RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8564
(341 letters)
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 321 bits (825), Expect = e-109
Identities = 126/341 (36%), Positives = 179/341 (52%), Gaps = 26/341 (7%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
LPW+ TK+ Y +W+SEIMLQQTQV TVIPYY+RFL++FP I +LA A + V++ W GLG
Sbjct: 26 LPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLG 85
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
YYSRARNLH A+ V ++ G FP + L LPG+G TA AI FA+ + +LDGNV
Sbjct: 86 YYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEPVLDGNV 145
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLL-PKKNIEIYTQGLMDFGSIICKKIKPKCK 180
KR+L R+ I+ + +K+LW A LL P + + Q +MD G+ IC KPKC
Sbjct: 146 KRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAMMDLGATICTAKKPKCS 205
Query: 181 VCPLQLCCISYKTNKINNFLIKNKKNIKNCSIIMFIVI-DDDYVLFQKRSNKGIWGGLLS 239
+CPL+ C +Y+ + +K K F+++ D VL +KR KG+ GGL
Sbjct: 206 LCPLRDNCAAYRNGTPEKYPVKKPKKKLPRRFAAFLILNRDGEVLLEKRPEKGLLGGLWC 265
Query: 240 FPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFIKNYLILPIISHKLTHLQFKIVPCH 299
FP E E L H TH +
Sbjct: 266 FP------------------QFEDEADLLDWLAADGLAAEPLGAFRHTFTHFRL-----T 302
Query: 300 IFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340
I L+ ++ WY + +++ +PAPV+K+L Q+ +
Sbjct: 303 IELRASASLVL-SDGRWYNLSDLESIGLPAPVKKLLQQLKK 342
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase. This equivalog
model identifies mutY members of the pfam00730
superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro
rich loop followed by a conserved aspartate). The major
members of the superfamily are nth and mutY [DNA
metabolism, DNA replication, recombination, and repair].
Length = 275
Score = 285 bits (731), Expect = 6e-96
Identities = 113/253 (44%), Positives = 160/253 (63%), Gaps = 2/253 (0%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
LPW+ K Y +WLSE+MLQQTQV TVIPY++RFL++FP + +LA A + V++LW GLG
Sbjct: 18 LPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLG 77
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
YY+RARNLH A+ V ++ G FP++F L LPG+G+ TA AI FA K ILDGNV
Sbjct: 78 YYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKPYPILDGNV 137
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
KR+L R+ + K +E +LW A LLPK + E + Q LMD G++IC + KPKC +
Sbjct: 138 KRVLSRLFAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMICTRKKPKCDL 197
Query: 182 CPLQLCCISYKTNKINNFLIKNKKN--IKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLS 239
CPLQ C++Y+ + +K K + + + + D VL ++R KG+WGGL
Sbjct: 198 CPLQDFCLAYQQGTWEEYPVKKPKAAPPERTTYFLVLQNYDGEVLLEQRPEKGLWGGLYC 257
Query: 240 FPEWILKDKIINF 252
FP++ +D +
Sbjct: 258 FPQFEDEDSLAFL 270
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 275 bits (706), Expect = 4e-91
Identities = 124/349 (35%), Positives = 186/349 (53%), Gaps = 34/349 (9%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
LPWQ K Y +WLSE+MLQQTQV TVIPY++RF+ +FP + LA A L+ V+ LW+GLG
Sbjct: 22 LPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLG 81
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
YY+RARNLH A+ V + G FP+ F + LPG+G+STA AI + GK ILDGNV
Sbjct: 82 YYARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNV 141
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
KR+L R ++ K +E +LW+ + + P +E + Q +MD G+++C + KPKC++
Sbjct: 142 KRVLARCYAVSGWPGKKEVENRLWQLSEQVTPAVGVERFNQAMMDLGAMVCTRSKPKCEL 201
Query: 182 CPLQLCCISYKTNKINNFLIKN-KKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLSF 240
CPLQ CI+Y + + K K+ + + ++ D V ++R G+WGGL F
Sbjct: 202 CPLQNGCIAYANHSWALYPGKKPKQTLPERTGYFLLLQHGDEVWLEQRPPSGLWGGLFCF 261
Query: 241 PE---------WILKDKIINFVDNNLKNLIELEIKKFISSFGFIKNYLILPIISHKLTHL 291
P+ W L + I +NL L H +H
Sbjct: 262 PQFADEEELRQW-LAQRGIA--ADNLTQLTAFR---------------------HTFSHF 297
Query: 292 QFKIVPCHIFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340
IVP + + ++ N +WY + + + + APV ++L Q+
Sbjct: 298 HLDIVPMWLPVSSFTGCMDEGNGLWYNLAQPPSVGLAAPVERLLQQLRT 346
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 145 bits (366), Expect = 4e-41
Identities = 104/318 (32%), Positives = 168/318 (52%), Gaps = 41/318 (12%)
Query: 19 MLQQTQVNTVIP-YYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVF 77
M QQTQ+NTV+ +Y FL+ FP + LA A LE V+ LW GLGYYSRA+NL A++
Sbjct: 1 MSQQTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICV 60
Query: 78 FKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNI 137
+++ P ++ SL+ LPGIG TA+AI F + +++A +D N+KR+L+R+ G++ +++
Sbjct: 61 KEHHSQLPNDYQSLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGLDPNIHA 120
Query: 138 KFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKIN 197
K ++ K A D L + Q L+D G++IC KPKC +CPL C+ N
Sbjct: 121 KDLQIK----ANDFLNLNESFNHNQALIDLGALICSP-KPKCAICPLNPYCLG--KNNPE 173
Query: 198 NFLIKNKKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFVDNNL 257
+K K+ I + +VI ++ + +K K ++ G+ FP NL
Sbjct: 174 KHTLKKKQEIVQEERYLGVVIQNNQIALEKIEQK-LYLGMHHFP--------------NL 218
Query: 258 KNLIELEIKKFISSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNNFIWY 317
K +E ++ L I H +H +FK+ ++ L +K+ KN +Y
Sbjct: 219 KENLEYKLP-------------FLGAIKH--SHTKFKL---NLNLYLAAIKDLKNPIRFY 260
Query: 318 PIKKIKNSPIPAPVRKIL 335
+K ++ PI + KIL
Sbjct: 261 SLKDLETLPISSMTLKIL 278
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 138 bits (350), Expect = 3e-40
Identities = 51/162 (31%), Positives = 81/162 (50%), Gaps = 8/162 (4%)
Query: 11 YYIWLSEIMLQQTQVNTVIPYYQRFLKKF-PNIMSLAQAKLENVMELWSGLGYYSRARNL 69
+ + +SEI+ QQT V Y+R +++ P +LA A E + EL LGY +A+ L
Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLGYRRKAKYL 60
Query: 70 HICAKLVFFKYNGIF---PKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILI 126
A+ + + G+ P L+ LPG+G+ TA+ + +FA G +D +V+R+L
Sbjct: 61 KELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLK 120
Query: 127 RVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFG 168
R+ I K ++L +LLPK Q LMD G
Sbjct: 121 RLGLI----PKKKTPEELEELLEELLPKPYWGEANQALMDLG 158
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 120 bits (302), Expect = 3e-33
Identities = 50/153 (32%), Positives = 78/153 (50%), Gaps = 5/153 (3%)
Query: 19 MLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG-YYSRARNLHICAKLVF 77
+ QQT V +R +KFP LA A E + EL GLG Y +AR L A+++
Sbjct: 1 LSQQTTDERVNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILV 60
Query: 78 FKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNI 137
+Y G P + L+ LPG+G+ TA+A+ FA GK +D +V RI R+ + +
Sbjct: 61 EEYGGEVPDDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLV----DK 116
Query: 138 KFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSI 170
K +++ + LLP+++ L+DFG
Sbjct: 117 KSTPEEVEKLLEKLLPEEDWRELNLLLIDFGRT 149
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 99.7 bits (249), Expect = 1e-25
Identities = 42/140 (30%), Positives = 75/140 (53%), Gaps = 8/140 (5%)
Query: 15 LSEIMLQQTQVNTVIPYYQRFLKK--FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHI 71
+S I+ QQT +R ++ FP LA+A E + EL GLG+Y +A+ +
Sbjct: 1 VSAILSQQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE 60
Query: 72 CAKLVFFKYNGIFPKNF---ISLINLPGIGQSTASAIRVFAYGKRNA--ILDGNVKRILI 126
A+++ Y G+ P + +L+ LPG+G+ TA A+ +FA G+ + +D +V+R+
Sbjct: 61 LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAK 120
Query: 127 RVLGINCSLNIKFIEKKLWR 146
R+ I+ K +E++L
Sbjct: 121 RLGLIDTKPPKKEVERELEE 140
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 99.2 bits (248), Expect = 1e-24
Identities = 53/195 (27%), Positives = 92/195 (47%), Gaps = 6/195 (3%)
Query: 3 PWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGY 62
+ K+ + + ++ I+ QT V K++P L A E + EL +G
Sbjct: 22 TELDFKDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGL 81
Query: 63 Y-SRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
Y ++A+N+ A+++ K+ G P L++LPG+G+ TA+ + FA+G +D +V
Sbjct: 82 YRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFAFGIPAIAVDTHV 141
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
R+ LG+ + +E+ L + L+PK+ L+ G ICK KP+C+
Sbjct: 142 HRV-SNRLGLVPGKTPEEVEEAL----MKLIPKELWTDLHHWLILHGRYICKARKPRCEE 196
Query: 182 CPLQLCCISYKTNKI 196
CPL C S
Sbjct: 197 CPLADLCPSAGKTGK 211
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 73.9 bits (182), Expect = 1e-15
Identities = 46/176 (26%), Positives = 87/176 (49%), Gaps = 12/176 (6%)
Query: 8 KNTYYIWLSEIMLQQT---QVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYY- 63
N + + ++ I+ Q VN + + +P +LAQA LE + E +G Y
Sbjct: 24 NNPFELLVATILSAQATDKSVNKATK---KLFEVYPTPQALAQAGLEELEEYIKSIGLYR 80
Query: 64 SRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKR 123
++A+N+ +++ +Y G P++ L+ LPG+G+ TA+ + A+G +D +V R
Sbjct: 81 NKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFR 140
Query: 124 ILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKC 179
+ R LG++ + +E++L + L+P++ L+ G CK KP C
Sbjct: 141 VSNR-LGLSKGKDPDKVEEEL----LKLIPREFWTKLHHWLILHGRYTCKARKPLC 191
>gnl|CDD|239523 cd03431, DNA_Glycosylase_C, DNA glycosylase (MutY in bacteria and
hMYH in humans) is responsible for repairing misread
A*oxoG residues to C*G by removing the inappropriately
paired adenine base from the DNA backbone. It belongs to
the Nudix hydrolase superfamily and is important for the
repair of various genotoxic lesions. Enzymes belonging
to this superfamily requires a divalent cation, such as
Mg2+ or Mn2+ for their activity. They are also
recognized by a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V). However, DNA
glycosylase does not seem to contain this signature
motif. DNA glycosylase consists of 2 domains: the
N-terminal domain contains the catalytic properties of
the enzyme and the C-terminal domain affects substrate
(oxoG) binding and enzymatic turnover. The C-terminal
domain is highly similar to MutT, based on secondary
structure and topology, despite low sequence identity.
MutT sanitizes the nucleotide precursor pool by
hydrolyzing oxo-dGTP to oxo-dGMO and inorganic
pyrophosphate. The similarity strongly suggests that the
two proteins share a common evolutionary origin.
Length = 118
Score = 62.0 bits (151), Expect = 5e-12
Identities = 29/126 (23%), Positives = 53/126 (42%), Gaps = 17/126 (13%)
Query: 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFP--EWILKDKIINFVDNNLKNLIELEIKKFI 269
I + ++ +D VL +KR KG+ GL FP EW + + + LK + L ++
Sbjct: 5 IAVVVIRNDGRVLLEKRPEKGLLAGLWEFPSVEWEEEADGEEALLSALKKALRLSLEPLG 64
Query: 270 SSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNNFIWYPIKKIKNSPIPA 329
+ + H TH + + L+ L + W P++++ +P
Sbjct: 65 T-------------VKHTFTHFRLTLHVYLARLEGDLLA--PDEGRWVPLEELDEYALPT 109
Query: 330 PVRKIL 335
+RKIL
Sbjct: 110 VMRKIL 115
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease
III [DNA replication, recombination, and repair].
Length = 215
Score = 43.1 bits (102), Expect = 7e-05
Identities = 50/203 (24%), Positives = 82/203 (40%), Gaps = 28/203 (13%)
Query: 4 WQNTKNTYYIWLSEIMLQQTQVNTV----IPYYQRFLKKFPNIMSLAQAKLENVMELWSG 59
W N I + I+ Q T V + I+ L + +L EL
Sbjct: 24 WWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELA---ELIRP 80
Query: 60 LGYY-SRARNLHICAKLV---FFKYNGIFPKNFIS-LINLPGIGQSTASAIRVFAYGKRN 114
G+Y +A+ L +K + F + L+++ GIG+ TA +I ++A +
Sbjct: 81 SGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYALDRPV 140
Query: 115 AILDGNVKRILIRVLGINCSL--NIK-FIEKKLWRYAIDLLPKKNIEIY--TQGLMD-FG 168
++D +R+L R+ GI IK E+ L +N+ +Y L+
Sbjct: 141 FVVDKYTRRLLSRLGGIEEKKYDEIKELFEENL---------PENLRLYQEFHALIVEHA 191
Query: 169 SIICKKIKPKCKVCPLQLCCISY 191
CKK KP C+ CPL+ C Y
Sbjct: 192 KHFCKK-KPLCEKCPLKEKCKKY 213
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 41.2 bits (96), Expect = 3e-04
Identities = 32/127 (25%), Positives = 63/127 (49%), Gaps = 5/127 (3%)
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
Y S+A N+ +++ ++NG P++ +L LPG+G+ TA+ + A+G +D ++
Sbjct: 82 YNSKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHI 141
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
R+ R N++ +E+KL + ++P + L+ G C KP+C
Sbjct: 142 FRVCNRT-QFAPGKNVEQVEEKLLK----VVPAEFKVDCHHWLILHGRYTCIARKPRCGS 196
Query: 182 CPLQLCC 188
C ++ C
Sbjct: 197 CIIEDLC 203
>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or
apyrimidinic site) lyase (subfamily of ENDO3).
Length = 21
Score = 36.4 bits (85), Expect = 6e-04
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 171 ICKKIKPKCKVCPLQLCCISY 191
IC KP+C CPL+ C +Y
Sbjct: 1 ICTARKPRCDECPLKDLCPAY 21
>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif. The helix-hairpin-helix
DNA-binding motif is found to be duplicated in the
central domain of RuvA. The HhH domain of DisA, a
bacterial checkpoint control protein, is a DNA-binding
domain.
Length = 30
Score = 35.5 bits (83), Expect = 0.001
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 79 KYNGIFPKNFISLINLPGIGQSTASAIRVF 108
G+ P + L+ LPG+G TA AI +
Sbjct: 1 SLEGLIPASREELLALPGVGPKTAEAILSY 30
>gnl|CDD|215841 pfam00293, NUDIX, NUDIX domain.
Length = 133
Score = 34.0 bits (78), Expect = 0.034
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 211 SIIMFIVIDDDYVLFQKRSNKGIWGGLLSFP 241
++ + ++ +D VL +RS ++ GL P
Sbjct: 4 AVGVVLLNEDGEVLLVRRSRPPVFPGLWELP 34
>gnl|CDD|204516 pfam10576, EndIII_4Fe-2S, Iron-sulfur binding domain of
endonuclease III. Escherichia coli endonuclease III (EC
4.2.99.18) is a DNA repair enzyme that acts both as a
DNA N-glycosylase, removing oxidized pyrimidines from
DNA, and as an apurinic/apyrimidinic (AP) endonuclease,
introducing a single-strand nick at the site from which
the damaged base was removed. Endonuclease III is an
iron-sulfur protein that binds a single 4Fe-4S cluster.
The 4Fe-4S cluster does not seem to be important for
catalytic activity, but is probably involved in the
proper positioning of the enzyme along the DNA strand.
The 4Fe-4S cluster is bound by four cysteines which are
all located in a 17 amino acid region at the C-terminal
end of endonuclease III. A similar region is also
present in the central section of mutY and in the
C-terminus of ORF-10 and of the Micro-coccus UV
endonuclease.
Length = 17
Score = 29.7 bits (68), Expect = 0.13
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 172 CKKIKPKCKVCPLQLCC 188
C KPKC+ CPL C
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 33.1 bits (76), Expect = 0.27
Identities = 26/126 (20%), Positives = 36/126 (28%), Gaps = 17/126 (13%)
Query: 197 NNFLIKNK---KNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFV 253
I + KNI N +II + + W F E L +I +
Sbjct: 14 KQIKIPDDLLVKNILNSAIIENLYVKKK---------SKNWEFHFLFAE-TLPIEIYKEL 63
Query: 254 DNNLKNLIELEIKKFISSF----GFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKE 309
+N L E + K I I + L K L K LK
Sbjct: 64 ENALSEEFEQLVAKVEFDIEVRNVDITEQEIQTYFKKIIEQLSVKSPIFKSLLNKLKLKV 123
Query: 310 NKNNFI 315
NN +
Sbjct: 124 KGNNIL 129
>gnl|CDD|240033 cd04677, Nudix_Hydrolase_18, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 132
Score = 30.7 bits (70), Expect = 0.53
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 216 IVIDD-DYVLFQKRSNKGIWG 235
I++++ VL QKRS+ G WG
Sbjct: 13 ILLNEQGEVLLQKRSDTGDWG 33
>gnl|CDD|223705 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit
[DNA replication, recombination, and repair].
Length = 201
Score = 29.5 bits (67), Expect = 2.0
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 88 FISLINLPGIGQSTASAI-RVFAYGK-RNAILDGNVKRILIRVLGIN 132
F LI++ GIG A AI + AI + +VK L ++ GI
Sbjct: 72 FRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVK-ALSKIPGIG 117
>gnl|CDD|223433 COG0356, AtpB, F0F1-type ATP synthase, subunit a [Energy production
and conversion].
Length = 246
Score = 28.4 bits (64), Expect = 5.3
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFVDNNLKNLIELEIKKFISS 271
++F+ + + L KR+ K + GG +F E I+ FV +K+ I + KKF
Sbjct: 40 GVVFLFL---FSLLAKRNTKLVPGGFQNFLEMIV-----EFVRGMVKDNIGGKGKKFAPL 91
Query: 272 FGFI 275
+
Sbjct: 92 ALTL 95
>gnl|CDD|223608 COG0534, NorM, Na+-driven multidrug efflux pump [Defense
mechanisms].
Length = 455
Score = 28.3 bits (64), Expect = 7.3
Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 87 NFISLINLPGIGQSTASAIRV-FAYGKRNAILDGNVKRILIRVLGIN 132
S I +P G + A I V G N +R L ++
Sbjct: 284 RIASFIFMPPFGIAQAVTILVGQNLGAGNY---KRARRAARLALKLS 327
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 28.3 bits (64), Expect = 7.7
Identities = 15/119 (12%), Positives = 41/119 (34%), Gaps = 18/119 (15%)
Query: 194 NKINNFLIKNKKNIKNCSIIMFIVIDD------------DYVLFQKRSNKGIWGGLLSFP 241
L ++ +I + + I +++ + ++ + + N ++ LL
Sbjct: 58 KLFKEKLKQSFSHIADIKVTFSIEVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQ 117
Query: 242 EWILKDKIIN------FVDNNLKNLIELEIKKFISSFGFIKNYLILPIISHKLTHLQFK 294
+ ++ + ++LK ++ K FGF + I K +F+
Sbjct: 118 KVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFE 176
>gnl|CDD|239079 cd02339, ZZ_Mind_bomb, Zinc finger, ZZ type. Zinc finger present in
Drosophila Mind bomb (D-mib) and related proteins. The
ZZ motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Mind bomb is an E3 ubiqitin ligase that has been shown
to regulate signaling by the Notch ligand Delta in
Drosophila melanogaster.
Length = 45
Score = 25.1 bits (55), Expect = 7.8
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 172 CKK-----IKPKCKVCP-LQLCCISYKTNK 195
C+K I+ KC CP LC Y +K
Sbjct: 6 CRKQGIIGIRWKCAECPNYDLCTTCYHGDK 35
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 28.0 bits (63), Expect = 8.9
Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 28/92 (30%)
Query: 254 DNNLKNLIELEIKKFISSFGFIKNYLILPIIS-HKLTHLQFKIVPCHIFLKKCFLKEN-- 310
D L L+ELE+++ +S + F + +PI+S L L+ L EN
Sbjct: 143 DEELLELVELEVRELLSKYDFPGDD--IPIVSGSALLALE-------------ALTENPK 187
Query: 311 --KNNFIWYPIKKIKN------SPIPAPVRKI 334
+ W + KI N S IP P R
Sbjct: 188 IKRGENKW--VDKIYNLMDAVDSYIPTPERDT 217
>gnl|CDD|217511 pfam03358, FMN_red, NADPH-dependent FMN reductase.
Length = 151
Score = 27.2 bits (61), Expect = 9.4
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 126 IRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEI 159
+++L I+ S +KL +A +LL + E+
Sbjct: 1 MKILVISGSPRKGSNTRKLAEWAAELLEEAGAEV 34
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
0.327 0.144 0.449
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,743,420
Number of extensions: 1776203
Number of successful extensions: 2227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2182
Number of HSP's successfully gapped: 75
Length of query: 341
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 243
Effective length of database: 6,590,910
Effective search space: 1601591130
Effective search space used: 1601591130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.4 bits)