RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6130
(295 letters)
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes human Ape1 (also known as Apex, Hap1,
or Ref-1) and related proteins. These are Escherichia
coli exonuclease III (ExoIII)-like AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity; for example, Ape1 and Ape2 in humans. Ape1 is
found in this subfamily, it exhibits strong
AP-endonuclease activity but shows weak 3'-5'
exonuclease and 3'-phosphodiesterase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes exonuclease III
(ExoIII) and endonuclease IV (EndoIV). This subfamily
belongs to the ExoIII family; the EndoIV family belongs
to a different superfamily.
Length = 253
Score = 309 bits (794), Expect = e-106
Identities = 118/222 (53%), Positives = 149/222 (67%), Gaps = 12/222 (5%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI SWNV GLRA +KK LDY+KKED DI CLQETK E +P E+K Y YW +
Sbjct: 1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA 60
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKNEHY-GRNC-----NSNIVNTFYIRKNVPNAGA 186
+ K GY+G + +K KP VTYG+G + GR N +VNT+ VPN+G
Sbjct: 61 AEKKGYSGTAILSKKKPLSVTYGIGIEEHDQEGRVITAEFENFYLVNTY-----VPNSGR 115
Query: 187 GLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEER 246
GL+ LD+R EWD F +L KLD++KPVI GDLNV+H+ IDLANP TN +SAGFT EER
Sbjct: 116 GLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEER 175
Query: 247 DSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
+SF+ LL+ GF D+FRHL+P + GAYT+WSY AR++N G
Sbjct: 176 ESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGN-ARAKNVG 216
>gnl|CDD|233064 TIGR00633, xth, exodeoxyribonuclease III (xth). All proteins in
this family for which functions are known are 5' AP
endonucleases that funciton in base excision repair and
the repair of abasic sites in DNA.This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 255
Score = 259 bits (663), Expect = 1e-86
Identities = 99/219 (45%), Positives = 130/219 (59%), Gaps = 7/219 (3%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSS 133
KI SWNV GLRA + K LD++K+E D+ CLQETK + Q P E+ Y ++ +
Sbjct: 2 KIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFE-ELGYHVFFHGA 60
Query: 134 PKAGYAGVGLYTKVKPNKVTYGLGTKNEHY--GRNCNSNIVNTFYIRKNVPNAGA-GLKT 190
GY+GV + +KV+P V YG G EH GR + + VPN G+ GL+
Sbjct: 61 KSKGYSGVAILSKVEPLDVRYGFGG-EEHDEEGRVITAEFDGFTVVNVYVPNGGSRGLER 119
Query: 191 LDKRLE-WDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSF 249
L+ +L+ WD LF + +LDA KPVI+ GD+NV+H IDL NP N +AGFT EER+ F
Sbjct: 120 LEYKLQFWDALFQYYEKELDAGKPVIICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWF 179
Query: 250 SSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
LL+ G D+FRH P GAYT+W Y S AR RN G
Sbjct: 180 DELLEAGLVDTFRHFNPDTEGAYTWWDYRSG-ARDRNRG 217
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III
(ExoIII)-like apurinic/apyrimidinic (AP) endonucleases.
The ExoIII family AP endonucleases belong to the large
EEP (exonuclease/endonuclease/phosphatase) superfamily
that contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, which is then
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, which have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a wide range of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two
functional AP endonucleases, for example, APE1/Ref-1 and
Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and
NExo in Neisseria meningitides, and exonuclease III
(ExoIII) and endonuclease IV (EndoIV) in Escherichia
coli. Usually, one of the two is the dominant AP
endonuclease, the other has weak AP endonuclease
activity, but exhibits strong 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, and 3'-phosphatase
activities. Class II AP endonucleases have been
classified into two families, designated ExoIII and
EndoIV, based on their homology to the Escherichia coli
enzymes. This family contains the ExoIII family; the
EndoIV family belongs to a different superfamily.
Length = 251
Score = 225 bits (575), Expect = 3e-73
Identities = 99/217 (45%), Positives = 133/217 (61%), Gaps = 5/217 (2%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSS 133
KI SWNV GLRA +KK L ++K+E DI CLQETK E +LP E++ Y +YW +
Sbjct: 1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEG-YHSYWSPA 59
Query: 134 PKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTLD 192
K GY+GV +K +P V+YG+G + + GR + + + I PN G GL+ LD
Sbjct: 60 RKKGYSGVATLSKEEPLDVSYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLD 119
Query: 193 KRLEWDKLFHEHLVKL-DAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFSS 251
+L + + F E L KL KPV++ GD NV+H+ IDLA P N ++AGFT EER F
Sbjct: 120 YKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFDK 179
Query: 252 LLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
LL G+ D+FRH +P+ GAYT+WSY AR RN G
Sbjct: 180 LLSLGYVDTFRHFHPE-PGAYTWWSYRGN-ARERNVG 214
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 215 bits (549), Expect = 3e-69
Identities = 84/228 (36%), Positives = 121/228 (53%), Gaps = 22/228 (9%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KIASWNV GLRA +KK LD++++E D+ CLQETK + Q P E + Y + +
Sbjct: 1 MKIASWNVNGLRARLKK-LLDWLEEEQPDVLCLQETKAQDEQFPREEL-EALGYHHVF-N 57
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKNEH--YGR--NC---NSNIVNTFYIRKNVPNAG 185
+ GY+GV + +K P+ V G + E GR ++N Y PN
Sbjct: 58 HGQKGYSGVAILSKKPPDDVRRGFPGEEEDDEEGRVIEAEFDGFRVIN-LY----FPNGS 112
Query: 186 A-GLKTLDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANP---TTNTRSAG 240
+ GL+ D +L + +L +L + KPV+L GD N++ + ID+ANP N ++G
Sbjct: 113 SIGLEKFDYKLRFLDALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSG 172
Query: 241 FTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F EER F LL+ GF D+FR +P YT+W Y + AR RN G
Sbjct: 173 FLPEERAWFRRLLNAGFVDTFRLFHP-EPEKYTWWDYRANAAR-RNRG 218
>gnl|CDD|197319 cd09085, Mth212-like_AP-endo, Methanothermobacter
thermautotrophicus Mth212-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes the thermophilic archaeon
Methanothermobacter thermautotrophicus Mth212and related
proteins. These are Escherichia coli exonuclease III
(ExoIII)-like AP endonucleases and they belong to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds. AP endonucleases participate in
the DNA base excision repair (BER) pathway. AP sites are
one of the most common lesions in cellular DNA. During
BER, the damaged DNA is first recognized by DNA
glycosylase. AP endonucleases then catalyze the
hydrolytic cleavage of the phosphodiester bond 5' to the
AP site, and this is followed by the coordinated actions
of DNA polymerase, deoxyribose phosphatase, and DNA
ligase. If left unrepaired, AP sites block DNA
replication, and have both mutagenic and cytotoxic
effects. AP endonucleases can carry out a variety of
excision and incision reactions on DNA, including 3'-5'
exonuclease, 3'-deoxyribose phosphodiesterase,
3'-phosphatase, and occasionally, nonspecific DNase
activities. Different AP endonuclease enzymes catalyze
the different reactions with different efficiences.
Mth212 is an AP endonuclease, and a DNA uridine
endonuclease (U-endo) that nicks double-stranded DNA at
the 5'-side of a 2'-d-uridine residue. After incision at
the 5'-side of a 2'-d-uridine residue by Mth212, DNA
polymerase B takes over the 3'-OH terminus and carries
out repair synthesis, generating a 5'-flap structure
that is resolved by a 5'-flap endonuclease. Finally, DNA
ligase seals the resulting nick. This U-endo activity
shares the same catalytic center as its AP-endo
activity, and is absent from other AP endonuclease
homologues.
Length = 252
Score = 205 bits (525), Expect = 1e-65
Identities = 91/223 (40%), Positives = 126/223 (56%), Gaps = 17/223 (7%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSS 133
KI SWNV GLRA KK LD+ K+E DI CLQETK QLP +++ Y +Y+ S+
Sbjct: 2 KIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNI-EGYHSYFNSA 60
Query: 134 PKAGYAGVGLYTKVKPNKVTYGLGTK---NEHYGR----NCNSNIVNTFYIRKNVPNAGA 186
+ GY+GV LY+K++P+ V GLG + NE GR + + + Y PN
Sbjct: 61 ERKGYSGVALYSKIEPDSVREGLGVEEFDNE--GRILIADFDDFTLFNIYF----PNGQM 114
Query: 187 GLKTLDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEE 245
+ LD +LE+ F E+L +L K VI+ GD N +HK IDLA P N + +GF EE
Sbjct: 115 SEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEE 174
Query: 246 RDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
R ++ G+ D+FR + G YT+WSY ++ AR RN G
Sbjct: 175 RAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTR-ARERNVG 215
>gnl|CDD|188032 TIGR00195, exoDNase_III, exodeoxyribonuclease III. The model
brings in reverse transcriptases at scores below 50,
model also contains eukaryotic apurinic/apyrimidinic
endonucleases which group in the same family [DNA
metabolism, DNA replication, recombination, and repair].
Length = 254
Score = 192 bits (491), Expect = 1e-60
Identities = 83/218 (38%), Positives = 116/218 (53%), Gaps = 9/218 (4%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSS 133
KI SWNV GLRA K GL ++K+ D+ CLQETK + Q P E K Y ++ S
Sbjct: 2 KIISWNVNGLRARPHK-GLAWLKENQPDVLCLQETKVQDEQFPLEPFHKE-GYHVFF--S 57
Query: 134 PKAGYAGVGLYTKVKPNKVTYGLGTKNE-HYGRNCNSNIVNTFYIRKNVPNAGA-GLKTL 191
+ GY+GV +++K +P V G G + E GR + + I PN + L
Sbjct: 58 GQKGYSGVAIFSKEEPISVRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRDDSEKL 117
Query: 192 DKRLEWDKLFHEHLVKL-DAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFS 250
+L+W + +L KL D +KPV++ GD+N++ IDL P N GF EER+
Sbjct: 118 PYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLD 177
Query: 251 SLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
LL+ G D+FR P GAY++W Y +K AR RN G
Sbjct: 178 RLLEAGLVDTFRKFNPD-EGAYSWWDYRTK-ARDRNRG 213
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional.
Length = 250
Score = 177 bits (449), Expect = 1e-54
Identities = 91/217 (41%), Positives = 131/217 (60%), Gaps = 6/217 (2%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
K+ SWNV GLRAC+ K +D+ DAD+FC+QE+K + Q +F Y +W
Sbjct: 1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQ----NTFEFKGYFDFWNC 56
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTK-NEHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL 191
+ K GY+GV +TK +P V+YG+ + ++ GR + + + PN+ L L
Sbjct: 57 AIKKGYSGVVTFTKKEPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRL 116
Query: 192 DKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFSS 251
R+ W+ F + L L+ +KPVI+ GDLNV+H IDL NP TN ++AGF+ EER FS
Sbjct: 117 SYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSE 176
Query: 252 LLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
LL+ GF D+FR+ YP + AYT+WSYM + AR +N G
Sbjct: 177 LLNAGFIDTFRYFYPNKEKAYTWWSYMQQ-ARDKNIG 212
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like
subfamily of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Neisseria
meningitides Nape and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity; for example, Neisseria meningitides Nape and
NExo. Nape, found in this subfamily, is the dominant AP
endonuclease. It exhibits strong AP endonuclease
activity, and also exhibits 3'-5'exonuclease and
3'-deoxyribose phosphodiesterase activities.
Length = 253
Score = 168 bits (427), Expect = 5e-51
Identities = 77/229 (33%), Positives = 120/229 (52%), Gaps = 28/229 (12%)
Query: 74 KIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE-YKTYWLS 132
++ S NV G+RA KK L+++ +DAD+ CLQE + E QL + PE Y Y+
Sbjct: 2 RVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDD--FFEPEGYNAYFFD 59
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKN----------V 181
+ K GYAGV +Y++ +P V YGLG + + GR YI + V
Sbjct: 60 AEKKGYAGVAIYSRTQPKAVIYGLGFEEFDDEGR----------YIEADFDNVSVASLYV 109
Query: 182 PNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKP-VILIGDLNVSHKPIDLANPTTNTRSAG 240
P+ +G + + ++ + F EHL +L ++ I+ GD N++H ID+ N N +++G
Sbjct: 110 PSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKNWKANQKNSG 169
Query: 241 FTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
F EER + + G+ D+FR L P G YT+WS + AR+ N G
Sbjct: 170 FLPEERAWLDQVFGELGYVDAFRELNPDE-GQYTWWSNRGQ-ARANNVG 216
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III
(ExoIII) and Neisseria meningitides NExo-like subfamily
of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Escherichia coli
ExoIII, Neisseria meningitides NExo,and related
proteins. These are ExoIII family AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiencies. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity. For example, Neisseria meningitides Nape and
NExo, and exonuclease III (ExoIII) and endonuclease IV
(EndoIV) in Escherichia coli. NExo and ExoIII are found
in this subfamily. NExo is the non-dominant AP
endonuclease. It exhibits strong 3'-5' exonuclease and
3'-deoxyribose phosphodiesterase activities. Escherichia
coli ExoIII is an active AP endonuclease, and in
addition, it exhibits double strand (ds)-specific 3'-5'
exonuclease, exonucleolytic RNase H,
3'-phosphomonoesterase and 3'-phosphodiesterase
activities, all catalyzed by a single active site. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes ExoIII and
endonuclease IV (EndoIV). This subfamily belongs to the
ExoIII family; the EndoIV family belongs to a different
superfamily.
Length = 254
Score = 142 bits (360), Expect = 5e-41
Identities = 72/232 (31%), Positives = 109/232 (46%), Gaps = 35/232 (15%)
Query: 73 FKIASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETKCHETQLPPEVKMKFPE------ 125
KIA+WNV +RA + E + D++K+ED D+ CLQETK + Q FP
Sbjct: 1 MKIATWNVNSIRA--RLEQVLDWLKEEDPDVLCLQETKVEDDQ--------FPADAFEAL 50
Query: 126 -YKTYWLSSPKAGYAGVGLYTKVKPNKVTYGL--GTKNEHY----GRNCNSNIVNTFYIR 178
Y Y GV + +++ V G ++ R ++N Y
Sbjct: 51 GYHVAVHGQK--AYNGVAILSRLPLEDVRTGFPGDPDDDQARLIAARVGGVRVIN-LY-- 105
Query: 179 KNVPNAGA-GLKTLDKRLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNT 236
VPN G G +L+W +L K L + P++L+GD N++ + ID+ +P
Sbjct: 106 --VPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDPKQLL 163
Query: 237 RSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
FT EER++ +LLD GF D+FR L+P +T+W Y + A RN G
Sbjct: 164 GKVLFTPEEREALRALLDLGFVDAFRALHP-DEKLFTWWDYRAG-AFERNRG 213
>gnl|CDD|197322 cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes human APE2, Saccharomyces cerevisiae
Apn2/Eth1, and related proteins. These are Escherichia
coli exonuclease III (ExoIII)-like AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity. For examples, Ape1 and Ape2 in humans, and
Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are
both found in this subfamily, and have the weaker AP
endonuclease activity. Ape2 shows strong 3'-5'
exonuclease and 3'-phosphodiesterase activities; it can
reduce the mutagenic consequences of attack by reactive
oxygen species by removing 3'-end adenine opposite from
8-oxoG, in addition to repairing 3'-damaged termini.
Apn2/Eth1 exhibits AP endonuclease activity, but has
30-40 fold more active 3'-phosphodiesterase and 3'-5'
exonuclease activities. Class II AP endonucleases have
been classified into two families, designated ExoIII and
EndoIV, based on their homology to the Escherichia coli
enzymes exonuclease III (ExoIII) and endonuclease IV
(EndoIV). This subfamily belongs to the ExoIII family;
the EndoIV family belongs to a different superfamily.
Length = 309
Score = 106 bits (267), Expect = 5e-27
Identities = 79/278 (28%), Positives = 110/278 (39%), Gaps = 69/278 (24%)
Query: 74 KIASWNVAGLRAC------VKKEGLDYIKKE-DADIFCLQETKCHETQLPPEVKMKFPE- 125
+I +WNV G+R K+ L DADI CLQETK +L E
Sbjct: 1 RIVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEP--SAIVEG 58
Query: 126 YKTYW-LSSPKAGYAGVGLYTK---VKPNKVTYGL----GTKNEHYGRNCNSNI-----V 172
Y +++ S + GY+GV Y + P GL + N+ + N +I +
Sbjct: 59 YDSFFSFSRGRKGYSGVATYCRDSAATPVAAEEGLTGVLSSPNQKNELSENDDIGCYGEM 118
Query: 173 NTFYIRK----------------------NV--PNAGAGLKTLDKRLEWDKLFHEHLVK- 207
F K NV P A + RLE+ F+ L +
Sbjct: 119 LEFTDSKELLELDSEGRCVLTDHGTFVLINVYCPRADPEKEE---RLEFKLDFYRLLEER 175
Query: 208 ----LDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDS---FSSLLDKG---- 256
L A + VIL+GD+NVSH+PID +P + G + E+ S LL
Sbjct: 176 VEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDNPSRQWLDQLLGDSGEGG 235
Query: 257 ------FTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
DSFR+ +P R GAYT W+ AR N G
Sbjct: 236 GSPGGLLIDSFRYFHPTRKGAYTCWN-TLTGARPTNYG 272
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily. This large superfamily includes the
catalytic domain (exonuclease/endonuclease/phosphatase
or EEP domain) of a diverse set of proteins including
the ExoIII family of apurinic/apyrimidinic (AP)
endonucleases, inositol polyphosphate 5-phosphatases
(INPP5), neutral sphingomyelinases (nSMases),
deadenylases (such as the vertebrate circadian-clock
regulated nocturnin), bacterial cytolethal distending
toxin B (CdtB), deoxyribonuclease 1 (DNase1), the
endonuclease domain of the non-LTR retrotransposon
LINE-1, and related domains. These diverse enzymes share
a common catalytic mechanism of cleaving phosphodiester
bonds; their substrates range from nucleic acids to
phospholipids and perhaps proteins.
Length = 241
Score = 79.4 bits (196), Expect = 2e-17
Identities = 56/221 (25%), Positives = 84/221 (38%), Gaps = 32/221 (14%)
Query: 75 IASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWL-S 132
+AS+NV GL A + G+ ++++ D DI CLQE K + ++ Y Y
Sbjct: 1 VASYNVNGLNAATRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGP 60
Query: 133 SPKAGYAGVGLYTK---VKPNKVTYGLGTKNEHYGRNCNSNIVNTFYIRKN---VPNA-- 184
S K GY GV + +K K + + + R +V F + V NA
Sbjct: 61 SRKEGYEGVAILSKTPKFKIVEKHQYKFGEGDSGERRA---VVVKFDVHDKELCVVNAHL 117
Query: 185 GAGLKTLDKRLEWDKLFHEHL--VKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFT 242
AG D R K E L ++ PV++ GD NV +D NP
Sbjct: 118 QAGGTRADVRDAQLKEVLEFLKRLRQPNSAPVVICGDFNVRPSEVDSENP---------- 167
Query: 243 IEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTAR 283
SS+L + + AYT+ +YM
Sbjct: 168 -------SSMLRLFVALNLVDSFETLPHAYTFDTYMHNVKS 201
>gnl|CDD|236970 PRK11756, PRK11756, exonuclease III; Provisional.
Length = 268
Score = 78.4 bits (194), Expect = 6e-17
Identities = 65/230 (28%), Positives = 101/230 (43%), Gaps = 36/230 (15%)
Query: 74 KIASWNVAGLRACVKK-EGLDYIKKEDADIFCLQETKCHETQLPPEV--KMKFPEYKTYW 130
K S+N+ GLRA + E + I+K D+ LQETK H+ P E + Y ++
Sbjct: 2 KFVSFNINGLRARPHQLEAI--IEKHQPDVIGLQETKVHDEMFPLEEVEALG---YHVFY 56
Query: 131 LSSPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGR----------NCNSNIVNTFYIRKN 180
K Y GV L +K P V G T +E R N N ++N ++
Sbjct: 57 HGQ-KGHY-GVALLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTPNGNLTVINGYF---- 110
Query: 181 VP---NAGAGLKTLDKRLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTN- 235
P + K KR + L + +L L + P++++GD+N+S +D+ N
Sbjct: 111 -PQGESRDHPTKFPAKRQFYQDLQN-YLETELSPDNPLLIMGDMNISPTDLDIGIGEENR 168
Query: 236 -----TRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSK 280
T F EER+ L+D G D+FR L P ++++ Y SK
Sbjct: 169 KRWLRTGKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSK 218
>gnl|CDD|197310 cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR
retrotransposon LINE-1 (L1), and related domains. This
family contains the endonuclease domain (L1-EN) of the
non-LTR retrotransposon LINE-1 (L1), and related
domains, including the endonuclease of Xenopus laevis
Tx1. These retrotranspons belong to the subtype 2,
L1-clade. LINES can be classified into two subtypes.
Subtype 2 has two ORFs: the second (ORF2) encodes a
modular protein consisting of an N-terminal
apurine/apyrimidine endonuclease domain (EN), a central
reverse transcriptase, and a zinc-finger-like domain at
the C-terminus. LINE-1/L1 elements (full length and
truncated) comprise about 17% of the human genome. This
endonuclease nicks the genomic DNA at the consensus
target sequence 5'TTTT-AA3' producing a ribose
3'-hydroxyl end as a primer for reverse transcription of
associated template RNA. This subgroup also includes the
endonuclease of Xenopus laevis Tx1, another member of
the L1-clade. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 236
Score = 62.8 bits (153), Expect = 1e-11
Identities = 52/219 (23%), Positives = 79/219 (36%), Gaps = 25/219 (11%)
Query: 75 IASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETKC-HETQLPPEVKMKFPEYKTYWLS 132
I + NV GLR+ K+ L + +K++ DI LQET E +L + + +
Sbjct: 1 IGTLNVRGLRSPGKRAQLLEELKRKKLDILGLQETHWTGEGELKKKRE----GGTILYSG 56
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGR----NCNSNIVNTFYIRKNV--PNAGA 186
S GV + + L GR I NV P A
Sbjct: 57 SDSGKSRGVAI--LLSKTAANKLLEYTKVVSGRIIMVRFKIKGKRLTII--NVYAPTARD 112
Query: 187 GLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEER 246
+K +D+L + L K+ +I+ GD N P D + R+ ER
Sbjct: 113 E---EEKEEFYDQL-QDVLDKVPRHDTLIIGGDFNAVLGPKDDGRKGLDKRNEN---GER 165
Query: 247 DSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSR 285
+ + + D +R PK YT W +RSR
Sbjct: 166 ALSALIEEHDLVDVWRENNPKTRE-YT-WRSPDHGSRSR 202
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
family. This large family of proteins includes
magnesium dependent endonucleases and a large number of
phosphatases involved in intracellular signalling. This
family includes: AP endonuclease proteins EC:4.2.99.18,
DNase I proteins EC:3.1.21.1, Synaptojanin an
inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
Sphingomyelinase EC:3.1.4.12 and Nocturnin.
Length = 143
Score = 46.5 bits (110), Expect = 2e-06
Identities = 27/156 (17%), Positives = 41/156 (26%), Gaps = 50/156 (32%)
Query: 76 ASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLSSPK 135
+WNV GL D ++ +D D+ LQ
Sbjct: 1 LTWNVNGLGNG-LAALADLLRAQDPDVLALQ----------------------------- 30
Query: 136 AGYAGVGLYTKVKPNKVTYGLGTKNEHYGRNCNSNIVNTFYIRKNV----------PNAG 185
+ ++ + T+ G I K G
Sbjct: 31 ------AILSRYPLEEKIVLDFTELGAGGIAVLRLSSGAHGIVKVSGQTLTLVNVHLPPG 84
Query: 186 AGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLN 221
GL+ D+R L L +PV+L GD N
Sbjct: 85 NGLREADERALLQLLSDL----LPDLRPVVLAGDFN 116
>gnl|CDD|197318 cd09084, EEP-2, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily; uncharacterized family 2. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of a
diverse set of proteins including the ExoIII family of
apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain of
the non-LTR retrotransposon LINE-1, and related domains.
These diverse enzymes share a common catalytic mechanism
of cleaving phosphodiester bonds; their substrates range
from nucleic acids to phospholipids and perhaps,
proteins.
Length = 246
Score = 46.1 bits (110), Expect = 7e-06
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 75 IASWNVAGLRAC----VKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYW 130
+ S+NV + LD+IKK+D DI CLQE E ++++ Y Y+
Sbjct: 1 VMSYNVRSFNRYKWKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYP-YY 59
Query: 131 LSSPKAGYAGVGL 143
K+ G GL
Sbjct: 60 YVVYKSDSGGTGL 72
>gnl|CDD|197314 cd09080, TDP2, Phosphodiesterase domain of human TDP2, a 5'-tyrosyl
DNA phosphodiesterase, and related domains. Human TDP2,
also known as TTRAP (TRAF/TNFR-associated factors, and
tumor necrosis factor receptor/TNFR-associated protein),
is a 5'-tyrosyl DNA phosphodiesterase. It is required
for the efficient repair of topoisomerase II-induced DNA
double strand breaks. The topoisomerase is covalently
linked by a phosphotyrosyl bond to the 5'-terminus of
the break. TDP2 cleaves the DNA 5'-phosphodiester bond
and restores 5'-phosphate termini, needed for subsequent
DNA ligation, and hence repair of the break. TDP2 and
3'-tyrosyl DNA phosphodiesterase (TDP1) are
complementary activities; together, they allow cells to
remove trapped topoisomerase from both 3'- and 5'-DNA
termini. TTRAP has been reported as being involved in
apoptosis, embryonic development, and transcriptional
regulation, and it may inhibit the activation of nuclear
factor-kB. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 248
Score = 37.7 bits (88), Expect = 0.004
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 73 FKIASWNVAGLRA-CVKK---EGLDYIKKEDADIFCLQE 107
K+ +WNV L + + L +++ D D+ LQE
Sbjct: 1 LKVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQE 39
>gnl|CDD|233198 TIGR00938, thrB_alt, homoserine kinase, Neisseria type. Homoserine
kinase is required in the biosynthesis of threonine from
aspartate.The member of this family from Pseudomonas
aeruginosa was shown by direct assay and complementation
to act specifically as a homoserine kinase [Amino acid
biosynthesis, Aspartate family].
Length = 307
Score = 32.1 bits (73), Expect = 0.28
Identities = 10/65 (15%), Positives = 21/65 (32%), Gaps = 9/65 (13%)
Query: 42 NKATGPMNEKLSLNKIDYSCNKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDAD 101
+ G + + L + N+KN L E +W++ A E ++
Sbjct: 118 CRPVGEVLAWMHLAGAHFPENRKNSLRLE------AWHIL---AEKCFEAAPQLEAHMGA 168
Query: 102 IFCLQ 106
+
Sbjct: 169 ELDKE 173
>gnl|CDD|169215 PRK08091, PRK08091, ribulose-phosphate 3-epimerase; Validated.
Length = 228
Score = 29.8 bits (67), Expect = 1.2
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 173 NTFYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANP 232
+ F + K AGA + TL ++E + L +K +LIG PI L P
Sbjct: 79 DQFEVAKACVAAGADIVTL--QVEQTHDLALTIEWLAKQKTTVLIGLCLCPETPISLLEP 136
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 30.3 bits (69), Expect = 1.4
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 2 GPKKAAAKVVDKEEKSSKKRKSEVEDSDANTKKTKSGSVENKATGPMNEK 51
G KKA K+ EK+ KKR+ E ++ K E + E+
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453
>gnl|CDD|235454 PRK05421, PRK05421, hypothetical protein; Provisional.
Length = 263
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 67 LGEEPNFKIASWNVA-GLRACVKKEGLDYIKKEDADIFCLQE 107
L E ++ WN+ RA L + K DAD+ LQE
Sbjct: 38 LSTEERLRLLVWNIYKQQRAGWLSV-LKNLGK-DADLVLLQE 77
>gnl|CDD|238886 cd01903, Ntn_AC_NAAA, AC_NAAA This conserved domain includes two
closely related proteins, acid ceramidase (AC, also
known as N-acylsphingosine amidohydrolase), and
N-acylethanolamine-hydrolyzing acid amidase (NAAA). AC
catalyzes the hydrolysis of ceramide to sphingosine and
fatty acid. Ceramide is required for the biosynthesis of
most sphingolipids and plays an important role in many
signal transduction pathways by inducing apoptosis
and/or arresting cell growth. An inherited deficiency of
AC activity leads to the lysosomal storage disorder
known as Farber disease. AC is considered a "rheostat"
important for maintaining the proper intracellular
levels of these lipids since hydrolysis of ceramide is
the only source of sphingosine in cells. NAAA is a
eukaryotic glycoprotein that hydrolyzes bioactive
N-acylethanolamines, including anandamide (an
endocannabinoid) and N-palmitoylethanolamine (an
anti-inflammatory and neuroprotective substance), to
fatty acids and ethanolamine at acidic pH. NAAA shows
structural and functional similarity to acid ceramidase,
but lacks the ceramide-hydrolyzing activity of AC.
Length = 231
Score = 27.6 bits (62), Expect = 7.0
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 136 AGYAGVGLYTKVKPNKVTYGLGTKNEHYGRNCNSNIVNTFYIRKNVP 182
AGY VGL T KP K + T NE + + N + + +P
Sbjct: 59 AGY--VGLLTGQKPGKFSL---TINERFSLDGGYNGILALLKKDGIP 100
>gnl|CDD|197331 cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4
and related domains. This subfamily contains the
C-terminal catalytic domain of the deadenylases,
Saccharomyces cerevisiae Ccr4p and two vertebrate
homologs (CCR4a and CCR4b), and related domains. CCR4
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1 (called Pop2 in
yeast), is a DEDD-type protein and does not belong in
this superfamily. Saccharomyces cerevisiae CCR4 (or
Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It
is the catalytic subunit of the yeast mRNA deadenylase
(Ccr4p/Pop2p/Not complex). This complex participates in
various ways in mRNA metabolism, including transcription
initiation and elongation, and mRNA degradation. Ccr4p
degrades both poly(A) and single-stranded DNA. There are
two vertebrate homologs of Ccr4p, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b (also called CNOT6-like or CNOT6L), which
independently associate with other components to form
distinct CCR4-NOT multisubunit complexes. The nuclease
domain of CNOT6 and CNOT6L exhibits Mg2+-dependent
deadenylase activity, with specificity for poly (A) RNA
as substrate. CCR4a is a component of P-bodies and is
necessary for foci formation. CCR4b regulates p27/Kip1
mRNA levels, thereby influencing cell cycle progression.
They both contribute to the prevention of cell death by
regulating insulin-like growth factor-binding protein 5.
Length = 329
Score = 27.7 bits (62), Expect = 7.8
Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 20/55 (36%)
Query: 89 KEGLDYIKKEDADIFCLQE--TKCHETQLPPEVKMKFPEYKTYWLSSPKAGYAGV 141
KE L Y +ADI CLQE T +E PE+K + GY GV
Sbjct: 36 KEILSY----NADILCLQEVETDQYEDFFLPELK--------------QHGYDGV 72
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 27.8 bits (62), Expect = 7.9
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 229 LANPTTNTRSAGFTIEERDSFSSLLDK 255
T+ GFT E+ F++LLDK
Sbjct: 1 SRTQNTDADDIGFTHED---FAALLDK 24
>gnl|CDD|197317 cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain;
uncharacterized family 1. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of a
diverse set of proteins including the ExoIII family of
apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain of
the non-LTR retrotransposon LINE-1, and related domains.
These diverse enzymes share a common catalytic mechanism
of cleaving phosphodiester bonds. Their substrates range
from nucleic acids to phospholipids and perhaps,
proteins.
Length = 252
Score = 27.2 bits (61), Expect = 9.5
Identities = 7/13 (53%), Positives = 7/13 (53%)
Query: 95 IKKEDADIFCLQE 107
IK D DI QE
Sbjct: 30 IKFYDPDIIGTQE 42
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.312 0.130 0.388
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,353,422
Number of extensions: 1324186
Number of successful extensions: 987
Number of sequences better than 10.0: 1
Number of HSP's gapped: 940
Number of HSP's successfully gapped: 42
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (26.6 bits)