RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6001
(327 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 = 341 bits (878), Expect = e-118
Identities = 129/255 (50%), Positives = 175/255 (68%), Gaps = 5/255 (1%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+ +WNVNGLRA +KK ++Y+ +E+PDI+ LQ+ + QE +VP+ ++ L YH +W
Sbjct: 2 KIISWNVNGLRALLKKG-LLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA 60
Query: 133 SD-KGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITVYVPNSGIKLKAI 190
++ KG G +L+K+KPL+V YGI +Q GRVITA+F+ F + YVPNSG L+ +
Sbjct: 61 AEKKGYSGTAILSKKKPLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERL 120
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
D R WD F Y++ +L S +I GDLNV + IDLANP N K+AG+T EER +F
Sbjct: 121 DRRKEWDVDFRAYLK-KLDSKKPVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFT 179
Query: 251 ELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
ELL+ G VD FRHL+PD+EGAYT+WS+R AR N GWRLDY LVSE+L + + D IR
Sbjct: 180 ELLEAGFVDTFRHLHPDKEGAYTFWSYRGN-ARAKNVGWRLDYFLVSERLKDRVVDSFIR 238
Query: 311 SDVQGSTHCPVVLRL 325
SD+ GS HCP+ L L
Sbjct: 239 SDIMGSDHCPIGLEL 253
>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 = 276 bits (709), Expect = 6e-93
Identities = 116/257 (45%), Positives = 168/257 (65%), Gaps = 6/257 (2%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ +WNVNGLRA + K ++++ EE PD++ LQ+ + +++ P + L YH+F+
Sbjct: 1 MKIISWNVNGLRARLHKLF-LDWLKEEQPDVLCLQETKVADEQFPAELFEELG-YHVFFH 58
Query: 132 GSD-KGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITVYVPNSG-IKLK 188
G+ KG GV +L+K +PL V+YG G ++ GRVITA+F FT + VYVPN G L+
Sbjct: 59 GAKSKGYSGVAILSKVEPLDVRYGFGGEEHDEEGRVITAEFDGFTVVNVYVPNGGSRGLE 118
Query: 189 AIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRN 248
+++++ + + Y + EL + +II GD+NV IDL NP +N AG+T EER
Sbjct: 119 RLEYKLQFWDALFQYYEKELDAGKPVIICGDMNVAHTEIDLGNPKENKGNAGFTPEEREW 178
Query: 249 FRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCI 308
F ELL+ GLVD FRH PD EGAYT+W +R+ AR N+GWR+DY LVSE LA + D
Sbjct: 179 FDELLEAGLVDTFRHFNPDTEGAYTWWDYRSG-ARDRNRGWRIDYFLVSEPLAERVVDSY 237
Query: 309 IRSDVQGSTHCPVVLRL 325
I S+++GS HCP+VL L
Sbjct: 238 IDSEIRGSDHCPIVLEL 254
>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 = 271 bits (695), Expect = 6e-91
Identities = 119/255 (46%), Positives = 162/255 (63%), Gaps = 6/255 (2%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+ +WNVNGLRA +KK ++++ EE PDI+ LQ+ + ED++PE + YH +W
Sbjct: 1 KIISWNVNGLRARLKKGV-LKWLKEEKPDILCLQETKADEDKLPEELQHVEG-YHSYWSP 58
Query: 133 SD-KGQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYVPNSGIKLKAI 190
+ KG GV L+KE+PL V YGI G + GRVITA+F F I VY PN G L+ +
Sbjct: 59 ARKKGYSGVATLSKEEPLDVSYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERL 118
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
D+++ + + F ++++ + ++I GD NV + IDLA P KN K AG+T EER F
Sbjct: 119 DYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFD 178
Query: 251 ELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
+LL G VD FRH +P E GAYT+WS+R AR N GWR+DY LVSE+LA +KD I
Sbjct: 179 KLLSLGYVDTFRHFHP-EPGAYTWWSYRGN-ARERNVGWRIDYFLVSEELAEKVKDSGIL 236
Query: 311 SDVQGSTHCPVVLRL 325
S V+GS H PV L L
Sbjct: 237 SKVKGSDHAPVTLEL 251
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 256 bits (656), Expect = 6e-85
Identities = 102/265 (38%), Positives = 156/265 (58%), Gaps = 15/265 (5%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+++WNVNGLRA +KK ++++ EE PD++ LQ+ + Q+++ P ++L YH +
Sbjct: 2 KIASWNVNGLRARLKKL--LDWLEEEQPDVLCLQETKAQDEQFPREELEALG-YHHVFNH 58
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGVSNQR--GRVITAKFKRFTFITVYVPNSG-IKLKA 189
KG GV +L+K+ P V+ G PG GRVI A+F F I +Y PN I L+
Sbjct: 59 GQKGYSGVAILSKKPPDDVRRGFPGEEEDDEEGRVIEAEFDGFRVINLYFPNGSSIGLEK 118
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDK---NVKTAGYTVEER 246
D+++ + +Y++ L+ +++ GD N+ + ID+ANP K N +G+ EER
Sbjct: 119 FDYKLRFLDALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEER 178
Query: 247 RNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKD 306
FR LL+ G VD FR +P+ E YT+W +R +AR N+GWR+DY LVS LA+ +KD
Sbjct: 179 AWFRRLLNAGFVDTFRLFHPEPEK-YTWWDYRANAAR-RNRGWRIDYILVSPALADRLKD 236
Query: 307 CIIRSDVQG----STHCPVVLRLSL 327
I +V+G S H PV + L L
Sbjct: 237 AGIDREVRGWEKPSDHAPVWVELDL 261
>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 = 244 bits (625), Expect = 2e-80
Identities = 99/259 (38%), Positives = 147/259 (56%), Gaps = 12/259 (4%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K+ +WNVNGLRA K + ++ E PD++ LQ+ + Q+++ P YH+F+ G
Sbjct: 2 KIISWNVNGLRARPHK--GLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEG-YHVFFSG 58
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITVYVPN-SGIKLKAI 190
KG GV + +KE+P++V+ G + GR+I A+F F I Y PN S + +
Sbjct: 59 Q-KGYSGVAIFSKEEPISVRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRDDSEKL 117
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
+++ W + +Y++ + + ++I GD+N+ IDL PD+N G+ EER
Sbjct: 118 PYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLD 177
Query: 251 ELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
LL+ GLVD FR PD EGAY++W +R K AR N+GWR+DY LVSE L DC I
Sbjct: 178 RLLEAGLVDTFRKFNPD-EGAYSWWDYRTK-ARDRNRGWRIDYFLVSEPLKERCVDCGID 235
Query: 311 SDVQG----STHCPVVLRL 325
D++G S HCPVVL
Sbjct: 236 YDIRGMEKPSDHCPVVLEF 254
>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 = 239 bits (611), Expect = 3e-78
Identities = 99/257 (38%), Positives = 151/257 (58%), Gaps = 8/257 (3%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ +WNVNGLRA KK +++ EE PDI+ LQ+ + Q +++PE +++ YH ++
Sbjct: 1 MKIISWNVNGLRAVHKKGF-LDWFKEEKPDILCLQETKAQPEQLPEDL-RNIEGYHSYFN 58
Query: 132 GSD-KGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLK 188
++ KG GV L +K +P +V+ G+ GV + GR++ A F FT +Y PN + +
Sbjct: 59 SAERKGYSGVALYSKIEPDSVREGL-GVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEE 117
Query: 189 AIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRN 248
+D+++ + F +Y+ S N+II GD N + IDLA P +N K +G+ EER
Sbjct: 118 RLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEERAW 177
Query: 249 FRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCI 308
+ ++ G VD FR E G YT+WS+R + AR N GWR+DY V+E+ +KD
Sbjct: 178 MDKFIENGYVDTFRMFNK-EPGQYTWWSYRTR-ARERNVGWRIDYFFVNEEFKPKVKDAG 235
Query: 309 IRSDVQGSTHCPVVLRL 325
I DV GS HCPV L L
Sbjct: 236 ILPDVMGSDHCPVSLEL 252
>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 = 205 bits (523), Expect = 7e-65
Identities = 88/259 (33%), Positives = 144/259 (55%), Gaps = 12/259 (4%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
K++TWNVN +RA + ++++ EE+PD++ LQ+ + ++D+ P ++L YH+ G
Sbjct: 2 KIATWNVNSIRA--RLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALG-YHVAVHG 58
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPG-VSNQRGRVITAKFKRFTFITVYVPNSG-IKLKAI 190
K GV +L++ V+ G PG + + R+I A+ I +YVPN G I
Sbjct: 59 Q-KAYNGVAILSRLPLEDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKF 117
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
+++ W Y+Q L+ + +++ GD N+ + ID+ +P + + +T EER R
Sbjct: 118 AYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALR 177
Query: 251 ELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
LLD G VDAFR L+PDE+ +T+W +R A N+G R+D+ L S LA+ +KD I
Sbjct: 178 ALLDLGFVDAFRALHPDEKL-FTWWDYRAG-AFERNRGLRIDHILASPALADRLKDVGID 235
Query: 311 SDVQG----STHCPVVLRL 325
+ +G S H PVV L
Sbjct: 236 REPRGWEKPSDHAPVVAEL 254
>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 = 204 bits (521), Expect = 1e-64
Identities = 83/254 (32%), Positives = 137/254 (53%), Gaps = 7/254 (2%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIG 132
+V + NVNG+RA KK +E++ ++ D++ LQ++R QE+++ + F + + F+
Sbjct: 2 RVISVNVNGIRAAAKK-GFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDA 60
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYVPNSGIKLK-AI 190
KG GV + ++ +P V YG+ + GR I A F + ++YVP SG
Sbjct: 61 EKKGYAGVAIYSRTQPKAVIYGLGFEEFDDEGRYIEADFDNVSVASLYVP-SGSSGDERQ 119
Query: 191 DFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFR 250
+ +M + F ++++ R I+ GD N+ ID+ N N K +G+ EER
Sbjct: 120 EAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLD 179
Query: 251 ELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
++ G VDAFR L PD EG YT+WS R + AR NN GWR+DY + + LA+ + I
Sbjct: 180 QVFGELGYVDAFRELNPD-EGQYTWWSNRGQ-ARANNVGWRIDYQIATPGLASKVVSAWI 237
Query: 310 RSDVQGSTHCPVVL 323
+ + S H P+++
Sbjct: 238 YREERFSDHAPLIV 251
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional.
Length = 250
Score = 194 bits (495), Expect = 5e-61
Identities = 105/256 (41%), Positives = 152/256 (59%), Gaps = 9/256 (3%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFW- 130
+K+ +WNVNGLRAC+ K +++ + D+ +Q+ + Q+++ F+ Y FW
Sbjct: 1 MKLISWNVNGLRACMTK-GFMDFFNSVDADVFCIQESKMQQEQNTFEFKG----YFDFWN 55
Query: 131 IGSDKGQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
KG GV TK++PL+V YGI ++ GRVIT +F+ F + VY PNS L
Sbjct: 56 CAIKKGYSGVVTFTKKEPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSR 115
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ +RM W+ F ++++ L +I+ GDLNV IDL NP N K AG++ EER F
Sbjct: 116 LSYRMSWEVEFKKFLKA-LELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKF 174
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
ELL+ G +D FR+ YP++E AYT+WS+ + AR N GWR+DY L S L +KD +I
Sbjct: 175 SELLNAGFIDTFRYFYPNKEKAYTWWSYMQQ-ARDKNIGWRIDYFLCSNPLKTRLKDALI 233
Query: 310 RSDVQGSTHCPVVLRL 325
D+ GS HCPV L L
Sbjct: 234 YKDILGSDHCPVGLEL 249
>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 = 144 bits (366), Expect = 6e-41
Identities = 83/315 (26%), Positives = 130/315 (41%), Gaps = 68/315 (21%)
Query: 73 KVSTWNVNGLRAC-----VKKNACVEYILEE-NPDIMALQQIRCQEDEVPESFRKSLSHY 126
++ TWNVNG+R K ++ L+ + DI+ LQ+ + DE+ E + Y
Sbjct: 1 RIVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEP-SAIVEGY 59
Query: 127 HMFW--IGSDKGQGGVGLLTK---EKPLTVKYGIPGV-----------SNQR-------- 162
F+ KG GV + P+ + G+ GV N
Sbjct: 60 DSFFSFSRGRKGYSGVATYCRDSAATPVAAEEGLTGVLSSPNQKNELSENDDIGCYGEML 119
Query: 163 --------------GRVITAKFKRFTFITVYVP-NSGIKLKAIDFRMIWDQHFYDYIQSE 207
GR + F I VY P K + ++F++ FY ++
Sbjct: 120 EFTDSKELLELDSEGRCVLTDHGTFVLINVYCPRADPEKEERLEFKL----DFYRLLEER 175
Query: 208 ----LRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEE---RRNFRELL------- 253
L++ +I+ GD+NV + ID +PD + G + E+ R+ +LL
Sbjct: 176 VEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDNPSRQWLDQLLGDSGEGG 235
Query: 254 --DTG-LVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
G L+D+FR+ +P +GAYT W+ AR N G R+DY L L +K I
Sbjct: 236 GSPGGLLIDSFRYFHPTRKGAYTCWNTL-TGARPTNYGTRIDYILADRGLLPWVKAADIL 294
Query: 311 SDVQGSTHCPVVLRL 325
+V+GS HCPV L
Sbjct: 295 PEVEGSDHCPVYADL 309
>gnl|CDD|236970 PRK11756, PRK11756, exonuclease III; Provisional.
Length = 268
Score = 118 bits (297), Expect = 3e-31
Identities = 82/270 (30%), Positives = 137/270 (50%), Gaps = 30/270 (11%)
Query: 73 KVSTWNVNGLRACVKKNACVEYILEE-NPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
K ++N+NGLRA + +E I+E+ PD++ LQ+ + ++ P ++L YH+F+
Sbjct: 2 KFVSFNINGLRARPHQ---LEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALG-YHVFYH 57
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVSN--QRGRVITAKFK----RFTFITVYVPNSGI 185
G KG GV LL+K+ P+ V+ G P QR R+I A T I Y P
Sbjct: 58 GQ-KGHYGVALLSKQTPIAVRKGFPTDDEEAQR-RIIMATIPTPNGNLTVINGYFPQGES 115
Query: 186 KLKAIDFRMIWDQHFY----DYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVK---- 237
+ F + FY +Y+++EL ++ ++I GD+N+ +D+ ++N K
Sbjct: 116 RDHPTKFPA--KRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLDIGIGEENRKRWLR 173
Query: 238 --TAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHL 295
+ EER L+D GLVD FR L PD ++++ +R+K +N+G R+D L
Sbjct: 174 TGKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGF-DDNRGLRIDLIL 232
Query: 296 VSEQLANNIKDCIIRSDVQG----STHCPV 321
++ LA + I D++G S H P+
Sbjct: 233 ATQPLAERCVETGIDYDIRGMEKPSDHAPI 262
>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 = 105 bits (264), Expect = 7e-27
Identities = 56/267 (20%), Positives = 105/267 (39%), Gaps = 41/267 (15%)
Query: 74 VSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIGS 133
V+++NVNGL A + + ++ E +PDI+ LQ+++ + + YH + G
Sbjct: 1 VASYNVNGLNAATRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGP 60
Query: 134 D--KGQGGVGLLTK---EKPLTVKYGIPGVSNQR-GRVITAKFKR----FTFITVYVPNS 183
+G GV +L+K K + G + R + KF + ++
Sbjct: 61 SRKEGYEGVAILSKTPKFKIVEKHQYKFGEGDSGERRAVVVKFDVHDKELCVVNAHLQAG 120
Query: 184 GIKLKAIDFRMIWDQHFYDYIQSELR-SNSNIIISGDLNVCLQSIDLANPDKNVKTAGYT 242
G + R + ++++ + +++ ++I GD NV +D NP
Sbjct: 121 GTRADV---RDAQLKEVLEFLKRLRQPNSAPVVICGDFNVRPSEVDSENP---------- 167
Query: 243 VEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLAN 302
+L + + AYT+ ++ +N RLDY VS+ L
Sbjct: 168 -------SSMLRLFVALNLVDSFETLPHAYTFDTYM------HNVKSRLDYIFVSKSLLP 214
Query: 303 NIKDCIIRSDVQ----GSTHCPVVLRL 325
++K I SD S H P+ + L
Sbjct: 215 SVKSSKILSDAARARIPSDHYPIEVTL 241
>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 = 103 bits (259), Expect = 3e-26
Identities = 65/260 (25%), Positives = 99/260 (38%), Gaps = 32/260 (12%)
Query: 74 VSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFW-IG 132
+ T NV GLR+ K+ +E + + DI+ LQ+ + +K + +
Sbjct: 1 IGTLNVRGLRSPGKRAQLLEELKRKKLDILGLQETHWTGE---GELKKKREGGTILYSGS 57
Query: 133 SDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFK----RFTFITVYVPNSGIKLK 188
GV +L + V + GR+I +FK R T I VY P +
Sbjct: 58 DSGKSRGVAILLSKTAANKLLEYTKVVS--GRIIMVRFKIKGKRLTIINVYAPTAR---- 111
Query: 189 AIDFRMIWDQHFYDYIQSELRSNS---NIIISGDLNVCLQSIDLANPDKNVKTAGYTVEE 245
+ + FYD +Q L +II GD N L D + + E
Sbjct: 112 DEEEKE----EFYDQLQDVLDKVPRHDTLIIGGDFNAVLGPKDDGRKGLDKRN---ENGE 164
Query: 246 RRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIK 305
R + + LVD +R P YT+ S + S R+D LVS++L +K
Sbjct: 165 RALSALIEEHDLVDVWRENNPKTRE-YTWRSPDHGSRS------RIDRILVSKRLRVKVK 217
Query: 306 DCIIRSDVQGSTHCPVVLRL 325
I GS H V L+L
Sbjct: 218 KTKITPGA-GSDHRLVTLKL 236
>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 = 57.0 bits (138), Expect = 2e-09
Identities = 56/244 (22%), Positives = 86/244 (35%), Gaps = 62/244 (25%)
Query: 73 KVSTWNVNGLRA-CVKK--NACVEYILEENPDIMALQQIRCQEDEVPESFRKSL------ 123
KV TWNV+ L + + A ++ + E +PD++ LQ EV F L
Sbjct: 2 KVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQ-------EVTPPFLAYLLSQPWV 54
Query: 124 -SHYHMFWIGSDK--GQGGVGLLTKEKPLTVKYGIPGVSNQRGR------VITAKFKRFT 174
+Y+ GV +L+K K L V+ +P S + GR + +
Sbjct: 55 RKNYYFSEGPPSPAVDPYGVLILSK-KSLVVRR-VPFTSTRMGRNLLAAEINLGSGEPLR 112
Query: 175 FITV----YVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLA 230
T +S R + ++ +N+I+ GD N+
Sbjct: 113 LATTHLESLKSHSSE-------RTAQLEEIAKKLKKPP-GAANVILGGDFNLR------- 157
Query: 231 NPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGW- 289
DK T G L G VDA+ L P E YT+ + +N R G
Sbjct: 158 --DKEDDTGG------------LPNGFVDAWEELGPPGEPGYTWDTQKNPMLRKGEAGPR 203
Query: 290 -RLD 292
R D
Sbjct: 204 KRFD 207
>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 = 53.4 bits (128), Expect = 7e-09
Identities = 29/146 (19%), Positives = 52/146 (35%), Gaps = 31/146 (21%)
Query: 76 TWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIGSDK 135
TWNVNGL A + + ++PD++ALQ I R L + ++
Sbjct: 2 TWNVNGLGN--GLAALADLLRAQDPDVLALQAIL---------SRYPLEEKIVL-DFTEL 49
Query: 136 GQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKAIDFRMI 195
G GG+ +L + G + T + V++P R
Sbjct: 50 GAGGIAVLRLSSGAHGIVKVSG-------------QTLTLVNVHLPPGN------GLREA 90
Query: 196 WDQHFYDYIQSELRSNSNIIISGDLN 221
++ + L ++++GD N
Sbjct: 91 DERALLQLLSDLLPDLRPVVLAGDFN 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 = 49.2 bits (118), Expect = 6e-07
Identities = 52/284 (18%), Positives = 92/284 (32%), Gaps = 70/284 (24%)
Query: 74 VSTWNVNGLRACVKKNAC---VEYILEENPDIMALQQIRCQEDEVPESFRKSLSHY--HM 128
V ++NV K+ +++I +++PDI+ LQ+ E + + R L Y +
Sbjct: 1 VMSYNVRSFNRYKWKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYPYYY 60
Query: 129 FWIGSDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRV---ITAKFKRFTFITVYVPNSGI 185
SD G G+ + +K P+ I + + I V++ + I
Sbjct: 61 VVYKSDSGGTGLAIFSK-YPILNSGSIDFPNTNNNAIFADIRVGGDTIRVYNVHLESFRI 119
Query: 186 KLKAIDFRMIWD------QHFYDYI---------QSEL------RSNSNIIISGDLNVCL 224
+ ++ + Q++L S +I+ GD N
Sbjct: 120 TPSDKELYKEEKKAKELSRNLLRKLAEAFKRRAAQADLLAADIAASPYPVIVCGDFN--- 176
Query: 225 QSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFR---HLYPDEEGAYTYWSFRNKS 281
+ A Y +R L GL DAF + YT+
Sbjct: 177 ------DTP-----ASYV------YRTLKK-GLTDAFVEAGSGFG-----YTF------- 206
Query: 282 ARLNNKGWRLDYHLVSEQLANNIKDCIIRSDVQGSTHCPVVLRL 325
R+DY L S+ + + S H P+V L
Sbjct: 207 -NGLFFPLRIDYILTSKGF--KVLRYRVDPGK-YSDHYPIVATL 246
>gnl|CDD|226098 COG3568, ElsH, Metal-dependent hydrolase [General function
prediction only].
Length = 259
Score = 38.9 bits (91), Expect = 0.002
Identities = 48/257 (18%), Positives = 83/257 (32%), Gaps = 60/257 (23%)
Query: 95 ILEENPDIMALQQI-------RCQEDEVPESFRKSLSHYHM-----FWIGSDKGQGGVGL 142
I E DI+ALQ++ R ++P + + F +GQ G +
Sbjct: 37 IREVGADIVALQEVDGAFGRHRDGLLDLPHLLGRLGLAPYWWSGAAFGAVYGEGQHGNAI 96
Query: 143 LTKEKPLTVK---YGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKAIDFRMIWDQH 199
L++ V+ P RG + A+ + + V N+ + L ++
Sbjct: 97 LSRLPIRDVENLALPDPTGLEPRG-ALLAEIELPGGKPLRVINAHLGL--------SEES 147
Query: 200 FYDYIQ-----SELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNFRELLD 254
+ L + + ++ GD N + E R R L+
Sbjct: 148 RLRQAAALLALAGLPALNPTVLMGDFN----------------NEPGSAEYRLAARSPLN 191
Query: 255 TGLVDAFRHLYPDEEGAYTYWSF-RNKSARLNNKGWRLDYHLVSEQLANNIKDCIIRSDV 313
P T +F N RLD VS++LA I+ + +D
Sbjct: 192 AQA-ALTGAFAPA--VGRTIRTFPSNTPLL------RLDRIFVSKELA--IRSVHVLTDR 240
Query: 314 ---QGSTHCPVVLRLSL 327
S H P++ L L
Sbjct: 241 LARVASDHLPLLAELRL 257
>gnl|CDD|197313 cd09079, RgfB-like, Streptococcus agalactiae RgfB, part of a
putative two component signal transduction system, and
related proteins. This family includes Streptococcus
agalactiae RgfB (for regulator of fibrinogen binding)
and related proteins. The function of RgfB is unknown.
It is part of a putative two component signal
transduction system designated rgfBDAC (the rgf locus
was identified in a screen for mutants of Streptococcus
agalactiae with altered binding to fibrinogen).
RgfA,-C,and -D do not belong to this superfamily: rgfA
encodes a putative response regulator, and rgfC, a
putative histidine kinase. All four genes are
co-transcribed, and may be involved in regulating
expression of bacterial cell surface components. 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 = 259
Score = 33.8 bits (78), Expect = 0.084
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 19/79 (24%)
Query: 87 KKNACVEYILEENPDIMALQQIRCQED----EVP-----------ESFRKSLSHYHMFW- 130
K + I EE+ D++ALQ++ D +VP E R+ + Y+ W
Sbjct: 17 KLERLAKIIAEEDYDVIALQEVNQSIDAPVSQVPIKEDNFALLLYEKLRELGATYYWTWI 76
Query: 131 ---IGSDKGQGGVGLLTKE 146
IG DK G+ +L+K
Sbjct: 77 LSHIGYDKYDEGLAILSKR 95
>gnl|CDD|197323 cd09089, INPP5c_Synj, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of synaptojanins. This
subfamily contains the INPP5c domains of two human
synaptojanins, synaptojanin 1 (Synj1) and synaptojanin 2
(Synj2), and related proteins. It belongs to a family of
Mg2+-dependent inositol polyphosphate 5-phosphatases,
which hydrolyze the 5-phosphate from the inositol ring
of various 5-position phosphorylated phosphoinositides
(PIs) and inositol phosphates (IPs). 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. Synj1 occurs as two main isoforms:
a brain enriched 145 KDa protein (Synj1-145) and a
ubiquitously expressed 170KDa protein (Synj1-170).
Synj1-145 participates in clathrin-mediated endocytosis.
The primary substrate of the Synj1-145 INPP5c domain is
PI(4,5)P2, which it converts to PI4P. Synj1-145 may work
with membrane curvature sensors/generators (such as
endophilin) to remove PI(4,5)P2 from curved membranes.
The recruitment of the INPP5c domain of Synj1-145 to
endophilin-induced membranes leads to a fragmentation
and condensation of these structures. The PI(4,5)P2 to
PI4P conversion may cooperate with dynamin to produce
membrane fission. In addition to this INPP5c domain,
Synjs contain an N-terminal Sac1-like domain; the Sac1
domain can dephosphorylate a variety of
phosphoinositides in vitro. Synj2 can hydrolyze
phosphatidylinositol diphosphate (PIP2) to
phosphatidylinositol phosphate (PIP). Synj2 occurs as
multiple alternative splice variants in various tissues.
These variants share the INPP5c domain and the Sac1
domain. Synj2A is recruited to the mitochondria via its
interaction with OMP25 (a mitochondrial outer membrane
protein). Synj2B is found at nerve terminals in the
brain and at the spermatid manchette in testis. Synj2B
undergoes further alternative splicing to give 2B1 and
2B2. In clathrin-mediated endocytosis, Synj2
participates in the formation of clathrin-coated pits,
and perhaps also in vesicle decoating. Rac1 GTPase
regulates the intracellular localization of Synj2 forms,
but not Synj1. Synj2 may contribute to the role of Rac1
in cell migration and invasion, and is a potential
target for therapeutic intervention in malignant tumors.
Length = 328
Score = 33.9 bits (78), Expect = 0.090
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 70 TKVKVSTWNVNG---LRACVKKNACVEYILEENPDIMALQQIRCQEDEVP 116
+V V TWNVNG R+ K+ + L +NP + +EDE P
Sbjct: 1 LRVFVGTWNVNGGKHFRSIAFKHQSMTDWLLDNPKLAGQCSNDSEEDEKP 50
>gnl|CDD|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and
I-clade non-long terminal repeat retrotransposons. This
family contains the endonuclease (EN) domain of various
non-long terminal repeat (non-LTR) retrotransposons,
long interspersed nuclear elements (LINEs) which belong
to the subtype 2, R1- and I-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. Most non-LTR
retrotransposons are inserted throughout the host
genome; however, many retrotransposons of the R1 clade
exhibit target-specific retrotransposition. This family
includes the endonucleases of SART1 and R1bm, from the
silkworm Bombyx mori, which belong to the R1-clade. It
also includes the endonuclease of snail (Biomphalaria
glabrata) Nimbus/Bgl and mosquito Aedes aegypti
(MosquI), both which belong to the I-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 = 205
Score = 30.3 bits (69), Expect = 1.0
Identities = 25/146 (17%), Positives = 51/146 (34%), Gaps = 28/146 (19%)
Query: 77 WNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWIGSDKG 136
N+N +A ++ ++ EE DI +Q+ P + + W+ +
Sbjct: 6 INLNRCKA--AQDLLLQTAREEGADIALIQE--------PYLVPVNNPN----WVTDE-- 49
Query: 137 QGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKAIDF-RMI 195
G ++ ++ I +S G V A+ T ++ Y P S + ++ +
Sbjct: 50 SGRAAIVVSDRLPRKP--IQRLSLGLGIVA-ARVGGITVVSCYAPPSESLEEFEEYLENL 106
Query: 196 WDQHFYDYIQSELRSNSNIIISGDLN 221
+ +II GD N
Sbjct: 107 VRIV--------RGLSRPVIIGGDFN 124
>gnl|CDD|197308 cd09074, INPP5c, Catalytic domain of inositol polyphosphate
5-phosphatases. Inositol polyphosphate 5-phosphatases
(5-phosphatases) are signal-modifying enzymes, which
hydrolyze the 5-phosphate from the inositol ring of
specific 5-position phosphorylated phosphoinositides
(PIs) and inositol phosphates (IPs), such as PI(4,5)P2,
PI(3,4,5)P3, PI(3,5)P2, I(1,4,5)P3, and I(1,3,4,5)P4.
These enzymes are Mg2+-dependent, 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. In addition to this INPP5c domain,
5-phosphatases often contain additional domains and
motifs, such as the SH2 domain, the Sac-1 domain, the
proline-rich domain (PRD), CAAX, RhoGAP
(RhoGTPase-activating protein), and SKICH [SKIP
(skeletal muscle- and kidney-enriched inositol
phosphatase) carboxyl homology] domains, that are
important for protein-protein interactions and/or for
the subcellular localization of these enzymes.
5-phosphatases incorporate into large signaling
complexes, and regulate diverse cellular processes
including postsynaptic vesicular trafficking, insulin
signaling, cell growth and survival, and endocytosis.
Loss or gain of function of 5-phosphatases is implicated
in certain human diseases. This family also contains a
functionally unrelated nitric oxide transport protein,
Cimex lectularius (bedbug) nitrophorin, which catalyzes
a heme-assisted S-nitrosation of a proximal thiolate;
the heme however binds at a site distinct from the
active site of the 5-phosphatases.
Length = 299
Score = 30.8 bits (70), Expect = 1.0
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 10/47 (21%)
Query: 70 TKVKVSTWNVNGLRACVKKNACVEYIL----EENPDIMALQQIRCQE 112
K+ V TWNV G + +E L E PDI A + QE
Sbjct: 1 VKIFVVTWNVGGGIS---PPENLENWLSPKGTEAPDIYA---VGVQE 41
>gnl|CDD|185247 PRK15349, PRK15349, type III secretion system protein SsaT;
Provisional.
Length = 259
Score = 29.1 bits (65), Expect = 2.5
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 194 MIWDQHFYDYIQSELRSNSNIIISGDLN--VCLQSIDLA 230
+++D+ F YIQ+E R+ + IS L +C+ DLA
Sbjct: 163 LLFDRQFLKYIQAEWRTLYQLCISFSLPAIICMVLADLA 201
>gnl|CDD|204098 pfam08929, DUF1911, Domain of unknown function (DUF1911). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 107
Score = 27.7 bits (62), Expect = 3.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 262 RHLYPDEEGAYTYWSF 277
RH DE G + YW+F
Sbjct: 66 RHKAADETGYFGYWAF 81
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 28.7 bits (64), Expect = 4.6
Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 4 SADVIQKSDDENQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFD 57
SAD +++ +E Q+ ++ K + K+ R+ + + + + IP +Q +
Sbjct: 21 SADELRRRREEQQVELRKQKREELLNKR---RNLADVSEEAESSFIPMEQQFYS 71
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 28.9 bits (66), Expect = 4.9
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 2 KRSADVIQKSDDENQIPKKQVKFDISRKKKKMKRSAD 38
K+ D++ ++++ KK+++ I +K+MK +A
Sbjct: 591 KKIRDILDSVYKKDKLSKKELEKLIKELEKQMKEAAK 627
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 5.3
Identities = 13/65 (20%), Positives = 37/65 (56%), Gaps = 7/65 (10%)
Query: 2 KRSADVIQKSDDENQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFDISHE 61
K+ A+ ++K+++EN+I + +K ++ K+ A+ +K++++ + + +K
Sbjct: 1646 KKKAEELKKAEEENKIKAAEEA----KKAEEDKKKAEEAKKAEEDEKKAAEALK---KEA 1698
Query: 62 EGSRK 66
E ++K
Sbjct: 1699 EEAKK 1703
>gnl|CDD|227509 COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA processing and
modification].
Length = 429
Score = 27.6 bits (61), Expect = 9.4
Identities = 23/112 (20%), Positives = 48/112 (42%), Gaps = 4/112 (3%)
Query: 6 DVIQKSD-DENQIPKKQVKFDISRKKKKMKRSADVIQKSDDENQIPKKQVKFDISHEEGS 64
DV+Q+ EN PK+ K + + + K +++ + +++ +++ + E S
Sbjct: 65 DVLQRFQVQENDTPKEITKDEKNMSRMKSRKAPTIHMEAEIDDEYGFEDRMKPYREESLS 124
Query: 65 RKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVP 116
R+ K K L+ V E+ PD M+L +++ + VP
Sbjct: 125 RQ---KKRKALQHRYEQLKLVVPYPEIFEWEDATCPDPMSLNRMKGCSNGVP 173
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
0.318 0.135 0.398
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,493,672
Number of extensions: 1571891
Number of successful extensions: 1522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1448
Number of HSP's successfully gapped: 42
Length of query: 327
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 230
Effective length of database: 6,635,264
Effective search space: 1526110720
Effective search space used: 1526110720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)