 79
>HECT A ubiquitin conjugating enzyme domain
Length = 255
Score = 20.5 bits (43), Expect = 8.2
Identities = 7/56 (12%), Positives = 22/56 (38%), Gaps = 8/56 (14%)
Query: 575 SKNKKTYIFAGDK--FWRYNEVKKKMDP---GFPKLIADAWNAIPDNLDAVVDLQG 625
N+K Y+ ++ +R +E+ +++ G ++ ++ + G
Sbjct: 179 FSNRKEYV---ERAIEYRLHEMDRQVAAVREGMSWIVPVPLLSLLTAKQLEQMVCG 231
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 20.1 bits (41), Expect = 8.3
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 475 FDGIAQIRGEIFFFKDRFIW 494
+DG+ Q+ E F +W
Sbjct: 169 YDGLTQLGNEFIFSDSADLW 188
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 12
Number of calls to ALIGN: 12
Length of query: 660
Total length of test sequences: 20182
Effective length of test sequences: 16839.0
Effective search space size: 10582953.8
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= tem7gi|116856|sp|P08253|COG2_HUMAN 72 KD TYPE IV COLLAGENASE
PRECURSOR (72 KD GELATINASE) (MATRIX METALLOPROTEINASE-2) (MMP-2)
(GELATINASE A) (TBE-1)
(660 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2829864 [79..325] Metzincin-like 252 1e-68
gi|116871 [267..480] 4-bladed beta-propeller 221 3e-59
gi|1616941 [10..247] Metzincin-like 211 4e-56
gi|1070649 [50..283] 4-bladed beta-propeller 184 5e-48
gi|1731806 [90..289] Metzincin-like 120 9e-29
gi|1815643 [227..431] Metzincin-like 32 0.036
gi|1938449 [68..180] DNA-binding 3-helical bundle 29 0.19
gi|2809057 [242..451] Metzincin-like 29 0.32
gi|1943527 [1..83] Zn2+ DD-carboxypeptidase, the N-terminal ... 28 0.39
gi|128242 [2..526] Nitrogenase iron-molybdenum protein, alph... 27 0.99
gi|544020 [86..429] Nitrogenase iron-molybdenum protein, alp... 25 3.8
gi|114277 [1..331] Glutaminase/Asparaginase 25 4.5
gi|1786987 [62..480] Aconitase, first 3 domains 25 4.8
gi|407037 [59..572] Heme-dependent peroxidases 24 6.9
gi|2497951 [161..384] Creatinase/methionine aminopeptidase 24 7.6
gi|1710095 [2..139] Lipocalins 24 8.6
gi|116280 [152..349] CheB methylesterase domain (C-terminal ... 24 8.8
gi|1075225 [35..246] R1 subunit of ribonucleotide reductase,... 24 9.4
>gi|2829864 [79..325] Metzincin-like
Length = 247
Score = 252 bits (639), Expect = 1e-68
Identities = 91/412 (22%), Positives = 125/412 (30%), Gaps = 200/412 (48%)
Query: 69 VLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVAN------------------- 109
+LK+ ++ Q+ F L TG LD+ T++ + PRCGNPDV N
Sbjct: 5 ILKNAVEMYQRNFQLNVTGVLDELTLKHVVIPRCGNPDVVNGTSTMHSGRKTFEVSFAGR 64
Query: 110 ---------YNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFS 160
Y+FFP +P+W +N+ + E V F+RAF W +VTPL F+
Sbjct: 65 GQRFHAVKHYSFFPGEPRWPRNRRDLTYAFDPRNALTEEVKSVFSRAFTRWEEVTPLTFT 124
Query: 161 RIH-DGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGEGQ 219
R+ +DI I F EHGDG PFDG LAHAF+P T G H D +E W +
Sbjct: 125 RVERFSTSDISIGFYSGEHGDGEPFDGPMRTLAHAFSPPT---GHFHLDGEENWIV---- 177
Query: 220 VVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEAL 279
Sbjct: 177 ------------------------------------------------------------ 177
Query: 280 FTMGGNAEGQPCKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMST 339
Sbjct: 177 ------------------------------------------------------------ 177
Query: 340 VGGNSEGAPCVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFC-PDQGYSLF 398
+ GF + L
Sbjct: 178 ------------------------------------------SGEGGDGFISVSEAVDLE 195
Query: 399 LVAAHEFGHAMGLEHSQDPGALMAPIY-TYTKNFRLSQDDIKGIQELYGASP 449
VA HE GH +GL HS G++M P T + L+ DD++G+Q LYGA+P
Sbjct: 196 SVAVHEIGHLLGLGHSSVEGSIMYPTIRTGRRKVDLTTDDVEGVQYLYGANP 247
>gi|116871 [267..480] 4-bladed beta-propeller
Length = 214
Score = 221 bits (558), Expect = 3e-59
Identities = 69/218 (31%), Positives = 102/218 (46%), Gaps = 12/218 (5%)
Query: 447 ASPDIDLGTGPTPTLGP-VTPEICKQDIVFDGIAQIRGEIFFFKDRFIWRTVTPRDKPMG 505
P + T L P P+ C + FD ++ IRGE+FFFK F+WR + +P
Sbjct: 5 LGPQAGIDTNEIAPLEPDAPPDAC--EASFDAVSTIRGELFFFKAGFVWRLRGGQLQPGY 62
Query: 506 PLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLERGYPKPLTSLGLPPDV 565
P L + W LP +DA +E Q FF G +YW+Y P PLT LGL
Sbjct: 63 PALASRHWQGLPSPVDAAFEDAQ-GHIWFFQGAQYWVYDGEKP-VLGPAPLTELGLVRFP 120
Query: 566 QRVDAAFNWSK-NKKTYIFAGDKFWRYNEVKKKMDPGFPKLIADAWNAIPDNLDAVVDLQ 624
V AA W K Y F G +WR++ +++D P+ D W +P +DA
Sbjct: 121 --VHAALVWGPEKNKIYFFRGRDYWRFHPSTRRVDSPVPRRATD-WRGVPSEIDAAF-QD 176
Query: 625 GGGHSYFFKGAYYLKLENQSLKSVKF--GSIKSDWLGC 660
G++YF +G Y K + +K+++ + D+ GC
Sbjct: 177 ADGYAYFLRGRLYWKFDPVKVKALEGFPRLVGPDFFGC 214
>gi|1616941 [10..247] Metzincin-like
Length = 238
Score = 211 bits (532), Expect = 4e-56
Identities = 33/248 (13%), Positives = 60/248 (23%), Gaps = 40/248 (16%)
Query: 70 LKDTLKKMQKFFGLPQTG----DLDQNTIETMRKPRCGNPDVANYN-----------FFP 114
+ + L + G +DQ + +R+ +
Sbjct: 9 VDNFLHAYARGPDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDF 68
Query: 115 RKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGE-ADIMINF 173
W Y + ++ + Q WSDVT + F G D+
Sbjct: 69 FNTPWKYVSDIYSLGKFSAFS--AQQQAQAKLSLQSWSDVTNIHFVDAGQGHQGDLTFGN 126
Query: 174 GRWEHGDGYPFDGKDGLLAHAFAPGTG--VGGDSHFDDDELWTLGEGQVVRVKYGNADGE 231
F G A AF P + G S + + ++ A+
Sbjct: 127 ----------FSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSAN--------VNPANAN 168
Query: 232 YCKFPFLFN-GKEYNSCTDTGRSDGFLWCSTTYNFEKD-GKYGFCPHEALFTMGGNAEGQ 289
Y + G T + + +D Y + G + +G
Sbjct: 169 YGRQTLTHEIGHTLGLSTPDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGA 228
Query: 290 PCKFPFRF 297
P
Sbjct: 229 YSSAPLLD 236
Score = 91.5 bits (225), Expect = 3e-20
Identities = 17/106 (16%), Positives = 25/106 (23%), Gaps = 7/106 (6%)
Query: 366 AGRSDGKMWCATTANYDDDRKW--GFCPDQGYSLFLVAAHEFGHAMGLEHSQDPGALMAP 423
A D + Y + + P HE GH +GL P
Sbjct: 137 AFLPDVPDALKGQSWYLINSSYSANVNPANANYGRQTLTHEIGHTLGLSTPDYNAGEGDP 196
Query: 424 IYT-YTKNFRLSQDDIKGIQELYGASPDIDLGTGPTPTLGPVTPEI 468
Y T + E D + P+ +I
Sbjct: 197 TYADATYAEDTRAYSVMSYWEEQNTGQDFK----GAYSSAPLLDDI 238
Score = 33.9 bits (77), Expect = 0.009
Identities = 9/58 (15%), Positives = 13/58 (21%), Gaps = 1/58 (1%)
Query: 299 GTSYDSCTTEGRTDGYRWCGTTEDYDRDK-KYGFCPETAMSTVGGNSEGAPCVFPFTF 355
G + T + Y D Y G + +GA P
Sbjct: 179 GHTLGLSTPDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLD 236
>gi|1070649 [50..283] 4-bladed beta-propeller
Length = 234
Score = 184 bits (463), Expect = 5e-48
Identities = 41/201 (20%), Positives = 73/201 (35%), Gaps = 25/201 (12%)
Query: 467 EICKQDIVFDGIA-QIRGEIFFFKDRFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYE 525
E C FD G + FFKD F+W++ L++ W +DA
Sbjct: 1 EQCSDGWSFDATTLDDNGTMLFFKDEFVWKS-----HRGIRELISERWKNFIGPVDAFRH 55
Query: 526 APQEEKAVFFAGNEYWIYSASTLERGYPKPLTSLGLPPDVQRVDAAFNWSK----NKKTY 581
G++ W+Y ++GYPK L P +DAA + ++
Sbjct: 56 GH--TSVYLIKGDKGWVYPPDKKDKGYPKLL-QDEFPLIPFPLDAAVECHRGECQDEGIL 112
Query: 582 IFAGDKFWRYNEVKKKMDPGFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLE 641
F G++ W ++ +W A+ + A+ + G Y F+G +L+
Sbjct: 113 FFQGNRKWFWDLTTGTKK-------ERSWPAVGNCTSAL---RWLGRYYCFQGNQFLRFN 162
Query: 642 NQSLKSVKF--GSIKSDWLGC 660
S + ++ +L C
Sbjct: 163 PVSGEVPPGYPLDVRDYFLSC 183
Score = 44.7 bits (105), Expect = 5e-06
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 558 SLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYN 592
D V +A + TY+F+G +WR +
Sbjct: 200 HESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRLD 234
Score = 36.5 bits (84), Expect = 0.001
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 610 WNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLE 641
PD + + + G +Y F G++Y +L+
Sbjct: 203 TRCDPDLVLSAMVSDNHGATYVFSGSHYWRLD 234
Score = 31.8 bits (72), Expect = 0.034
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 513 WPELPEKIDAVYEAPQEEKAVFFAGNEYWIY 543
P+ + + + F+G+ YW
Sbjct: 203 TRCDPDLVLSAMVSDNHGATYVFSGSHYWRL 233
>gi|1731806 [90..289] Metzincin-like
Length = 200
Score = 120 bits (298), Expect = 9e-29
Identities = 17/105 (16%), Positives = 28/105 (26%), Gaps = 5/105 (4%)
Query: 113 FPRKPKWDKNQITYRIIGYTPDLDPETVD-DAFARAFQVWSDVTPLRFSRIHDGEADIMI 171
+ W K+ + Y F +A Q + +T +RF + I
Sbjct: 4 NDARFLWPKSADGIVPVPYNLSYSYNADQLALFKKAIQEFEALTCVRFVPWTTEVNFLNI 63
Query: 172 NFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLG 216
+G GK+G G + LG
Sbjct: 64 MS----NGGCGSLIGKNGGAQRLELDANGCMNMGIIQHELNHALG 104
Score = 66.3 bits (160), Expect = 1e-12
Identities = 15/87 (17%), Positives = 24/87 (27%), Gaps = 11/87 (12%)
Query: 389 FCPDQGYSLFLVAAHEFGHAMGLEHSQDPG------ALMAPIY--TYTKNFRLSQDDIKG 440
G + HE HA+G H Q+ + + K F + G
Sbjct: 83 ELDANGCMNMGIIQHELNHALGFYHEQNRSDRDDYVIIHTENIIPDFLKMFEKYNTNNLG 142
Query: 441 IQELYGASPDID---LGTGPTPTLGPV 464
I+ Y + T+ P
Sbjct: 143 IEYDYASVMHYSRYHYSINGDITIEPK 169
>gi|1815643 [227..431] Metzincin-like
Length = 205
Score = 31.9 bits (72), Expect = 0.036
Identities = 9/47 (19%), Positives = 14/47 (29%), Gaps = 10/47 (21%)
Query: 392 DQGYSLFLVA---AHEFGHAMGLEHSQD-------PGALMAPIYTYT 428
+ ++ A GH +GLEH P +M
Sbjct: 123 VEQFATHWNGELLAQSIGHLLGLEHDTTACSCEPSPECVMRQQPGRV 169
>gi|1938449 [68..180] DNA-binding 3-helical bundle
Length = 113
Score = 29.4 bits (65), Expect = 0.19
Identities = 17/55 (30%), Positives = 23/55 (40%), Gaps = 8/55 (14%)
Query: 603 PKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKFGSIKSDW 657
P +A+ W A N D G YF+ N +LK V +G +KS W
Sbjct: 36 PHKVAELWGAATGNPGMNYDKMSRGLRYFY--------TNNTLKKVSWGFLKSFW 82
>gi|2809057 [242..451] Metzincin-like
Length = 210
Score = 28.8 bits (64), Expect = 0.32
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 392 DQGYSLFLVAAHEFGHAMGLEH 413
D G AHE GH + H
Sbjct: 133 DDGLQAAFTTAHELGHVFNMPH 154
>gi|1943527 [1..83] Zn2+ DD-carboxypeptidase, the N-terminal domain
Length = 83
Score = 28.4 bits (63), Expect = 0.39
Identities = 6/28 (21%), Positives = 11/28 (38%)
Query: 71 KDTLKKMQKFFGLPQTGDLDQNTIETMR 98
K +++ Q +GL G T +
Sbjct: 47 KAAVQRFQSAYGLAADGIAGPATFNKIY 74
>gi|128242 [2..526] Nitrogenase iron-molybdenum protein, alpha and beta chains
Length = 525
Score = 26.8 bits (59), Expect = 0.99
Identities = 11/35 (31%), Positives = 14/35 (39%), Gaps = 3/35 (8%)
Query: 53 YLNTFYGCPKESCNLFVLKDT---LKKMQKFFGLP 84
+ T YG P CN + L+ M K F P
Sbjct: 271 MMETKYGIPWIKCNFIGVDGIVETLRDMAKCFDDP 305
>gi|544020 [86..429] Nitrogenase iron-molybdenum protein, alpha and beta chains
Length = 344
Score = 25.2 bits (55), Expect = 3.8
Identities = 6/35 (17%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 53 YLNTFYGCPKESCNLFVLKDT---LKKMQKFFGLP 84
Y +G P S D ++++Q++
Sbjct: 147 YFEKEFGMPYISTIPMGAVDMAECIRQIQRYVNTL 181
>gi|114277 [1..331] Glutaminase/Asparaginase
Length = 331
Score = 25.0 bits (54), Expect = 4.5
Identities = 16/101 (15%), Positives = 28/101 (26%), Gaps = 15/101 (14%)
Query: 511 TFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSAS----TLERGYPKPLTSLGLPPDVQ 566
L +++ + + P V G + +A + P L P
Sbjct: 65 KELLSLARQVNDLVKKPSVNGVVITHGTDTMEETAFFLNLVVHTDKPIVLVGSMRPSTAL 124
Query: 567 RVDAAFNW-----------SKNKKTYIFAGDKFWRYNEVKK 596
D N +KNK + D + +V K
Sbjct: 125 SADGPLNLYSAVALASSNEAKNKGVMVLMNDSIFAARDVTK 165
>gi|1786987 [62..480] Aconitase, first 3 domains
Length = 419
Score = 24.9 bits (54), Expect = 4.8
Identities = 8/26 (30%), Positives = 10/26 (37%)
Query: 193 HAFAPGTGVGGDSHFDDDELWTLGEG 218
A +G DSH L T+ G
Sbjct: 85 MAGGGKMILGSDSHTRYGALGTMAVG 110
>gi|407037 [59..572] Heme-dependent peroxidases
Length = 514
Score = 24.1 bits (52), Expect = 6.9
Identities = 3/23 (13%), Positives = 9/23 (39%)
Query: 434 SQDDIKGIQELYGASPDIDLGTG 456
++ ++ LY ++L
Sbjct: 412 EKEMAAELKALYHDIDAMELYPA 434
>gi|2497951 [161..384] Creatinase/methionine aminopeptidase
Length = 224
Score = 24.1 bits (52), Expect = 7.6
Identities = 7/47 (14%), Positives = 16/47 (33%), Gaps = 7/47 (14%)
Query: 403 HEFGHAMGLEHSQDP-------GALMAPIYTYTKNFRLSQDDIKGIQ 442
G+A+G++ S+ + P T+ ++ G
Sbjct: 159 SRCGYAIGIDWSEPTASLKDGDMTKLKPNMTFHLMLGNWIEEDFGYV 205
>gi|1710095 [2..139] Lipocalins
Length = 138
Score = 24.1 bits (52), Expect = 8.6
Identities = 12/79 (15%), Positives = 26/79 (32%), Gaps = 12/79 (15%)
Query: 556 LTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFW-------RYNEVKKKMDPGFPKLIAD 608
L +LG+ ++++ A + D F+ R E+ K+ F + D
Sbjct: 19 LKALGVNMMMRKIAVAAASKPAVEIKQENDDTFYIKTSTTVRTTEINFKIGEEFEEQTVD 78
Query: 609 AWNAIPDNLDAVVDLQGGG 627
++V +
Sbjct: 79 G-----RPCKSLVKWESEN 92
>gi|116280 [152..349] CheB methylesterase domain (C-terminal residues 152-349)
Length = 198
Score = 23.7 bits (51), Expect = 8.8
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 598 MDPGFPKLIADAWNAI--PDNLDAVVDLQ-GGGHSYFFKGAYYLKLENQS 644
M PGF + A+ N + +A + GH+Y G +++L
Sbjct: 40 MPPGFTRSFAERLNKLCQISVKEAEDGERVLPGHAYIAPGDKHMELARSG 89
>gi|1075225 [35..246] R1 subunit of ribonucleotide reductase, N-terminal domain
Length = 212
Score = 23.7 bits (51), Expect = 9.4
Identities = 9/65 (13%), Positives = 18/65 (26%), Gaps = 6/65 (9%)
Query: 488 FKDRFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSAST 547
F ++ V + M A E+ D + + + + +
Sbjct: 88 FDPPRLYDHVKKLVR-MEKYDQALLDDYTREEWDTMDGFIDHWRDM-----TFSYAAVKQ 141
Query: 548 LERGY 552
LE Y
Sbjct: 142 LEGKY 146
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 18
Number of calls to ALIGN: 26
Length of query: 660
Total length of test sequences: 256703
Effective length of test sequences: 211865.0
Effective search space size: 131976727.9
Initial X dropoff for ALIGN: 25.0 bits