RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12564
(1033 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 = 278 bits (713), Expect = 2e-86
Identities = 113/304 (37%), Positives = 155/304 (50%), Gaps = 58/304 (19%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE--- 791
KI SWNVNG+RA + K ++++ D ++ C+QE + +P+
Sbjct: 1 LKIISWNVNGLRALLK------------KGLLDYVKKEDPDILCLQETKLQEGDVPKELK 48
Query: 792 -CPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDM 850
+GYH +W ++GY+G A+LSK KP+ VT+G G EH
Sbjct: 49 ELLKGYHQYWNAAEKKGYSGTAILSKKKPLSVTYGI---------------GIEEH---- 89
Query: 851 ESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFL 910
E GRV+T E+E FYLVN Y P + L L + W+
Sbjct: 90 -----DQE--------------GRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDF 130
Query: 911 RGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVH 970
R +LK L+ KPV+ GDLNVAH ID+A P TN +GFT +ER F+ L+ GF+D
Sbjct: 131 RAYLKKLDSKKPVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELLEAGFVDTF 190
Query: 971 RHLYPNHRI-YTYWPY--YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQ 1027
RHL+P+ YT+W Y R K GWRLDYFL+S++LK + D I D+ GSDH P
Sbjct: 191 RHLHPDKEGAYTFWSYRGNARA-KNVGWRLDYFLVSERLKDRVVDSFIRSDIMGSDHCPI 249
Query: 1028 ILYL 1031
L L
Sbjct: 250 GLEL 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 = 227 bits (581), Expect = 6e-68
Identities = 103/304 (33%), Positives = 150/304 (49%), Gaps = 57/304 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE---C 792
KI SWNVNG+RA K ++++ +V C+QE + E+ P
Sbjct: 2 KIISWNVNGLRAR------------LHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFE 49
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
GYH F+ +GY+GVA+LSK +P+ V +GF G EH
Sbjct: 50 ELGYHVFFHGAKSKGYSGVAILSKVEPLDVRYGF---------------GGEEH------ 88
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAP-AAKEDLSMLSVKLL-WNSFL 910
D +GRV+T E++ F +VNVY P L L KL W++
Sbjct: 89 -------------DE----EGRVITAEFDGFTVVNVYVPNGGSRGLERLEYKLQFWDALF 131
Query: 911 RGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVH 970
+ + K L+ KPV++ GD+NVAH ID+ P N G +GFT +ER +F L+ G +D
Sbjct: 132 QYYEKELDAGKPVIICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLEAGLVDTF 191
Query: 971 RHLYPNHR-IYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQI 1028
RH P+ YT+W Y + +GWR+DYFL+S+ L + D I ++ GSDH P +
Sbjct: 192 RHFNPDTEGAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIV 251
Query: 1029 LYLN 1032
L L+
Sbjct: 252 LELD 255
>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 = 218 bits (558), Expect = 9e-65
Identities = 107/301 (35%), Positives = 151/301 (50%), Gaps = 55/301 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE---C 792
KI SWNVNG+RA + L ++++ ++ C+QE + +KLPE
Sbjct: 1 KIISWNVNGLRARLKKGVL------------KWLKEEKPDILCLQETKADEDKLPEELQH 48
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGYH++W P ++GY+GVA LSK +P+ V++G G E
Sbjct: 49 VEGYHSYWSPARKKGYSGVATLSKEEPLDVSYGI---------------GGEEFD----- 88
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRG 912
+GRV+T E++ FYL+NVY P L L KL +
Sbjct: 89 ------------------SEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLE 130
Query: 913 HLKSL-NEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHR 971
L+ L KPVV+ GD NVAH ID+A P N +GFT +ER +F L LG++D R
Sbjct: 131 FLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFDKLLSLGYVDTFR 190
Query: 972 HLYPNHRIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQILY 1030
H +P YT+W Y + + GWR+DYFL+S++L + D I V+GSDHAP L
Sbjct: 191 HFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKVKGSDHAPVTLE 250
Query: 1031 L 1031
L
Sbjct: 251 L 251
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 210 bits (536), Expect = 2e-61
Identities = 102/312 (32%), Positives = 140/312 (44%), Gaps = 64/312 (20%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE--- 791
KI SWNVNG+RA L ++ + +V C+QE + E+ P
Sbjct: 1 MKIASWNVNGLRA-------RLKKLLD------WLEEEQPDVLCLQETKAQDEQFPREEL 47
Query: 792 CPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
GYH + G + GY+GVA+LSK P V GF G E
Sbjct: 48 EALGYHHVFNHGQK-GYSGVAILSKKPPDDVRRGFP--------------GEEED----- 87
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKE-DLSMLSVKLLWNSFL 910
++GRV+ E++ F ++N+Y P L KL + L
Sbjct: 88 ------------------DEEGRVIEAEFDGFRVINLYFPNGSSIGLEKFDYKLRFLDAL 129
Query: 911 RGHLKSL-NEIKPVVLAGDLNVAHNHIDVALP---LTNLGKSGFTIQERNYFSNFLDLGF 966
R +L+ L + KPVVL GD N+A IDVA P N G SGF +ER +F L+ GF
Sbjct: 130 RNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRRLLNAGF 189
Query: 967 LDVHRHLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEG---- 1021
+D R +P YT+W Y ++ GWR+DY L+S L L D I +V G
Sbjct: 190 VDTFRLFHPEPEKYTWWDYRANAARRNRGWRIDYILVSPALADRLKDAGIDREVRGWEKP 249
Query: 1022 SDHAPQILYLNL 1033
SDHAP + L+L
Sbjct: 250 SDHAPVWVELDL 261
>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 = 195 bits (498), Expect = 1e-56
Identities = 88/296 (29%), Positives = 137/296 (46%), Gaps = 55/296 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE---C 792
KI SWNVNG+RA + +K + ++ ++ C+QE + E+LPE
Sbjct: 2 KIISWNVNGLRA------------VHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRN 49
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGYH+++ R+GY+GVA+ SK +P V G ++ F+
Sbjct: 50 IEGYHSYFNSAERKGYSGVALYSKIEPDSVREGLGVEE--------FDN----------- 90
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRG 912
+GR++ +++ F L N+Y P + L KL +
Sbjct: 91 -------------------EGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLE 131
Query: 913 HLKSL-NEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHR 971
+L L + K V++ GD N AH ID+A P N SGF +ER + F++ G++D R
Sbjct: 132 YLNELRDSGKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFIENGYVDTFR 191
Query: 972 HLYPNHRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAP 1026
YT+W Y R + GWR+DYF ++++ K + D I DV GSDH P
Sbjct: 192 MFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPDVMGSDHCP 247
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional.
Length = 250
Score = 187 bits (476), Expect = 1e-53
Identities = 109/294 (37%), Positives = 152/294 (51%), Gaps = 52/294 (17%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECPE 794
K+ SWNVNG+RA K F D +VFCIQE + E+ +
Sbjct: 1 MKLISWNVNGLRA------------CMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK 48
Query: 795 GYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMESGP 854
GY FW ++GY+GV +K +P+ V++G +++ EH +
Sbjct: 49 GYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGINIE---------------EHDKE----- 88
Query: 855 SHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRGHL 914
GRV+T E+E FYLVNVY P +++ LS LS ++ W + L
Sbjct: 89 ------------------GRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFL 130
Query: 915 KSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHRHLY 974
K+L KPV++ GDLNVAHN ID+ P TN +GF+ +ER FS L+ GF+D R+ Y
Sbjct: 131 KALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFY 190
Query: 975 PN-HRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAP 1026
PN + YT+W Y + K GWR+DYFL S LK+ L D I+ D+ GSDH P
Sbjct: 191 PNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGSDHCP 244
>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 = 186 bits (475), Expect = 2e-53
Identities = 94/301 (31%), Positives = 148/301 (49%), Gaps = 63/301 (20%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECP-- 793
KI SWNVNG+RA + G ++++++ +V C+QE + E+ P P
Sbjct: 2 KIISWNVNGLRA-------------RPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFH 48
Query: 794 -EGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGYH F+ ++GY+GVA+ SK +P+ V GF G E D E
Sbjct: 49 KEGYHVFFSG--QKGYSGVAIFSKEEPISVRRGF---------------GVEEE--DAE- 88
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAP-AAKEDLSMLSVKLLWNSFLR 911
GR++ E++ F ++N Y P +++D L KL W L+
Sbjct: 89 --------------------GRIIMAEFDSFLVINGYFPNGSRDDSEKLPYKLQWLEALQ 128
Query: 912 GHLKSL-NEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVH 970
+L+ L ++ KPV++ GD+N+A ID+ +P N +GF +ER + L+ G +D
Sbjct: 129 NYLEKLVDKDKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLDRLLEAGLVDTF 188
Query: 971 RHLYPNHRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEG----SDHA 1025
R P+ Y++W Y + + +GWR+DYFL+S+ LK D I D+ G SDH
Sbjct: 189 RKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIRGMEKPSDHC 248
Query: 1026 P 1026
P
Sbjct: 249 P 249
>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 = 180 bits (459), Expect = 3e-51
Identities = 80/300 (26%), Positives = 130/300 (43%), Gaps = 56/300 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE---C 792
++ S NVNGIRA +K ++ D +V C+QE+R E+L +
Sbjct: 2 RVISVNVNGIRA------------AAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFE 49
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
PEGY+A++F ++GYAGVA+ S+T+P V +G
Sbjct: 50 PEGYNAYFFDAEKKGYAGVAIYSRTQPKAVIYGLGF------------------------ 85
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRG 912
+ D G R + +++ + ++Y P+ K+ +
Sbjct: 86 ----------EEFDDEG----RYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLE 131
Query: 913 HLKSLNEIKP-VVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLD-LGFLDVH 970
HLK L + ++ GD N+AH ID+ N SGF +ER + LG++D
Sbjct: 132 HLKELRRKRREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAF 191
Query: 971 RHLYPNHRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQIL 1029
R L P+ YT+W + + GWR+DY + + L S + I+ + SDHAP I+
Sbjct: 192 RELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREERFSDHAPLIV 251
>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 = 166 bits (422), Expect = 3e-46
Identities = 88/303 (29%), Positives = 127/303 (41%), Gaps = 65/303 (21%)
Query: 735 FKIGSWNVNGIRA-WSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECP 793
KI +WNVN IRA QV ++++ D +V C+QE + ++ P
Sbjct: 1 MKIATWNVNSIRARLEQV--------------LDWLKEEDPDVLCLQETKVEDDQFPADA 46
Query: 794 ---EGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDM 850
GYH G + Y GVA+LS+ V GF
Sbjct: 47 FEALGYHVAVH-GQK-AYNGVAILSRLPLEDVRTGF------------------------ 80
Query: 851 ESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKE-DLSMLSVKLLWNSF 909
P P+ D R++ ++N+Y P + + KL W
Sbjct: 81 ---PGDPDD-----------DQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDR 126
Query: 910 LRGHLKS-LNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLD 968
L +L+ L P+VL GD N+A IDV P LGK FT +ER LDLGF+D
Sbjct: 127 LIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALRALLDLGFVD 186
Query: 969 VHRHLYPNHRIYTYWPYY-DRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEG----SD 1023
R L+P+ +++T+W Y + +G R+D+ L S L L D+ I + G SD
Sbjct: 187 AFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPRGWEKPSD 246
Query: 1024 HAP 1026
HAP
Sbjct: 247 HAP 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 = 128 bits (323), Expect = 2e-32
Identities = 84/323 (26%), Positives = 138/323 (42%), Gaps = 51/323 (15%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQH-DLNVFCIQEIRCPLEKLPE--- 791
+I +WNVNGIR +++ D ++ C+QE + ++L E
Sbjct: 1 RIVTWNVNGIRT------RLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSA 54
Query: 792 CPEGYHAFW-FPGTRQGYAGVAVL---SKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHG 847
EGY +F+ F R+GY+GVA S PV G + GV+ + +E+
Sbjct: 55 IVEGYDSFFSFSRGRKGYSGVATYCRDSAATPVAAEEGLT----GVLSSPNQKNELSEND 110
Query: 848 SDMESGPSHPELTTIQYADASGID-DGRVMTVEYEQFYLVNVYAPAA-KEDLSMLSVKLL 905
G + + + +D +GR + ++ F L+NVY P A E L KL
Sbjct: 111 DIGCYGEMLEFTDSKELLE---LDSEGRCVLTDHGTFVLINVYCPRADPEKEERLEFKLD 167
Query: 906 WNSFLRGHLKSLNEI-KPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQE---RNYFSNF 961
+ L +++L + + V+L GD+NV+H ID P + G + ++ R +
Sbjct: 168 FYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDNPSRQWLDQL 227
Query: 962 L-DLG---------FLDVHRHLYPNHR-IYTYWPYYDRPSKMK-------GWRLDYFLIS 1003
L D G +D R+ +P + YT W + + G R+DY L
Sbjct: 228 LGDSGEGGGSPGGLLIDSFRYFHPTRKGAYTCW------NTLTGARPTNYGTRIDYILAD 281
Query: 1004 KQLKSHLSDLEIHGDVEGSDHAP 1026
+ L + +I +VEGSDH P
Sbjct: 282 RGLLPWVKAADILPEVEGSDHCP 304
>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 = 88.7 bits (220), Expect = 2e-19
Identities = 65/306 (21%), Positives = 100/306 (32%), Gaps = 76/306 (24%)
Query: 737 IGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP----EC 792
+ S+NVNG + + ++R+ D ++ C+QE++
Sbjct: 1 VASYNVNG---LNAATRA--------SGIARWVRELDPDIVCLQEVKDSQYSAVALNQLL 49
Query: 793 PEGYHAFWFPGTR-QGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
PEGYH + +R +GY GVA+LSKT ++ K G R
Sbjct: 50 PEGYHQYQSGPSRKEGYEGVAILSKTPKFKIVEKHQYKFG---EGDSGERR--------- 97
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLS--MLSVKLLWNSF 909
D +VN + A +K + F
Sbjct: 98 ----------AVVVKFDVHDKE---------LCVVNAHLQAGGTRADVRDAQLKEVLE-F 137
Query: 910 LRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDV 969
L+ + + PVV+ GD NV + +D P F+ L +D
Sbjct: 138 LKRLRQPNSA--PVVICGDFNVRPSEVDSENP-----------SSMLRL--FVALNLVDS 182
Query: 970 HRHLYPNHRIYTYWPYYDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDV----EGSDHA 1025
L YT+ Y RLDY +SK L + +I D SDH
Sbjct: 183 FETL---PHAYTFDTYMHNV----KSRLDYIFVSKSLLPSVKSSKILSDAARARIPSDHY 235
Query: 1026 PQILYL 1031
P + L
Sbjct: 236 PIEVTL 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 = 75.9 bits (187), Expect = 3e-15
Identities = 60/299 (20%), Positives = 105/299 (35%), Gaps = 81/299 (27%)
Query: 737 IGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEK-LPECPEG 795
IG+ NV G+R+ + +L +++ L++ +QE E L + EG
Sbjct: 1 IGTLNVRGLRSPGKRAQLL-----------EELKRKKLDILGLQETHWTGEGELKKKREG 49
Query: 796 YHAFWFPGTRQGYAGVAVL----SKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
+ GVA+L + K + T
Sbjct: 50 GTILYSGSDSGKSRGVAILLSKTAANKLLEYTK--------------------------- 82
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTV----EYEQFYLVNVYAPAAKEDLSMLSVKLLWN 907
+ GR++ V + ++ ++NVYAP A+++ K +
Sbjct: 83 ------------------VVSGRIIMVRFKIKGKRLTIINVYAPTARDE----EEKEEFY 120
Query: 908 SFLRGHLKSLNEIKPVVLAGDLN-VAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGF 966
L+ L + +++ GD N V D L ++G ER + +
Sbjct: 121 DQLQDVLDKVPRHDTLIIGGDFNAVLGPKDDGRKGLDKRNENG----ERALSALIEEHDL 176
Query: 967 LDVHRHLYPNHRIYTYWPYYDRPSKMKGW-RLDYFLISKQLKSHLSDLEIHGDVEGSDH 1024
+DV R P R YT+ R R+D L+SK+L+ + +I GSDH
Sbjct: 177 VDVWRENNPKTREYTW-----RSPDHGSRSRIDRILVSKRLRVKVKKTKI-TPGAGSDH 229
>gnl|CDD|236970 PRK11756, PRK11756, exonuclease III; Provisional.
Length = 268
Score = 73.8 bits (182), Expect = 3e-14
Identities = 77/324 (23%), Positives = 126/324 (38%), Gaps = 97/324 (29%)
Query: 736 KIGSWNVNGIRA-WSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRC-----PLEKL 789
K S+N+NG+RA Q+ + + +H +V +QE + PLE++
Sbjct: 2 KFVSFNINGLRARPHQLEAI--------------IEKHQPDVIGLQETKVHDEMFPLEEV 47
Query: 790 PECPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSD 849
GYH F+ G + Y GVA+LSK P+ V GF +D
Sbjct: 48 EAL--GYHVFYH-GQKGHY-GVALLSKQTPIAVRKGFP--------------------TD 83
Query: 850 MESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPA-----------AKE--- 895
E + + +G +TV +N Y P AK
Sbjct: 84 DEE--AQRRIIMATIPTPNGN-----LTV-------INGYFPQGESRDHPTKFPAKRQFY 129
Query: 896 -DLSMLSVKLLWNSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTN------LGKS 948
DL ++L L N P+++ GD+N++ +D+ + N GK
Sbjct: 130 QDL---------QNYLETELSPDN---PLLIMGDMNISPTDLDIGIGEENRKRWLRTGKC 177
Query: 949 GFTIQERNYFSNFLDLGFLDVHRHLYP-NHRIYTYWPYYDRP-SKMKGWRLDYFLISKQL 1006
F +ER + +D G +D R L P + ++++ Y + +G R+D L ++ L
Sbjct: 178 SFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPL 237
Query: 1007 KSHLS----DLEIHGDVEGSDHAP 1026
D +I G + SDHAP
Sbjct: 238 AERCVETGIDYDIRGMEKPSDHAP 261
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 33.9 bits (77), Expect = 0.62
Identities = 31/121 (25%), Positives = 47/121 (38%), Gaps = 14/121 (11%)
Query: 445 STKRRGRPKKTTTPSGGIISSPSKNTRKHDKKYTTNSESIQTSVSNIRDSTSRNLKTKSV 504
S G T P+G H + T + Q+ ++ S+S N
Sbjct: 530 SAPYGGNAATTADPNG------IAKREDHPEGGTNRQKYEQSDEESVESSSSENSSENEN 583
Query: 505 NIEDKSESASTATLKTIGKEDKDFISRPVKSSRVSTKIQLDHSVKKSQKQGLT-KYESQP 563
+ DK E + KTI + D + I RP+ +++ K KK+ K T KY S P
Sbjct: 584 EVTDKGEEIYSLLKKTINRIDMNKIPRPIINTQEKKK-------KKNLKVFETCKYISPP 636
Query: 564 S 564
S
Sbjct: 637 S 637
>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 = 32.7 bits (75), Expect = 0.83
Identities = 14/52 (26%), Positives = 18/52 (34%), Gaps = 9/52 (17%)
Query: 980 YTYWPYYDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQILYL 1031
YT+ R+DY L SK K + SDH P + L
Sbjct: 204 YTF------NGLFFPLRIDYILTSKGFKVL--RYRVDPGK-YSDHYPIVATL 246
>gnl|CDD|240448 cd13425, Peptidase_G1_like, Peptidases of the G1 family and
homologs that might lack peptidase activity. Some
members of this family had been classified earlier as
carboxyl peptidases insensitive to pepstatin, and the
family has also been called the eqolisin family, due to
the fact that the conserved catalytic dyad of the family
consists of a glutamate (E) and glutamine (Q) residue.
The family is found in fungi and bacteria. This family
also includes homologous uncharacterized proteins that
might lack peptidase activity.
Length = 195
Score = 31.9 bits (72), Expect = 0.97
Identities = 27/126 (21%), Positives = 50/126 (39%), Gaps = 10/126 (7%)
Query: 420 EKYTFRKRKGKTKTTRIKTTKYSDKSTKRRGRPKKTTTPSGGIIS------SPSKNTRKH 473
EK+T+ K T + K S + GR T +G I+S SP+ T +
Sbjct: 70 EKFTYNKGFRPGDTVQXTVYKTSSGN----GRATLENTTTGQIVSEIQGTNSPATLTISN 125
Query: 474 DKKYTTNSESIQTSVSNIRDSTSRNLKTKSVNIEDKSESASTATLKTIGKEDKDFISRPV 533
+ + S ++ I+ + S +++ + KS TA + ++ K F V
Sbjct: 126 AETIAEDFVSYESQRDAIKATFSVEFTNCTIDNKGKSYGLVTAVITQDQQDGKVFTKVSV 185
Query: 534 KSSRVS 539
+ V+
Sbjct: 186 AGNNVT 191
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 33.1 bits (76), Expect = 1.1
Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 10/178 (5%)
Query: 341 KKTFKTTAGSSENILLKGLLMNRKSTQPRHSISTSKNRSPTQNEIDMIVENFISVQRKFS 400
KK K++A S+ + G S + R N+ + D + + K S
Sbjct: 1179 KKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKS 1238
Query: 401 LNTVRPVTHF----LNVSNEESYEKYTFRKRKGKTKTTRIKTTKYSDKSTKRRGRPKKTT 456
+ N+E ++ K K R+ +YS +R +
Sbjct: 1239 SVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNG 1298
Query: 457 TPSGGIISSPSKNTRKHDKKYTTNSESIQTSVSNIRDSTSRNLKTKSVNIEDKSESAS 514
S PS T+K KK S + T+R K+K+ + + +S
Sbjct: 1299 G------SKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSS 1350
>gnl|CDD|215299 PLN02543, PLN02543, pfkB-type carbohydrate kinase family protein.
Length = 496
Score = 31.8 bits (72), Expect = 1.9
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 3/76 (3%)
Query: 432 KTTRIKTTKYSDKSTKRRGRPKKTTTPSGGIISSPSKNTRKHDKKYTTNSESIQTSVSNI 491
KT R K S + +R RP + + +G + K +R+ KK T+S +
Sbjct: 30 KTRRFPKPKASLHPSIKRSRPGR-CSTNGAAVPESPKPSRRGRKKKPTSSPPKAKTTR-- 86
Query: 492 RDSTSRNLKTKSVNIE 507
R + + + E
Sbjct: 87 RRTKKTDQELDPEGAE 102
>gnl|CDD|150784 pfam10151, DUF2359, Uncharacterized conserved protein (DUF2359).
This is a 450 amino acid region of a family of proteins
conserved from insects to humans. The mouse protein,
Q8BM55, is annotated as being a putative Vitamin
K-dependent carboxylation gamma-carboxyglutamic (GLA)
domain containing protein, but this could not be
confirmed. The function is not known.
Length = 469
Score = 31.8 bits (72), Expect = 2.2
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 16/78 (20%)
Query: 656 LYNEWEYRPPKRKKASRKNVFSFKLNEIHVGTGKIENRLGCDSSNETSYAEVEEVPIIDF 715
L W P K +K+ ++ V SFK+ T G S + + D
Sbjct: 205 LLKTWNTLPKKLRKSLQETVQSFKV------TNSELTSKGSASLQD----------LEDC 248
Query: 716 NDPFRILEHKRRQDQYPW 733
+ ++L K + +PW
Sbjct: 249 DTACQVLLEKMQGSSFPW 266
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 31.7 bits (72), Expect = 2.2
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 16/84 (19%)
Query: 384 EIDMIVENFISVQRKFSLNTVRPVTHFLNVSNEESYEKYTFRKRKGKTKTTRIKTTKYSD 443
+I + +V K++ P YEK T K K K+ +T+ K K
Sbjct: 724 ACSVIGNSIDAVITKYAGTPKTP------------YEKKT--KAKKKSASTKGKAAKTVK 769
Query: 444 KSTKRRGRPKKTTTPSGGIISSPS 467
K +K + KKTT G + +PS
Sbjct: 770 KKSKAKS--KKTTKKRAGPLYTPS 791
>gnl|CDD|115650 pfam07010, Endomucin, Endomucin. This family consists of several
mammalian endomucin proteins. Endomucin is an early
endothelial-specific antigen that is also expressed on
putative hematopoietic progenitor cells.
Length = 259
Score = 31.2 bits (70), Expect = 2.3
Identities = 40/161 (24%), Positives = 61/161 (37%), Gaps = 19/161 (11%)
Query: 431 TKTTRIKTTKYSDKSTKRRGRPKKTTTPSGGIISSPSK----------NTRKHDKKYTT- 479
T TT+ T + S K +P T P G S K T KH+ K TT
Sbjct: 34 TSTTKASITTPNTVSLKNVNKPTTGTPPKGTTTSELLKTSLMSTATSLTTPKHELKTTTT 93
Query: 480 -----NSESIQTSVSNIRDSTSRNLKTKSVNIEDKSESASTATLKTIGKEDKDFISRPVK 534
S + + +V+N+ S + + S N + S T + D + P K
Sbjct: 94 GVRKNESSTSKVTVTNVTLSNAVSTLQSSQNKTENQSSIRTTEISPTSVLQPD--ASPKK 151
Query: 535 SSRVSTKIQLDHSVKKSQKQGLTKYESQPSST-STSTDVLP 574
+ S + + +SQ K S S+T S S+ +LP
Sbjct: 152 TGTTSASLTTAETTSQSQDTEDGKIASTSSTTPSYSSIILP 192
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 31.3 bits (71), Expect = 3.1
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 263 HVSEMEENNDDSNIKLHREVKSDVNEDQESNIKIVRDLDSEVINSEQTVDRTESSEDKYS 322
H + +E+ DS I+ +VK V+ + D + + E TV S +
Sbjct: 842 HQAIIEQRTQDSGIR--NDVKHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHH 899
Query: 323 KSQHGDLNDIY 333
K++ N+ Y
Sbjct: 900 KTEALSQNNKY 910
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 31.0 bits (70), Expect = 3.5
Identities = 27/163 (16%), Positives = 54/163 (33%), Gaps = 9/163 (5%)
Query: 257 MGNSELHVSEMEENNDDSNIKLHREVKSDVNEDQESNIKIVRDLDSEVINSEQTVDRTES 316
M + EE + E+ +N + E RDL E E ++
Sbjct: 203 MTPETSKQDQKEERRAAVERR-LAELVEMINWNLEERR---RDLRKEQELEENVERDSDD 258
Query: 317 SEDKYSKSQHGDLNDIYFPSNLYHKKTFKTTAGSSENILLKGLLMNRKSTQPRHSISTSK 376
++ S+ G+ + ++ Y ++ + E + +M + S + I T K
Sbjct: 259 EDEHGEDSEDGETKPESYITSEYIERISEIRKMKDERLSSLASMMPQASGEFDGMIFTKK 318
Query: 377 NRSPTQNEIDMIVENFISVQRKFSLNTVRPVTHFLNVSNEESY 419
++ + N +K+ L +V VS S
Sbjct: 319 -----CKWDNVPLYNIDEDSKKYELQSVGSCERVAFVSKGLSL 356
>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 = 29.9 bits (67), Expect = 3.6
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 878 VEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRGHLKSLNEIKPVVLAGDLN 930
V + LVNV+ P + + L+ L +++PVVLAGD N
Sbjct: 69 VSGQTLTLVNVHLPPGNGL-----READERALLQLLSDLLPDLRPVVLAGDFN 116
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 30.9 bits (70), Expect = 4.1
Identities = 43/244 (17%), Positives = 77/244 (31%), Gaps = 33/244 (13%)
Query: 268 EENNDDSNIKLHREVKSDVNEDQESNIKIVRDLDSEVINSEQTVDRTESSEDKYSKSQHG 327
+ D + + K N+D+ S +D D N+ D + S
Sbjct: 29 DPQKDSTAKTTSHDSKKS-NDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSD 87
Query: 328 DLNDIYFPSNLYHKKT----FKTTAGSSENILLKGLLMN-----------------RKST 366
N+I +T T +N L L+ N KST
Sbjct: 88 S-NNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNSEKST 146
Query: 367 QPRHSISTSKNRSPTQNEIDMIVENFISVQRKFSLNTVRPVTHFLNVSNEESYEKYTFRK 426
+ S S ++ T + ++ Q+ S N +P T ++ + T
Sbjct: 147 NDSNKNSDSSIKNDTDTQSSK--QDKADNQKAPSSNNTKPSTSNKQPNSPKP----TQPN 200
Query: 427 RKGKTKTTRIKTTKYSDKSTKRRGRPKKTTTPSGGIISSPSKNTRKHDKKYTTNSESIQT 486
+ + T S+K + S I+ S++ +K K Y + S+ +T
Sbjct: 201 QSNSQPAS--DDTANQKSSSKDNQSMSDSALDS--ILDQYSEDAKKTQKDYASQSKKDKT 256
Query: 487 SVSN 490
SN
Sbjct: 257 ETSN 260
>gnl|CDD|221121 pfam11489, DUF3210, Protein of unknown function (DUF3210). This is
a family of proteins conserved in yeasts. The function
is not known. The Schizosaccharomyces pombe member is
SPBC18E5.07 and the Saccharomyces cerevisiae member is
AIM21.
Length = 671
Score = 30.7 bits (69), Expect = 4.4
Identities = 32/197 (16%), Positives = 67/197 (34%), Gaps = 36/197 (18%)
Query: 470 TRKHDKKYTTNSESIQTSVSNIRDSTSRNLKTKSVNIEDKSESASTATLKTIGKEDKDFI 529
+ + +K + ES S N + ++ + L+ + + + F
Sbjct: 334 SFEREKSEKSRHESDPKSRENSKPASIYG---------SVPDLIRHTPLEDVEEYEPLF- 383
Query: 530 SRPVKSSRVSTKIQLDHSVKKSQKQGLT-----KYESQPSSTS----TSTDVLPAHKMSL 580
P S ++ K + S ++ +++ +E PSS ST P + S
Sbjct: 384 --PEDESEIAVKPPTEESSRRPEEEKHRFPSEDVWEDSPSSLQDTATVSTPSNPPPRASE 441
Query: 581 APERKIAQFNNRNKLVLLHTKTTHVKTVPSENVQNTKGKFELLKEIKFERTGSEDTSEDV 640
PE++ ++ ++ ++ + K + E+ +R S D ED
Sbjct: 442 TPEQETSR-------------SSSEVSLDPHQSELKSEKKKARPEVSKQRFPSRDVWEDA 488
Query: 641 EESGFF--TVEPIPDSN 655
ES T E +
Sbjct: 489 PESQELVTTEETPEEVK 505
>gnl|CDD|226883 COG4477, EzrA, Negative regulator of septation ring formation [Cell
division and chromosome partitioning].
Length = 570
Score = 30.4 bits (69), Expect = 5.5
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 4/75 (5%)
Query: 256 LMGNSELHVSEMEENNDDSNIKLHREVKSDVNED----QESNIKIVRDLDSEVINSEQTV 311
+ E H+ E E D + D+ + +E +I+ DL+ V + E+
Sbjct: 79 SFADVEEHLFEAEALADKFRFNKAKHEIDDIEQQLTLIEEDIEQILEDLNELVESEEKNS 138
Query: 312 DRTESSEDKYSKSQH 326
+ + + Y + +
Sbjct: 139 EEIDHVLELYEELRR 153
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 30.3 bits (69), Expect = 6.9
Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 18/89 (20%)
Query: 616 TKGKFELLKE------IKFERTGSEDTSEDVE--------ESGFFTVEP----IPDSNLY 657
++G+ E L E I ++ D ++ E ESGF + I +S L
Sbjct: 386 SEGRRERLLELLAEHDIPPQKVDRLDEAKKGEVYIAVGPLESGFILPDEKLAVITESELL 445
Query: 658 NEWEYRPPKRKKASRKNVFSFKLNEIHVG 686
R +RK+ + L E+ G
Sbjct: 446 GSRVKRRRRRKRRKKNATRIKDLAELKPG 474
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
0.314 0.131 0.377
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 50,492,620
Number of extensions: 4864432
Number of successful extensions: 2917
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2848
Number of HSP's successfully gapped: 81
Length of query: 1033
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 926
Effective length of database: 6,191,724
Effective search space: 5733536424
Effective search space used: 5733536424
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 (22.0 bits)
S2: 64 (28.4 bits)