analysis of sequence from tem1
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRACRELGGDLATPRTPEEAQRV
DSLVGAGPASRLLWIGLQRQARQCQLQRPLRGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEH
RWLEGSCTLAVDGYLCQFGFEGACPALQDEAGQAGPAVYTTPFHLVSTEFEWLPFGSVAAVQCQAGRGAS
LLCVKQPEGGVGWSRAGPLCLGTGCSPDNGGCEHECVEEVDGHVSCRCTEGFRLAADGRSCEDPCAQAPC
EQQCEPGGPQGYSCHCRLGFRPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISC
SPAGAMGAQASQDLGDELLDDGEDEEDEDEAWKAFNGGWTEMPGILWMEPTQPPDFALAYRPSFPEDREP
QIPYPEPTWPPPLSAPRVPYHSSVLSVTRPVVVSATHPTLPSAHQPPVIPATHPALSRDHQIPVIAANYP
DLPSAYQPGILSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAGTQTTTHLPGIPPNHAPLVTT
LGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPVSPAHQISVPAATQPAALPTLLPSQSPTNQT
SPISPTHPHSKAPQIPREDGPSPKLALWLPSPAPTAAPTALGEAGLAEHSQRDDRWLLVALLVPTCVFLV
VLLALGIVYCTRCGPHAPNKRITDCYRWVIHAGSKSPTEPMPPRGSLTGVQTCRTSV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|9857400|gb|AAG00867.1|AF279142_1
. . . . .
1 MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRA 50
___HHHHHHHHH______________________EEEHHHHHHHHHHHHH
. . . . .
51 CRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPL 100
HHH___________HHHHHHH________HHHHHHHHHHHHHHHHHH___
. . . . .
101 RGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSCTLA 150
__EEE_________________________HHHHHH__________EEEE
. . . . .
151 VDGYLCQFGFEGACPALQDEAGQAGPAVYTTPFHLVSTEFEWLPFGSVAA 200
E_EEEE_____________________EEE________________HHHH
. . . . .
201 VQCQAGRGASLLCVKQPEGGVGWSRAGPLCLGTGCSPDNGGCEHECVEEV 250
HHHH_____EEEEEE_____________________________EEEE__
. . . . .
251 DGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGF 300
___EEEEE__________________________________EEE_____
. . . . .
301 RPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISC 350
________EEE_____HHHHHHHHHHH_____EEEEE_____________
. . . . .
351 SPAGAMGAQASQDLGDELLDDGEDEEDEDEAWKAFNGGWTEMPGILWMEP 400
____HHHHHHHHHH_______________HHHHHH_______________
. . . . .
401 TQPPDFALAYRPSFPEDREPQIPYPEPTWPPPLSAPRVPYHSSVLSVTRP 450
_____EEEEE_________________________________EEEE_EE
. . . . .
451 VVVSATHPTLPSAHQPPVIPATHPALSRDHQIPVIAANYPDLPSAYQPGI 500
EEEEE__________________________EEEEEE____________E
. . . . .
501 LSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAGTQTTTHLPGI 550
EEEE______________________________________________
. . . . .
551 PPNHAPLVTTLGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPV 600
_____EEEEEE__________HHHHHHHHH____________EEE_____
. . . . .
601 SPAHQISVPAATQPAALPTLLPSQSPTNQTSPISPTHPHSKAPQIPREDG 650
__________________________________________________
. . . . .
651 PSPKLALWLPSPAPTAAPTALGEAGLAEHSQRDDRWLLVALLVPTCVFLV 700
____EEEE____________HHHHHHHHHH____HHHHHHH____HHHHH
. . . . .
701 VLLALGIVYCTRCGPHAPNKRITDCYRWVIHAGSKSPTEPMPPRGSLTGV 750
HHHHHHEEEE_______________EEEEEE_________________EE
751 QTCRTSV 757
EEEE___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 29.5 %
beta-contents : 0.0 %
coil-contents : 70.5 %
class : alpha
method : 2
alpha-contents : 0.0 %
beta-contents : 0.0 %
coil-contents : 100.0 %
class : irregular
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-10.51 0.00 -0.01 -0.32 0.00 0.00 0.00 0.00 0.00 -5.86 -1.86 -12.00 -12.00 0.00 -12.00 0.00 -54.55
1.96 -1.48 -3.19 -5.14 0.00 0.00 -20.00 0.00 0.00 -6.69 -1.86 -12.00 0.00 0.00 0.00 0.00 -48.40
ID: gi|9857400|gb|AAG00867.1|AF279142_1 AC: xxx Len: 757 1:I 745 Sc: -48.40 Pv: 2.073175e-01 NO_GPI_SITE
GPI: learning from protozoa
-15.59 -0.10 -0.01 -0.07 -4.00 0.00 -24.00 0.00 0.00 -5.79 -7.25 -12.00 0.00 0.00 0.00 0.00 -68.82
1.29 -1.64 -0.23 -1.49 0.00 0.00 -20.00 0.00 0.00 -5.79 -7.25 -12.00 -12.00 0.00 0.00 0.00 -59.12
ID: gi|9857400|gb|AAG00867.1|AF279142_1 AC: xxx Len: 757 1:I 745 Sc: -59.12 Pv: 2.153983e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857400| 0.856 18 Y 0.793 714 Y 0.990 697 Y 0.142 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857400| 0.619 667 Y 0.459 18 Y 0.988 3 Y 0.715 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857400| 0.633 279 Y 0.385 715 Y 0.985 695 Y 0.224 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
1-1 M
llrlllawaaa 2-12
13-86 GPTLGQDPWAAEPRAACGPSSCYALFPRRR
TFLEAWRACRELGGDLATPRTPEEAQRVDS
LVGAGPASRLLWIG
lqrqarqcqlqrplr 87-101
102-362 GFTWTTGDQDTAFTNWAQPASGGPCPAQRC
VALEASGEHRWLEGSCTLAVDGYLCQFGFE
GACPALQDEAGQAGPAVYTTPFHLVSTEFE
WLPFGSVAAVQCQAGRGASLLCVKQPEGGV
GWSRAGPLCLGTGCSPDNGGCEHECVEEVD
GHVSCRCTEGFRLAADGRSCEDPCAQAPCE
QQCEPGGPQGYSCHCRLGFRPAEDDPHRCV
DTDECQIAGVCQQMCVNYVGGFECYCSEGH
ELEADGISCSPAGAMGAQASQ
dlgdellddgedeedede 363-380
381-608 AWKAFNGGWTEMPGILWMEPTQPPDFALAY
RPSFPEDREPQIPYPEPTWPPPLSAPRVPY
HSSVLSVTRPVVVSATHPTLPSAHQPPVIP
ATHPALSRDHQIPVIAANYPDLPSAYQPGI
LSVSHSAQPPAHQPPMISTKYPELFPAHQS
PMFPDTRVAGTQTTTHLPGIPPNHAPLVTT
LGAQLPPQAPDALVLRTQATQLPIIPTAQP
SLTTTSRSPVSPAHQISV
paatqpaalptllpsqspt 609-627
628-654 NQTSPISPTHPHSKAPQIPREDGPSPK
lalwlpspaptaaptalgeaglae 655-678
679-757 HSQRDDRWLLVALLVPTCVFLVVLLALGIV
YCTRCGPHAPNKRITDCYRWVIHAGSKSPT
EPMPPRGSLTGVQTCRTSV
low complexity regions: SEG 25 3.0 3.3
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
1-1 M
llrlllawaaagptlgqdpwaaepraa 2-28
29-264 CGPSSCYALFPRRRTFLEAWRACRELGGDL
ATPRTPEEAQRVDSLVGAGPASRLLWIGLQ
RQARQCQLQRPLRGFTWTTGDQDTAFTNWA
QPASGGPCPAQRCVALEASGEHRWLEGSCT
LAVDGYLCQFGFEGACPALQDEAGQAGPAV
YTTPFHLVSTEFEWLPFGSVAAVQCQAGRG
ASLLCVKQPEGGVGWSRAGPLCLGTGCSPD
NGGCEHECVEEVDGHVSCRCTEGFRL
aadgrscedpcaqapceqqcepggpqg 265-291
292-362 YSCHCRLGFRPAEDDPHRCVDTDECQIAGV
CQQMCVNYVGGFECYCSEGHELEADGISCS
PAGAMGAQASQ
dlgdellddgedeedede 363-380
381-406 AWKAFNGGWTEMPGILWMEPTQPPDF
alayrpsfpedrepqipypeptwppplsap 407-486
rvpyhssvlsvtrpvvvsathptlpsahqp
pvipathpalsrdhqipvia
487-535 ANYPDLPSAYQPGILSVSHSAQPPAHQPPM
ISTKYPELFPAHQSPMFPD
trvagtqttthlpgippnhaplvttlgaql 536-646
ppqapdalvlrtqatqlpiiptaqpslttt
srspvspahqisvpaatqpaalptllpsqs
ptnqtspispthphskapqip
647-650 REDG
pspklalwlpspaptaaptalgeaglae 651-678
679-686 HSQRDDRW
llvallvptcvflvvllal 687-705
706-757 GIVYCTRCGPHAPNKRITDCYRWVIHAGSK
SPTEPMPPRGSLTGVQTCRTSV
low complexity regions: SEG 45 3.4 3.75
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
1-337 MLLRLLLAWAAAGPTLGQDPWAAEPRAACG
PSSCYALFPRRRTFLEAWRACRELGGDLAT
PRTPEEAQRVDSLVGAGPASRLLWIGLQRQ
ARQCQLQRPLRGFTWTTGDQDTAFTNWAQP
ASGGPCPAQRCVALEASGEHRWLEGSCTLA
VDGYLCQFGFEGACPALQDEAGQAGPAVYT
TPFHLVSTEFEWLPFGSVAAVQCQAGRGAS
LLCVKQPEGGVGWSRAGPLCLGTGCSPDNG
GCEHECVEEVDGHVSCRCTEGFRLAADGRS
CEDPCAQAPCEQQCEPGGPQGYSCHCRLGF
RPAEDDPHRCVDTDECQIAGVCQQMCVNYV
GGFECYC
segheleadgiscspagamgaqasqdlgde 338-388
llddgedeededeawkafngg
389-399 WTEMPGILWME
ptqppdfalayrpsfpedrepqipypeptw 400-695
ppplsaprvpyhssvlsvtrpvvvsathpt
lpsahqppvipathpalsrdhqipviaany
pdlpsayqpgilsvshsaqppahqppmist
kypelfpahqspmfpdtrvagtqttthlpg
ippnhaplvttlgaqlppqapdalvlrtqa
tqlpiiptaqpsltttsrspvspahqisvp
aatqpaalptllpsqsptnqtspispthph
skapqipredgpspklalwlpspaptaapt
algeaglaehsqrddrwllvallvpt
696-757 CVFLVVLLALGIVYCTRCGPHAPNKRITDC
YRWVIHAGSKSPTEPMPPRGSLTGVQTCRT
SV
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
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRACRELGGDLAT
PRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPLRGFTWTTGDQDTAFTNWAQP
ASGGPCPAQRCVALEASGEHRWLEGSCTLAVDGYLCQFGFEGACPALQDEAGQAGPAVYT
TPFHLVSTEFEWLPFGSVAAVQCQAGRGASLLCVKQPEGGVGWSRAGPLCLGTGCSPDNG
GCEHECVEEVDGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGF
RPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISCSPAGAMGAQA
sqdlgdellddgedeededeAWKAFNGGWTEMPGILWMEPTQPPDFALAYRPSFPEDREP
QIPYPEPTWPPPLSAPRVPYHSSVLSVTRPVVVSATHPTLPSAHQPPVIPATHPALSRDH
QIPVIAANYPDLPSAYQPGILSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAG
TQTTTHLPGIPPNHAPLVTTLGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPV
SPAHQIsvpaatqpaalptllpsqsptNQTSPISPTHPHSKAPQIPREDGPSPKLALWLp
spaptaaptaLGEAGLAEHSQRDDRWLLVALLVPTCVFLVVLLALGIVYCTRCGPHAPNK
RITDCYRWVIHAGSKSPTEPMPPRGSLTGVQTCRTSV
1 - 360 MLLRLLLAWA AAGPTLGQDP WAAEPRAACG PSSCYALFPR RRTFLEAWRA CRELGGDLAT
PRTPEEAQRV DSLVGAGPAS RLLWIGLQRQ ARQCQLQRPL RGFTWTTGDQ DTAFTNWAQP
ASGGPCPAQR CVALEASGEH RWLEGSCTLA VDGYLCQFGF EGACPALQDE AGQAGPAVYT
TPFHLVSTEF EWLPFGSVAA VQCQAGRGAS LLCVKQPEGG VGWSRAGPLC LGTGCSPDNG
GCEHECVEEV DGHVSCRCTE GFRLAADGRS CEDPCAQAPC EQQCEPGGPQ GYSCHCRLGF
RPAEDDPHRC VDTDECQIAG VCQQMCVNYV GGFECYCSEG HELEADGISC SPAGAMGAQA
361 - 380 sqdlgdelld dgedeedede
381 - 606 AWKAFNGGWT EMPGILWMEP TQPPDFALAY RPSFPEDREP QIPYPEPTWP PPLSAPRVPY
HSSVLSVTRP VVVSATHPTL PSAHQPPVIP ATHPALSRDH QIPVIAANYP DLPSAYQPGI
LSVSHSAQPP AHQPPMISTK YPELFPAHQS PMFPDTRVAG TQTTTHLPGI PPNHAPLVTT
LGAQLPPQAP DALVLRTQAT QLPIIPTAQP SLTTTSRSPV SPAHQI
607 - 627 svpa atqpaalptl lpsqspt
628 - 659 NQT SPISPTHPHS KAPQIPREDG PSPKLALWL
660 - 670 p spaptaapta
671 - 757 LGEAGLAEHS QRDDRWLLVA LLVPTCVFLV VLLALGIVYC TRCGPHAPNK RITDCYRWVI
HAGSKSPTEP MPPRGSLTGV QTCRTSV
low complexity regions: DUST
>gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRACRELGGDLAT
PRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPLRGFTWTTGDQDTAFTNWAQP
ASGGPCPAQRCVALEASGEHRWLEGSCTLAVDGYLCQFGFEGACPALQDEAGQAGPAVYT
TPFHLVSTEFEWLPFGSVAAVQCQAGRGASLLCVKQPEGGVGWSRAGPLCLGTGCSPDNG
GCEHECVEEVDGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGF
RPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISCSPAGAMGAQA
SQDLGDELLDDGEDEEDEDEAWKAFNGGWTEMPGILWMEPTQPPDFALAYRPSFPEDREP
QIPYPEPTWPPPLSAPRVPYHSSVLSVTRPVVVSATHPTLPSAHQPPVIPATHPALSRDH
QIPVIAANYPDLPSAYQPGILSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAG
TQTTTHLPGIPPNHAPLVTTLGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPV
SPAHQISVPAATQPAALPTLLPSQSPTNQTSPISPTHPHSKAPQIPREDGPSPKLALWLP
SPAPTAAPTALGEAGLAEHSQRDDRWLLVALLVPTCVFLVVLLALGIVYCTRCGPHAPNK
RITDCYRWVIHAGSKSPTEPMPPRGSLTGVQTCRTSV
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|9857400|gb|AAG00867.1|AF279142_1
sequence: 757 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MLLRLLLAWA AAGPTLGQDP WAAEPRAACG PSSCYALFPR RRTFLEAWRA CRELGGDLAT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PRTPEEAQRV DSLVGAGPAS RLLWIGLQRQ ARQCQLQRPL RGFTWTTGDQ DTAFTNWAQP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
ASGGPCPAQR CVALEASGEH RWLEGSCTLA VDGYLCQFGF EGACPALQDE AGQAGPAVYT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
TPFHLVSTEF EWLPFGSVAA VQCQAGRGAS LLCVKQPEGG VGWSRAGPLC LGTGCSPDNG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GCEHECVEEV DGHVSCRCTE GFRLAADGRS CEDPCAQAPC EQQCEPGGPQ GYSCHCRLGF
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
RPAEDDPHRC VDTDECQIAG VCQQMCVNYV GGFECYCSEG HELEADGISC SPAGAMGAQA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
SQDLGDELLD DGEDEEDEDE AWKAFNGGWT EMPGILWMEP TQPPDFALAY RPSFPEDREP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
QIPYPEPTWP PPLSAPRVPY HSSVLSVTRP VVVSATHPTL PSAHQPPVIP ATHPALSRDH
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
QIPVIAANYP DLPSAYQPGI LSVSHSAQPP AHQPPMISTK YPELFPAHQS PMFPDTRVAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
TQTTTHLPGI PPNHAPLVTT LGAQLPPQAP DALVLRTQAT QLPIIPTAQP SLTTTSRSPV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 660
SPAHQISVPA ATQPAALPTL LPSQSPTNQT SPISPTHPHS KAPQIPREDG PSPKLALWLP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 720
SPAPTAAPTA LGEAGLAEHS QRDDRWLLVA LLVPTCVFLV VLLALGIVYC TRCGPHAPNK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | .
RITDCYRWVI HAGSKSPTEP MPPRGSLTGV QTCRTSV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~
---------- ---------- ---------- -------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem1.___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: tem1.___inter___
(1 sequences)
MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRA
CRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPL
RGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSCTLA
VDGYLCQFGFEGACPALQDEAGQAGPAVYTTPFHLVSTEFEWLPFGSVAA
VQCQAGRGASLLCVKQPEGGVGWSRAGPLCLGTGCSPDNGGCEHECVEEV
DGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGF
RPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISC
SPAGAMGAQASQDLGDELLDDGEDEEDEDEAWKAFNGGWTEMPGILWMEP
TQPPDFALAYRPSFPEDREPQIPYPEPTWPPPLSAPRVPYHSSVLSVTRP
VVVSATHPTLPSAHQPPVIPATHPALSRDHQIPVIAANYPDLPSAYQPGI
LSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAGTQTTTHLPGI
PPNHAPLVTTLGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPV
SPAHQISVPAATQPAALPTLLPSQSPTNQTSPISPTHPHSKAPQIPREDG
PSPKLALWLPSPAPTAAPTALGEAGLAEHSQRDDRWLLVALLVPTCVFLV
VLLALGIVYCTRCGPHAPNKRITDCYRWVIHAGSKSPTEPMPPRGSLTGV
QTCRTSV
(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 8 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 170 190 0.626 Putative
2 605 625 0.834 Putative
3 652 672 0.929 Putative
4 686 706 2.332 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4
Loop length 169 414 26 13 51
K+R profile + 3.00 7.00
+ 2.00
CYT-EXT prof -0.82 - -
0.23 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 8.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2 3 4
Loop length 604 26 13 51
K+R profile + 2.00
3.00 7.00
CYT-EXT prof -0.07 -
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -8.00
Tm probability: 0.48
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): 0.3204
NEG: 68.0000
POS: 35.0000
-> Orientation: N-in
CYT-EXT difference: -0.07
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 4
Loop length 169 495 51
K+R profile + 7.00
+
CYT-EXT prof -0.82 -
0.26
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 7.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.08
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 4
Loop length 685 51
K+R profile +
7.00
CYT-EXT prof 0.00
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -7.00
Tm probability: 1.00
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -4.00
(NEG-POS)/(NEG+POS): 0.2982
NEG: 74.0000
POS: 40.0000
-> Orientation: N-out
CYT-EXT difference: 0.00
-> Orientation: N-out
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 3 4
Loop length 169 461 13 51
K+R profile + 2.00
+ 7.00
CYT-EXT prof -0.82 -
0.30 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -5.00
Tm probability: 0.05
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 3 4
Loop length 651 13 51
K+R profile + 7.00
2.00
CYT-EXT prof 0.02 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.82
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.2963
NEG: 70.0000
POS: 38.0000
-> Orientation: N-in
CYT-EXT difference: 0.02
-> Orientation: N-out
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 4
Loop length 169 414 60 51
K+R profile + 5.00
+ 7.00
CYT-EXT prof -0.82 -
0.23 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -2.00
Tm probability: 0.04
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 2 4
Loop length 604 60 51
K+R profile + 7.00
5.00
CYT-EXT prof -0.07 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.59
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): 0.3204
NEG: 68.0000
POS: 35.0000
-> Orientation: N-in
CYT-EXT difference: -0.07
-> Orientation: N-in
----------------------------------------------------------------------
"tem1" 757
170 190 #f 0.626042
605 625 #f 0.834375
652 672 #f 0.929167
686 706 #t 2.33229
************************************
*TOPPREDM with prokaryotic function*
************************************
tem1.___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: tem1.___inter___
(1 sequences)
MLLRLLLAWAAAGPTLGQDPWAAEPRAACGPSSCYALFPRRRTFLEAWRA
CRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPL
RGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSCTLA
VDGYLCQFGFEGACPALQDEAGQAGPAVYTTPFHLVSTEFEWLPFGSVAA
VQCQAGRGASLLCVKQPEGGVGWSRAGPLCLGTGCSPDNGGCEHECVEEV
DGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGF
RPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEGHELEADGISC
SPAGAMGAQASQDLGDELLDDGEDEEDEDEAWKAFNGGWTEMPGILWMEP
TQPPDFALAYRPSFPEDREPQIPYPEPTWPPPLSAPRVPYHSSVLSVTRP
VVVSATHPTLPSAHQPPVIPATHPALSRDHQIPVIAANYPDLPSAYQPGI
LSVSHSAQPPAHQPPMISTKYPELFPAHQSPMFPDTRVAGTQTTTHLPGI
PPNHAPLVTTLGAQLPPQAPDALVLRTQATQLPIIPTAQPSLTTTSRSPV
SPAHQISVPAATQPAALPTLLPSQSPTNQTSPISPTHPHSKAPQIPREDG
PSPKLALWLPSPAPTAAPTALGEAGLAEHSQRDDRWLLVALLVPTCVFLV
VLLALGIVYCTRCGPHAPNKRITDCYRWVIHAGSKSPTEPMPPRGSLTGV
QTCRTSV
(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 8 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 170 190 0.626 Putative
2 605 625 0.834 Putative
3 652 672 0.929 Putative
4 686 706 2.332 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4
Loop length 169 414 26 13 51
K+R profile + 3.00 7.00
+ 2.00
CYT-EXT prof -0.82 - -
0.23 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 8.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2 3 4
Loop length 604 26 13 51
K+R profile + 2.00
3.00 7.00
CYT-EXT prof -0.07 -
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -8.00
Tm probability: 0.48
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): 0.3204
NEG: 68.0000
POS: 35.0000
-> Orientation: N-in
CYT-EXT difference: -0.07
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 4
Loop length 169 495 51
K+R profile + 7.00
+
CYT-EXT prof -0.82 -
0.26
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 7.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.08
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 4
Loop length 685 51
K+R profile +
7.00
CYT-EXT prof 0.00
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -7.00
Tm probability: 1.00
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -4.00
(NEG-POS)/(NEG+POS): 0.2982
NEG: 74.0000
POS: 40.0000
-> Orientation: N-out
CYT-EXT difference: 0.00
-> Orientation: N-out
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 3 4
Loop length 169 461 13 51
K+R profile + 2.00
+ 7.00
CYT-EXT prof -0.82 -
0.30 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -5.00
Tm probability: 0.05
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 3 4
Loop length 651 13 51
K+R profile + 7.00
2.00
CYT-EXT prof 0.02 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.82
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.2963
NEG: 70.0000
POS: 38.0000
-> Orientation: N-in
CYT-EXT difference: 0.02
-> Orientation: N-out
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 4
Loop length 169 414 60 51
K+R profile + 5.00
+ 7.00
CYT-EXT prof -0.82 -
0.23 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -2.00
Tm probability: 0.04
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0303
NEG: 17.0000
POS: 16.0000
-> Orientation: N-out
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 2 4
Loop length 604 60 51
K+R profile + 7.00
5.00
CYT-EXT prof -0.07 -
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.59
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): 0.3204
NEG: 68.0000
POS: 35.0000
-> Orientation: N-in
CYT-EXT difference: -0.07
-> Orientation: N-in
----------------------------------------------------------------------
"tem1" 757
170 190 #f 0.626042
605 625 #f 0.834375
652 672 #f 0.929167
686 706 #t 2.33229
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem1.___saps___
SAPS. Version of April 11, 1996.
Date run: Fri Oct 13 19:31:57 2000
File: /people/maria/tem1.___saps___
ID gi|9857400|gb|AAG00867.1|AF279142_1
DE tumor endothelial marker 1 precursor
number of residues: 757; molecular weight: 80.9 kdal
1 MLLRLLLAWA AAGPTLGQDP WAAEPRAACG PSSCYALFPR RRTFLEAWRA CRELGGDLAT
61 PRTPEEAQRV DSLVGAGPAS RLLWIGLQRQ ARQCQLQRPL RGFTWTTGDQ DTAFTNWAQP
121 ASGGPCPAQR CVALEASGEH RWLEGSCTLA VDGYLCQFGF EGACPALQDE AGQAGPAVYT
181 TPFHLVSTEF EWLPFGSVAA VQCQAGRGAS LLCVKQPEGG VGWSRAGPLC LGTGCSPDNG
241 GCEHECVEEV DGHVSCRCTE GFRLAADGRS CEDPCAQAPC EQQCEPGGPQ GYSCHCRLGF
301 RPAEDDPHRC VDTDECQIAG VCQQMCVNYV GGFECYCSEG HELEADGISC SPAGAMGAQA
361 SQDLGDELLD DGEDEEDEDE AWKAFNGGWT EMPGILWMEP TQPPDFALAY RPSFPEDREP
421 QIPYPEPTWP PPLSAPRVPY HSSVLSVTRP VVVSATHPTL PSAHQPPVIP ATHPALSRDH
481 QIPVIAANYP DLPSAYQPGI LSVSHSAQPP AHQPPMISTK YPELFPAHQS PMFPDTRVAG
541 TQTTTHLPGI PPNHAPLVTT LGAQLPPQAP DALVLRTQAT QLPIIPTAQP SLTTTSRSPV
601 SPAHQISVPA ATQPAALPTL LPSQSPTNQT SPISPTHPHS KAPQIPREDG PSPKLALWLP
661 SPAPTAAPTA LGEAGLAEHS QRDDRWLLVA LLVPTCVFLV VLLALGIVYC TRCGPHAPNK
721 RITDCYRWVI HAGSKSPTEP MPPRGSLTGV QTCRTSV
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 83(11.0%); C+ : 35( 4.6%); D : 33( 4.4%); E : 43( 5.7%); F : 18( 2.4%)
G : 61( 8.1%); H : 23( 3.0%); I : 19( 2.5%); K- : 7( 0.9%); L : 67( 8.9%)
M : 8( 1.1%); N- : 8( 1.1%); P+ : 95(12.5%); Q : 46( 6.1%); R : 40( 5.3%)
S : 50( 6.6%); T : 51( 6.7%); V : 40( 5.3%); W : 16( 2.1%); Y : 14( 1.8%)
KR : 47 ( 6.2%); ED : 76 ( 10.0%); AGP + : 239 ( 31.6%);
KRED : 123 ( 16.2%); KR-ED : -29 ( -3.8%); FIKMNY--: 74 ( 9.8%);
LVIFM : 152 ( 20.1%); ST : 101 ( 13.3%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 000+000000 00000000-0 000-0+0000 000000000+ ++000-00+0 0+-000-000
61 0+00--00+0 -000000000 +0000000+0 0+00000+00 +0000000-0 -000000000
121 000000000+ 0000-000-0 +00-000000 0-00000000 -0000000-- 0000000000
181 00000000-0 -000000000 000000+000 0000+00-00 0000+00000 0000000-00
241 00-0-00--0 -00000+00- 00+000-0+0 0--0000000 -000-00000 000000+000
301 +00---00+0 0-0--00000 0000000000 000-0000-0 0-0-0-0000 0000000000
361 00-00--00- -0-------- 00+0000000 -0000000-0 0000-00000 +0000--+-0
421 00000-0000 000000+000 00000000+0 0000000000 0000000000 0000000+-0
481 0000000000 -000000000 0000000000 000000000+ 00-0000000 0000-0+000
541 0000000000 0000000000 0000000000 -0000+0000 0000000000 000000+000
601 0000000000 0000000000 0000000000 0000000000 +00000+--0 000+000000
661 0000000000 00-0000-00 0+--+00000 0000000000 0000000000 0+0000000+
721 +00-00+000 0000+000-0 000+000000 000+000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 7/30 or 10/45 or 12/60): none
Negative charge clusters (cmin = 10/30 or 13/45 or 16/60):
1) From 363 to 383: DLGDELLDDGEDEEDEDEAWK
-00--00--0--------00+
quartile: 2; size: 21, +count: 1, -count: 13, 0count: 7; t-value: 7.18 *
L: 3 (14.3%); E: 6 (28.6%); D: 7 (33.3%);
Mixed charge clusters (cmin = 13/30 or 18/45 or 22/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
______________________________________
High scoring negative charge segments:
score= 2.00 frequency= 0.100 ( ED )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.838 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency= 0.062 ( KR )
Expected score/letter: -0.761
M_0.01= 10.71; M_0.05= 8.98
1) From 363 to 382: length= 20, score=19.00 **
363 DLGDELLDDG EDEEDEDEAW
L: 3(15.0%); G: 2(10.0%); E: 6(30.0%); D: 7(35.0%);
___________________________________
High scoring mixed charge segments:
score= 1.00 frequency= 0.162 ( KEDR )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.838 ( LAGSVTIPNFQYHMCW )
Expected score/letter: -0.675
M_0.01= 6.48; M_0.05= 5.48
1) From 366 to 385: length= 20, score= 6.00 *
(pocket at 381 to 382: length= 2, score=-2.00)
(pocket at 368 to 369: length= 2, score=-2.00)
366 DE |LL| DDGEDE EDEDE |AW| KAF
L: 2(10.0%); A: 2(10.0%); E: 6(30.0%); D: 6(30.0%);
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 4 | 5 | 6 | 53 | 8 | 10 | 12 | 10 | 12 | 15 | 7 | 9 |
lmin1 5 | 6 | 8 | 64 | 10 | 12 | 14 | 13 | 15 | 18 | 9 | 12 |
lmin2 6 | 7 | 9 | 72 | 12 | 13 | 16 | 14 | 17 | 20 | 10 | 13 |
(Significance level: 0.010000; Minimal displayed length: 6)
(-) 10(1,0,0); at 370- 380: DDGEDEEDEDE
(2. quartile) --0--------
Run count statistics:
+ runs >= 3: 1, at 40;
- runs >= 3: 2, at 304; 373;
* runs >= 4: 3, at 373; 416; 682;
0 runs >= 35: 1, at 598;
--------------------------------------------------------------------------------
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: -1.753
M_0.01= 23.49; M_0.05= 19.64
1) From 686 to 710: length= 25, score=33.00 **
686 WLLVALLVPT CVFLVVLLAL GIVYC
L: 8(32.0%); V: 6(24.0%);
____________________________________
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: -3.410
M_0.01= 52.51; M_0.05= 43.68; M_0.30= 33.17
1) From 687 to 708: length= 22, score=77.00 **
687 LLVALLVPTC VFLVVLLALG IV
L: 8(36.4%); V: 6(27.3%);
2. SPACINGS OF C.
H2N-28-C-4-C-16-C-42-C-31-C-4-C-15-C-8-C-7-C-38-C-9-C-16-C-4-C-6-C-3-C-9-C-1-C-12-C-3-C-4-C-3-C-9-C-1-C-13-C-5-C-5-C-3-C-8-C-1-C-12-C-345-C-13-C-2-C-11-C-27-C-4-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-28-C-4-C-16-C-42-C-31-C-4-C-8-H-6-C-8-C-7-C-19-H-18-C-9-C-16-C-4-C-6-C-1-H-1-C-6-H-2-C-1-C-12-C-3-C-4-C-3-C-9-C-H-C-11-H-1-C-5-C-5-C-3-C-8-C-1-C-3-H-8-C-90-H-15-H-6-H-8-H-6-H-24-H-6-H-15-H-17-H-7-H-49-H-32-H-1-H-39-H-16-C-13-C-2-C-2-H-8-C-5-H-21-C-4-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
Aligned matching blocks:
[ 463- 467] AHQPP
[ 511- 515] AHQPP
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: 52 (Expected range: 28-- 70)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 14 (6-10) 13 (11-20) 18 (>=21) 8
3. Clusters of amino acid multiplets (cmin = 12/30 or 15/45 or 18/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 14 (Expected range: 0-- 19)
2 +plets (f+: 6.2%), 12 -plets (f-: 10.0%)
Total number of charge altplets: 6 (Critical number: 21)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 2 (6-10) 1 (11-20) 0 (>=21) 12
3. Long charge multiplets (>= 5; Letter/Length/Position):
-/8/373
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
220- 247 7 G...... 4 4 0
415- 434 5 P....
4 4 0
450- 529 8 P....A.. 8 4 /2/././././3/././
614- 629 4 P... 4 4 0
656- 683 7 A...... 4 4 0
689- 704 4 V.L. 4 4 /0/./1/./
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8)
Location Period Element Copies Core Errors
370- 380 1 - 10 8 ! 1
444- 539 8 i.000000 11 8 ! /1/./1/4/1/2/2/3/
687- 708 2 i. 10 6 1
697- 703 1 i 7 7 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
51- 94 (1.) C( 43)C 2 of 36 0.9952 small 2. maximal spacing
116- 239 (1.) N( 123)N 1 of 9 0.9983 small maximal spacing
350- 696 (3.) C( 346)C 1 of 36 0.0000 large 1. maximal spacing
394- 499 (3.) G( 105)G 1 of 62 0.0045 large 1. maximal spacing
562- 650 (4.) G( 88)G 2 of 62 0.0001 large 2. maximal spacing
719- 758 (4.) N( 39)N 9 of 9 0.0068 large minimal 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: tem1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
EGF EGF-like domain 56.5 5.6e-13 3
lectin_c Lectin C-type domain 34.7 2.2e-06 1
sushi Sushi domain (SCR repeat) 8.4 0.72 1
Xlink Extracellular link domain 6.4 0.034 1
TIL Trypsin Inhibitor like cysteine rich 5.6 0.17 1
defensins Mammalian defensin 1.9 69 1
ATP-synt_DE ATP synthase, Delta/Epsilon chain 1.5 49 1
Luteo_ORF2 Putative replicase 1 (ORF2) -0.4 24 1
Flavi_NS1 Flavivirus non-structural Protein NS1 -0.7 83 1
late_protein_L1 L1 (late) protein -1.9 83 1
Arthro_defensin Arthropod defensin -5.6 67 1
Metallothio_5 Metallothionein family 5 -5.8 28 1
W2 eIF4-gamma/eIF5/eIF2-epsilon -34.8 51 1
Keratin_B2 Keratin, high sulfur B2 protein -95.8 58 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Xlink 1/1 43 61 .. 16 34 .. 6.4 0.034
Flavi_NS1 1/1 61 80 .. 358 377 .] -0.7 83
Luteo_ORF2 1/1 119 132 .. 674 687 .] -0.4 24
lectin_c 1/1 49 156 .. 1 111 [] 34.7 2.2e-06
sushi 1/1 176 230 .. 1 62 [] 8.4 0.72
Arthro_defensin 1/1 232 259 .. 1 36 [] -5.6 67
EGF 1/3 235 271 .. 1 45 [] 33.6 4.6e-06
Metallothio_5 1/1 254 298 .. 1 41 [] -5.8 28
defensins 1/1 294 300 .. 1 7 [. 1.9 69
Keratin_B2 1/1 195 303 .. 1 177 [] -95.8 58
EGF 2/3 275 310 .. 1 45 [] 11.5 2.1
TIL 1/1 258 316 .. 1 67 [] 5.6 0.17
EGF 3/3 316 350 .. 1 45 [] 27.4 0.00035
W2 1/1 323 380 .. 1 87 [] -34.8 51
ATP-synt_DE 1/1 549 561 .. 32 44 .. 1.5 49
late_protein_L1 1/1 655 663 .. 1 9 [. -1.9 83
Alignments of top-scoring domains:
Xlink: domain 1 of 1, from 43 to 61: score 6.4, E = 0.034
*->tFeEAqaaClrqgAriATt<-*
tF EA +aC++ g+ +AT+
gi|9857400 43 TFLEAWRACRELGGDLATP 61
Flavi_NS1: domain 1 of 1, from 61 to 80: score -0.7, E = 83
*->PvkekEenLVkSqVtAgnge<-*
P++ +E++ V S+V Ag++
gi|9857400 61 PRTPEEAQRVDSLVGAGPAS 80
Luteo_ORF2: domain 1 of 1, from 119 to 132: score -0.4, E = 24
*->qeaSgGPsSaqklN<-*
q+aSgGP +aq+
gi|9857400 119 QPASGGPCPAQRCV 132
lectin_c: domain 1 of 1, from 49 to 156: score 34.7, E = 2.2e-06
*->laCqrekpgghLvsIqsqeEqdFlqslvkavn...yaWIGLtdinkg
aC+++ gg+L++++ +eE+ + slv+a + ++ +WIGL ++
gi|9857400 49 RACREL--GGDLATPRTPEEAQRVDSLVGAGPasrLLWIGLQRQARQ 93
eptegt...WvWsdGslpvnytnWak.ipgePnnwrhkggkedCvelytk
+ +++ ++++W++G++ + +tnWa++ +g P + Cv+l +
gi|9857400 94 CQLQRPlrgFTWTTGDQDTAFTNWAQpASGGPCP------AQRCVALEAS 137
tpkangkWnDepCdskl.pyvC<-*
+ +W +C ++y+C
gi|9857400 138 GE---HRWLEGSCTLAVdGYLC 156
sushi: domain 1 of 1, from 176 to 230: score 8.4, E = 0.72
*->Cp.pPdieNGrvsss.gtyeypvGdtvtytCneGYrlvGsssitCte
p + + +++ vs++ + ++ G+++ +C+ G +G +s+ C++
gi|9857400 176 -PaVYTTPFHLVSTEfEWLPF--GSVAAVQCQAG---RG-ASLLCVK 215
dg.g.GgWsppllGelPkC<-*
+ +g+ gWs + P C
gi|9857400 216 QPeGgVGWSRAG----PLC 230
Arthro_defensin: domain 1 of 1, from 232 to 259: score -5.6, E = 67
*->gkgcpvNhsaCaaHClakGGrrGGyCnglkavCvCR<-*
g gc +++ C C+ g C+C
gi|9857400 232 GTGCSPDNGGCEHECVEEV-------DG-HVSCRCT 259
EGF: domain 1 of 3, from 235 to 271: score 33.6, E = 4.6e-06
*->Capnn.pCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<
C+p+n++C + +Cv+ + g+ +C+C++G ++l+ +G+ C
gi|9857400 235 CSPDNgGCEH--ECVEEVD------GHVSCRCTEG-FRLAADGRSC 271
-*
gi|9857400 - -
Metallothio_5: domain 1 of 1, from 254 to 298: score -5.8, E = 28
*->MvCkGCGsnCkCaa..QktkdsCa...CnkDCkCvgdkkskdqCse<
C+ C + + aa++ + d Ca+ +C + C +g ++ + C
gi|9857400 254 VSCR-CTEGFRLAAdgRSCEDPCAqapCEQQCEPGGPQGYSCHCRL 298
-*
gi|9857400 - -
defensins: domain 1 of 1, from 294 to 300: score 1.9, E = 69
*->CyCRrrl<-*
C+CR ++
gi|9857400 294 CHCRLGF 300
Keratin_B2: domain 1 of 1, from 195 to 303: score -95.8, E = 58
*->qtScCGfptCStlgtrPsCGsscCQPsCCeSCCQpsCcqpSCCqPtc
+S + +g C+ QP + + S P
gi|9857400 195 FGSVAAVQCQAGRGASLLCVK---QP--------EGGVGWSRAGP-- 228
sqtscCqPtcfqssCCrPsCcqTSCCqPtCcqsssCqtgCgigGsiGyGQ
+c + C + ++ +C+ C
gi|9857400 229 --------LCLGT-----GCSP---------DNGGCEHEC---------V 247
eGsSGAvScrirWCRPdCrvegtClPpCCvvsCtaPTCCqpvsaQasC..
e G vScr + eg l+ + sC P +aQa+C++
gi|9857400 248 EEVDGHVSCR--------CTEGFRLAADGR-SCEDP------CAQAPCeq 282
.CRPsCqPyCgqsCCRP.aCccsvtCtrTccePc<-*
+C P g ++ +C c +P
gi|9857400 283 qCEPG-----G---PQGySCHCR-----LGFRPA 303
EGF: domain 2 of 3, from 275 to 310: score 11.5, E = 2.1
*->CapnnpCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-
Ca+ pC + +C +++ +gy+C+C G+ + + +rC
gi|9857400 275 CAQA-PCEQ--QCEPGGP------QGYSCHCRLGFRPAEDDPHRC 310
*
gi|9857400 - -
TIL: domain 1 of 1, from 258 to 316: score 5.6, E = 0.17
*->CpaneqyteCgpsCepsCsnpdgplettppCegtSpkvPstCkeg..
C++ + + g sCe C+ +pCe +C++g++
gi|9857400 258 CTEGFRLAADGRSCEDPCAQ--------APCE-------QQCEPGgp 289
....CvCqpGyVrnndgd.kCVprseC<-*
++ +C C+ G+ +d++++CV eC
gi|9857400 290 qgysCHCRLGFRPAEDDPhRCVDTDEC 316
EGF: domain 3 of 3, from 316 to 350: score 27.4, E = 0.00035
*->CapnnpCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-
C+ +C++ Cvn+ g g++C C +G ++l+ +G+ C
gi|9857400 316 CQIAGVCQQ--MCVNYVG-------GFECYCSEG-HELEADGISC 350
*
gi|9857400 - -
W2: domain 1 of 1, from 323 to 380: score -34.8, E = 51
*->eeeqidlLlaiEefcvkleeelvikllakiLkslYDaDileEeaIlk
++ ++ ++++E++c + el +aD ++ + +
gi|9857400 323 QQMCVNYVGGFECYCSEG-HEL-------------EADGISCSPAGA 355
WyekadsadeskEgkskvrkqakkFitWLkeAeEEEseee<-*
+++a+ d + ++++ + e+EE+e+e
gi|9857400 356 MGAQASQ-D----LGDELL----------DDGEDEEDEDE 380
ATP-synt_DE: domain 1 of 1, from 549 to 561: score 1.5, E = 49
*->GiLpgHAPlitaL<-*
Gi p+HAPl+t+L
gi|9857400 549 GIPPNHAPLVTTL 561
late_protein_L1: domain 1 of 1, from 655 to 663: score -1.9, E = 83
*->MAlWlpsqn<-*
+AlWlps +
gi|9857400 655 LALWLPSPA 663
//
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: tem1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
EGF EGF-like domain 51.2 9.5e-13 3
lectin_c Lectin C-type domain 34.3 7.8e-11 1
sushi Sushi domain (SCR repeat) 11.8 0.21 1
Xlink Extracellular link domain 6.4 0.034 1
gla Vitamin K-dependent carboxylation/gam 4.2 14 1
GBP_PSP Paralytic/GBP/PSP peptide 2.7 93 1
Bcl-2 Apoptosis regulator proteins, Bcl-2 f 2.1 4.4 1
defensins Mammalian defensin 1.9 69 1
EB EB module 1.7 66 1
ATP-synt_DE ATP synthase, Delta/Epsilon chain 1.5 49 1
ANATO Anaphylotoxin-like domain 0.5 13 1
COX3 Cytochrome c oxidase subunit III 0.0 84 1
Luteo_ORF2 Putative replicase 1 (ORF2) -0.4 24 1
Flavi_NS1 Flavivirus non-structural Protein NS1 -0.7 83 1
DegT_DnrJ_EryC1 DegT/DnrJ/EryC1/StrS family -1.5 97 1
late_protein_L1 L1 (late) protein -1.9 83 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Xlink 1/1 43 61 .. 16 34 .. 6.4 0.034
Flavi_NS1 1/1 61 80 .. 358 377 .] -0.7 83
lectin_c 1/1 49 120 .. 1 72 [. 34.3 7.8e-11
Luteo_ORF2 1/1 119 132 .. 674 687 .] -0.4 24
COX3 1/1 181 187 .. 1 7 [. 0.0 84
sushi 1/1 182 230 .. 7 62 .] 11.8 0.21
GBP_PSP 1/1 253 269 .. 1 18 [. 2.7 93
EB 1/1 256 271 .. 43 56 .] 1.7 66
EGF 1/3 235 271 .. 1 45 [] 31.8 2.9e-07
ANATO 1/1 258 272 .. 1 17 [. 0.5 13
defensins 1/1 294 300 .. 1 7 [. 1.9 69
EGF 2/3 275 310 .. 1 45 [] 9.7 0.5
EGF 3/3 316 350 .. 1 45 [] 25.6 1.6e-05
gla 1/1 373 387 .. 28 42 .] 4.2 14
DegT_DnrJ_EryC1 1/1 371 389 .. 1 19 [. -1.5 97
Bcl-2 1/1 382 389 .. 101 108 .] 2.1 4.4
ATP-synt_DE 1/1 549 561 .. 32 44 .. 1.5 49
late_protein_L1 1/1 655 663 .. 1 9 [. -1.9 83
Alignments of top-scoring domains:
Xlink: domain 1 of 1, from 43 to 61: score 6.4, E = 0.034
*->tFeEAqaaClrqgAriATt<-*
tF EA +aC++ g+ +AT+
gi|9857400 43 TFLEAWRACRELGGDLATP 61
Flavi_NS1: domain 1 of 1, from 61 to 80: score -0.7, E = 83
*->PvkekEenLVkSqVtAgnge<-*
P++ +E++ V S+V Ag++
gi|9857400 61 PRTPEEAQRVDSLVGAGPAS 80
lectin_c: domain 1 of 1, from 49 to 120: score 34.3, E = 7.8e-11
*->laCqrekpgghLvsIqsqeEqdFlqslvkavn...yaWIGLtdinkg
aC+++ gg+L++++ +eE+ + slv+a + ++ +WIGL ++
gi|9857400 49 RACREL--GGDLATPRTPEEAQRVDSLVGAGPasrLLWIGLQRQARQ 93
eptegt...WvWsdGslpvnytnWakipgeP<-*
+ +++ ++++W++G++ + +tnWa +P
gi|9857400 94 CQLQRPlrgFTWTTGDQDTAFTNWA----QP 120
Luteo_ORF2: domain 1 of 1, from 119 to 132: score -0.4, E = 24
*->qeaSgGPsSaqklN<-*
q+aSgGP +aq+
gi|9857400 119 QPASGGPCPAQRCV 132
COX3: domain 1 of 1, from 181 to 187: score 0.0, E = 84
*->HPFHLVs<-*
PFHLVs
gi|9857400 181 TPFHLVS 187
sushi: domain 1 of 1, from 182 to 230: score 11.8, E = 0.21
*->eNGrvsss.gtyeypvGdtvtytCneGYrlvGsssitCtedg.g.Gg
+++ vs++ + ++ G+++ +C+ G +G +s+ C+++ +g+ g
gi|9857400 182 PFHLVSTEfEWLPF--GSVAAVQCQAG---RG-ASLLCVKQPeGgVG 222
WsppllGelPkC<-*
Ws + P C
gi|9857400 223 WSRAG----PLC 230
GBP_PSP: domain 1 of 1, from 253 to 269: score 2.7, E = 93
*->EnFagGCipGylRtADGR<-*
+ C+ G+ ADGR
gi|9857400 253 -HVSCRCTEGFRLAADGR 269
EB: domain 1 of 1, from 256 to 271: score 1.7, E = 66
*->CqCpeGf..tavnGvC<-*
C+C+eGf+ a++ C
gi|9857400 256 CRCTEGFrlAADGRSC 271
EGF: domain 1 of 3, from 235 to 271: score 31.8, E = 2.9e-07
*->Capnn.pCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<
C+p+n++C + +Cv+ + g+ +C+C++G ++l+ +G+ C
gi|9857400 235 CSPDNgGCEH--ECVEEVD------GHVSCRCTEG-FRLAADGRSC 271
-*
gi|9857400 - -
ANATO: domain 1 of 1, from 258 to 272: score 0.5, E = 13
*->CCeDGmrenplmgqsCe<-*
C G r+++ g+sCe
gi|9857400 258 -CTEGFRLAA-DGRSCE 272
defensins: domain 1 of 1, from 294 to 300: score 1.9, E = 69
*->CyCRrrl<-*
C+CR ++
gi|9857400 294 CHCRLGF 300
EGF: domain 2 of 3, from 275 to 310: score 9.7, E = 0.5
*->CapnnpCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-
Ca+ pC + +C +++ +gy+C+C G+ + + +rC
gi|9857400 275 CAQA-PCEQ--QCEPGGP------QGYSCHCRLGFRPAEDDPHRC 310
*
gi|9857400 - -
EGF: domain 3 of 3, from 316 to 350: score 25.6, E = 1.6e-05
*->CapnnpCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-
C+ +C++ Cvn+ g g++C C +G ++l+ +G+ C
gi|9857400 316 CQIAGVCQQ--MCVNYVG-------GFECYCSEG-HELEADGISC 350
*
gi|9857400 - -
gla: domain 1 of 1, from 373 to 387: score 4.2, E = 14
*->edtegtqefwrkYyd<-*
ed+e+ +e+w+++ +
gi|9857400 373 EDEEDEDEAWKAFNG 387
DegT_DnrJ_EryC1: domain 1 of 1, from 371 to 389: score -1.5, E = 97
*->psideeelaavtevlrsgw<-*
+dee++++++ + ++gw
gi|9857400 371 DGEDEEDEDEAWKAFNGGW 389
Bcl-2: domain 1 of 1, from 382 to 389: score 2.1, E = 4.4
*->WiqenGGW<-*
W++ nGGW
gi|9857400 382 WKAFNGGW 389
ATP-synt_DE: domain 1 of 1, from 549 to 561: score 1.5, E = 49
*->GiLpgHAPlitaL<-*
Gi p+HAPl+t+L
gi|9857400 549 GIPPNHAPLVTTL 561
late_protein_L1: domain 1 of 1, from 655 to 663: score -1.9, E = 83
*->MAlWlpsqn<-*
+AlWlps +
gi|9857400 655 LALWLPSPA 663
//
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: tem1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
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: Fri Oct 13 19:33:56 2000
Sequence file: tem1
----------------------------------------
Sequence gi|9857400|gb|AAG00867.1|AF279142_1 (757 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
628: NQTS
Total matches: 1
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
40: RRRT
720: KRIT
Total matches: 2
Matching pattern PS00005 PKC_PHOSPHO_SITE:
60: TPR
255: SCR
518: STK
595: TSR
652: SPK
680: SQR
752: TCR
Total matches: 7
Matching pattern PS00006 CK2_PHOSPHO_SITE:
43: TFLE
63: TPEE
106: TTGD
188: TEFE
270: SCED
413: SFPE
680: SQRD
736: SPTE
Total matches: 8
Matching pattern PS00008 MYRISTYL:
55: GGDLAT
75: GAGPAS
162: GACPAL
196: GSVAAV
220: GVGWSR
287: GGPQGY
331: GGFECY
354: GAMGAQ
357: GAQASQ
540: GTQTTT
549: GIPPNH
706: GIVYCT
745: GSLTGV
749: GVQTCR
Total matches: 14
Matching pattern PS00010 ASX_HYDROXYL:
326: CVNYVGGFECYC
Total matches: 1
Matching pattern PS01186 EGF_2:
256: CRCTEGFRLAADGRSC
Total matches: 1
Matching pattern PS01187 EGF_CA:
312: DTDECQIAGVCQQMCVNYVGGFEC
Total matches: 1
Total no of hits in this sequence: 35
========================================
1314 pattern(s) searched in 1 sequence(s), 757 residues.
Total no of hits in all sequences: 35.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
L=0 16.2564 1253 pos. 30 - 147 PS50041|C_TYPE_LECTIN_2 C-type lectin domain profile.
#
# P 1 YGGHCYYFSterktwaeAELFCqQQrpggHlLVSIQSqeeqefLTSLVKasn--syVWIG -60
# S 30 GPSSCYALFPRRRTFLEAWRACREL--GGD-LATPRTPEEAQRVDSLVGAGPasRLLWIG -672
#
# P 59 LNDItt-------egkWTWSDGt-pvSYTNWapgepnn--kgerEDCVELys---gKWND -13
# S 87 LQRQARqcqlqrpLRGFTWTTGDqDTAFTNWA--QPASggPCPAQRCVALEAsgeHRWLE -614
#
# P 106 ENC -10
# S 145 GSC -611
#
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
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 tem1
***** 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, 757 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: tem1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
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: tem1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1 precursor
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= gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1
precursor
(757 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
PP2C PP2C type phosphatase domain 25 0.56
HISDAC Histone deacetylase domain 24 0.96
INSL Insulinase like Metallo protease domain 23 0.98
PCNA Proliferating Cell nuclear antigen like domain 23 1.1
SNARE Alpha helical domains which are involved in vesicle fu... 23 1.2
KELCH Kelch repeat- beta propeller like domain 23 1.6
DNASE1 DNASE-1/Sphingomyelinase like domain 23 1.8
BZIP Basic Zipper domain (A DNA binding domain) 21 6.4
RGS Regulator of heterotrimeric G protein signalling (G-prot... 21 6.9
HECT A ubiquitin conjugating enzyme domain 21 6.9
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 20 9.1
>PP2C PP2C type phosphatase domain
Length = 254
Score = 24.5 bits (53), Expect = 0.56
Identities = 11/104 (10%), Positives = 20/104 (18%), Gaps = 30/104 (28%)
Query: 281 EQQCEPGGPQGYSCHCRLGFRPAEDDPHRCVDTDECQIAGVCQQMCVNYVGGFECYCSEG 340
E R D E + V +G
Sbjct: 3 EVNLSVVSCSSTGKTDPGLVRQYNQDSFYLD--PEGRFYIVA----------------DG 44
Query: 341 HELEADGISCSPAGAMGAQ-ASQDLGDELLDDGEDEEDEDEAWK 383
G G + AS+ + + D + + +
Sbjct: 45 M-----------GGHAGGEEASRIAVERVRDYLDTYWQSEITSE 77
>HISDAC Histone deacetylase domain
Length = 433
Score = 23.7 bits (51), Expect = 0.96
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 362 QDLGDELLDDGEDEEDEDEA 381
+ D G+ EED EA
Sbjct: 392 NHTPRDAEDLGDVEEDSAEA 411
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 23.4 bits (50), Expect = 0.98
Identities = 4/43 (9%), Positives = 9/43 (20%)
Query: 621 LPSQSPTNQTSPISPTHPHSKAPQIPREDGPSPKLALWLPSPA 663
+ P P + ++ + PA
Sbjct: 227 EEGRPVPKVQIPTEPEQIGIRFKKLKDPRIEKAYWIIGWRVPA 269
Score = 21.0 bits (44), Expect = 5.2
Identities = 11/63 (17%), Positives = 14/63 (21%), Gaps = 6/63 (9%)
Query: 440 YHSS--VLSVTRPV----VVSATHPTLPSAHQPPVIPATHPALSRDHQIPVIAANYPDLP 493
Y + + V V T PV P I P +
Sbjct: 198 YQPRNMAVVIVGKVNPKEVEEEVMKTFGKEEGRPVPKVQIPTEPEQIGIRFKKLKDPRIE 257
Query: 494 SAY 496
AY
Sbjct: 258 KAY 260
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 23.3 bits (50), Expect = 1.1
Identities = 5/28 (17%), Positives = 13/28 (45%), Gaps = 2/28 (7%)
Query: 245 ECVEEVDGHVSCRCTE-GFRLAADGRSC 271
+ + + H +C T+ G ++ + C
Sbjct: 32 KAIHFRE-HATCFATKNGIKVTVENAKC 58
>SNARE Alpha helical domains which are involved in vesicle fusion
Length = 254
Score = 23.3 bits (50), Expect = 1.2
Identities = 7/31 (22%), Positives = 15/31 (47%), Gaps = 2/31 (6%)
Query: 677 AEHSQRDDRWLLVALLVPT--CVFLVVLLAL 705
S +D ++A + T C++ ++ L L
Sbjct: 217 LLQSDGEDFSYMIAFFLGTAACLYQMICLCL 247
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 23.0 bits (49), Expect = 1.6
Identities = 8/52 (15%), Positives = 17/52 (32%)
Query: 706 GIVYCTRCGPHAPNKRITDCYRWVIHAGSKSPTEPMPPRGSLTGVQTCRTSV 757
G T C P +P+ + + + P+ S V + + +
Sbjct: 125 GHTAATGCLPASPSVSLKQVEHYDPTINKWTMVAPLREGVSNAAVVSAKLKL 176
>DNASE1 DNASE-1/Sphingomyelinase like domain
Length = 388
Score = 22.8 bits (48), Expect = 1.8
Identities = 11/51 (21%), Positives = 19/51 (36%), Gaps = 3/51 (5%)
Query: 57 DLATPRTPEEAQRVDSLVGAGPASRLL--WIGLQRQARQCQLQRPLRGFTW 105
D + P P+E + +RL + L+ ++ Q R R W
Sbjct: 56 DQSEPLDPKELLDECQVALQDRPARLHRDFFSLRSESSSQQ-PRTFRVMQW 105
>BZIP Basic Zipper domain (A DNA binding domain)
Length = 89
Score = 21.0 bits (43), Expect = 6.4
Identities = 12/25 (48%), Positives = 13/25 (52%)
Query: 558 VTTLGAQLPPQAPDALVLRTQATQL 582
V TL AQ A A +LR Q QL
Sbjct: 42 VKTLKAQNSELASTANMLREQVAQL 66
>RGS Regulator of heterotrimeric G protein signalling (G-protein GTP hydrolysis activating protein)
Length = 117
Score = 20.9 bits (44), Expect = 6.9
Identities = 10/87 (11%), Positives = 21/87 (23%), Gaps = 9/87 (10%)
Query: 242 CEHE-CVEEVDGHVSCRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQ--GYSCHCRL 298
+ E E +D +SC E ++ A+ + + R
Sbjct: 19 LKSEYSEENIDFWISC---EEYKKIKSPSKLSP-KAKKIYNEFISVQATKEVNLDSCTRE 74
Query: 299 GFRPAEDDPHRCVDTDECQIAGVCQQM 325
+P + + M
Sbjct: 75 ETSRNMLEPTI--TCFDEAQKKIFNLM 99
>HECT A ubiquitin conjugating enzyme domain
Length = 255
Score = 20.9 bits (44), Expect = 6.9
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 652 SPKLALWLPSPAPTA 666
+ + L +PSP TA
Sbjct: 43 TGIVDLLIPSPNATA 57
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 20.2 bits (42), Expect = 9.1
Identities = 7/19 (36%), Positives = 9/19 (46%), Gaps = 2/19 (10%)
Query: 293 SCHCRLGFRPAEDDPHRCV 311
+ + GF A DD R V
Sbjct: 16 TGMVKAGF--AGDDAPRAV 32
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 11
Number of calls to ALIGN: 12
Length of query: 757
Total length of test sequences: 20182
Effective length of test sequences: 16738.0
Effective search space size: 12123929.4
Initial X dropoff for ALIGN: 25.0 bits
Y. Wolf's SCOP PSSM
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|9857400|gb|AAG00867.1|AF279142_1 tumor endothelial marker 1
precursor
(757 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2502062 [25..167] C-type lectin-like 84 6e-18
gi|1469029 [26..148] C-type lectin-like 72 4e-14
gi|1078939 [54..180] C-type lectin-like 61 4e-11
gi|1053218 [103..244] C-type lectin-like 61 5e-11
gi|1109918 [24..147] C-type lectin-like 59 3e-10
gi|2706599 [57..185] C-type lectin-like 58 8e-10
gi|128081 [13..98] Neurophysin II 31 0.057
gi|139813 [192..507] Periplasmic binding protein-like II 26 1.8
gi|949974 [58..232] Periplasmic binding protein-like I 26 1.9
gi|1173357 [36..558] Periplasmic binding protein-like II 26 2.0
gi|2500694 [73..586] Periplasmic binding protein-like II 26 2.1
gi|2665716 [42..473] Periplasmic binding protein-like II 26 2.5
gi|1723074 [152..573] Periplasmic binding protein-like II 26 2.7
gi|2648784 [24..191] Periplasmic binding protein-like II 26 2.9
gi|1703166 [11..338] beta/alpha (TIM)-barrel 26 3.0
gi|462710 [40..510] Periplasmic binding protein-like II 25 3.3
gi|1685117 [55..161] C-type lectin-like 25 3.7
gi|2665705 [26..489] Periplasmic binding protein-like II 25 4.0
gi|2146709 [57..529] Periplasmic binding protein-like II 25 4.0
gi|1174715 [357..558] Thiamin-binding 25 4.2
gi|538698 [52..502] Periplasmic binding protein-like II 25 4.4
gi|1175188 [41..508] Periplasmic binding protein-like II 25 4.7
gi|1168472 [55..543] Periplasmic binding protein-like II 25 5.3
gi|1942958 [8..338] ATP pyrophoshatases 25 5.8
gi|1652862 [45..566] Periplasmic binding protein-like II 24 7.2
gi|2696483 [229..706] Periplasmic binding protein-like II 24 7.3
gi|1787052 [35..512] Periplasmic binding protein-like II 24 7.5
gi|628630 [25..232] Ribosome inactivating proteins (RIP) 24 7.7
gi|1742427 [67..555] Periplasmic binding protein-like II 24 8.9
gi|1334744 [1415..1521] Spectrin repeat unit 24 9.9
>gi|2502062 [25..167] C-type lectin-like
Length = 143
Score = 84.4 bits (206), Expect = 6e-18
Identities = 47/133 (35%), Positives = 61/133 (45%), Gaps = 8/133 (6%)
Query: 34 CYALFPRRRTFLEAWRACRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQ 93
C+ALF TFL+A +AC+ L G L T R+ A + LV WIGLQ
Sbjct: 11 CFALFQDPVTFLDASQACQRLQGHLMTVRSSVAADVISLLVSDSSMDSRPWIGLQLPQGC 70
Query: 94 CQLQ--RPLRGFTWTTGDQDTAFTNWAQPASGGPCPA-QRCVALEASGEH-----RWLEG 145
PLRGF W TGD T+++ WA+P P CV + + E W E
Sbjct: 71 GDPVHLGPLRGFQWVTGDNHTSYSRWARPNDQSPPLCGPLCVTVSTATEAAPGEPAWEEK 130
Query: 146 SCTLAVDGYLCQF 158
C G+LC+F
Sbjct: 131 PCENETKGFLCEF 143
>gi|1469029 [26..148] C-type lectin-like
Length = 123
Score = 71.6 bits (173), Expect = 4e-14
Identities = 27/126 (21%), Positives = 44/126 (34%), Gaps = 14/126 (11%)
Query: 32 SSCYALFPRRRTFLEAWRACRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQA 91
S CY R TF EA C+ LGG A E + S A W+G+ R
Sbjct: 12 SYCYLTSDRYMTFAEADGYCQSLGGSQAFMMNSYEFTFMKSYTQGMFAQ--PWLGVTRNL 69
Query: 92 RQCQLQRPLRGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSCTLAV 151
+ + G + W +G P CV+ +++ + C ++
Sbjct: 70 TNNK-------WYNNDG-TTPYSSWW---IAGEPSLNGDCVSFKSTDKQGIRATQCW-SI 117
Query: 152 DGYLCQ 157
+C+
Sbjct: 118 QPVICK 123
>gi|1078939 [54..180] C-type lectin-like
Length = 127
Score = 61.4 bits (147), Expect = 4e-11
Identities = 24/127 (18%), Positives = 42/127 (32%), Gaps = 17/127 (13%)
Query: 34 CYALFPRRRTFLEAWRACRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQ 93
+ F ++ A AC++ G+L P P E+ + ++ S ++ +
Sbjct: 14 YISAFADIQSHSGAQAACKQQKGELFWPDLPYESFFLKKVLQRVKTST-NFVWTNGEKHN 72
Query: 94 CQLQRPLRGFTWTTGDQDTAFTNWA--QPASGGPCPAQRCVALEASGEHRWLEGSCTLAV 151
Q + W TG W+ QP G C SG + C
Sbjct: 73 GQ-------WNWGTGHPAFTAPRWSPGQPDGQGEC----LAVYTHSG--FLDDKQCE-TQ 118
Query: 152 DGYLCQF 158
Y+C+
Sbjct: 119 YNYICKT 125
>gi|1053218 [103..244] C-type lectin-like
Length = 142
Score = 61.5 bits (147), Expect = 5e-11
Identities = 25/136 (18%), Positives = 41/136 (29%), Gaps = 15/136 (11%)
Query: 33 SCYALFPRRRTFLEAWRACREL-GGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQA 91
SCY R + +A C + L + E+ + A S R
Sbjct: 11 SCYVFDTTLRNWNDAALYCNNMNSATLPLVESAEDQAFFAGYLQAMIPS--NPPADMRPP 68
Query: 92 R-------QCQLQRPLRGFTWTTGDQDTAFTNWA--QPASGGPCPAQRCVALEA-SGEHR 141
+ + + G T WA +P + CVAL++ S
Sbjct: 69 PDGIWTAVRGVNNVTRASWVYYPGSFLVTDTFWAPQEP-NIYVNYNDVCVALQSDSFYRE 127
Query: 142 WLEGSCTLAVDGYLCQ 157
W CT + +C+
Sbjct: 128 WTTALCT-ILKYTVCK 142
>gi|1109918 [24..147] C-type lectin-like
Length = 124
Score = 58.7 bits (140), Expect = 3e-10
Identities = 28/129 (21%), Positives = 37/129 (27%), Gaps = 18/129 (13%)
Query: 33 SCYALFPRRRTFLEAWRACRELGG---DLATPRTPEEAQRVDSLVGAGPASRLLWIGLQR 89
CYA T A CR+ G L TP T E V V A+ W+
Sbjct: 11 KCYAALGMDMTRDNALAYCRKTYGPYARLTTPLTYAENNFVTEQVQ-LHANWHTWLEYVA 69
Query: 90 QARQCQLQRPLRGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSCTL 149
G +TN+A C+ + +G W C
Sbjct: 70 DGTY---------IVGDDGKP-PIYTNFA-VGEPFSVNVGYCITIGMNG--YWYAQPCP- 115
Query: 150 AVDGYLCQF 158
LC+F
Sbjct: 116 DSHSVLCEF 124
>gi|2706599 [57..185] C-type lectin-like
Length = 129
Score = 57.6 bits (137), Expect = 8e-10
Identities = 27/130 (20%), Positives = 46/130 (34%), Gaps = 16/130 (12%)
Query: 33 SCYALFPRRRTFLEAWRACRELGGD-LATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQA 91
C+ L + +A AC LGG L + R+ E + + V LW GL
Sbjct: 11 KCWKLITGPQRRADADEACMNLGGSTLFSIRSDIENRALVDFV-KDKRIENLWTGLICVG 69
Query: 92 RQCQLQRPLRGFTWTTGDQDTAFTNWA--QPASGGPCPAQRCVALEASGEH--RWLEGSC 147
+ + +G + N+A P + C+ +G +W GSC
Sbjct: 70 K----NSFSCTWDVNSGTA-AVYNNFAEGYPNNVY----GDCIHYMTTGTQAGQWASGSC 120
Query: 148 TLAVDGYLCQ 157
++C+
Sbjct: 121 N-ETMSFVCE 129
>gi|128081 [13..98] Neurophysin II
Length = 86
Score = 31.3 bits (69), Expect = 0.057
Identities = 12/85 (14%), Positives = 15/85 (17%), Gaps = 5/85 (5%)
Query: 256 CRCTEGFRLAADGRSCEDPCAQAPCEQQCEPGGPQGYSCHCRLGFRPAEDDPHRCVDTDE 315
L + C G G + R P
Sbjct: 3 SDTELRQCLPCGPGGQGRCFGPSICCADA-LGCFVGTAEALRCQEENYLPSPC-QSGQKP 60
Query: 316 CQIAGVCQ---QMCVNYVGGFECYC 337
C G C C + E C
Sbjct: 61 CGSGGRCAANGVCCNDESCVIEPEC 85
>gi|139813 [192..507] Periplasmic binding protein-like II
Length = 316
Score = 26.5 bits (58), Expect = 1.8
Identities = 9/34 (26%), Positives = 13/34 (37%), Gaps = 4/34 (11%)
Query: 366 DELLDDGEDEEDEDEAWKAFNGGWTEMPGILWME 399
DE LD G +D A+ E+ L +
Sbjct: 273 DEALDAGRRSQDPKVRAAAYR----EIQKALVAD 302
Score = 24.1 bits (52), Expect = 8.9
Identities = 10/48 (20%), Positives = 13/48 (26%), Gaps = 1/48 (2%)
Query: 370 DDGEDEEDEDEAWKAFN-GGWTEMPGILWMEPTQPPDFALAYRPSFPE 416
E D A + + GW G + Q F L Y
Sbjct: 149 RGIERPRDLAAAGRILDEAGWKPGSGGIRARDGQRASFTLYYPSGDKV 196
>gi|949974 [58..232] Periplasmic binding protein-like I
Length = 175
Score = 26.1 bits (57), Expect = 1.9
Identities = 17/95 (17%), Positives = 23/95 (23%), Gaps = 13/95 (13%)
Query: 466 PPVIPATHPALSRDHQIPVIAAN--YPDLPS----AYQPGILSVSHSAQPPAHQPPMIST 519
I H + +PVI + DL YQ G L Q +
Sbjct: 65 ATEITDQHLEVINKINVPVIIVGQAHDDLHCIIHNDYQAGYLVGDMLGQQGYNDIKFFGV 124
Query: 520 KYPELFPAHQSPMFPDTRVAGTQTTTHLPGIPPNH 554
++ Q R G I P
Sbjct: 125 TESDIAVGVQ-------RKEGLIAGLEAHNIQPEI 152
>gi|1173357 [36..558] Periplasmic binding protein-like II
Length = 523
Score = 26.1 bits (57), Expect = 2.0
Identities = 5/21 (23%), Positives = 8/21 (37%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+ +D KA+N
Sbjct: 459 DQFMDRAITTSHLSSRAKAYN 479
>gi|2500694 [73..586] Periplasmic binding protein-like II
Length = 514
Score = 26.1 bits (57), Expect = 2.1
Identities = 5/34 (14%), Positives = 11/34 (31%), Gaps = 4/34 (11%)
Query: 366 DELLDDGEDEEDEDEAWKAFNGGWTEMPGILWME 399
D L++ +D + A + +L
Sbjct: 471 DALIERVIFAKDRETLVAATK----ALDRVLLAH 500
>gi|2665716 [42..473] Periplasmic binding protein-like II
Length = 432
Score = 25.7 bits (56), Expect = 2.5
Identities = 3/21 (14%), Positives = 10/21 (47%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+ ++ E D ++ + +
Sbjct: 409 DKQIEAARTETDPNKQIELWK 429
>gi|1723074 [152..573] Periplasmic binding protein-like II
Length = 422
Score = 25.7 bits (56), Expect = 2.7
Identities = 5/21 (23%), Positives = 8/21 (37%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D ++ E D +A N
Sbjct: 371 DAAIERTLAELDPGKARALAN 391
>gi|2648784 [24..191] Periplasmic binding protein-like II
Length = 168
Score = 25.7 bits (56), Expect = 2.9
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
DELL+ +E K +
Sbjct: 104 DELLEKASTATSMEEREKLYK 124
>gi|1703166 [11..338] beta/alpha (TIM)-barrel
Length = 328
Score = 25.7 bits (56), Expect = 3.0
Identities = 14/79 (17%), Positives = 27/79 (33%), Gaps = 10/79 (12%)
Query: 366 DELLDDG--EDEEDEDEAWKAFNGGWTE-----MPGILWMEPTQPPDFALAYRPSFPEDR 418
D +L +G + E+ +E +K F + G + DF F +
Sbjct: 26 DIILPEGFPKSVEELNEKYKKF-RDLQDFLDYYYIGTNVL--ISEQDFFDLAWAYFKKVH 82
Query: 419 EPQIPYPEPTWPPPLSAPR 437
+ + + E + P R
Sbjct: 83 KQGLVHAEVFYDPQSHTSR 101
>gi|462710 [40..510] Periplasmic binding protein-like II
Length = 471
Score = 25.3 bits (55), Expect = 3.3
Identities = 3/21 (14%), Positives = 8/21 (37%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+ + + DE + +
Sbjct: 415 DKEIGEVLATHDETQRQALYR 435
>gi|1685117 [55..161] C-type lectin-like
Length = 107
Score = 25.2 bits (54), Expect = 3.7
Identities = 24/108 (22%), Positives = 40/108 (36%), Gaps = 9/108 (8%)
Query: 43 TFLEAWRACRELGGDLATPRTPEEAQRVDSLVGAGPAS---RLLWIGLQRQARQCQLQRP 99
+F +A C++ GG L + + S + + +L+WIG Q++
Sbjct: 5 SFDKAQAICKQTGGHLVHDFRGATSSYILSELERRKSELKPQLVWIGAQKEPGITS---- 60
Query: 100 LRGFTWTTGDQDTAFTNWAQPASGGPCPAQRCVALEASGEHRWLEGSC 147
R + W GD T W + Q CV L+ W + C
Sbjct: 61 -RTWKWVNGDVVQKPT-WGKDQPNNYNGEQNCVVLDGGRNWLWNDVGC 106
>gi|2665705 [26..489] Periplasmic binding protein-like II
Length = 464
Score = 25.3 bits (55), Expect = 4.0
Identities = 7/21 (33%), Positives = 12/21 (56%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
++LLD G D+ E K ++
Sbjct: 412 NDLLDKGRATVDKAERVKIYD 432
>gi|2146709 [57..529] Periplasmic binding protein-like II
Length = 473
Score = 25.3 bits (55), Expect = 4.0
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D L+ + + E +K FN
Sbjct: 419 DSLITEARKITNMSERYKKFN 439
>gi|1174715 [357..558] Thiamin-binding
Length = 202
Score = 25.2 bits (55), Expect = 4.2
Identities = 6/23 (26%), Positives = 6/23 (26%)
Query: 665 TAAPTALGEAGLAEHSQRDDRWL 687
T LGE G L
Sbjct: 134 THDSVGLGEDGPTHQPIEHLAAL 156
>gi|538698 [52..502] Periplasmic binding protein-like II
Length = 451
Score = 24.9 bits (54), Expect = 4.4
Identities = 8/34 (23%), Positives = 12/34 (34%), Gaps = 4/34 (11%)
Query: 366 DELLDDGEDEEDEDEAWKAFNGGWTEMPGILWME 399
+EL + E + A+N M I E
Sbjct: 403 NELCQKVTVLPNGKERFDAYN----RMRDIFEEE 432
>gi|1175188 [41..508] Periplasmic binding protein-like II
Length = 468
Score = 24.9 bits (54), Expect = 4.7
Identities = 3/21 (14%), Positives = 6/21 (28%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D L + E + +
Sbjct: 403 DRLFESAMTTISEKVRLENYA 423
>gi|1168472 [55..543] Periplasmic binding protein-like II
Length = 489
Score = 24.9 bits (54), Expect = 5.3
Identities = 5/34 (14%), Positives = 14/34 (40%), Gaps = 4/34 (11%)
Query: 366 DELLDDGEDEEDEDEAWKAFNGGWTEMPGILWME 399
D+L+ D + D + K + ++ + +
Sbjct: 420 DKLMKDAKSISDRKQYSKEYE----QIYQKIAED 449
>gi|1942958 [8..338] ATP pyrophoshatases
Length = 331
Score = 24.7 bits (53), Expect = 5.8
Identities = 1/25 (4%), Positives = 3/25 (12%)
Query: 373 EDEEDEDEAWKAFNGGWTEMPGILW 397
D + +
Sbjct: 169 IDMASPFIVMRDPVLYRIKFAEHHQ 193
>gi|1652862 [45..566] Periplasmic binding protein-like II
Length = 522
Score = 24.1 bits (52), Expect = 7.2
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+L E D ++ + F
Sbjct: 467 DQLWQKAVAELDPEKRQQLFI 487
>gi|2696483 [229..706] Periplasmic binding protein-like II
Length = 478
Score = 24.1 bits (52), Expect = 7.3
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 372 GEDEEDEDEAWKAF--NGGWTEMPGILWMEP 400
D + +AWKA+ G ++ P
Sbjct: 203 ASDYGKKPDAWKAYVQKGSTDATHQLMHKYP 233
>gi|1787052 [35..512] Periplasmic binding protein-like II
Length = 478
Score = 24.1 bits (52), Expect = 7.5
Identities = 4/21 (19%), Positives = 7/21 (33%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+ L D E + +
Sbjct: 411 DDFLAQALKTNDPAEKTRLYK 431
>gi|628630 [25..232] Ribosome inactivating proteins (RIP)
Length = 208
Score = 24.0 bits (51), Expect = 7.7
Identities = 21/79 (26%), Positives = 32/79 (39%), Gaps = 6/79 (7%)
Query: 41 RRTFLEAWRACRELGGDLATPRTPEEAQRVDSLVGAGPASRLLWIGLQRQARQCQLQRPL 100
R + + ++ A E G+ T +A R A L + +QR+ RQ L
Sbjct: 131 RHSLVSSYLALMEFSGNTMT----RDASRAVLRFVTVTAEALRFRQIQREFRQA-LSETA 185
Query: 101 RGFTWTTGDQDTAFTNWAQ 119
+T T GD D NW +
Sbjct: 186 PVYTMTPGDVDLTL-NWGR 203
>gi|1742427 [67..555] Periplasmic binding protein-like II
Length = 489
Score = 24.1 bits (52), Expect = 8.9
Identities = 4/21 (19%), Positives = 10/21 (47%)
Query: 366 DELLDDGEDEEDEDEAWKAFN 386
D+LL + D+ + + +
Sbjct: 428 DKLLRNALATTDQTQRTRDYQ 448
>gi|1334744 [1415..1521] Spectrin repeat unit
Length = 107
Score = 23.7 bits (51), Expect = 9.9
Identities = 4/32 (12%), Positives = 8/32 (24%), Gaps = 1/32 (3%)
Query: 362 QDLGDELLDDGEDEEDEDEAW-KAFNGGWTEM 392
Q D+L+ + W +
Sbjct: 63 QSFADQLIAADHYAKGVIANRRNEVLDRWRRL 94
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 30
Number of calls to ALIGN: 31
Length of query: 757
Total length of test sequences: 256703
Effective length of test sequences: 210706.0
Effective search space size: 151418078.0
Initial X dropoff for ALIGN: 25.0 bits