analysis of sequence from tem19
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem19partial
RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVALTATLVLIC
AGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIV
FSTRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS
VIIALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVN
DGFQALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKI
NDSVTLNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHCSDG
SILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEEDDDGLPKKKWPTVD
ASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMR
RPSSPRKWYSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPL
NNAYHTSSPPPAPIYTPPPPAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPS
RPPPRPSV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem19partial
. . . . .
1 RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA 50
___________EEEEEEE____________________________HHHH
. . . . .
51 LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV 100
HHHHHHEEE__________________EEEEEE_____EEEE_HHHHHHH
. . . . .
101 EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG 150
HHHHHHH_HHHHHHHEEEE______EEE_____HHHHHHHHHHHHH____
. . . . .
151 DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN 200
_______HHHHHHHHHHH_______EEEEEEE_______EEEEEHHHHHH
. . . . .
201 RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL 250
H_____EEEEEEE_____HHHHHHHHHH_EEEE_____HHHHHHHHHHHH
. . . . .
251 KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT 300
_HHHHHHHH__________EEEEEEE___________EEEEE______EE
. . . . .
301 LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH 350
E_________EEE_____HHHHH_HHHHHHHHH_____EEEEEEEEEE__
. . . . .
351 CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED 400
_______HHHHHHHHHHHHHHHHHH____EEEEEEEE_____________
. . . . .
401 DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA 450
___________________________EEE_______HHHHHHHHHHHHH
. . . . .
451 RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD 500
HH__________________________________HHHHHHHHHHH___
. . . . .
501 RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP 550
_EEEEE_______EEEEEEE______________________________
. . . .
551 PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV 598
________________________________________________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 21.4 %
beta-contents : 13.6 %
coil-contents : 65.0 %
class : mixed
method : 2
alpha-contents : 0.0 %
beta-contents : 13.6 %
coil-contents : 86.4 %
class : beta
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-5.59 -1.12 -1.50 -1.27 0.00 -4.00 0.00 0.00 0.00 -12.94 -3.96 -12.00 -12.00 -4.00 -12.00 0.00 -70.38
-10.18 -0.05 -0.10 -0.20 0.00 -4.00 0.00 0.00 0.00 -9.97 -3.96 -12.00 -12.00 -4.00 -12.00 0.00 -68.47
ID: tem19partial AC: xxx Len: 590 1:I 561 Sc: -68.47 Pv: 5.332868e-01 NO_GPI_SITE
GPI: learning from protozoa
-23.32 -0.03 -0.11 -0.01 -4.00 -4.00 0.00 0.00 0.00 -8.65 -13.18 -12.00 -12.00 -4.00 -12.00 0.00 -93.29
-12.30 -1.22 -0.08 -0.26 0.00 -4.00 0.00 0.00 0.00 -10.89 -13.18 -12.00 -12.00 -4.00 -12.00 0.00 -81.93
ID: tem19partial AC: xxx Len: 590 1:I 572 Sc: -81.93 Pv: 5.441371e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem19partia 1.000 372 Y 0.750 383 Y 0.999 368 Y 0.171 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem19partia 0.474 284 N 0.410 372 Y 0.986 364 Y 0.176 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem19partia 0.524 33 Y 0.367 33 Y 0.992 363 Y 0.311 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem19partial
1-9 RTREEGPAD
gaslrvvassrsvgrsg 10-26
27-339 PCSPRAAGHGHGGAESPRHRLPVALTATLV
LICAGQGGRREDGGPACYGGFDLYFILDKS
GSVLHHWNEIYYFVEQLAHKFISPQLRMSF
IVFSTRGTTLMKLTEDREQIRQGLEELQKV
LPGGDTYMHEGFERASEQIYYENRQGYRTA
SVIIALTDGELHEDLFFYSEREANRSRDLG
AIVYCVGVKDFNETQLARIADSKDHVFPVN
DGFQALQGIIHSILKKSCIEILAAEPSTIC
AGESFQVVVRGNGFRHARNVDRVLCSFKIN
DSVTLNEKPFSVEDTYLLCPAPILKEVGMK
AALQVSMNDGLSF
isssviittt 340-349
350-355 HCSDGS
ilaiallilflllalallwwfw 356-377
378-386 PLCCTVIIK
evppppaeeseee 387-399
400-537 DDDGLPKKKWPTVDASYYGGRGVGGIKRME
VRWGEKGSTEEGAKLEKAKNARVKMPEQEY
EFPEPRNLNNNMRRPSSPRKWYSPIKGKLD
ALWVLLRKGYDRVSVMRPQPGDTGRCINFT
RVKNNQPAKYPLNNAYHT
sspppapiytppppaphcpppppsaptppi 538-597
psppstlppppqapppnrapppsrppprps
598-598 V
low complexity regions: SEG 25 3.0 3.3
>tem19partial
rtreegpadgaslrvvassrsvgrsgpcsp 1-57
raaghghggaesprhrlpvaltatlvl
58-355 ICAGQGGRREDGGPACYGGFDLYFILDKSG
SVLHHWNEIYYFVEQLAHKFISPQLRMSFI
VFSTRGTTLMKLTEDREQIRQGLEELQKVL
PGGDTYMHEGFERASEQIYYENRQGYRTAS
VIIALTDGELHEDLFFYSEREANRSRDLGA
IVYCVGVKDFNETQLARIADSKDHVFPVND
GFQALQGIIHSILKKSCIEILAAEPSTICA
GESFQVVVRGNGFRHARNVDRVLCSFKIND
SVTLNEKPFSVEDTYLLCPAPILKEVGMKA
ALQVSMNDGLSFISSSVIITTTHCSDGS
ilaiallilflllalallwwfw 356-377
378-385 PLCCTVII
kevppppaeeseeedddglpkkkwp 386-410
411-537 TVDASYYGGRGVGGIKRMEVRWGEKGSTEE
GAKLEKAKNARVKMPEQEYEFPEPRNLNNN
MRRPSSPRKWYSPIKGKLDALWVLLRKGYD
RVSVMRPQPGDTGRCINFTRVKNNQPAKYP
LNNAYHT
sspppapiytppppaphcpppppsaptppi 538-597
psppstlppppqapppnrapppsrppprps
598-598 V
low complexity regions: SEG 45 3.4 3.75
>tem19partial
rtreegpadgaslrvvassrsvgrsgpcsp 1-76
raaghghggaesprhrlpvaltatlvlica
gqggrredggpacygg
77-355 FDLYFILDKSGSVLHHWNEIYYFVEQLAHK
FISPQLRMSFIVFSTRGTTLMKLTEDREQI
RQGLEELQKVLPGGDTYMHEGFERASEQIY
YENRQGYRTASVIIALTDGELHEDLFFYSE
REANRSRDLGAIVYCVGVKDFNETQLARIA
DSKDHVFPVNDGFQALQGIIHSILKKSCIE
ILAAEPSTICAGESFQVVVRGNGFRHARNV
DRVLCSFKINDSVTLNEKPFSVEDTYLLCP
APILKEVGMKAALQVSMNDGLSFISSSVII
TTTHCSDGS
ilaiallilflllalallwwfw 356-377
378-537 PLCCTVIIKEVPPPPAEESEEEDDDGLPKK
KWPTVDASYYGGRGVGGIKRMEVRWGEKGS
TEEGAKLEKAKNARVKMPEQEYEFPEPRNL
NNNMRRPSSPRKWYSPIKGKLDALWVLLRK
GYDRVSVMRPQPGDTGRCINFTRVKNNQPA
KYPLNNAYHT
sspppapiytppppaphcpppppsaptppi 538-597
psppstlppppqapppnrapppsrppprps
598-598 V
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
>tem19partial
RTREEGPADGASLRVVASSRSVGRSGPCSPRAAghghggaesprhrlpvaltatlvliCA
GQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIVFS
TRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVII
ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQ
ALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT
LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFIsssviitttHCSDGSIlaia
llilflllalallwwfwPLcctviikevppppaeeseeedddGLPKKKWPTVDASYYGGR
GVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKW
YSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHtssp
ppapiytppppaphcpppppsaptppipsppstlppppqapppnrapppsrppprpsV
1 - 33 RTREEGPADG ASLRVVASSR SVGRSGPCSP RAA
34 - 58 ghghgga esprhrlpva ltatlvli
59 - 340 CA GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIV
FS TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASV
II ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDG
FQ ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDS
VT LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI
341 - 349 sssviittt
350 - 356 H CSDGSI
357 - 377 laia llilflllal allwwfw
378 - 379 PL
380 - 402 c ctviikevpp ppaeeseeed dd
403 - 536 GLPKKKWP TVDASYYGGR GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FP
EPRNLNNN MRRPSSPRKW YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VK
NNQPAKYP LNNAYH
537 - 597 tssp ppapiytppp paphcppppp saptppipsp pstlppppqa pppnrappps rppprp
s
598 - 598 V
low complexity regions: DUST
>tem19partial
RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVALTATLVLICA
GQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIVFS
TRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVII
ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQ
ALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT
LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHCSDGSILAIA
LLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEEDDDGLPKKKWPTVDASYYGGR
GVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKW
YSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSP
PPAPIYTPPPPAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem19partial
sequence: 590 amino acids, 25 residue(s) in coiled coil state
Coil 1 * 123* 148* TTLMKLTEDREQIRQGLEELQKVLPG
. | . | . | . | . | . 60
RTREEGPADG ASLRVVASSR SVGRSGPCSP RAAGHGHGGA ESPRHRLPVA LTATLVLICA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIVFS
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASVII
~~29999999 9999999999 999999962~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
--efgabcde fgabcdefga bcdefgabc- ---------- ---------- ---------- * 21 M'95 -w register
~~89999999 9999999999 999999997~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~15777777 7777777777 7777766~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~1555566 9999999999 9999877~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDGFQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDSVT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI SSSVIITTTH CSDGSILAIA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
LLILFLLLAL ALLWWFWPLC CTVIIKEVPP PPAEESEEED DDGLPKKKWP TVDASYYGGR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FPEPRNLNNN MRRPSSPRKW
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~111111 11111111~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 540
YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VKNNQPAKYP LNNAYHTSSP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . |
PPAPIYTPPP PAPHCPPPPP SAPTPPIPSP PSTLPPPPQA PPPNRAPPPS
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem8.___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: tem8.___inter___
(1 sequences)
RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA
LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV
EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG
DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN
RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL
KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT
LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH
CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED
DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA
RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD
RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP
PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV
(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 45 65 1.189 Certain
2 332 352 1.038 Certain
3 356 376 2.603 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 44 266 3 222
K+R profile 9.00 0.00
+ +
CYT-EXT prof - -
0.28 0.83
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 9.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -0.3333
NEG: 4.0000
POS: 8.0000
-> Orientation: N-in
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem8" 598
45 65 #t 1.18854
332 352 #t 1.0375
356 376 #t 2.60313
************************************
*TOPPREDM with prokaryotic function*
************************************
tem8.___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: tem8.___inter___
(1 sequences)
RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA
LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV
EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG
DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN
RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL
KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT
LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH
CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED
DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA
RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD
RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP
PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV
(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 45 65 1.189 Certain
2 332 352 1.038 Certain
3 356 376 2.603 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 44 266 3 222
K+R profile 9.00 0.00
+ +
CYT-EXT prof - -
0.28 0.83
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 9.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -0.3333
NEG: 4.0000
POS: 8.0000
-> Orientation: N-in
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem8" 598
45 65 #t 1.18854
332 352 #t 1.0375
356 376 #t 2.60313
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem8.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Dec 14 16:46:48 2000
File: /people/maria/tem8.___saps___
ID tem19partial
DE -
number of residues: 598; molecular weight: 66.0 kdal
1 RTREEGPADG ASLRVVASSR SVGRSGPCSP RAAGHGHGGA ESPRHRLPVA LTATLVLICA
61 GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIVFS
121 TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASVII
181 ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDGFQ
241 ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDSVT
301 LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI SSSVIITTTH CSDGSILAIA
361 LLILFLLLAL ALLWWFWPLC CTVIIKEVPP PPAEESEEED DDGLPKKKWP TVDASYYGGR
421 GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FPEPRNLNNN MRRPSSPRKW
481 YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VKNNQPAKYP LNNAYHTSSP
541 PPAPIYTPPP PAPHCPPPPP SAPTPPIPSP PSTLPPPPQA PPPNRAPPPS RPPPRPSV
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 43( 7.2%); C : 13( 2.2%); D : 25( 4.2%); E : 40( 6.7%); F : 21( 3.5%)
G : 46( 7.7%); H : 14( 2.3%); I : 32( 5.4%); K : 28( 4.7%); L : 50( 8.4%)
M : 9( 1.5%); N : 21( 3.5%); P+ : 64(10.7%); Q : 17( 2.8%); R : 41( 6.9%)
S : 45( 7.5%); T : 26( 4.3%); V : 36( 6.0%); W : 8( 1.3%); Y : 19( 3.2%)
KR : 69 ( 11.5%); ED : 65 ( 10.9%); AGP : 153 ( 25.6%);
KRED : 134 ( 22.4%); KR-ED : 4 ( 0.7%); FIKMNY : 130 ( 21.7%);
LVIFM : 148 ( 24.7%); ST : 71 ( 11.9%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 +0+--000-0 000+00000+ 000+000000 +000000000 -00+0+0000 0000000000
61 0000++--00 0000000-00 000-+00000 0000-00000 -0000+0000 00+0000000
121 0+00000+00 --+-00+000 --00+00000 -0000-00-+ 00-0000-0+ 000+000000
181 000-0-00-- 00000-+-00 +0+-000000 0000+-00-0 000+00-0+- 000000-000
241 0000000000 ++000-0000 -0000000-0 00000+0000 +00+00-+00 000+00-000
301 00-+0000-- 0000000000 +-000+0000 0000-00000 0000000000 00-0000000
361 0000000000 0000000000 00000+-000 000--0---- --000+++00 00-000000+
421 00000++0-0 +00-+000-- 00+0-+0+00 +0+00-0-0- 00-0+00000 0++0000++0
481 0000+0+0-0 00000++00- +0000+0000 -00+00000+ 0+00000+00 0000000000
541 0000000000 0000000000 0000000000 0000000000 0000+00000 +000+000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Mixed charge clusters (cmin = 15/30 or 21/45 or 26/60):
1) From 394 to 465: see sequence above
see sequence above
quartile: 3; size: 72, +count: 14, -count: 18, 0count: 40; t-value: 4.48 *
G: 9 (12.5%); K: 9 (12.5%); E: 14 (19.4%);
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.
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.776 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.224 ( KEDR )
Expected score/letter: -1.017
M_0.01= 41.93; M_0.05= 34.23
1) From 336 to 385: length= 50, score=41.00 *
336 GLSFISSSVI ITTTHCSDGS ILAIALLILF LLLALALLWW FWPLCCTVII
L: 12(24.0%); S: 6(12.0%); I: 8(16.0%);
2) From 529 to 584: length= 56, score=56.00 **
529 YPLNNAYHTS SPPPAPIYTP PPPAPHCPPP PPSAPTPPIP SPPSTLPPPP
579 QAPPPN
P: 28(50.0%);
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 7 | 37 | 10 | 10 | 13 | 12 | 11 | 15 | 7 | 9 |
lmin1 6 | 6 | 9 | 45 | 12 | 12 | 16 | 14 | 14 | 19 | 8 | 11 |
lmin2 8 | 7 | 10 | 50 | 13 | 13 | 18 | 16 | 16 | 21 | 10 | 12 |
(Significance level: 0.010000; Minimal displayed length: 6)
(0) 57(2,0,0); at 327- 385: see sequence above
(3. quartile)
L: 13 (22.0%); A: 6 (10.2%); S: 7 (11.9%); I: 8 (13.6%);
LVIFM: 28 (47.5%); ST: 11 (18.6%);
(-) 8(1,0,0); at 394- 402: EESEEEDDD
(3. quartile) --0------
(0) 61(1,0,0); at 523- 584: see sequence above
(4. quartile)
P: 29 (46.8%);
(0) 64(2,0,0); at 529- 594: see sequence above
(4. quartile)
P: 34 (51.5%); ST: 10 (15.2%);
Run count statistics:
+ runs >= 3: 1, at 406;
- runs >= 3: 1, at 397;
* runs >= 5: 1, at 397;
0 runs >= 25: 2, at 354; 529;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
__________________________________
High scoring hydrophobic segments:
2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ)
-8.00 (KEDR)
Expected score/letter: -2.072
M_0.01= 23.31; M_0.05= 19.43
1) From 356 to 385: length= 30, score=41.00 **
356 ILAIALLILF LLLALALLWW FWPLCCTVII
L: 11(36.7%); A: 4(13.3%); I: 5(16.7%); W: 3(10.0%);
____________________________________
High scoring transmembrane segments:
5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST)
-6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED)
Expected score/letter: -3.973
M_0.01= 54.08; M_0.05= 44.84; M_0.30= 33.84
1) From 356 to 385: length= 30, score=90.00 **
356 ILAIALLILF LLLALALLWW FWPLCCTVII
L: 11(36.7%); A: 4(13.3%); I: 5(16.7%); W: 3(10.0%);
2. SPACINGS OF C.
H2N-27-C-30-C-13-C-137-C-42-C-11-C-24-C-23-C-35-C-28-C-C-133-C-39-C-43-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-27-C-6-H-1-H-7-H-13-C-13-C-17-H-H-12-H-49-H-32-H-22-C-19-H-15-H-6-C-11-C-15-H-8-C-23-C-34-H-C-28-C-C-133-C-20-H-17-H-C-43-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
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
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 57 (Expected range: 17-- 52) high
1 ...EE..... ....VV.SS. .......... .AA....GG. .......... ..........
61 ..GGRR..GG ....GG.... .......... HH....YY.. .......... ..........
121 ...TT..... .......... EE......GG .......... .....YY... ........II
181 .......... .FF....... .......... .......... .......... ..........
241 ....II.... KK......AA .......... ..VVV..... .......... ..........
301 .......... ..LL...... ......AA.. .......... SSS.IITTT. ..........
361 LL...LLL.. .LLWW....C C..II...PP PP.EE.EEED DD...KKK.. .....YYGG.
421 ..GG...... ........EE .......... .......... .......NNN .RR.SS....
481 .......... ...LL..... .......... .......... ..NN...... .NN....SSP
541 PP.....PPP P....PPPPP ....PP...P P...PPPP.. PPP...PPP. .PPP....
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 34 (6-10) 6 (11-20) 12 (>=21) 6
3. Clusters of amino acid multiplets (cmin = 15/30 or 19/45 or 23/60): none
4. Long amino acid multiplets (>= 5; Letter/Length/Position):
P/5/556
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 16 (Expected range: 2-- 25)
7 +plets (f+: 11.5%), 9 -plets (f-: 10.9%)
Total number of charge altplets: 16 (Critical number: 28)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 5 (6-10) 1 (11-20) 3 (>=21) 8
3. Long charge multiplets (>= 5; Letter/Length/Position):
-/6/397
---------------------------------------------------------------
-----------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
362- 373 2 L. 6 6 ! 0
389- 392 1 P 4 4 0
541- 579 3 PP. 10 4 /3/4/./
548- 551 1 P 4 4 0
548- 597 5 P..P. 9 5 ! /1/././3/./
556- 560 1 P 5 5 ! 0
575- 578 1 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
81- 134 9 i..0.*.0. 6 6 /0/././2/./2/./2/./
225- 284 10 i..0....00 6 6 /0/././1/././././2/2/
361- 368 1 i 8 8 0
361- 390 3 i.. 9 7 1
362- 373 2 i. 6 6 0
394- 402 1 - 8 6 ! 1
399- 440 7 *..00.. 6 6 /0/././2/1/././
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
148- 234 (2.) P( 86)P 1 of 65 0.0017 large 1. maximal spacing
288- 420 (3.) R( 132)R 1 of 42 0.0010 large 1. maximal spacing
318- 378 (3.) P( 60)P 2 of 65 0.0005 large 2. maximal spacing
322- 387 (3.) E( 65)E 2 of 41 0.0294 large 2. maximal spacing
353- 386 (3.) *( 33)* 2 of 135 0.0002 large 2. maximal spacing
463- 599 (4.) E( 136)E 1 of 41 0.0009 large 1. maximal spacing
511- 599 (4.) -( 88)- 1 of 66 0.0011 large maximal spacing
520- 585 (4.) R( 65)R 2 of 42 0.0238 large 2. maximal spacing
528- 585 (4.) *( 57)* 1 of 135 0.0000 large 1. 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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem19partial
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
vwa von Willebrand factor type A domain 37.9 2.3e-07 1
Man-6-P_recep Cation-dependent mannose-6-phosphate r 0.9 20 1
beta-lactamase Beta-lactamase 0.6 38 1
Glyco_hydro_1 Glycosyl hydrolase family 1 -1.2 57 1
Bacteriofer Bacterioferritin -110.1 1e+02 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
vwa 1/1 78 249 .. 1 200 [] 37.9 2.3e-07
Bacteriofer 1/1 132 255 .. 1 155 [] -110.1 1e+02
Glyco_hydro_1 1/1 271 284 .. 515 528 .] -1.2 57
Man-6-P_recep 1/1 394 406 .. 266 278 .] 0.9 20
beta-lactamase 1/1 438 452 .. 1 15 [. 0.6 38
Alignments of top-scoring domains:
vwa: domain 1 of 1, from 78 to 249: score 37.9, E = 2.3e-07
*->DivFLlDGSgSigsqnFervKdFvervverLdvgprdkkeedavrVg
D++F+lD SgS+ ++ ++++ Fve+++ ++ + + r +
tem19parti 78 DLYFILDKSGSVLHH-WNEIYYFVEQLAHKFIS---PQ-----LRMS 115
lvQYSdnvrtEikfklndyqnkdevlqalqkiryedyyggggtnTgaALq
+ +S++ +t++k + + q + l+ lqk++ gg t ++
tem19parti 116 FIVFSTRGTTLMKLTEDREQIRQ-GLEELQKVL-----PGGDTYMHEGFE 159
yvvrnlft.easGsRiepvaeegapkvlVvlTDGrsqddpspTi.dirdv
+ ++++ + ++G R + v++ lTDG+ ++d + + ++
tem19parti 160 RASEQIYYeNRQGYR--------TASVIIALTDGELHED-L--FfYSERE 198
lnelkkeagvevfaiGvGnadnnnleeLreIAskpddhvfkvsdfea.Ld
+n+ ++ g +v+ +Gv++ +n + +L +IA + dhvf v+d ++ L+
tem19parti 199 ANRSRD-LGAIVYCVGVKD-FN--ETQLARIADSK-DHVFPVNDGFQaLQ 243
tlqelL<-*
+++ +
tem19parti 244 GIIHSI 249
Bacteriofer: domain 1 of 1, from 132 to 255: score -110.1, E = 1e+02
*->MKGdpkVIeyLNklLggELaAinQYFlHsRmyedWGltkLaererhE
d++ I++ + L L + Y m e G+++ e ++ E
tem19parti 132 ---DREQIRQGLEELQKVLPGGDTY-----MHE--GFERASEQIYYE 168
SieEMkHADklIeRILfLEGlPNLqeLdkLrIGetvrEmLeaDLalEyev
+ A+ +I+ L + Ge + + + E e+
tem19parti 169 NRQGYRTASVIIA----------LTD------GELHEDLFFY---SEREA 199
.rkaLkeAialCeevqDYvSRdLleeilaDTEEdHiDWLEtQLdLidKIG
+r + Ai +C v+D +L + +aD dH+ ++ I
tem19parti 200 nRSRDLGAIVYCVGVKDFNETQL--ARIAD-SKDHVFPVNDGFQALQGII 246
lenYlQsqa<-*
s++
tem19parti 247 HSILKKSCI 255
Glyco_hydro_1: domain 1 of 1, from 271 to 284: score -1.2, E = 57
*->YkevirnNgfplkr<-*
++ v+r+Ngf+ +r
tem19parti 271 FQVVVRGNGFRHAR 284
Man-6-P_recep: domain 1 of 1, from 394 to 406: score 0.9, E = 20
*->EEsEERDDHLLPm<-*
EEsEE DD LP
tem19parti 394 EESEEEDDDGLPK 406
beta-lactamase: domain 1 of 1, from 438 to 452: score 0.6, E = 38
*->eedlaalekqfdArl<-*
+e++a+lek ++Ar+
tem19parti 438 TEEGAKLEKAKNARV 452
//
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem19partial
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
vwa von Willebrand factor type A domain 36.1 1.7e-09 1
GIDA Glucose inhibited division protein A 4.0 2.9 1
TarH Tar ligand binding domain homologues 2.5 20 1
IRS PTB domain (IRS-1 type) 2.5 30 1
CBFB_NFYA CCAAT-binding transcription factor (CB 1.6 15 1
Man-6-P_recep Cation-dependent mannose-6-phosphate r 0.9 20 1
SIS SIS domain 0.6 77 1
beta-lactamase Beta-lactamase 0.6 38 1
Flavi_capsid Flavivirus capsid protein C 0.5 94 1
Glyco_hydro_1 Glycosyl hydrolase family 1 -1.2 57 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CBFB_NFYA 1/1 133 156 .. 17 40 .. 1.6 15
TarH 1/1 154 177 .. 119 142 .] 2.5 20
vwa 1/1 78 249 .. 1 200 [] 36.1 1.7e-09
SIS 1/1 203 249 .. 94 140 .. 0.6 77
Glyco_hydro_1 1/1 271 284 .. 515 528 .] -1.2 57
IRS 1/1 267 291 .. 1 28 [. 2.5 30
GIDA 1/1 331 348 .. 140 157 .. 4.0 2.9
Flavi_capsid 1/1 352 371 .. 107 126 .] 0.5 94
Man-6-P_recep 1/1 394 406 .. 266 278 .] 0.9 20
beta-lactamase 1/1 438 452 .. 1 15 [. 0.6 38
Alignments of top-scoring domains:
CBFB_NFYA: domain 1 of 1, from 133 to 156: score 1.6, E = 15
*->RRqaRakleaelklikarkkYLHe<-*
R q R+ le+ +k+ Y+He
tem19parti 133 REQIRQGLEELQKVLPGGDTYMHE 156
TarH: domain 1 of 1, from 154 to 177: score 2.5, E = 20
*->mqdgfdpayrdwlqqavklkgeav<-*
m +gf+ a ++++ ++ + +++a+
tem19parti 154 MHEGFERASEQIYYENRQGYRTAS 177
vwa: domain 1 of 1, from 78 to 249: score 36.1, E = 1.7e-09
*->DivFLlDGSgSigsqnFervKdFvervverLdvgprdkkeedavrVg
D++F+lD SgS+ ++ ++++ Fve+++ ++ + + r +
tem19parti 78 DLYFILDKSGSVLHH-WNEIYYFVEQLAHKFIS---PQ-----LRMS 115
lvQYSdnvrtEikfklndyqnkdevlqalqkiryedyyggggtnTgaALq
+ +S++ +t++k + + q + l+ lqk++ gg t ++
tem19parti 116 FIVFSTRGTTLMKLTEDREQIRQ-GLEELQKVL-----PGGDTYMHEGFE 159
yvvrnlft.easGsRiepvaeegapkvlVvlTDGrsqddpspTi.dirdv
+ ++++ + ++G R + v++ lTDG+ ++d + + ++
tem19parti 160 RASEQIYYeNRQGYR--------TASVIIALTDGELHED-L--FfYSERE 198
lnelkkeagvevfaiGvGnadnnnleeLreIAskpddhvfkvsdfea.Ld
+n+ ++ g +v+ +Gv++ +n + +L +IA + dhvf v+d ++ L+
tem19parti 199 ANRSRD-LGAIVYCVGVKD-FN--ETQLARIADSK-DHVFPVNDGFQaLQ 243
tlqelL<-*
+++ +
tem19parti 244 GIIHSI 249
SIS: domain 1 of 1, from 203 to 249: score 0.6, E = 77
*->karga.akiiaiTnndgsslareasiddlilripaepealqaastsa
+++ga ++++ + +++ lar a d++++++ + +alq+ ++++
tem19parti 203 RDLGAiVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQG-IIHS 248
i<-*
i
tem19parti 249 I 249
Glyco_hydro_1: domain 1 of 1, from 271 to 284: score -1.2, E = 57
*->YkevirnNgfplkr<-*
++ v+r+Ngf+ +r
tem19parti 271 FQVVVRGNGFRHAR 284
IRS: domain 1 of 1, from 267 to 291: score 2.5, E = 30
*->gkevwvvnvkteglercknLlsGsyrLr<-*
+ e+++v+v+++g +++n + +L+
tem19parti 267 AGESFQVVVRGNGFRHARN---VDRVLC 291
GIDA: domain 1 of 1, from 331 to 348: score 4.0, E = 2.9
*->VvtqdGlefrAkaVviTT<-*
V ++dGl f +++V+iTT
tem19parti 331 VSMNDGLSFISSSVIITT 348
Flavi_capsid: domain 1 of 1, from 352 to 371: score 0.5, E = 94
*->SedsltwlflllaLlpmamA<-*
S +s+ ++ll+ l+ a+A
tem19parti 352 SDGSILAIALLILFLLLALA 371
Man-6-P_recep: domain 1 of 1, from 394 to 406: score 0.9, E = 20
*->EEsEERDDHLLPm<-*
EEsEE DD LP
tem19parti 394 EESEEEDDDGLPK 406
beta-lactamase: domain 1 of 1, from 438 to 452: score 0.6, E = 38
*->eedlaalekqfdArl<-*
+e++a+lek ++Ar+
tem19parti 438 TEEGAKLEKAKNARV 452
//
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem19partial
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Thu Dec 14 16:49:06 2000
Sequence file: tem8
----------------------------------------
Sequence tem19partial (598 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
200: NRSR
218: NETQ
296: NDSV
517: NFTR
Total matches: 4
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
472: RRPS
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
12: SLR
18: SSR
29: SPR
42: SPR
120: STR
195: SER
292: SFK
476: SPR
512: TGR
Total matches: 9
Matching pattern PS00006 CK2_PHOSPHO_SITE:
2: TREE
183: TDGE
195: SERE
253: SCIE
300: TLNE
307: SVED
332: SMND
396: SEEE
437: STEE
Total matches: 9
Matching pattern PS00008 MYRISTYL:
69: GGPACY
244: GIIHSI
324: GMKAAL
354: GSILAI
Total matches: 4
Matching pattern PS00009 AMIDATION:
63: GGRR
Total matches: 1
Total no of hits in this sequence: 28
========================================
1314 pattern(s) searched in 1 sequence(s), 598 residues.
Total no of hits in all sequences: 28.
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 tem8
***** 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, 598 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: tem8
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Query: tem19partial
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: tem8
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem19partial
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= tem19partial
(598 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
VWA Von Willebrand factor A domain 79 2e-17
PCNA Proliferating Cell nuclear antigen like domain 26 0.21
SGTP Small GTPAses 25 0.24
ARR Arrestin domain 24 0.61
INSL Insulinase like Metallo protease domain 24 0.66
14-3-3 14-3-3 protein alpha Helical domain 23 1.3
PAP Papain/bleomycin hydrolase like domain 22 2.6
KIN Protein kinase domain 22 3.4
DSP Dual specificity protein phosphatase 21 3.6
SH3 Src Homology domain 3 21 3.8
RHOGAP RHO-type GTPase GTP hydrolysis activating protein 21 4.1
PP2C PP2C type phosphatase domain 21 5.9
CBS cystathionine beta -synthase domain (A predicted ligand... 20 6.7
BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 20 8.3
SNARE Alpha helical domains which are involved in vesicle fu... 20 8.5
AP2 A plant specific DNA binding domain (Apetala 2 like) 20 9.4
>VWA Von Willebrand factor A domain
Length = 255
Score = 78.7 bits (192), Expect = 2e-17
Identities = 20/202 (9%), Positives = 20/202 (9%), Gaps = 22/202 (10%)
Query: 78 DLYFILDKSGSV-LHHWNEIYYFVEQLAHKFI-------SPQLRMSFIVFSTRGT-TLMK 128
Sbjct: 55 SLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQLVSQ 114
Query: 129 LTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELH 188
Sbjct: 115 VSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARG--LLLPVPAHCTREVLIVFGSLSTT 172
Query: 189 EDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIAD---SKD-HVFPVNDGFQALQG 244
Sbjct: 173 DPG--DIHQTIDSLVSEKIRVKVLGL-SAQVAICKELCKATNYGDESFYKILLDETHLK- 228
Query: 245 IIHSILKKSCIEILAAEPSTIC 266
Sbjct: 229 ---ELFNEAVTPLPVNKINKGF 247
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 25.6 bits (56), Expect = 0.21
Identities = 5/64 (7%), Positives = 5/64 (7%), Gaps = 2/64 (3%)
Query: 292 SFKINDSVTLNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHC 351
Sbjct: 125 EGGVVTVCKITTQEPEETLDFDFCSTNVMNKIILQSEGLREAFSELDMTGDVLQITVS-- 182
Query: 352 SDGS 355
Sbjct: 183 PDKP 186
>SGTP Small GTPAses
Length = 164
Score = 25.1 bits (55), Expect = 0.24
Identities = 13/65 (20%), Positives = 13/65 (20%), Gaps = 7/65 (10%)
Query: 284 RNVDRVLCSFKINDSVTLNEKPFSVEDTYLLCP--APILKEVGMKAAL----QVSMNDGL 337
Sbjct: 71 RGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIIL-CGNKKDLDADREVTFLEAS 129
Query: 338 SFISS 342
Sbjct: 130 RFAQE 134
>ARR Arrestin domain
Length = 454
Score = 23.7 bits (51), Expect = 0.61
Identities = 5/25 (20%), Positives = 5/25 (20%)
Query: 569 SPPSTLPPPPQAPPPNRAPPPSRPP 593
Sbjct: 380 SKPPESPERTDRGLPSIEATNGSEP 404
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 23.8 bits (51), Expect = 0.66
Identities = 15/80 (18%), Positives = 15/80 (18%), Gaps = 13/80 (16%)
Query: 155 HEGFERASEQIYYENRQGYRTASVIIALTDGELHE-------DLFFYSEREANRSRDLGA 207
Sbjct: 327 PENYEKVKKRVFEL------LKETYENLTDEQVEEAKSRIINSRLFEEERVENDAFDIGY 380
Query: 208 IVYCVGVKDFNETQLARIAD 227
Sbjct: 381 SYTVVRDLDFYRFFDKNLSR 400
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 22.6 bits (48), Expect = 1.3
Identities = 16/52 (30%), Positives = 16/52 (30%), Gaps = 2/52 (3%)
Query: 126 LMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS 177
Sbjct: 12 LAKLAEQAERYEGMVENMKSVASTDQELTVE--ERNLLSVAYKNVIGARRAS 61
>PAP Papain/bleomycin hydrolase like domain
Length = 376
Score = 21.9 bits (46), Expect = 2.6
Identities = 4/19 (21%), Positives = 4/19 (21%)
Query: 560 PSAPTPPIPSPPSTLPPPP 578
Sbjct: 358 PLTARVQKPDMKPRVSCPP 376
Score = 20.8 bits (43), Expect = 4.7
Identities = 4/16 (25%), Positives = 4/16 (25%)
Query: 542 PAPIYTPPPPAPHCPP 557
Sbjct: 361 ARVQKPDMKPRVSCPP 376
Score = 20.0 bits (41), Expect = 9.2
Identities = 3/16 (18%), Positives = 3/16 (18%)
Query: 526 PAKYPLNNAYHTSSPP 541
Sbjct: 361 ARVQKPDMKPRVSCPP 376
>KIN Protein kinase domain
Length = 313
Score = 21.6 bits (45), Expect = 3.4
Identities = 9/67 (13%), Positives = 9/67 (13%), Gaps = 4/67 (5%)
Query: 125 TLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTD 184
Sbjct: 61 KISKAFDNLKDTKRTLREIHLL----RHFKHENLISIKDILKPNSKEQFEDVYIVSELMD 116
Query: 185 GELHEDL 191
Sbjct: 117 TDLHQII 123
>DSP Dual specificity protein phosphatase
Length = 185
Score = 21.5 bits (45), Expect = 3.6
Identities = 4/27 (14%), Positives = 4/27 (14%)
Query: 317 APILKEVGMKAALQVSMNDGLSFISSS 343
Sbjct: 48 IPKLQKLGITHVLNAAEGRSFMHVNTN 74
>SH3 Src Homology domain 3
Length = 90
Score = 21.3 bits (45), Expect = 3.8
Identities = 6/17 (35%), Positives = 6/17 (35%)
Query: 576 PPPQAPPPNRAPPPSRP 592
Sbjct: 1 PRVQAWSPPVRGIPQLP 17
Score = 20.9 bits (44), Expect = 4.5
Identities = 5/14 (35%), Positives = 5/14 (35%)
Query: 558 PPPSAPTPPIPSPP 571
Sbjct: 1 PRVQAWSPPVRGIP 14
>RHOGAP RHO-type GTPase GTP hydrolysis activating protein
Length = 194
Score = 21.0 bits (44), Expect = 4.1
Identities = 4/26 (15%), Positives = 4/26 (15%), Gaps = 4/26 (15%)
Query: 126 LMKLT----EDREQIRQGLEELQKVL 147
Sbjct: 164 ILQHSHGIEEERQDLTTALGLVKELL 189
>PP2C PP2C type phosphatase domain
Length = 254
Score = 20.6 bits (43), Expect = 5.9
Identities = 7/49 (14%), Positives = 7/49 (14%)
Query: 181 ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSK 229
Sbjct: 79 LLRDALMDANEGILEDQKINLERRDMGTTAVLIAFREDGAWRAHVGDSR 127
>CBS cystathionine beta -synthase domain (A predicted ligand binding domain)
Length = 214
Score = 20.3 bits (42), Expect = 6.7
Identities = 7/76 (9%), Positives = 7/76 (9%), Gaps = 8/76 (10%)
Query: 273 VVVRGN----GFRHARNVDRVL---CSFKINDSVTLNEKPFSV-EDTYLLCPAPILKEVG 324
Sbjct: 36 PIVDKEDRLVGWVTTLELLGISEKDFKKPITEFMRPVEEVITVYEDDEARNVVLKFVKYK 95
Query: 325 MKAALQVSMNDGLSFI 340
Sbjct: 96 VVSIPVLTRDGRVIGM 111
Score = 20.3 bits (42), Expect = 6.8
Identities = 9/53 (16%), Positives = 9/53 (16%), Gaps = 3/53 (5%)
Query: 209 VYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSILKKSCIEILAAE 261
Sbjct: 75 VITVYEDDEARNVVLKFVKYKVVSIPVLTRDGRVIGMVR---NCDVVKTLAKL 124
>BRIGHT BRIGHT domain (Alpha helical DNA binding domain)
Length = 172
Score = 20.3 bits (42), Expect = 8.3
Identities = 6/29 (20%), Positives = 6/29 (20%), Gaps = 1/29 (3%)
Query: 16 VASSRSVGRSGPCSPRAAGHGHGGAESPR 44
Sbjct: 125 IDGNRREGRRSSYGQYEAMH-NQMPMTPI 152
>SNARE Alpha helical domains which are involved in vesicle fusion
Length = 254
Score = 20.2 bits (42), Expect = 8.5
Identities = 4/20 (20%), Positives = 4/20 (20%)
Query: 357 LAIALLILFLLLALALLWWF 376
Sbjct: 187 PATLSGIVAFILSLLCGALN 206
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 20.1 bits (41), Expect = 9.4
Identities = 7/25 (28%), Positives = 7/25 (28%)
Query: 446 KAKNARVKMPEQEYEFPEPRNLNNN 470
Sbjct: 83 KGASAILNFPDLAGSFPRPSSLSPR 107
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 16
Number of calls to ALIGN: 20
Length of query: 598
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 9391311.1
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= tem19partial
(598 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|420193 [185..357] Integrin A (or I) domain 86 1e-18
gi|2582830 [161..353] Integrin A (or I) domain 81 4e-17
gi|2645090 [1..155] Integrin A (or I) domain 76 2e-15
gi|102029 [2..423] Phosphoglycerate kinase 28 0.38
gi|1001744 [209..396] alpha/beta-Hydrolases 28 0.45
gi|2499877 [3..454] Cysteine proteinases 28 0.45
gi|555731 [3..383] Serpins 28 0.64
gi|1346563 [21..174] Periplasmic binding protein-like I 27 0.78
gi|543771 [1..98] Ferredoxin-like 27 0.89
gi|116871 [267..480] 4-bladed beta-propeller 27 1.1
gi|2622097 [427..630] ATP-grasp 26 1.7
gi|1572759 [30..280] Trypsin-like serine proteases 25 3.1
gi|124505 [1..400] Sugar phosphatases 25 4.3
gi|398985 [18..447] PLP-dependent transferases 24 5.1
gi|416621 [37..465] Serpins 25 5.2
gi|127815 [6..138] Bleomycin resistance protein/Dihydroxybip... 24 5.7
gi|2194029 [140..303] Ferredoxin reductase-like, C-terminal ... 24 6.5
gi|1001472 [191..704] N-terminal nucleophile aminohydrolases... 24 7.3
gi|1086887 [26..189] P-loop containing nucleotide triphospha... 24 7.4
gi|1350557 [4..271] P-loop containing nucleotide triphosphat... 24 7.7
gi|483174 [15..156] Four-helical up-and-down bundle 24 8.1
gi|229680 [2..306] Periplasmic binding protein-like I 24 8.8
gi|1706496 [2..127] DNA clamp 24 8.9
gi|2414449 [42..312] alpha/beta-Hydrolases 24 9.5
>gi|420193 [185..357] Integrin A (or I) domain
Length = 173
Score = 86.1 bits (211), Expect = 1e-18
Identities = 36/179 (20%), Positives = 36/179 (20%), Gaps = 20/179 (11%)
Query: 78 DLYFILDKSGSV-LHHWNEIYYFVEQL------AHKFISP-QLRMSFIVFSTRGTTLMKL 129
Sbjct: 1 DIVFLLDGSERLGEQNFHKVRRFVEDVSRRLTLARRDDDPLNARMALLQYGSQNQQQVAF 60
Query: 130 TE--DREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS--VIIALTDG 185
Sbjct: 61 PLTYNVTTIHEALERAT--YLNSFSHVGTGIVHAINNVVRGARGGARRHAELSFVFLTDG 118
Query: 186 ELHEDLFFYSEREANRSRDLGAIVYCVGVK-DFNETQLARIA-DSKDHVFPVNDGFQAL 242
Sbjct: 119 VTGND---SLEESVHSMRKQNVVPTVVAVGGDVDMDVLTKISLGDRAAIFREKD-FDSL 173
>gi|2582830 [161..353] Integrin A (or I) domain
Length = 193
Score = 81.5 bits (199), Expect = 4e-17
Identities = 34/196 (17%), Positives = 34/196 (17%), Gaps = 26/196 (13%)
Query: 78 DLYFILDKSGSVLHHWNEIYYFVEQLAHKF-ISPQL-RMSFIVFSTRGTTLMKLTEDREQ 135
Sbjct: 2 DIVIVLDGSNSI-YPWESVTAFLNSLLRNMDIGPQQTQVGIVQYGQTVVHEFYLN-TYST 59
Query: 136 IRQGLEELQKV--LPGGDTYMHEGFERASEQIYYE---NRQGYRTASVIIALTDGELHED 190
Sbjct: 60 TEEVMDAALRIRQRGGTQTMTALGIDTAREEAFTEAHGARRGVQK--VMVIVTDGE--SH 115
Query: 191 LFFYSEREANRSRDLGAIVYCVGVK-DFNETQLARIADSK-----------DHVFPVNDG 238
Sbjct: 116 DNYRLQEVIDKCEDENIQRFAIAILGSYSRGNLSTEKFVEEIKSIASKPTEKHFFNVSD- 174
Query: 239 FQALQGIIHSILKKSC 254
Sbjct: 175 ELALVTIVEALGERIF 190
>gi|2645090 [1..155] Integrin A (or I) domain
Length = 155
Score = 76.0 bits (185), Expect = 2e-15
Identities = 34/159 (21%), Positives = 34/159 (21%), Gaps = 16/159 (10%)
Query: 79 LYFILDKSGSV-LHHWNEIYYFVEQLAHKFISPQL--RMSFIVFSTRGTTLMKLTE--DR 133
Sbjct: 1 MLFLLDSSGSVGDENFDKMKEFVKSIVLNFDVDNQLTRIGIIRFDSDAEIIIQLSDHKTL 60
Query: 134 EQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDG-----ELH 188
Sbjct: 61 KDLLNDIDSI-RYNEGIQTRIDKALERAMEAFSEKNGGRADATKALVLLADGQNSFIEGS 119
Query: 189 EDLFFYSEREANRSRDLGAIVYCVGV-KDFNETQLARIA 226
Sbjct: 120 QDL----NEELKPLIDAKVFRYVIGIGRELDLKELEDIA 154
>gi|102029 [2..423] Phosphoglycerate kinase
Length = 422
Score = 28.3 bits (63), Expect = 0.38
Identities = 17/74 (22%), Positives = 17/74 (22%), Gaps = 10/74 (13%)
Query: 172 GYRTASVIIALTDGE--LHEDLFFYSEREANRSRDLGAIVYCVGVKDFNE--TQLARIAD 227
Sbjct: 106 GPEVEAIVNKADNGAVILLENLRFHIEEEGSSKDKEGNKTK-ADKAKVEEFRKGLTALGD 164
Query: 228 SKDHVFPVNDGFQA 241
Sbjct: 165 ----VY-VNDAFGT 173
>gi|1001744 [209..396] alpha/beta-Hydrolases
Length = 188
Score = 28.0 bits (62), Expect = 0.45
Identities = 12/72 (16%), Positives = 12/72 (16%), Gaps = 10/72 (13%)
Query: 117 IVFSTRGT-TLMKLTEDREQIRQGLEELQKVLPG-GDTYMHEGFERASEQIYYE-----N 169
Sbjct: 10 NLIVFRGTQTTMEWVNN---LRAQQIPFTERRSGQYFGKIHQGFIENYLRIVSPIPREIA 66
Query: 170 RQGYRTASVIIA 181
Sbjct: 67 QQLDPAVPCYVT 78
>gi|2499877 [3..454] Cysteine proteinases
Length = 452
Score = 27.8 bits (61), Expect = 0.45
Identities = 4/23 (17%), Positives = 4/23 (17%)
Query: 556 PPPPPSAPTPPIPSPPSTLPPPP 578
Sbjct: 424 KKHVPEEVLAVLEQEPIVLPAWD 446
>gi|555731 [3..383] Serpins
Length = 381
Score = 27.6 bits (61), Expect = 0.64
Identities = 9/68 (13%), Positives = 9/68 (13%), Gaps = 11/68 (16%)
Query: 108 ISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLE----ELQKVLPGGDTYMHEGFERASE 163
Sbjct: 25 VLFTLGILLGSGGAQGKT-------SYQIAKTMRLKSANFPWNISETQQEMKSLYKELSD 77
Query: 164 QIYYENRQ 171
Sbjct: 78 SLTMENTS 85
>gi|1346563 [21..174] Periplasmic binding protein-like I
Length = 154
Score = 27.2 bits (60), Expect = 0.78
Identities = 22/155 (14%), Positives = 22/155 (14%), Gaps = 25/155 (16%)
Query: 135 QIRQGLEELQKVLPGGDTYM-HEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFF 193
Sbjct: 17 LLRNGMEDYAKTLDGVDLQIEDALNDVAKQQSQIQNFIAAGVDAIIVQPVDTDATTVM-- 74
Query: 194 YSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVND-----GFQALQGIIHS 248
Sbjct: 75 --SKLAA-DAGIPLVYV--------NREPVNIDTLPEKQAFVASNEVDSGTLQTREICKL 123
Query: 249 ILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHA 283
Sbjct: 124 LDGKGKAVVIMGELSNQAARM------RTKDIHDV 152
>gi|543771 [1..98] Ferredoxin-like
Length = 98
Score = 26.8 bits (59), Expect = 0.89
Identities = 11/52 (21%), Positives = 11/52 (21%), Gaps = 6/52 (11%)
Query: 98 YFVEQLAHKFISPQLRMSFIVFST-RGTTLMKLTEDREQIRQGLEELQKVLP 148
Sbjct: 24 MYTEGEAKK-----IGVVGWVKNTSKGTVTGQVQGPEEKVNSMKSWLSKVGS 70
>gi|116871 [267..480] 4-bladed beta-propeller
Length = 214
Score = 26.8 bits (59), Expect = 1.1
Identities = 6/26 (23%), Positives = 6/26 (23%), Gaps = 2/26 (7%)
Query: 557 PPPPSAPTPPIPSPPSTLPPPPQAPP 582
Sbjct: 2 TPALGPQAGIDTNEIA--PLEPDAPP 25
>gi|2622097 [427..630] ATP-grasp
Length = 204
Score = 26.1 bits (57), Expect = 1.7
Identities = 13/100 (13%), Positives = 13/100 (13%), Gaps = 11/100 (11%)
Query: 127 MKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGE 186
Sbjct: 52 MEIVYDDVELEEYMREAVRVSPEHPILVDKFLEDAIEVDVDALCDGTDVYIGGIMEHIEE 111
Query: 187 LHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIA 226
Sbjct: 112 -----------AGVHSGDSACVIPPQSIPEDIIDTIKEYT 140
>gi|1572759 [30..280] Trypsin-like serine proteases
Length = 251
Score = 25.1 bits (54), Expect = 3.1
Identities = 5/88 (5%), Positives = 5/88 (5%), Gaps = 8/88 (9%)
Query: 460 EFPEPRNLNNNMRRPSSPRKWYSPIKGK--LDALWVLLRKGYDRVSVMRPQPGDTGRCIN 517
Sbjct: 116 RISSDLSKLGIKPVCLVHDDSKLLKQYKNGVVIGYGLTLGEDSSGEPKLINS-QTLQSTS 174
Query: 518 FTRVKNNQPAKYPLNNAYHTSSPPPAPI 545
Sbjct: 175 VPIISDDD-----CVKTWRFLSLLSVKI 197
>gi|124505 [1..400] Sugar phosphatases
Length = 400
Score = 24.6 bits (53), Expect = 4.3
Identities = 17/71 (23%), Positives = 17/71 (23%), Gaps = 4/71 (5%)
Query: 149 GGDTYMHEGFERASEQIYYENRQGYR----TASVIIALTDGELHEDLFFYSEREANRSRD 204
Sbjct: 289 AGAGYKSLCVILGLADIYIFSEDTTFKWDSCAAHAILRAMGGGMVDLKECLERNPDTGLD 348
Query: 205 LGAIVYCVGVK 215
Sbjct: 349 LPQLVYHVGNE 359
>gi|398985 [18..447] PLP-dependent transferases
Length = 430
Score = 24.4 bits (52), Expect = 5.1
Identities = 7/43 (16%), Positives = 7/43 (16%)
Query: 221 QLARIADSKDHVFPVNDGFQALQGIIHSILKKSCIEILAAEPS 263
Sbjct: 95 GPFYLAHDRISFVQTLSGTGALAVAAKFLALFISRDIWIPDPS 137
>gi|416621 [37..465] Serpins
Length = 429
Score = 24.6 bits (53), Expect = 5.2
Identities = 10/89 (11%), Positives = 10/89 (11%), Gaps = 13/89 (14%)
Query: 107 FISP---QLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASE 163
Sbjct: 74 FLSPLSISTAFAMTKLGACNDT-------LKQLMEVF-KFDTISEKTSDQIHFFFAKLNC 125
Query: 164 QIYYENRQGY--RTASVIIALTDGELHED 190
Sbjct: 126 RLYRKANKSSDLVSANRLFGDKSLTFNES 154
>gi|127815 [6..138] Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Length = 133
Score = 24.1 bits (52), Expect = 5.7
Identities = 5/42 (11%), Positives = 5/42 (11%), Gaps = 4/42 (9%)
Query: 65 RREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHK 106
Sbjct: 89 VCDKVEAQERMVLGLMKTEDPGG----NPTEIFWGPRIDMSN 126
>gi|2194029 [140..303] Ferredoxin reductase-like, C-terminal NADP-linked domain
Length = 164
Score = 24.1 bits (52), Expect = 6.5
Identities = 7/75 (9%), Positives = 7/75 (9%), Gaps = 15/75 (20%)
Query: 134 EQIRQGLEELQKVLPGGDTYMH----EGFERASEQIYYENRQGYRTASVIIALTDGELHE 189
Sbjct: 99 DRVAEHADQLWQLIKNQKTHTYICGLRGMEEGIDAALSA-----------AAAKEGVTWS 147
Query: 190 DLFFYSEREANRSRD 204
Sbjct: 148 DYQKDLKKAGRWHVE 162
>gi|1001472 [191..704] N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Length = 514
Score = 23.8 bits (51), Expect = 7.3
Identities = 13/89 (14%), Positives = 13/89 (14%), Gaps = 7/89 (7%)
Query: 457 QEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYDRVSVMR------PQPG 510
Sbjct: 366 QWNPAD-PLNTPSGMADINKFMAVLEGVAAQVKFLYDDLAISWGEVVQMQVGNFTAPANG 424
Query: 511 DTGRCINFTRVKNNQPAKYPLNNAYHTSS 539
Sbjct: 425 APSNLGSFRVLALSTIANQRFQAVAGDSY 453
>gi|1086887 [26..189] P-loop containing nucleotide triphosphate hydrolases
Length = 164
Score = 24.1 bits (51), Expect = 7.4
Identities = 13/120 (10%), Positives = 13/120 (10%), Gaps = 14/120 (11%)
Query: 144 QKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREANRSR 203
Sbjct: 47 TVELIEKDLGGLTNEDNGFKKTEMRDVDA---VLLFYAADDLESFKQLKENLVHVQRKIP 103
Query: 204 DLGAIVYCVGVKD-----FNETQLARIADSKD-HVFPV----NDGF-QALQGIIHSILKK 252
Sbjct: 104 PNANITVVGTKADVKEMQVQWQEVDSFAENQGFSCFETSSKTGVNVEIILHDILETIFER 163
>gi|1350557 [4..271] P-loop containing nucleotide triphosphate hydrolases
Length = 268
Score = 23.9 bits (50), Expect = 7.7
Identities = 10/71 (14%), Positives = 10/71 (14%), Gaps = 4/71 (5%)
Query: 443 KLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYDRV 502
Sbjct: 3 EKEKAIELAMSAVERQFGKGSIMRLGNDEPMMRDVQAIPTGSISLDIALGVGGVPKGRII 62
Query: 503 SVMRPQPGDTG 513
Sbjct: 63 EIF----GPES 69
>gi|483174 [15..156] Four-helical up-and-down bundle
Length = 142
Score = 23.7 bits (51), Expect = 8.1
Identities = 5/20 (25%), Positives = 5/20 (25%)
Query: 128 KLTEDREQIRQGLEELQKVL 147
Sbjct: 118 HMRKLRKRVLRDAEDLQRRL 137
>gi|229680 [2..306] Periplasmic binding protein-like I
Length = 305
Score = 23.8 bits (51), Expect = 8.8
Identities = 19/162 (11%), Positives = 19/162 (11%), Gaps = 32/162 (19%)
Query: 161 ASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNET 220
Sbjct: 43 EKTLNAIDSLAASGAKGFVICTPDPKLGSAI----VAKARG-YDMKVIAV-----DDQFV 92
Query: 221 QLARIADSKDHVFPVND-----GFQALQGIIHSILKK-----SCIEILAAEPSTICAGES 270
Sbjct: 93 NAK--GKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARR- 149
Query: 271 FQVVVRGNGFRHARNVDRVLCSFKINDSVTLNEKPFSVEDTY 312
Sbjct: 150 -----RTTGSMDALKAA----GFPEKQIYQVPTKSNDIPGAF 182
>gi|1706496 [2..127] DNA clamp
Length = 126
Score = 23.7 bits (51), Expect = 8.9
Identities = 6/26 (23%), Positives = 6/26 (23%)
Query: 127 MKLTEDREQIRQGLEELQKVLPGGDT 152
Sbjct: 1 MEFTIKRDYFITQLNDTLKAISPRTT 26
>gi|2414449 [42..312] alpha/beta-Hydrolases
Length = 271
Score = 23.7 bits (51), Expect = 9.5
Identities = 11/70 (15%), Positives = 11/70 (15%), Gaps = 11/70 (15%)
Query: 117 IVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGGD-TYMHEGFERASEQIYYENR----- 170
Sbjct: 54 ITVVFRGT-----KTSSQLLLEGWTTLKPSSDFYGMGLVNTYFRSGHEKTWQYVQDALSI 108
Query: 171 QGYRTASVII 180
Sbjct: 109 SQYRNYDVYV 118
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 24
Number of calls to ALIGN: 24
Length of query: 598
Total length of test sequences: 256703
Effective length of test sequences: 209547.0
Effective search space size: 117038708.7
Initial X dropoff for ALIGN: 25.0 bits