RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4002
(378 letters)
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 203 bits (520), Expect = 2e-64
Identities = 73/220 (33%), Positives = 117/220 (53%), Gaps = 37/220 (16%)
Query: 147 RYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKH 206
+ +L++++LS+QT DEV + A L + T E++ N E+ L +LI +G ++ KAK+
Sbjct: 29 PFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKN 88
Query: 207 IKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSP 266
IK + IL + + ++P+T E L LPGVG K A++ ++ A+G
Sbjct: 89 IKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFAFG----------------- 131
Query: 267 SSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESL 326
IP + VD HVHR+S+RLG KTPE+ + L +P+ L
Sbjct: 132 -------------------IPAIAVDTHVHRVSNRLGLVPG-KTPEEVEEALMKLIPKEL 171
Query: 327 WSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELA 366
W++++H L+ G+ ICK+++P CE C DLCP K
Sbjct: 172 WTDLHHWLILHGRYICKARKPRCEECPLADLCPSAGKTGK 211
>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 = 143 bits (362), Expect = 9e-42
Identities = 61/184 (33%), Positives = 86/184 (46%), Gaps = 36/184 (19%)
Query: 156 LSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILK 215
LS QT DE + A RL E T E++ E+ L +LI +GF++ KA+++ + IL
Sbjct: 1 LSQQTTDERVNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILV 60
Query: 216 KNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSE 275
+ Y ++P+ E L KLPGVG K A+ ++ A G
Sbjct: 61 EEYGGEVPDDREELLKLPGVGRKTANAVLSFALGKPF----------------------- 97
Query: 276 LICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWSEVNHLLV 335
+ VD HV RI+ RLG TPE+ K LE LPE W E+N LL+
Sbjct: 98 -------------IPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPEEDWRELNLLLI 144
Query: 336 GFGQ 339
FG+
Sbjct: 145 DFGR 148
>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 = 7e-40
Identities = 57/195 (29%), Positives = 84/195 (43%), Gaps = 41/195 (21%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEH-GLTIENICNTSEDVLGKLIIPVGFWKTKAKH 206
+ VL+S +LS QT D+ + A RL E G T E + E+ L +LI +G+ + KAK+
Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLGY-RRKAKY 59
Query: 207 IKMASDILKKNYNNDI---PNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPI 263
+K + + + + + P+ E L LPGVG K A++ + A G
Sbjct: 60 LKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG-------------- 105
Query: 264 LSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLP 323
VD HV R+ RLG KTPE+ + LE LP
Sbjct: 106 ----------------------PDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP 143
Query: 324 ESLWSEVNHLLVGFG 338
+ W E N L+ G
Sbjct: 144 KPYWGEANQALMDLG 158
>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 = 121 bits (305), Expect = 7e-33
Identities = 58/202 (28%), Positives = 98/202 (48%), Gaps = 37/202 (18%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
+ +L++ +LS+Q D+ + A +L E T + + + L + I +G ++ KAK+I
Sbjct: 27 FELLVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNI 86
Query: 208 KMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPS 267
IL + Y ++P E L KLPGVG K A++ +N A+GI
Sbjct: 87 IALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVAFGI----------------- 129
Query: 268 SRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLW 327
P + VD HV R+S+RLG +K K P+ +EL +P W
Sbjct: 130 -------------------PAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIPREFW 169
Query: 328 SEVNHLLVGFGQQICKSQRPSC 349
++++H L+ G+ CK+++P C
Sbjct: 170 TKLHHWLILHGRYTCKARKPLC 191
>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 = 108 bits (271), Expect = 2e-28
Identities = 48/177 (27%), Positives = 71/177 (40%), Gaps = 39/177 (22%)
Query: 152 ISLMLSSQTKDEVNHAAMGRLKEH--GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKM 209
+S +LS QT D+ + RL E T E++ E+ L +LI +GF++ KAK+IK
Sbjct: 1 VSAILSQQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE 60
Query: 210 ASDILKKNYNNDIPNTI---ELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSP 266
+ IL + Y +P + E L LPGVG A + A G
Sbjct: 61 LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAVLLFALG----------------- 103
Query: 267 SSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLP 323
+ VD HV R++ RLG ++ +ELE P
Sbjct: 104 -----------------RPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVERELEELWP 143
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 70.4 bits (172), Expect = 4e-14
Identities = 49/216 (22%), Positives = 93/216 (43%), Gaps = 37/216 (17%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
+ +LI+++LS+Q D + A +L T + + + I +G + +KA+++
Sbjct: 30 FELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENV 89
Query: 208 KMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPS 267
IL + +N ++P L LPGVG K A++ +N A+G
Sbjct: 90 IKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFG------------------ 131
Query: 268 SRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLW 327
P + VD H+ R+ +R + K E ++L +P
Sbjct: 132 ------------------WPTIAVDTHIFRVCNRTQFAP-GKNVEQVEEKLLKVVPAEFK 172
Query: 328 SEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKK 363
+ +H L+ G+ C +++P C +C+ +DLC +K
Sbjct: 173 VDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 63.5 bits (155), Expect = 3e-11
Identities = 53/237 (22%), Positives = 91/237 (38%), Gaps = 44/237 (18%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
Y V +S ++ QT+ R E TI+ + ED + K +G++ ++A+++
Sbjct: 35 YRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYY-SRARNL 93
Query: 208 KMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPS 267
A+ + + + + P+ E L LPGVGP A ILS +
Sbjct: 94 HKAAQEVVERHGGEFPDDEEELAALPGVGPYTAG--------------------AILSFA 133
Query: 268 SRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL----GWTKVFKTPEDTRKELESWL- 322
+ P +D +V R+ RL G KT ++ + E L
Sbjct: 134 --------------FNQPEP--VLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLT 177
Query: 323 PESLWSEVNHLLVGFGQQICKSQRPSCETC-LNKDLCP-QGKKELAERVKKSPKKRK 377
P+ + N ++ G IC +++P C C L + + VKK KK
Sbjct: 178 PDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKLP 234
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease
III [DNA replication, recombination, and repair].
Length = 215
Score = 56.2 bits (136), Expect = 3e-09
Identities = 54/223 (24%), Positives = 91/223 (40%), Gaps = 45/223 (20%)
Query: 143 PEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLT-IENICNTSEDVLGKLIIPVGFWK 201
P + ++I +L+ T + A+ LK G+ ++ I E+ L +LI P GF+
Sbjct: 26 PADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYN 85
Query: 202 TKAKHIKMASDILKK---NYNNDIPN-TIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKD 257
KAK +K S L K N + E L + G+G + A + +A
Sbjct: 86 QKAKRLKALSKNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYA---------- 135
Query: 258 ESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKE 317
++ P VD + R+ RLG + K ++ ++
Sbjct: 136 ------------------------LDR--PVFVVDKYTRRLLSRLGGIEE-KKYDEIKEL 168
Query: 318 LESWLPES--LWSEVNHLLVGFGQQICKSQRPSCETCLNKDLC 358
E LPE+ L+ E + L+V + CK ++P CE C K+ C
Sbjct: 169 FEENLPENLRLYQEFHALIVEHAKHFCK-KKPLCEKCPLKEKC 210
>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 = 48.9 bits (117), Expect = 2e-06
Identities = 51/238 (21%), Positives = 89/238 (37%), Gaps = 46/238 (19%)
Query: 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHI 207
Y V +S ++ QT+ R E T++ + N +D + KL +G++ +A+++
Sbjct: 27 YRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYY-ARARNL 85
Query: 208 KMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPS 267
A+ + + + + P E L LPGVG A G + ++ PIL +
Sbjct: 86 HKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTA--------GAILSFALNK-PYPILDGN 136
Query: 268 -----SRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWL 322
SR + +K E ++ L ES L
Sbjct: 137 VKRVLSRLFAVEGWPGKKKVENRLWTLA----------------------------ESLL 168
Query: 323 PESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKE--LAERVKKSPKKRKS 378
P++ N L+ G IC ++P C+ C +D C ++ E K PK
Sbjct: 169 PKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFC-LAYQQGTWEEYPVKKPKAAPP 225
>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 = 43.9 bits (105), Expect = 2e-06
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 218 YNNDIPNTIELLCKLPGVGPKMAHLCMNH 246
IP + E L LPGVGPK A +++
Sbjct: 2 LEGLIPASREELLALPGVGPKTAEAILSY 30
>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or
apyrimidinic site) lyase (subfamily of ENDO3).
Length = 21
Score = 34.1 bits (79), Expect = 0.004
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 341 ICKSQRPSCETCLNKDLCP 359
IC +++P C+ C KDLCP
Sbjct: 1 ICTARKPRCDECPLKDLCP 19
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 36.9 bits (85), Expect = 0.011
Identities = 34/153 (22%), Positives = 61/153 (39%), Gaps = 37/153 (24%)
Query: 200 WKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDES 259
+ ++AK++K +++I K +++ +PN + L KLPG+G A
Sbjct: 45 YYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTA------------------- 85
Query: 260 RQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELE 319
+ ++C EK CVD ++ R+ RL +D + +
Sbjct: 86 --------------NAILCFGFREKSA---CVDANIKRVLLRLFGLDPNIHAKDLQIKAN 128
Query: 320 SWLPESLWSEVNHLLVGFGQQICKSQRPSCETC 352
+L + N L+ G IC S +P C C
Sbjct: 129 DFLNLNESFNHNQALIDLGALIC-SPKPKCAIC 160
>gnl|CDD|220339 pfam09674, DUF2400, Protein of unknown function (DUF2400). Members
of this uncharacterized protein family are found
sporadically, so far only among spirochetes, epsilon and
delta proteobacteria, and Bacteroides. The function is
unknown and its gene neighborhoods show little
conservation.
Length = 230
Score = 36.4 bits (85), Expect = 0.015
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 11/38 (28%)
Query: 269 RQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTK 306
+ IS S+LI P +D H HR++ +LG K
Sbjct: 166 KSISPSQLII--------P---LDTHTHRVARKLGLLK 192
>gnl|CDD|223430 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 198
Score = 34.1 bits (79), Expect = 0.068
Identities = 15/33 (45%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 216 KNYNNDIPNTIELLCKLPGVGPKMA-----HLC 243
Y I I+ L KLPGVGPK A HL
Sbjct: 1 MMYPPPIEKLIDALKKLPGVGPKSAQRLAFHLL 33
>gnl|CDD|234616 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 33.1 bits (77), Expect = 0.13
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 218 YNNDIPNTIELLCKLPGVGPK----MA-HLCMN 245
Y I IE L KLPG+GPK +A HL
Sbjct: 2 YPPPIEKLIEALRKLPGIGPKSAQRLAFHLLQR 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 = 28.2 bits (64), Expect = 0.47
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 342 CKSQRPSCETCLNKDLC 358
C +++P CE C DLC
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg). All proteins
in this family for which functions are known are
8-oxo-guanaine DNA glycosylases that function in base
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). This family is distantly realted
to the Nth-MutY superfamily [DNA metabolism, DNA
replication, recombination, and repair].
Length = 310
Score = 31.8 bits (72), Expect = 0.56
Identities = 34/108 (31%), Positives = 45/108 (41%), Gaps = 41/108 (37%)
Query: 227 ELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKI 286
E LC+LPGVGPK+A C+ + G+ K ++ +
Sbjct: 220 EALCELPGVGPKVAD-CI-----CLMGLDKPQA--------------------------V 247
Query: 287 PQLCVDVHVHRISHRL-GW---TKVFKTP-EDTRKELESWLPESLWSE 329
P VDVHV RI++R W T K P RKEL + SLW
Sbjct: 248 P---VDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGN-FFRSLWGP 291
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 31.3 bits (71), Expect = 0.74
Identities = 24/109 (22%), Positives = 34/109 (31%), Gaps = 21/109 (19%)
Query: 151 LISLMLSSQTKDEVNHAAMGRLKE----------HGLTIENICNTSEDVLGKLIIPVGFW 200
L+ +LS Q RL T E + E+ L + G
Sbjct: 109 LVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRC----GLS 164
Query: 201 KTKAKHIK-----MASDILKKN--YNNDIPNTIELLCKLPGVGPKMAHL 242
KA++I A L + IE L L G+GP A +
Sbjct: 165 GRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEM 213
>gnl|CDD|197622 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 27.3 bits (62), Expect = 0.94
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 227 ELLCKLPGVGPKMA 240
E L K+PG+GPK A
Sbjct: 1 EELLKVPGIGPKTA 14
>gnl|CDD|223705 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit
[DNA replication, recombination, and repair].
Length = 201
Score = 29.9 bits (68), Expect = 1.4
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 226 IELLCKLPGVGPKMAH 241
++ L K+PG+G K A
Sbjct: 107 VKALSKIPGIGKKTAE 122
>gnl|CDD|233054 TIGR00615, recR, recombination protein RecR. All proteins in this
family for which functions are known are involved in the
initiation of recombination and recombinational repair.
RecF is also required. 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 = 195
Score = 30.0 bits (68), Expect = 1.6
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 217 NYNNDIPNTIELLCKLPGVGPKMA 240
Y I IE L KLPG+GPK A
Sbjct: 1 QYPPPISKLIESLKKLPGIGPKSA 24
>gnl|CDD|184390 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Provisional.
Length = 218
Score = 29.8 bits (67), Expect = 1.8
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 143 PEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGL-------TIENICNTSEDVLGKLII 195
P ++ L+ +L+ TK E ++ LK + ++ I L + +
Sbjct: 26 PNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVR 85
Query: 196 PVGFWKTKAKH-IKMASDILK 215
P GF+ KAK I ++ +ILK
Sbjct: 86 PSGFYNQKAKRLIDLSENILK 106
>gnl|CDD|234645 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
Length = 192
Score = 29.3 bits (67), Expect = 2.4
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 226 IELLCKLPGVGPKMA 240
++ L K+PG+G K A
Sbjct: 107 VKALTKVPGIGKKTA 121
>gnl|CDD|205097 pfam12836, HHH_3, Helix-hairpin-helix motif. The HhH domain is a
short DNA-binding domain.
Length = 65
Score = 26.7 bits (60), Expect = 4.3
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 225 TIELLCKLPGVGPKMA 240
+ ELL ++PG+GPK+A
Sbjct: 12 SAELLQRVPGIGPKLA 27
>gnl|CDD|129193 TIGR00084, ruvA, Holliday junction DNA helicase, RuvA subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions [DNA metabolism,
DNA replication, recombination, and repair].
Length = 191
Score = 28.1 bits (63), Expect = 5.2
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 224 NTIELLCKLPGVGPKMA 240
++ L K+PGVG K A
Sbjct: 104 EEVKALVKIPGVGKKTA 120
>gnl|CDD|149881 pfam08950, DUF1861, Protein of unknown function (DUF1861). This
hypothetical protein, found in bacteria and in the
eukaryote Leishmania, has no known function.
Length = 298
Score = 28.4 bits (64), Expect = 5.3
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 17/74 (22%)
Query: 236 GPKMAHLCMNHAWGIVTGIG---KDESRQPI---------LSPSSRQISRSELI----CV 279
G A+L + G + I KD +R P+ L P + + S ++I C
Sbjct: 189 GVNQAYLLSSGKIGCIGHIAYFDKDGNRHPLNVYYNTSFVLDPDTNEYSDEKIIGTRGCF 248
Query: 280 RKCEKKIPQLCVDV 293
C K P L D
Sbjct: 249 PDCPAKRPDL-ADC 261
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also
known as Pol kappa, DinB, and Dpo4, is a translesion
synthesis (TLS) polymerase. Translesion synthesis is a
process that allows the bypass of a variety of DNA
lesions. TLS polymerases lack proofreading activity and
have low fidelity and low processivity. They use
damaged DNA as templates and insert nucleotides opposite
the lesions. Known primarily as Pol IV in prokaryotes
and Pol kappa in eukaryotes, this polymerase has a
propensity for generating frameshift mutations. The
eukaryotic Pol kappa differs from Pol IV and Dpo4 by an
N-terminal extension of ~75 residues known as the
"N-clasp" region. The structure of Pol kappa shows DNA
that is almost totally encircled by Pol kappa, with the
N-clasp region augmenting the interactions between DNA
and the polymerase. Pol kappa is more resistant than Pol
eta and Pol iota to bulky guanine adducts and is
efficient at catalyzing the incorporation of dCTP.
Bacterial pol IV has a higher error rate than other
Y-family polymerases.
Length = 334
Score = 28.3 bits (64), Expect = 6.4
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 208 KMASDILKKN-----YNNDIPNTIELL--CKLPGVGPKMA-HLCMNHAWGIVTG 253
K+ASD+ K N D+ + L K+PGVG A L GI T
Sbjct: 145 KIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKL---KELGIKTI 195
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated.
Length = 343
Score = 28.2 bits (64), Expect = 8.8
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 21/59 (35%)
Query: 208 KMASDILKKN------YNN------DIPNTIELLCKLPGVGPKMA-HLCMNHAWGIVTG 253
K+ASD K N +P + K+PGVG A L HA GI T
Sbjct: 142 KIASDWNKPNGLFVITPEEVDAFLATLP-----VEKIPGVGKVTAEKL---HALGIYTC 192
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol beta,
Pol lambda, Pol mu, and terminal deoxyribonucleotidyl
transferase (TdT). Pol beta and Pol lambda are primarily
DNA template-dependent polymerases. TdT is a DNA
template-independent polymerase. Pol mu has both
template dependent and template independent activities.
This subgroup belongs to the Pol beta-like NT
superfamily. In the majority of enzymes in this
superfamily, two carboxylates, Dx[D/E], together with a
third more distal carboxylate, coordinate two divalent
metal cations involved in a two-metal ion mechanism of
nucleotide addition. These three carboxylate residues
are fairly well conserved in this family.
Length = 307
Score = 27.9 bits (63), Expect = 9.8
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 220 NDIPNTIELLCKLPGVGPKMA 240
D+P + LL ++PGVGPK A
Sbjct: 78 EDVPPGLLLLLRVPGVGPKTA 98
>gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase
(isomerizing). The member from Methanococcus jannaschii
contains an intein [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan,
Central intermediary metabolism, Amino sugars].
Length = 607
Score = 28.0 bits (63), Expect = 9.8
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 139 VDIAPEVRRYHVLI---SLML----SSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVL 190
V+IA E R ++ +L++ S +T D + AA+ KE G ICN L
Sbjct: 323 VEIASEFRYRKPVVDKDTLVIAISQSGETADTL--AALRLAKELGAKTLGICNVPGSTL 379
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
0.315 0.131 0.400
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: 18,685,041
Number of extensions: 1748922
Number of successful extensions: 1585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1575
Number of HSP's successfully gapped: 41
Length of query: 378
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 279
Effective length of database: 6,546,556
Effective search space: 1826489124
Effective search space used: 1826489124
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 (21.6 bits)
S2: 60 (26.7 bits)