analysis of sequence from tem28
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKLTACLQGQQGAEADKRSKKLP
LTTLAQCLMEGSAILGDDTLLGKMLKLCGETEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRK
HLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSADMYSFVAKEID
YANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAWVEKPSFGKPLEEHLTISGREIAFPIEACVTMLL
ECGMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQA
SNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNIT
EMMTTVSLQIVGIIEPIIQHADWFFPGEIEFNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPEQARR
PLSVATDNMMLEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAPPAELAAPLPSPL
PEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSAQKGSPGSSQGTACAGTQPGAQPGAQPGASP
SPSQPPADQSPHTLRKVSKKLAPIPPKVPFGQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSL
ASGQLSPAAAPPLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSASSPQSTEAPMLDGMSPGESM
STDLVHFDIPSIHIELGSTLRLSPLEHMRRHSVTDKRDSEEESESTAL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|3327158|dbj|BAA31647.1|
. . . . .
1 MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKL 50
___HHHHHHHHHHHHHH_____HHHHHHHHHHHHHHHHHHHH____HHHH
. . . . .
51 TACLQGQQGAEADKRSKKLPLTTLAQCLMEGSAILGDDTLLGKMLKLCGE 100
HHHHHH___HHHHHHHH____HHHHHHHHHHH________HHHHHHHH__
. . . . .
101 TEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRKHLAKLVLDMD 150
_HHHHHHHHHHHHHHHHHHH_HHHHHHHHH____HHHHHHHHHHHHHHH_
. . . . .
151 SSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSAD 200
___HHHHHHH_______________HHHHHHHHHHHHHHHHHHHHHHHHH
. . . . .
201 MYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAWVEK 250
HHHHHHH____HHHHHHHHHHHHHHH___HHHHHHHHHHHHHHHHHHH__
. . . . .
251 PSFGKPLEEHLTISGREIAFPIEACVTMLLECGMQEEGLFRVAPSASKLK 300
________________EEEEHHHHHHHHHHHH______EEEEE___HHHH
. . . . .
301 KLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQA 350
HHHHHHHHHH___________HHHHHHHHHHH______HHHHHHHHHHHH
. . . . .
351 SNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPS 400
HHHHHHHHHHHHHHHHHHH_______HHHHHHHHHHHHH___________
. . . . .
401 NMAIVLGPNLLWPQAEGNITEMMTTVSLQIVGIIEPIIQHADWFFPGEIE 450
_EEEEE______________HHHHHHHHHHHHEEEE____________EE
. . . . .
451 FNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPEQARRPLSVATDNMM 500
EEE_______EEE____________________________________E
. . . . .
501 LEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAPPA 550
EEEE_____EEE_____EEE_____________EEEE_____________
. . . . .
551 ELAAPLPSPLPEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSA 600
__________________________________________________
. . . . .
601 QKGSPGSSQGTACAGTQPGAQPGAQPGASPSPSQPPADQSPHTLRKVSKK 650
__________EEE______________________________HHHHHHH
. . . . .
651 LAPIPPKVPFGQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSL 700
________________HHHHH_____________________________
. . . . .
701 ASGQLSPAAAPPLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSA 750
__________________________________________________
. . . . .
751 SSPQSTEAPMLDGMSPGESMSTDLVHFDIPSIHIELGSTLRLSPLEHMRR 800
_______________________________EEEE__________HHHHH
.
801 HSVTDKRDSEEESESTAL 818
HH_______HHHHHH___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 49.2 %
beta-contents : 0.0 %
coil-contents : 50.8 %
class : alpha
method : 2
alpha-contents : 15.4 %
beta-contents : 0.0 %
coil-contents : 84.6 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-7.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -7.94 -3.24 -12.00 -12.00 0.00 -12.00 0.00 -54.48
-3.96 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -7.27 -3.24 -12.00 -12.00 0.00 -12.00 0.00 -50.47
ID: gi|3327158|dbj|BAA31647.1| AC: xxx Len: 770 1:I 751 Sc: -50.47 Pv: 2.309833e-01 NO_GPI_SITE
GPI: learning from protozoa
-17.65 0.00 0.00 0.00 -4.00 0.00 0.00 0.00 0.00 -6.27 -11.21 -12.00 -12.00 0.00 -12.00 0.00 -75.13
-11.95 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -6.83 -11.21 -12.00 -12.00 0.00 -12.00 0.00 -65.98
ID: gi|3327158|dbj|BAA31647.1| AC: xxx Len: 770 1:I 750 Sc: -65.98 Pv: 2.920596e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|3327158| 0.649 243 Y 0.273 243 N 0.467 242 N 0.072 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|3327158| 0.511 668 Y 0.379 175 Y 0.897 300 Y 0.176 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|3327158| 0.443 325 Y 0.350 245 Y 0.935 297 N 0.190 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
1-159 MKKQFNRMRQLANQTVGRAEKTEVLSEDLL
QVEKRLELVKQVSHSTHKKLTACLQGQQGA
EADKRSKKLPLTTLAQCLMEGSAILGDDTL
LGKMLKLCGETEDKLAQELIHFELQVERDV
IEPLFLLAEVEIPNIQKQRKHLAKLVLDMD
SSRTRWQQT
skssglsssl 160-169
170-294 QPAGAKADALREEMEEAANRVEICRDQLSA
DMYSFVAKEIDYANYFQTLIEVQAEYHRKS
LTLLQAVLPQIKAQQEAWVEKPSFGKPLEE
HLTISGREIAFPIEACVTMLLECGMQEEGL
FRVAP
sasklkklkaal 295-306
307-538 DCCVVDVQEYSADPHAIAGALKSYLRELPE
PLMTFELYDEWIQASNVQEQDKKLQALWNA
CEKLPKANHNNIRYLIKFLSKLSEYQDVNK
MTPSNMAIVLGPNLLWPQAEGNITEMMTTV
SLQIVGIIEPIIQHADWFFPGEIEFNITGN
YGSPVHVNHNANYSSMPSPDMDPADRRQPE
QARRPLSVATDNMMLEFYKKDGLRKIQSMG
VRVMDTNWVARRGSSAGRKVSC
appsmqppappaelaaplpsplpeqpldsp 539-580
aapalspsglgl
581-613 QPGPERTSTTKSKELSPGSAQKGSPGSSQG
TAC
agtqpgaqpgaqpgaspspsqppadqsp 614-641
642-674 HTLRKVSKKLAPIPPKVPFGQPGAMADQSA
GQL
spvslsptppstpspyglsyp 675-695
696-698 QGY
slasgqlspaaapplasps 699-717
718-726 VFTSTLSKS
rptpkprqrptlpppqppt 727-745
746-818 VNLSASSPQSTEAPMLDGMSPGESMSTDLV
HFDIPSIHIELGSTLRLSPLEHMRRHSVTD
KRDSEEESESTAL
low complexity regions: SEG 25 3.0 3.3
>gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
1-525 MKKQFNRMRQLANQTVGRAEKTEVLSEDLL
QVEKRLELVKQVSHSTHKKLTACLQGQQGA
EADKRSKKLPLTTLAQCLMEGSAILGDDTL
LGKMLKLCGETEDKLAQELIHFELQVERDV
IEPLFLLAEVEIPNIQKQRKHLAKLVLDMD
SSRTRWQQTSKSSGLSSSLQPAGAKADALR
EEMEEAANRVEICRDQLSADMYSFVAKEID
YANYFQTLIEVQAEYHRKSLTLLQAVLPQI
KAQQEAWVEKPSFGKPLEEHLTISGREIAF
PIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSY
LRELPEPLMTFELYDEWIQASNVQEQDKKL
QALWNACEKLPKANHNNIRYLIKFLSKLSE
YQDVNKMTPSNMAIVLGPNLLWPQAEGNIT
EMMTTVSLQIVGIIEPIIQHADWFFPGEIE
FNITGNYGSPVHVNHNANYSSMPSPDMDPA
DRRQPEQARRPLSVATDNMMLEFYKKDGLR
KIQSMGVRVMDTNWV
arrgssagrkvscappsmqppappaelaap 526-756
lpsplpeqpldspaapalspsglglqpgpe
rtsttkskelspgsaqkgspgssqgtacag
tqpgaqpgaqpgaspspsqppadqsphtlr
kvskklapippkvpfgqpgamadqsagqls
pvslsptppstpspyglsypqgyslasgql
spaaapplaspsvftstlsksrptpkprqr
ptlpppqpptvnlsasspqst
757-818 EAPMLDGMSPGESMSTDLVHFDIPSIHIEL
GSTLRLSPLEHMRRHSVTDKRDSEEESEST
AL
low complexity regions: SEG 45 3.4 3.75
>gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
1-528 MKKQFNRMRQLANQTVGRAEKTEVLSEDLL
QVEKRLELVKQVSHSTHKKLTACLQGQQGA
EADKRSKKLPLTTLAQCLMEGSAILGDDTL
LGKMLKLCGETEDKLAQELIHFELQVERDV
IEPLFLLAEVEIPNIQKQRKHLAKLVLDMD
SSRTRWQQTSKSSGLSSSLQPAGAKADALR
EEMEEAANRVEICRDQLSADMYSFVAKEID
YANYFQTLIEVQAEYHRKSLTLLQAVLPQI
KAQQEAWVEKPSFGKPLEEHLTISGREIAF
PIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSY
LRELPEPLMTFELYDEWIQASNVQEQDKKL
QALWNACEKLPKANHNNIRYLIKFLSKLSE
YQDVNKMTPSNMAIVLGPNLLWPQAEGNIT
EMMTTVSLQIVGIIEPIIQHADWFFPGEIE
FNITGNYGSPVHVNHNANYSSMPSPDMDPA
DRRQPEQARRPLSVATDNMMLEFYKKDGLR
KIQSMGVRVMDTNWVARR
gssagrkvscappsmqppappaelaaplps 529-774
plpeqpldspaapalspsglglqpgperts
ttkskelspgsaqkgspgssqgtacagtqp
gaqpgaqpgaspspsqppadqsphtlrkvs
kklapippkvpfgqpgamadqsagqlspvs
lsptppstpspyglsypqgyslasgqlspa
aapplaspsvftstlsksrptpkprqrptl
pppqpptvnlsasspqsteapmldgmspge
smstdl
775-818 VHFDIPSIHIELGSTLRLSPLEHMRRHSVT
DKRDSEEESESTAL
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|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKLTACLQGQQGA
EADKRSKKLPLTTLAQCLMEGSAILGDDTLLGKMLKLCGETEDKLAQELIHFELQVERDV
IEPLFLLAEVEIPNIQKQRKHLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPAGAKADALR
EEMEEAANRVEICRDQLSADMYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQI
KAQQEAWVEKPSFGKPLEEHLTISGREIAFPIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQASNVQEQDKKL
QALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNIT
EMMTTVSLQIVGIIEPIIQHADWFFPGEIEFNITGNYGSPVHVNHNANYSSMPSPDMDPA
DRRQPEQARRPLSVATDNMMLEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAp
psmqppappaelaaplpsplpeqpldspaapalspsGLGLQPGPERTSTTKSKELSPGSA
QKGSPGSSQGTACagtqpgaqpgaqpgaspspsqppadqspHTLRKVSKKLAPIPPKVPF
GQPGAMADQSAGQLSPVSLsptppstpspyglsypqgyslasgqlspaaapplaspsvft
stlsksrptpkprqrptlpppqpptvnlsasspQSTEAPMLDGMSPGESMSTDLVHFDIP
SIHIELGSTLRLSPLEHMRRHSVTDKRDSEEESESTAL
1 - 539 MKKQFNRMRQ LANQTVGRAE KTEVLSEDLL QVEKRLELVK QVSHSTHKKL TACLQGQQGA
EADKRSKKLP LTTLAQCLME GSAILGDDTL LGKMLKLCGE TEDKLAQELI HFELQVERDV
IEPLFLLAEV EIPNIQKQRK HLAKLVLDMD SSRTRWQQTS KSSGLSSSLQ PAGAKADALR
EEMEEAANRV EICRDQLSAD MYSFVAKEID YANYFQTLIE VQAEYHRKSL TLLQAVLPQI
KAQQEAWVEK PSFGKPLEEH LTISGREIAF PIEACVTMLL ECGMQEEGLF RVAPSASKLK
KLKAALDCCV VDVQEYSADP HAIAGALKSY LRELPEPLMT FELYDEWIQA SNVQEQDKKL
QALWNACEKL PKANHNNIRY LIKFLSKLSE YQDVNKMTPS NMAIVLGPNL LWPQAEGNIT
EMMTTVSLQI VGIIEPIIQH ADWFFPGEIE FNITGNYGSP VHVNHNANYS SMPSPDMDPA
DRRQPEQARR PLSVATDNMM LEFYKKDGLR KIQSMGVRVM DTNWVARRGS SAGRKVSCA
540 - 576 p psmqppappa elaaplpspl peqpldspaa palsps
577 - 613 GLGL QPGPERTSTT KSKELSPGSA QKGSPGSSQG TAC
614 - 641 agtqpga qpgaqpgasp spsqppadqs p
642 - 679 HTLRKVSKK LAPIPPKVPF GQPGAMADQS AGQLSPVSL
680 - 753 s ptppstpspy glsypqgysl asgqlspaaa pplaspsvft stlsksrptp kprqrptlp
p pqpptvnlsa ssp
754 - 818 QSTEAPM LDGMSPGESM STDLVHFDIP SIHIELGSTL RLSPLEHMRR HSVTDKRDSE EES
ESTAL
low complexity regions: DUST
>gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKLTACLQGQQGA
EADKRSKKLPLTTLAQCLMEGSAILGDDTLLGKMLKLCGETEDKLAQELIHFELQVERDV
IEPLFLLAEVEIPNIQKQRKHLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPAGAKADALR
EEMEEAANRVEICRDQLSADMYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQI
KAQQEAWVEKPSFGKPLEEHLTISGREIAFPIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQASNVQEQDKKL
QALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNIT
EMMTTVSLQIVGIIEPIIQHADWFFPGEIEFNITGNYGSPVHVNHNANYSSMPSPDMDPA
DRRQPEQARRPLSVATDNMMLEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAP
PSMQPPAPPAELAAPLPSPLPEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSA
QKGSPGSSQGTACAGTQPGAQPGAQPGASPSPSQPPADQSPHTLRKVSKKLAPIPPKVPF
GQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSLASGQLSPAAAPPLASPSVFT
STLSKSRPTPKPRQRPTLPPPQPPTVNLSASSPQSTEAPMLDGMSPGESMSTDLVHFDIP
SIHIELGSTLRLSPLEHMRRHSVTDKRDSEEESESTAL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|3327158|dbj|BAA31647.1|
sequence: 770 amino acids, 30 residue(s) in coiled coil state
Coil 1 * 171* 201* AGAKADALREEMEEAANRVEICRDQLSADMY
. | . | . | . | . | . 60
MKKQFNRMRQ LANQTVGRAE KTEVLSEDLL QVEKRLELVK QVSHSTHKKL TACLQGQQGA
~~~~~~~~~~ ~~~~~~~~14 4444444444 4444444444 311~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- --------ef gabcdefgab cdefgabcde fga------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~1 1111111111 1111111111 ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~14 4444444444 4444444444 311~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
2222222222 2222~~~~~~ ~~55555555 5555555544 3~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 120
EADKRSKKLP LTTLAQCLME GSAILGDDTL LGKMLKLCGE TEDKLAQELI HFELQVERDV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~11111111 11111111~~ * 14 M'95 -w local
. | . | . | . | . | . 180
IEPLFLLAEV EIPNIQKQRK HLAKLVLDMD SSRTRWQQTS KSSGLSSSLQ PAGAKADALR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~111144 4999999999 * 21 M'95 -w border
---------- ---------- ---------- ---------- ----defgab cdefgabcde * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~24888899 9999999999 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~122 2999999999 * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~14444466 6999999999 * 28 M'95 -w signif.
~~~~~~~~11 1111111111 11~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~999999999 * 14 M'95 -w local
. | . | . | . | . | . 240
EEMEEAANRV EICRDQLSAD MYSFVAKEID YANYFQTLIE VQAEYHRKSL TLLQAVLPQI
9999999999 9999999997 7~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
fgabcdefga bcdefgabcg a--------- ---------- ---------- ---------- * 21 M'95 -w register
9999999999 9999999994 4~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
9999999999 9999999882 2~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
9999999999 9999999999 951~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
9999999999 99664441~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 300
KAQQEAWVEK PSFGKPLEEH LTISGREIAF PIEACVTMLL ECGMQEEGLF RVAPSASKLK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- -------gab * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~11222 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 360
KLKAALDCCV VDVQEYSADP HAIAGALKSY LRELPEPLMT FELYDEWIQA SNVQEQDKKL
1111111111 11111111~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
cdefgabcde fgabcdef-- ---------- ---------- ---------- ---------- * 21 M'95 -w register
2222222222 222222222~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~1 1111111111 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~1 1111111111 * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~12 2222222222 * 14 M'95 -w local
. | . | . | . | . | . 420
QALWNACEKL PKANHNNIRY LIKFLSKLSE YQDVNKMTPS NMAIVLGPNL LWPQAEGNIT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
1111111111 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
1111111111 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
222~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 480
EMMTTVSLQI VGIIEPIIQH ADWFFPGEIE FNITGNYGSP VHVNHNANYS SMPSPDMDPA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
DRRQPEQARR PLSVATDNMM LEFYKKDGLR KIQSMGVRVM DTNWVARRGS SAGRKVSCAP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PSMQPPAPPA ELAAPLPSPL PEQPLDSPAA PALSPSGLGL QPGPERTSTT KSKELSPGSA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
QKGSPGSSQG TACAGTQPGA QPGAQPGASP SPSQPPADQS PHTLRKVSKK LAPIPPKVPF
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GQPGAMADQS AGQLSPVSLS PTPPSTPSPY GLSYPQGYSL ASGQLSPAAA PPLASPSVFT
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . |
STLSKSRPTP KPRQRPTLPP PQPPTVNLSA SSPQSTEAPM LDGMSPGESM
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem12.___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: tem12.___inter___
(1 sequences)
MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKL
TACLQGQQGAEADKRSKKLPLTTLAQCLMEGSAILGDDTLLGKMLKLCGE
TEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRKHLAKLVLDMD
SSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSAD
MYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAWVEK
PSFGKPLEEHLTISGREIAFPIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQA
SNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPS
NMAIVLGPNLLWPQAEGNITEMMTTVSLQIVGIIEPIIQHADWFFPGEIE
FNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPEQARRPLSVATDNMM
LEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAPPA
ELAAPLPSPLPEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSA
QKGSPGSSQGTACAGTQPGAQPGAQPGASPSPSQPPADQSPHTLRKVSKK
LAPIPPKVPFGQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSL
ASGQLSPAAAPPLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSA
SSPQSTEAPMLDGMSPGESMSTDLVHFDIPSIHIELGSTLRLSPLEHMRR
HSVTDKRDSEEESESTAL
(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 4 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 418 438 0.892 Putative
2 674 694 0.692 Putative
3 704 724 1.205 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 417 235 9 94
K+R profile + 0.00
+ +
CYT-EXT prof -0.48 -
0.97 0.25
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.17
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.0714
NEG: 60.0000
POS: 52.0000
-> Orientation: N-in
CYT-EXT difference: -1.70
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2 3
Loop length 673 9 94
K+R profile + +
0.00
CYT-EXT prof 0.21 0.25
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.23
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): 0.0327
NEG: 79.0000
POS: 74.0000
-> Orientation: undecided
CYT-EXT difference: 0.45
-> Orientation: N-out
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 3
Loop length 417 265 94
K+R profile + +
+
CYT-EXT prof -0.48 0.25
1.13
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.73
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.0714
NEG: 60.0000
POS: 52.0000
-> Orientation: N-in
CYT-EXT difference: -1.36
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 3
Loop length 703 94
K+R profile +
+
CYT-EXT prof 0.39
0.25
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): -5.00
(NEG-POS)/(NEG+POS): 0.0327
NEG: 79.0000
POS: 74.0000
-> Orientation: N-out
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
"tem12" 818
418 438 #f 0.891667
674 694 #f 0.691667
704 724 #t 1.20521
************************************
*TOPPREDM with prokaryotic function*
************************************
tem12.___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: tem12.___inter___
(1 sequences)
MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKL
TACLQGQQGAEADKRSKKLPLTTLAQCLMEGSAILGDDTLLGKMLKLCGE
TEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRKHLAKLVLDMD
SSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSAD
MYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAWVEK
PSFGKPLEEHLTISGREIAFPIEACVTMLLECGMQEEGLFRVAPSASKLK
KLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQA
SNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPS
NMAIVLGPNLLWPQAEGNITEMMTTVSLQIVGIIEPIIQHADWFFPGEIE
FNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPEQARRPLSVATDNMM
LEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAPPA
ELAAPLPSPLPEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSA
QKGSPGSSQGTACAGTQPGAQPGAQPGASPSPSQPPADQSPHTLRKVSKK
LAPIPPKVPFGQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSL
ASGQLSPAAAPPLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSA
SSPQSTEAPMLDGMSPGESMSTDLVHFDIPSIHIELGSTLRLSPLEHMRR
HSVTDKRDSEEESESTAL
(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 4 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 418 438 0.892 Putative
2 674 694 0.692 Putative
3 704 724 1.205 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3
Loop length 417 235 9 94
K+R profile + 0.00
+ +
CYT-EXT prof -0.48 -
0.97 0.25
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.17
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.0714
NEG: 60.0000
POS: 52.0000
-> Orientation: N-in
CYT-EXT difference: -1.70
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2 3
Loop length 673 9 94
K+R profile + +
0.00
CYT-EXT prof 0.21 0.25
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.23
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): 0.0327
NEG: 79.0000
POS: 74.0000
-> Orientation: undecided
CYT-EXT difference: 0.45
-> Orientation: N-out
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 3
Loop length 417 265 94
K+R profile + +
+
CYT-EXT prof -0.48 0.25
1.13
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.73
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): 0.0714
NEG: 60.0000
POS: 52.0000
-> Orientation: N-in
CYT-EXT difference: -1.36
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 3
Loop length 703 94
K+R profile +
+
CYT-EXT prof 0.39
0.25
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): -5.00
(NEG-POS)/(NEG+POS): 0.0327
NEG: 79.0000
POS: 74.0000
-> Orientation: N-out
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
"tem12" 818
418 438 #f 0.891667
674 694 #f 0.691667
704 724 #t 1.20521
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem12.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Oct 12 15:13:10 2000
File: /people/maria/tem12.___saps___
ID gi|3327158|dbj|BAA31647.1|
DE KIAA0672 protein [Homo sapiens]
number of residues: 818; molecular weight: 89.3 kdal
1 MKKQFNRMRQ LANQTVGRAE KTEVLSEDLL QVEKRLELVK QVSHSTHKKL TACLQGQQGA
61 EADKRSKKLP LTTLAQCLME GSAILGDDTL LGKMLKLCGE TEDKLAQELI HFELQVERDV
121 IEPLFLLAEV EIPNIQKQRK HLAKLVLDMD SSRTRWQQTS KSSGLSSSLQ PAGAKADALR
181 EEMEEAANRV EICRDQLSAD MYSFVAKEID YANYFQTLIE VQAEYHRKSL TLLQAVLPQI
241 KAQQEAWVEK PSFGKPLEEH LTISGREIAF PIEACVTMLL ECGMQEEGLF RVAPSASKLK
301 KLKAALDCCV VDVQEYSADP HAIAGALKSY LRELPEPLMT FELYDEWIQA SNVQEQDKKL
361 QALWNACEKL PKANHNNIRY LIKFLSKLSE YQDVNKMTPS NMAIVLGPNL LWPQAEGNIT
421 EMMTTVSLQI VGIIEPIIQH ADWFFPGEIE FNITGNYGSP VHVNHNANYS SMPSPDMDPA
481 DRRQPEQARR PLSVATDNMM LEFYKKDGLR KIQSMGVRVM DTNWVARRGS SAGRKVSCAP
541 PSMQPPAPPA ELAAPLPSPL PEQPLDSPAA PALSPSGLGL QPGPERTSTT KSKELSPGSA
601 QKGSPGSSQG TACAGTQPGA QPGAQPGASP SPSQPPADQS PHTLRKVSKK LAPIPPKVPF
661 GQPGAMADQS AGQLSPVSLS PTPPSTPSPY GLSYPQGYSL ASGQLSPAAA PPLASPSVFT
721 STLSKSRPTP KPRQRPTLPP PQPPTVNLSA SSPQSTEAPM LDGMSPGESM STDLVHFDIP
781 SIHIELGSTL RLSPLEHMRR HSVTDKRDSE EESESTAL
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 73( 8.9%); C : 11( 1.3%); D : 33( 4.0%); E : 59( 7.2%); F : 17( 2.1%)
G : 44( 5.4%); H : 16( 2.0%); I : 30( 3.7%); K : 49( 6.0%); L : 87(10.6%)
M : 26( 3.2%); N : 22( 2.7%); P+ : 80( 9.8%); Q : 54( 6.6%); R : 35( 4.3%)
S : 82(10.0%); T : 40( 4.9%); V : 38( 4.6%); W : 7( 0.9%); Y : 15( 1.8%)
KR : 84 ( 10.3%); ED : 92 ( 11.2%); AGP : 197 ( 24.1%);
KRED : 176 ( 21.5%); KR-ED : -8 ( -1.0%); FIKMNY : 159 ( 19.4%);
LVIFM : 198 ( 24.2%); ST : 122 ( 14.9%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0++000+0+0 0000000+0- +0-000--00 00-++0-00+ 0000000++0 0000000000
61 -0-++0++00 000000000- 000000--00 00+00+000- 0--+000-00 00-000-+-0
121 0-000000-0 -00000+0++ 000+000-0- 00+0+00000 +000000000 0000+0-00+
181 --0--000+0 -00+-0000- 000000+-0- 000000000- 000-00++00 0000000000
241 +000-000-+ 0000+00--0 00000+-000 00-0000000 -0000--000 +000000+0+
301 +0+000-000 0-00-000-0 0000000+00 0+-00-0000 0-00--0000 0000-0-++0
361 0000000-+0 0+000000+0 00+000+00- 00-00+0000 0000000000 00000-0000
421 -000000000 0000-00000 0-00000-0- 0000000000 0000000000 00000-0-00
481 -++00-00++ 000000-000 0-00++-00+ +000000+00 -00000++00 000++00000
541 0000000000 -000000000 0-000-0000 0000000000 0000-+0000 +0+-000000
601 0+00000000 0000000000 0000000000 0000000-00 0000++00++ 000000+000
661 0000000-00 0000000000 0000000000 0000000000 0000000000 0000000000
721 0000+0+000 +0+0+00000 0000000000 000000-000 0-00000-00 00-0000-00
781 0000-00000 +0000-00++ 0000-++-0- --0-0000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Negative charge clusters (cmin = 11/30 or 14/45 or 17/60): none
Mixed charge clusters (cmin = 16/30 or 22/45 or 27/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
There are no high scoring negative charge segments.
There are no high scoring mixed charge segments.
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.785 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.215 ( KEDR )
Expected score/letter: -0.936
M_0.01= 46.13; M_0.05= 37.84
1) From 603 to 724: length=122, score=59.00 **
(pocket at 638 to 657: length= 20, score=-34.00)
603 GSPGSSQGTA CAGTQPGAQP GAQPGASPSP SQPPA |DQSPH TLRKVSKKLA
653 PIPPK| VPFGQ PGAMADQSAG QLSPVSLSPT PPSTPSPYG
L SYPQGYSLAS
703 GQLSPAAAPP LASPSVFTST LS
A: 15(12.3%); G: 13(10.7%); S: 22(18.0%); P: 25(20.5%);
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 7 | 40 | 10 | 10 | 13 | 12 | 12 | 16 | 7 | 8 |
lmin1 6 | 7 | 9 | 49 | 12 | 12 | 16 | 14 | 15 | 19 | 8 | 10 |
lmin2 7 | 8 | 10 | 54 | 13 | 14 | 18 | 16 | 17 | 21 | 9 | 12 |
(Significance level: 0.010000; Minimal displayed length: 6)
(0) 66(1,0,0); at 658- 724: see sequence above
(4. quartile)
L: 7 (10.4%); A: 8 (11.9%); S: 14 (20.9%); P: 13 (19.4%);
ST: 18 (26.9%);
Run count statistics:
+ runs >= 3: 0
- runs >= 3: 1, at 810;
* runs >= 5: 0
0 runs >= 27: 2, at 603; 669;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
There are no high scoring hydrophobic segments.
There are no high scoring transmembrane segments.
2. SPACINGS OF C.
H2N-52-C-23-C-20-C-94-C-81-C-6-C-25-C-C-57-C-170-C-74-C-205-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-43-H-2-H-5-C-23-C-20-C-12-H-29-H-51-C-32-H-33-H-14-C-6-C-25-C-C-11-H-45-C-7-H-64-H-21-H-2-H-72-C-74-C-28-H-133-H-6-H-13-H-3-H-17-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
Aligned matching blocks:
[ 672- 676] GQLSP
[ 703- 707] GQLSP
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: 58 (Expected range: 30-- 72)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 21 (6-10) 12 (11-20) 13 (>=21) 13
3. Clusters of amino acid multiplets (cmin = 12/30 or 15/45 or 19/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 28 (Expected range: 4-- 30)
19 +plets (f+: 10.3%), 9 -plets (f-: 11.2%)
Total number of charge altplets: 19 (Critical number: 34)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 6 (6-10) 5 (11-20) 8 (>=21) 10
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
172- 179 2 A. 4 4 0
473- 496 6 P..... 4 4 0
555- 562 2 P. 4 4 0
561- 588 7 P.....S 4 4 /0/./././././1/
615- 630 4 GAQP 4 4 /0/1/1/0/
670- 689 5 S.... 4 4 0
728- 747 4 P... 5 5 ! 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
There are no periodicities of the prescribed length.
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
396- 482 (3.) +( 86)+ 1 of 85 0.0044 large 1. maximal spacing
577- 579 (3.) G( 2)G 45 of 45 0.0059 large minimal spacing
594- 757 (4.) E( 163)E 1 of 60 0.0001 large maximal spacing
602- 638 (4.) *( 36)* 2 of 177 0.0002 large 2. maximal spacing
657- 725 (4.) +( 68)+ 2 of 85 0.0003 large 2. maximal spacing
668- 725 (4.) *( 57)* 1 of 177 0.0001 large 1. maximal spacing
668- 757 (4.) -( 89)- 1 of 93 0.0012 large maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem12
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RhoGAP RhoGAP domain 196.1 5.4e-55 1
ATP-gua_Ptrans ATP:guanido phosphotransferase 0.5 25 1
Carboxyl_trans Carboxyl transferase domain 0.0 36 1
GST Glutathione S-transferases. -0.3 70 1
Glutelin Beta type Zein -59.7 40 1
SNAP-25 SNAP-25 family -63.0 37 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
SNAP-25 1/1 28 229 .. 1 215 [] -63.0 37
GST 1/1 359 371 .. 195 207 .] -0.3 70
Carboxyl_trans 1/1 358 378 .. 570 591 .] 0.0 36
ATP-gua_Ptrans 1/1 378 403 .. 371 398 .] 0.5 25
RhoGAP 1/1 269 419 .. 1 170 [] 196.1 5.4e-55
Glutelin 1/1 515 694 .. 1 210 [] -59.7 40
Alignments of top-scoring domains:
SNAP-25: domain 1 of 1, from 28 to 229: score -63.0, E = 37
*->eldEiqreieqitdeSLeSTRRmLklaee..........SkdaGirT
+l ++++ e +++ S ST + L + ++++ + +++Sk+ T
gi|3327158 28 DLLQVEKRLELVKQVS-HSTHKKLTACLQgqqgaeadkrSKKLPLTT 73
lvmLdeQgEqLdriEeglDqInkdmkeAeknLseLkKccGsilkvhvsnP
l + + g l ++ k e+e +L+ + l+v
gi|3327158 74 LAQCLMEGSAILGDDTLLGKMLKLCGETEDKLAQELIHFE--LQV----- 116
fnskklcvkPcektknfkvdkaykkewgsnqdgkstqrieGavvanqpsr
+ ++P + +++ +++ + k +v + s+
gi|3327158 117 ---ERDVIEPLFLLAEVEIPNI---QKQRKHLAK--------LVLDMDSS 152
vvddreqqktvmeasggyikriteenDArEnEmdeNLdqvssiignL.rk
++ ++ k + +s + + DA +Em+e v+ L+ +
gi|3327158 153 RTRWQQTSKSSGLSSSLQPAGAK--ADALREEMEEAANRVEICRDQLsAD 200
mAldmGkEiDsQnrqidRIeeKadsndar<-*
m + kEiD n Ie a+ +
gi|3327158 201 MYSFVAKEIDYANYFQTLIEVQAEYHRKS 229
GST: domain 1 of 1, from 359 to 371: score -0.3, E = 70
*->nLkawrervaarp<-*
+L+a+++ ++ +p
gi|3327158 359 KLQALWNACEKLP 371
Carboxyl_trans: domain 1 of 1, from 358 to 378: score 0.0, E = 36
*->ialallwtkrrrffpwrkhgni<-*
++l++lw++ + ++p+ h ni
gi|3327158 358 KKLQALWNACE-KLPKANHNNI 378
ATP-gua_Ptrans: domain 1 of 1, from 378 to 403: score 0.5, E = 25
*->VklLvemEkkLekgqdGaiedvlPvqkl<-*
+++L++ kL ++qd ++ + P
gi|3327158 378 IRYLIKFLSKLSEYQD--VNKMTPSNMA 403
RhoGAP: domain 1 of 1, from 269 to 419: score 196.1, E = 5.4e-55
*->PiivekcveyIeklYPLaerGlqeEGIYRvsGsasrvkeLreafdkd
+e+cv + + G+qeEG++Rv +sas++k+L++a+d+
gi|3327158 269 AFPIEACVTMLLE------CGMQEEGLFRVAPSASKLKKLKAALDCC 309
gapdslelsekewfDvhvvaglLKlYLReLPePLipydlyeefiraakeq
+++ +++ D+h++ag+LK YLReLPePL++++ly+e+i a++
gi|3327158 310 --VVDVQEYSA---DPHAIAGALKSYLRELPEPLMTFELYDEWIQASN-- 352
iedpderlralkellsSkLPrahynTLryLltHLnrvaeiyiensavNkM
+++ d +l+al ++++ kLP+a+ n+ ryL+++L +++e +++vNkM
gi|3327158 353 VQEQDKKLQALWNACE-KLPKANHNNIRYLIKFLSKLSE----YQDVNKM 397
narNLAivFgPtLlrppdkesnd<-*
+++N Aiv+gP+Ll+p + e n+
gi|3327158 398 TPSNMAIVLGPNLLWPQA-EGNI 419
Glutelin: domain 1 of 1, from 515 to 694: score -59.7, E = 40
*->mkvLlvALALLALaAsaaststsGgCGCqtPhlPPPPvHLPPPvhlP
m v ++ +A s+a ++s C +P + PP PP l
gi|3327158 515 MGVRVMDTNWVARRGSSAGRKVS----CAPPSMQPP----APPAELA 553
PPvhLPPPqvhyPtqpPrpqphPtlppq...phPCptqpphPsPcqlqqp
P LP P +P+qp P+l p + +++P p +l p
gi|3327158 554 AP--LPSP---LPEQPLDSPAAPALSPSglgLQPGPERTSTTKSKELS-P 597
GsCgvgsgpvttpiLGqCvEFLRHqCsPaAtPYcsPq.CqaLrqqCCqql
Gs gs p +++ G P A P +sP + q q + l
gi|3327158 598 GSAQKGS-PGSSQ--GTACAGTQPGAQPGAQPGASPSpSQPPADQSPHTL 644
RqvEPlHRyqAifGvvLqsilqqqPqgeqlaaLlAAqiAqqLtamCGlql
R+v L i + P g+ ++ +A q A qL +
gi|3327158 645 RKVSKK----------LAPIPPKVPFGQ--PGAMADQSAGQLSPVSLSPT 682
pqpsPCpcsaaAGGvqy<-*
p ++P p+ G y
gi|3327158 683 PPSTPSPY-----GLSY 694
//
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: tem12
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RhoGAP RhoGAP domain 194.2 2e-54 1
UVR UvrB/uvrC motif 3.4 25 1
ATP-gua_Ptrans ATP:guanido phosphotransferase 0.5 25 1
Carboxyl_trans Carboxyl transferase domain 0.0 36 1
GST Glutathione S-transferases. -0.3 70 1
XRCC1_N XRCC1 N terminal domain -0.5 42 1
ANATO Anaphylotoxin-like domain -1.2 57 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
UVR 1/1 173 188 .. 1 16 [. 3.4 25
ANATO 1/1 303 309 .. 31 37 .] -1.2 57
GST 1/1 359 371 .. 195 207 .] -0.3 70
Carboxyl_trans 1/1 358 378 .. 570 591 .] 0.0 36
ATP-gua_Ptrans 1/1 378 403 .. 371 398 .] 0.5 25
RhoGAP 1/1 269 419 .. 1 170 [] 194.2 2e-54
XRCC1_N 1/1 683 699 .. 139 155 .] -0.5 42
Alignments of top-scoring domains:
UVR: domain 1 of 1, from 173 to 188: score 3.4, E = 25
*->ekeikeLekeMeeAae<-*
++ ++L++eMeeAa+
gi|3327158 173 GAKADALREEMEEAAN 188
ANATO: domain 1 of 1, from 303 to 309: score -1.2, E = 57
*->kaFlqCC<-*
ka l+CC
gi|3327158 303 KAALDCC 309
GST: domain 1 of 1, from 359 to 371: score -0.3, E = 70
*->nLkawrervaarp<-*
+L+a+++ ++ +p
gi|3327158 359 KLQALWNACEKLP 371
Carboxyl_trans: domain 1 of 1, from 358 to 378: score 0.0, E = 36
*->ialallwtkrrrffpwrkhgni<-*
++l++lw++ + ++p+ h ni
gi|3327158 358 KKLQALWNACE-KLPKANHNNI 378
ATP-gua_Ptrans: domain 1 of 1, from 378 to 403: score 0.5, E = 25
*->VklLvemEkkLekgqdGaiedvlPvqkl<-*
+++L++ kL ++qd ++ + P
gi|3327158 378 IRYLIKFLSKLSEYQD--VNKMTPSNMA 403
RhoGAP: domain 1 of 1, from 269 to 419: score 194.2, E = 2e-54
*->PiivekcveyIeklYPLaerGlqeEGIYRvsGsasrvkeLreafdkd
+e+cv + + G+qeEG++Rv +sas++k+L++a+d+
gi|3327158 269 AFPIEACVTMLLE------CGMQEEGLFRVAPSASKLKKLKAALDCC 309
gapdslelsekewfDvhvvaglLKlYLReLPePLipydlyeefiraakeq
+++ +++ D+h++ag+LK YLReLPePL++++ly+e+i a++
gi|3327158 310 --VVDVQEYSA---DPHAIAGALKSYLRELPEPLMTFELYDEWIQASN-- 352
iedpderlralkellsSkLPrahynTLryLltHLnrvaeiyiensavNkM
+++ d +l+al ++++ kLP+a+ n+ ryL+++L +++e +++vNkM
gi|3327158 353 VQEQDKKLQALWNACE-KLPKANHNNIRYLIKFLSKLSE----YQDVNKM 397
narNLAivFgPtLlrppdkesnd<-*
+++N Aiv+gP+Ll+p + e n+
gi|3327158 398 TPSNMAIVLGPNLLWPQA-EGNI 419
XRCC1_N: domain 1 of 1, from 683 to 699: score -0.5, E = 42
*->PYsKDsPyGLsFvrFHs<-*
P s sPyGLs+ + s
gi|3327158 683 PPSTPSPYGLSYPQGYS 699
//
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: tem12
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Thu Oct 12 15:18:13 2000
Sequence file: tem12
----------------------------------------
Sequence gi|3327158|dbj|BAA31647.1| (818 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
13: NQTV
418: NITE
452: NITG
468: NYSS
747: NLSA
Total matches: 5
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
48: KKLT
527: RRGS
534: RKVS
645: RKVS
799: RRHS
806: KRDS
Total matches: 6
Matching pattern PS00005 PKC_PHOSPHO_SITE:
46: THK
66: SKK
151: SSR
159: TSK
264: SGR
589: TTK
643: TLR
648: SKK
729: TPK
789: TLR
804: TDK
Total matches: 11
Matching pattern PS00006 CK2_PHOSPHO_SITE:
217: TLIE
264: SGRE
765: SPGE
793: SPLE
802: SVTD
809: SEEE
Total matches: 6
Matching pattern PS00008 MYRISTYL:
56: GQQGAE
164: GLSSSL
325: GALKSY
529: GSSAGR
603: GSPGSS
606: GSSQGT
610: GTACAG
615: GTQPGA
619: GAQPGA
623: GAQPGA
661: GQPGAM
763: GMSPGE
Total matches: 12
Matching pattern PS00009 AMIDATION:
532: AGRK
Total matches: 1
Total no of hits in this sequence: 41
========================================
1314 pattern(s) searched in 1 sequence(s), 818 residues.
Total no of hits in all sequences: 41.
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 tem12
***** 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, 818 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: tem12
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem12
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
(818 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
AP2 A plant specific DNA binding domain (Apetala 2 like) 24 0.63
PUM Pumilio repeat RNA binding domain 24 0.76
ARM Armadillo repeat 23 1.1
VWA Von Willebrand factor A domain 23 1.3
KELCH Kelch repeat- beta propeller like domain 23 1.4
PDE cyclic NMP phosphodiesterase domain 22 3.0
UBHYD Ubiquitin C-terminal hydrolase domain 22 3.2
CYCL cyclophilin like peptidyl prolyl isomerases 22 3.5
GAF GAF domain (Predicted Small-ligand binding domain) 21 5.4
RASGEF RAS-type GTPase GDP exchange factor 21 5.9
PCNA Proliferating Cell nuclear antigen like domain 21 8.0
HECT A ubiquitin conjugating enzyme domain 20 8.4
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 24.4 bits (52), Expect = 0.63
Identities = 11/67 (16%), Positives = 21/67 (30%), Gaps = 12/67 (17%)
Query: 470 SSMPSPDMDPADRRQPEQARRPLSVATDNMMLEFYKKDGLRKIQSMGVRVMDT-NWVARR 528
+S + + + RQ + + V KD + GVR + WV+
Sbjct: 3 ASESTKSWEASAVRQENEEEKKKPV-----------KDSGKHPVYRGVRKRNWGKWVSEI 51
Query: 529 GSSAGRK 535
+
Sbjct: 52 REPRKKS 58
>PUM Pumilio repeat RNA binding domain
Length = 337
Score = 24.1 bits (52), Expect = 0.76
Identities = 21/147 (14%), Positives = 44/147 (29%), Gaps = 43/147 (29%)
Query: 130 VEIPNIQKQRKHLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANR 189
VEI + + KL D R ++ S + D + E+++
Sbjct: 2 VEISALPLRDLDYIKLATDQFGCRFLQKKLETPS-------ESNMVRDLMYEQIKPFF-- 52
Query: 190 VEICRD-------------------------------QLSADMYS--FVAKEIDYANYFQ 216
+++ D Q+S + Y + K ID +
Sbjct: 53 LDLILDPFGNYLVQKLCDYLTAEQKTLLIQTIYPNVFQISINQYGTRSLQKIIDTVDNEV 112
Query: 217 TLIEVQAEYHRKSLTLLQAVLPQIKAQ 243
I++ + + T ++ V+ I
Sbjct: 113 Q-IDLIIKGFSQEFTSIEQVVTLINDL 138
Score = 20.9 bits (44), Expect = 6.5
Identities = 6/56 (10%), Positives = 15/56 (26%), Gaps = 7/56 (12%)
Query: 87 DDTLLGKMLKLCGETEDKLA----QELIHFELQVERDVIEPLFLLAEVEIPNIQKQ 138
+ L ++ +L K + ++ I ++ I A
Sbjct: 236 FNRLSNELCQLSC---LKFSSNVVEKFIKKLFRIITGFIVNNNGGASQRTAVASDD 288
>ARM Armadillo repeat
Length = 532
Score = 23.4 bits (50), Expect = 1.1
Identities = 14/84 (16%), Positives = 27/84 (31%), Gaps = 6/84 (7%)
Query: 113 ELQVERDVIEPLFLLAEVEIPNIQKQRKHLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPA 172
+ VE+ I+PL L P I + +L + + T + + + A
Sbjct: 406 KYLVEQGCIKPLCDLLVCPDPRIITVCLEGLENILKVGEAEKNLGHTGDMNYYAQLIDDA 465
Query: 173 GAKADALR------EEMEEAANRV 190
E+ E A ++
Sbjct: 466 EGLEKIENLQSHDNNEIYEKAVKI 489
Score = 21.8 bits (46), Expect = 3.1
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 354 QEQDKKLQALWNACEKLPKANHNNIRYLIK 383
E D K +A W +H+ I+YL++
Sbjct: 381 AEFDIKKEAAWAISNATSGGSHDQIKYLVE 410
Score = 20.6 bits (43), Expect = 8.5
Identities = 4/20 (20%), Positives = 7/20 (35%)
Query: 798 MRRHSVTDKRDSEEESESTA 817
M++ + S S A
Sbjct: 46 MKKRREGMQALQGFPSASAA 65
>VWA Von Willebrand factor A domain
Length = 255
Score = 23.4 bits (50), Expect = 1.3
Identities = 5/35 (14%), Positives = 15/35 (42%)
Query: 268 IAFPIEACVTMLLECGMQEEGLFRVAPSASKLKKL 302
++ + C + +E +++ + LK+L
Sbjct: 196 LSAQVAICKELCKATNYGDESFYKILLDETHLKEL 230
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 23.0 bits (49), Expect = 1.4
Identities = 3/14 (21%), Positives = 4/14 (28%)
Query: 453 ITGNYGSPVHVNHN 466
+T P H
Sbjct: 13 VTSLCARPRKTGHA 26
>PDE cyclic NMP phosphodiesterase domain
Length = 350
Score = 22.0 bits (46), Expect = 3.0
Identities = 18/74 (24%), Positives = 40/74 (53%), Gaps = 10/74 (13%)
Query: 188 NRVEICRDQLSADMYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAW 247
++ + R +++AD FVA + FQ++ A++ ++S LL+ V+ + + +A+
Sbjct: 260 DKTKTTRARIAADFIDFVASPL-----FQSM----AKFLKESQFLLK-VISKNRENWQAY 309
Query: 248 VEKPSFGKPLEEHL 261
+E GK ++ L
Sbjct: 310 MELQKEGKCNDDDL 323
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 21.9 bits (46), Expect = 3.2
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 496 TDNMMLEFYKKDGLR 510
TD M+L+F+K G R
Sbjct: 614 TDPMLLQFFKSQGYR 628
>CYCL cyclophilin like peptidyl prolyl isomerases
Length = 165
Score = 21.7 bits (46), Expect = 3.5
Identities = 7/18 (38%), Positives = 7/18 (38%)
Query: 770 MSTDLVHFDIPSIHIELG 787
M V FDI LG
Sbjct: 1 MVNPTVFFDIAVDGEPLG 18
>GAF GAF domain (Predicted Small-ligand binding domain)
Length = 160
Score = 21.0 bits (44), Expect = 5.4
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 254 GKPLEEHLTISGREIAFPI 272
LEE L EI FP+
Sbjct: 46 DAVLEECLVAPDSEIVFPL 64
>RASGEF RAS-type GTPase GDP exchange factor
Length = 196
Score = 20.9 bits (44), Expect = 5.9
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 643 TLRKVSKKLAPIPPKVPF 660
T+R + + P+ VPF
Sbjct: 151 TIRNLLNSVNPLVGCVPF 168
Score = 20.5 bits (43), Expect = 7.4
Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 362 ALWNACEKLPKANHNN----IRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPN 409
W E L + I+ I +Q+ N + M I+L +
Sbjct: 68 VDWIISEILLTKSSKMKRNVIQRFIHVADHCRTFQNFNTL----MEIILALS 115
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 20.6 bits (43), Expect = 8.0
Identities = 7/57 (12%), Positives = 14/57 (24%), Gaps = 5/57 (8%)
Query: 89 TLLGKMLKLCGETEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRKHLAKL 145
T+L L + G + + Q + E + K +
Sbjct: 87 TILLDCLSIFGSSPTPGTLTALRMCYQGYGHPLMLFL-----EEGGVVTVCKITTQE 138
>HECT A ubiquitin conjugating enzyme domain
Length = 255
Score = 20.5 bits (43), Expect = 8.4
Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 9/92 (9%)
Query: 88 DTLLGKMLKLCGETEDK-LAQELIHFELQVERDVIEPLFLLAEVE-------IPNIQKQR 139
D L + L ED + +E H + ++ V + V IP R
Sbjct: 124 DLLYVQTLNSILHIEDSGITEESFHEMIPLDSFVGQSADGK-MVPIIPGGNSIPLTFSNR 182
Query: 140 KHLAKLVLDMDSSRTRWQQTSKSSGLSSSLQP 171
K + ++ Q + G+S +
Sbjct: 183 KEYVERAIEYRLHEMDRQVAAVREGMSWIVPV 214
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 12
Number of calls to ALIGN: 16
Length of query: 818
Total length of test sequences: 20182
Effective length of test sequences: 16037.0
Effective search space size: 12488779.1
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= gi|3327158|dbj|BAA31647.1| KIAA0672 protein [Homo sapiens]
(818 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2285879 [10..385] ATP-grasp 30 0.15
gi|2506153 [10..236] NAD(P)-binding Rossmann-fold domains 29 0.35
gi|121822 [1..340] beta/alpha (TIM)-barrel 27 1.2
gi|625921 [2..242] NAD(P)-binding Rossmann-fold domains 27 1.4
gi|1708072 [225..439] ATP pyrophoshatases 26 1.9
gi|465501 [6..186] N-terminal domain of DNA photolyase 26 2.3
gi|132176 [36..260] near-membrane domain of membrane proteins 26 3.0
gi|461667 [103..306] Photosynthetic reaction centre (cytochr... 26 3.5
gi|1073919 [251..447] NAD(P)-binding Rossmann-fold domains 25 4.0
gi|2494172 [22..295] DNase I-like 25 4.6
gi|1125790 [25..414] Phosphoglycerate mutase-like 25 4.7
gi|483174 [15..156] Four-helical up-and-down bundle 25 5.0
gi|124505 [1..400] Sugar phosphatases 25 6.5
gi|121769 [3..207] Class I glutamine amidotransferases 25 6.6
gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains 24 7.3
gi|2500207 [212..776] R1 subunit of ribonucleotide reductase... 24 9.3
>gi|2285879 [10..385] ATP-grasp
Length = 376
Score = 30.0 bits (67), Expect = 0.15
Identities = 14/46 (30%), Positives = 24/46 (51%), Gaps = 1/46 (2%)
Query: 200 DMYSFVAKEIDYANYFQTLIEVQAEYHRKSLTLLQAV-LPQIKAQQ 244
DM+S V I + ++ + L E++A K+ T L A L ++ Q
Sbjct: 139 DMFSDVVMGIPHEHFGEKLEEMKATKGVKNDTDLSADDLKELVVQY 184
>gi|2506153 [10..236] NAD(P)-binding Rossmann-fold domains
Length = 227
Score = 28.6 bits (62), Expect = 0.35
Identities = 16/201 (7%), Positives = 35/201 (16%), Gaps = 19/201 (9%)
Query: 274 ACVTMLLECGMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSADPHAIAGALKSYLRE 333
A + +R A +Q + + L+
Sbjct: 12 ALAWHFINQKQPVIVSYRTHYPAIDGLINA-----GAQCIQADFSTNDGVMAFADEVLKS 66
Query: 334 LPEPLMTFELYDEWIQASNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQD 393
W+ L + P + L + L
Sbjct: 67 THGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTP---YLLNHALERLLRGHGHAAS 123
Query: 394 VNKMTPSNMAIVLGPNLLWPQAEGNITEMMT-----------TVSLQIVGIIEPIIQHAD 442
+ + A + MT V+ +I
Sbjct: 124 DIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSLILFNEHDDA 183
Query: 443 WFFPGEIEFNITGNYGSPVHV 463
+ + ++ V
Sbjct: 184 EYRQQALNKSLMKTAPGEKEV 204
>gi|121822 [1..340] beta/alpha (TIM)-barrel
Length = 340
Score = 27.1 bits (59), Expect = 1.2
Identities = 12/138 (8%), Positives = 34/138 (23%), Gaps = 11/138 (7%)
Query: 369 KLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNITEMMTTVSL 428
L + + I Y F + + S MA + +P I E +
Sbjct: 184 NLADIDDDYIVYNFHFYNPFFFTHQKAHWSESAMAYNRT--VKYPGQYEGIEEFVKNNPK 241
Query: 429 QIVGIIEPIIQHADWFFPGEIE--FNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPE 486
+ ++ +++ ++ + + R +
Sbjct: 242 YSFMMELNNLKLNKELLRKDLKPAIEFREKKKCKLYCGEFGVI------AIADLESR-IK 294
Query: 487 QARRPLSVATDNMMLEFY 504
+S+ + +
Sbjct: 295 WHEDYISLLEEYDIGGAV 312
>gi|625921 [2..242] NAD(P)-binding Rossmann-fold domains
Length = 241
Score = 26.6 bits (57), Expect = 1.4
Identities = 11/122 (9%), Positives = 27/122 (22%), Gaps = 6/122 (4%)
Query: 274 ACVTMLLECGMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSADPHAIAGALKSYLRE 333
A V L G A++ ++ ++ V + + L+
Sbjct: 15 AAVEALTRDGYTVVCHDATFADAAERQRFESENPGTVA------LAEQKPERLVDATLQH 68
Query: 334 LPEPLMTFELYDEWIQASNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQD 393
+ + + + E L ++ I L
Sbjct: 69 GEAIDTIVSNDYIPRPMNRLPIEGTSEADIRQVFEALSIFPILLLQSAIAPLRAAGGASV 128
Query: 394 VN 395
+
Sbjct: 129 IF 130
>gi|1708072 [225..439] ATP pyrophoshatases
Length = 215
Score = 26.1 bits (57), Expect = 1.9
Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 5/64 (7%)
Query: 180 REEMEEAANRVEICRDQLSADMYSFVAKEIDYANYFQTLIEVQAEYHRKSLT--LLQAVL 237
R+ ++ +L + A Y I + RK ++ L
Sbjct: 52 RKRESQSVEEAL---KKLGIQVKVINAAHSFYNGTTTLPISDEDRTPRKRISKTLNMTTS 108
Query: 238 PQIK 241
P+ K
Sbjct: 109 PEEK 112
>gi|465501 [6..186] N-terminal domain of DNA photolyase
Length = 181
Score = 26.0 bits (57), Expect = 2.3
Identities = 8/63 (12%), Positives = 16/63 (24%), Gaps = 3/63 (4%)
Query: 315 EYSADPHAIAGALKSYLRELPEPLMTFE---LYDEWIQASNVQEQDKKLQALWNACEKLP 371
+ + + L +L + L+ + + W LP
Sbjct: 97 DVEPYARERDRVVAATLNDLGIAVHRQWDQLLHPPSAVQTQQGQPYTVYTPFWRNWSALP 156
Query: 372 KAN 374
KA
Sbjct: 157 KAA 159
>gi|132176 [36..260] near-membrane domain of membrane proteins
Length = 225
Score = 25.6 bits (55), Expect = 3.0
Identities = 20/82 (24%), Positives = 29/82 (34%), Gaps = 19/82 (23%)
Query: 696 QGYSL--ASGQLSPAAAP-PLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSASS 752
+GY L G + P PL P F P R T+P P+ ++ +
Sbjct: 3 EGYPLENEDGTPAANQGPFPLPKPKTFI--------LPHGRGTLTVPGPESEDRPIALAR 54
Query: 753 PQSTEA--------PMLDGMSP 766
+E PM DG+ P
Sbjct: 55 TAVSEGFPHAPTGDPMKDGVGP 76
>gi|461667 [103..306] Photosynthetic reaction centre (cytochrome subunit)
Length = 204
Score = 25.5 bits (55), Expect = 3.5
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 502 EFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAP 548
E+ +K R + + VR ++ ++ + G V CA P
Sbjct: 42 EYPQKIAARNMLRL-VRDVNAEFIVNLPNWQGNYVQCATCHNNAPNN 87
>gi|1073919 [251..447] NAD(P)-binding Rossmann-fold domains
Length = 197
Score = 25.4 bits (54), Expect = 4.0
Identities = 14/192 (7%), Positives = 46/192 (23%), Gaps = 18/192 (9%)
Query: 364 WNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNITEMM 423
+ + K + + + + K + + A + +
Sbjct: 18 AHIIDVAKKFGIKTYSLSRSNGVDVGDVKSIEKAFAGIYGKEHKIDHIVNTAAVLNHKTL 77
Query: 424 TTVSLQIVGIIEPIIQHADWFFPGEIEFNITGNYGSPVHVNHNANYSSMPSPDMDPADRR 483
++S + + + + +GS + ++ P + +
Sbjct: 78 ASMSYEEIVTSINVNYTGMINAVITAYPYLKQTHGSFLGFTSSSYTRGRPFYAIYSS--- 134
Query: 484 QPEQARRPLSVATDNMMLEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSM 543
A+ + T + E+ +++ N + + P
Sbjct: 135 ----AKAAVVNLTQAISEEWLPD---------NIKINCVNPERTKTPMRTKAFGIEP--E 179
Query: 544 QPPAPPAELAAP 555
P +A
Sbjct: 180 GTLLDPKTVAFA 191
>gi|2494172 [22..295] DNase I-like
Length = 274
Score = 24.9 bits (54), Expect = 4.6
Identities = 10/38 (26%), Positives = 14/38 (36%)
Query: 719 FTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSASSPQST 756
F++ + R P P +R PPP P P
Sbjct: 113 FSAPGTGERAPPLPSRRALTPPPLPAAAQNLVLIPLHA 150
>gi|1125790 [25..414] Phosphoglycerate mutase-like
Length = 390
Score = 24.9 bits (54), Expect = 4.7
Identities = 13/105 (12%), Positives = 32/105 (30%), Gaps = 9/105 (8%)
Query: 283 GMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSAD-PHAIAGALKSYLRELPEPLMTF 341
+ + +++ ++ + L Q D I AL L T
Sbjct: 152 LAKTSDEVKSFVNSADVQAVLGNLTN--YCGQPVDIDNLWIITNALYIEQIYYNATLRTK 209
Query: 342 -ELY--DEWIQASNVQEQDKKLQ-ALWNACEKLPKANHNNIRYLI 382
+ + +A + +Q + Q ++ N +++ L
Sbjct: 210 NNWFTDAFYAKADAINDQVQLFQNGIFK--TVPNIVNGHDVGVLT 252
>gi|483174 [15..156] Four-helical up-and-down bundle
Length = 142
Score = 24.8 bits (54), Expect = 5.0
Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 9/90 (10%)
Query: 165 LSSSLQPAGAKADALREEM----EEAANRVEIC----RDQLSADMYSFVAKEIDYANYFQ 216
+ +++ A L E++ E RV + +L ADM + Y Q
Sbjct: 42 MDETMKEVKAYKAELDEQLGPMTSETQARVAKELQAAQARLRADMEDVRNRLTQYRGELQ 101
Query: 217 TLIEVQAEYHRKSL-TLLQAVLPQIKAQQE 245
++ +E R + ++ + ++ E
Sbjct: 102 AMLGQSSEELRARFASHMRKLRKRVLRDAE 131
>gi|124505 [1..400] Sugar phosphatases
Length = 400
Score = 24.6 bits (53), Expect = 6.5
Identities = 12/71 (16%), Positives = 26/71 (35%), Gaps = 15/71 (21%)
Query: 155 RWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSADMYSFVAKEIDYANY 214
Q+ + S ++++ A + + L + + E E K +A
Sbjct: 4 ILQELLRVSEKAANIARACRQQETLFQLLIEEKKEGE---------------KNKKFAVD 48
Query: 215 FQTLIEVQAEY 225
F+TL +V +
Sbjct: 49 FKTLADVLVQE 59
>gi|121769 [3..207] Class I glutamine amidotransferases
Length = 205
Score = 24.6 bits (53), Expect = 6.6
Identities = 13/116 (11%), Positives = 30/116 (25%), Gaps = 17/116 (14%)
Query: 372 KANHNNIRYLIKFLSKL------SEYQDVNKMTPSNMAIVLGPNLLWPQAEGNITEM--M 423
+ R + + + PS + + GP E + +
Sbjct: 16 QYTQLVARRVRELGVYCELWAWDVTEAQIRDFNPSGIILSGGPE--STTEENSPRAPQYV 73
Query: 424 TTVSLQIVGII--EPIIQHADWFFPGEIEFNITGNYG--SPVHVNHNANYSSMPSP 475
+ + G+ + G +E + +G VN +A +
Sbjct: 74 FEAGVPVFGVCYGMQTMAMQ---LGGHVEASNEREFGYAQVEVVNDSALVRGIEDA 126
>gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains
Length = 178
Score = 24.2 bits (51), Expect = 7.3
Identities = 11/97 (11%), Positives = 24/97 (24%), Gaps = 1/97 (1%)
Query: 274 ACVTMLLECGMQEEGLFRVAPSASKLKKLKAALDCCV-VDVQEYSADPHAIAGALKSYLR 332
L + + + A + SK + V D++ G + + +
Sbjct: 13 YLTARLAQNPLINRVIAVDAIAPSKDMLRRMGRAEFVRADIRNPFIAKVIRNGEVDTVVH 72
Query: 333 ELPEPLMTFELYDEWIQASNVQEQDKKLQALWNACEK 369
++ NV + A A
Sbjct: 73 AAAASYAPRSGGSAALKELNVMGAMQLFAACQKAPSV 109
>gi|2500207 [212..776] R1 subunit of ribonucleotide reductase, C-terminal domain
Length = 565
Score = 24.0 bits (52), Expect = 9.3
Identities = 9/52 (17%), Positives = 15/52 (28%), Gaps = 5/52 (9%)
Query: 274 ACVTMLLECGMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSADPHAIAG 325
+C + EG+F + L K + D + I G
Sbjct: 4 SCY--IGSTPDNIEGIFDSYKEMALLSKYGGGIG---WDFSLVRSIGSYIDG 50
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 16
Number of calls to ALIGN: 16
Length of query: 818
Total length of test sequences: 256703
Effective length of test sequences: 201489.0
Effective search space size: 155528848.3
Initial X dropoff for ALIGN: 25.0 bits