RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026681
(235 letters)
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 223 bits (572), Expect = 3e-74
Identities = 74/190 (38%), Positives = 115/190 (60%), Gaps = 9/190 (4%)
Query: 25 RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKAC 84
F +L++ +LS+ T D+V + A L + T E + ADE +++LI + Y KA
Sbjct: 29 PFELLVAVILSAQTTDEVVNKATPALFKR-YPTPEDLLNADEEELEELIKSIGLYRNKAK 87
Query: 85 NMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICN 144
N+K++A+I L K+ G++P + +ELL+LPG+G K AN+V++ F + I VDTHVHR+ N
Sbjct: 88 NIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFA-FGIPAIAVDTHVHRVSN 146
Query: 145 RLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTV 204
RLG V +PE+ EAL + +PKE W ++ L+ G+ IC +PRC C +
Sbjct: 147 RLGLV-------PGKTPEEVEEALMKLIPKELWTDLHHWLILHGRYICKARKPRCEECPL 199
Query: 205 SEYCPSAFKE 214
++ CPSA K
Sbjct: 200 ADLCPSAGKT 209
>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 = 160 bits (407), Expect = 5e-50
Identities = 60/166 (36%), Positives = 89/166 (53%), Gaps = 11/166 (6%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
F VL+S +LS T DK + A +RL + T EA+ ADE +++LI + + RKA
Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLGYR-RKAKY 59
Query: 86 MKKIAKICLTKYDGDI---PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRI 142
+K++A+ + + G + P + +ELLALPG+G K AN+V+ VDTHV R+
Sbjct: 60 LKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFA-LGPDAFPVDTHVRRV 118
Query: 143 CNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFG 188
RLG + K +PE+ E L+ LPK W N L+ G
Sbjct: 119 LKRLGLIP------KKKTPEELEELLEELLPKPYWGEANQALMDLG 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 = 148 bits (375), Expect = 2e-45
Identities = 62/157 (39%), Positives = 93/157 (59%), Gaps = 8/157 (5%)
Query: 34 LSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC 93
LS T D+ + A +RL + T E + ADE +++LI + FY RKA + ++A+I
Sbjct: 1 LSQQTTDERVNKATERLFEKFP-TPEDLAAADEEELEELIRGLGFYRRKARYLIELARIL 59
Query: 94 LTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPG 153
+ +Y G++P +ELL LPG+G K AN V++ I VDTHV RI RLG V
Sbjct: 60 VEEYGGEVPDDREELLKLPGVGRKTANAVLSFAL-GKPFIPVDTHVLRIAKRLGLV---- 114
Query: 154 TKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQT 190
K S+PE+ + L++ LP+E+W +N LL+ FG+T
Sbjct: 115 --DKKSTPEEVEKLLEKLLPEEDWRELNLLLIDFGRT 149
>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 = 149 bits (378), Expect = 3e-45
Identities = 55/174 (31%), Positives = 98/174 (56%), Gaps = 9/174 (5%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
F +L++ +LS+ DK + A ++L + T +A+ +A +++ I + Y KA N
Sbjct: 27 FELLVATILSAQATDKSVNKATKKLFEV-YPTPQALAQAGLEELEEYIKSIGLYRNKAKN 85
Query: 86 MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNR 145
+ + +I + +Y G++P +EL+ LPG+G K AN+V+ + F + I VDTHV R+ NR
Sbjct: 86 IIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVA-FGIPAIAVDTHVFRVSNR 144
Query: 146 LGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRC 199
LG +K K P++ E L + +P+E W +++ L+ G+ C +P C
Sbjct: 145 LGL-----SKGKD--PDKVEEELLKLIPREFWTKLHHWLILHGRYTCKARKPLC 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 = 122 bits (308), Expect = 2e-35
Identities = 51/150 (34%), Positives = 76/150 (50%), Gaps = 11/150 (7%)
Query: 30 LSALLSSLTKDKVADGALQRLLQ-NGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK 88
+SA+LS T DK A+ +RL + G T E + +ADE +++LI + FY RKA +K+
Sbjct: 1 VSAILSQQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE 60
Query: 89 IAKICLTKYDGDIPSSLDE---LLALPGIGPKMANMVMTLGW-FNVQGICVDTHVHRICN 144
+A+I + Y G +P L+E LLALPG+G A V+ VDTHV R+
Sbjct: 61 LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAK 120
Query: 145 RLGWVTQPGTKQKTSSPEQTREALQRWLPK 174
RLG + ++ L+ P
Sbjct: 121 RLGLI------DTKPPKKEVERELEELWPP 144
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 94.3 bits (234), Expect = 8e-24
Identities = 62/191 (32%), Positives = 96/191 (50%), Gaps = 15/191 (7%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACN 85
F +L++ LLS+ D + A +L +T A+ + +K I + Y KA N
Sbjct: 30 FELLIAVLLSAQATDVSVNKATAKLYPVA-NTPAAMLELGVEGVKTYIKTIGLYNSKAEN 88
Query: 86 MKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVM--TLGWFNVQGICVDTHVHRIC 143
+ K +I L +++G++P L ALPG+G K AN+V+ GW I VDTH+ R+C
Sbjct: 89 VIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGW---PTIAVDTHIFRVC 145
Query: 144 NRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCT 203
NR + PG + EQ E L + +P E V + L+ G+ C +PRCG C
Sbjct: 146 NRTQFA--PG-----KNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCI 198
Query: 204 VSEYCPSAFKE 214
+ + C +KE
Sbjct: 199 IEDLC--EYKE 207
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 91.3 bits (227), Expect = 1e-21
Identities = 46/178 (25%), Positives = 86/178 (48%), Gaps = 6/178 (3%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
T +A+ A E + + +Y+R A N+ K A+ + ++ G+ P +EL ALPG+GP
Sbjct: 65 TIKALAAAPEDEVLKAWEGLGYYSR-ARNLHKAAQEVVERHGGEFPDDEEELAALPGVGP 123
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
A +++ FN +D +V R+ +RL G K + ++ E ++ L +
Sbjct: 124 YTAGAILSFA-FNQPEPVLDGNVKRVLSRL--FAISGDIGKPKTKKELWELAEQLLTPDR 180
Query: 177 WVR-INPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKKSESSSLRKL 233
N ++ G TICT +P+C +C + + C +A++ + KK + R+
Sbjct: 181 RPGDFNQAMMDLGATICTAKKPKCSLCPLRDNC-AAYRNGTPEKYPVKKPKKKLPRRF 237
>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 = 78.2 bits (193), Expect = 3e-17
Identities = 44/168 (26%), Positives = 82/168 (48%), Gaps = 5/168 (2%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGP 116
T +A+ A + + L + +Y R A N+ K A+ + ++ G+ P ++L ALPG+G
Sbjct: 57 TVQALANAPQDEVLKLWEGLGYYAR-ARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGR 115
Query: 117 KMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEE 176
A +++ N +D +V R+ +RL V K+K + + + LPK +
Sbjct: 116 YTAGAILSFA-LNKPYPILDGNVKRVLSRLFAVEGWPGKKKVEN--RLWTLAESLLPKAD 172
Query: 177 WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
N L+ G ICT +P+C +C + ++C A+++ + KK
Sbjct: 173 PEAFNQALMDLGAMICTRKKPKCDLCPLQDFC-LAYQQGTWEEYPVKK 219
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 72.0 bits (176), Expect = 6e-15
Identities = 42/134 (31%), Positives = 66/134 (49%), Gaps = 16/134 (11%)
Query: 79 YTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH 138
Y +A N+KK A+IC+ ++ +P+ LL LPGIG AN ++ G F + CVD +
Sbjct: 45 YYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKSACVDAN 103
Query: 139 VHRICNRLGWVTQPGTKQKTSSPEQTREALQR----WLPKEEWVRINPLLVGFGQTICTP 194
+ R+ RL + P + LQ +L E N L+ G IC+P
Sbjct: 104 IKRVLLRLFGL----------DPNIHAKDLQIKANDFLNLNESFNHNQALIDLGALICSP 153
Query: 195 LRPRCGMCTVSEYC 208
+P+C +C ++ YC
Sbjct: 154 -KPKCAICPLNPYC 166
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease
III [DNA replication, recombination, and repair].
Length = 215
Score = 61.2 bits (149), Expect = 2e-11
Identities = 48/194 (24%), Positives = 88/194 (45%), Gaps = 15/194 (7%)
Query: 21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYT 80
P + + +++ A+L+ T K + AL+ L G+ + I K DE + +LI P FY
Sbjct: 26 PADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYN 85
Query: 81 RKACNMKKIAKICL---TKYDGDIPSSL-DELLALPGIGPKMANMVMTLGWFNVQGICVD 136
+KA +K ++K + L +ELL++ GIG + A+ + L + VD
Sbjct: 86 QKAKRLKALSKNLAKFFINLESFKSEVLREELLSIKGIGKETAD-SILLYALDRPVFVVD 144
Query: 137 THVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN--PLLVGFGQTICTP 194
+ R+ +RLG + + ++ +E + LP+ + L+V + C
Sbjct: 145 KYTRRLLSRLGGI-------EEKKYDEIKELFEENLPENLRLYQEFHALIVEHAKHFCKK 197
Query: 195 LRPRCGMCTVSEYC 208
+P C C + E C
Sbjct: 198 -KPLCEKCPLKEKC 210
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 56.3 bits (136), Expect = 2e-09
Identities = 43/151 (28%), Positives = 70/151 (46%), Gaps = 13/151 (8%)
Query: 78 FYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDT 137
+Y R A N+ K A+ T + G+ P + +E+ ALPG+G A +++L I +D
Sbjct: 82 YYAR-ARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPI-LDG 139
Query: 138 HVHRICNRL----GWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTICT 193
+V R+ R GW PG K+ + Q E + P R N ++ G +CT
Sbjct: 140 NVKRVLARCYAVSGW---PGKKEVENRLWQLSEQVT---PAVGVERFNQAMMDLGAMVCT 193
Query: 194 PLRPRCGMCTVSEYCPSAFKESSTSSSKSKK 224
+P+C +C + C A+ S + KK
Sbjct: 194 RSKPKCELCPLQNGC-IAYANHSWALYPGKK 223
>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 = 46.2 bits (111), Expect = 1e-07
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 96 KYDGDIPSSLDELLALPGIGPKMANMVM 123
+G IP+S +ELLALPG+GPK A ++
Sbjct: 1 SLEGLIPASREELLALPGVGPKTAEAIL 28
>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 = 42.6 bits (100), Expect = 8e-05
Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 108 LLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRL-GWVTQPGTKQKTSSPEQTRE 166
L LPG+GPK+A+ + +G Q + VD HV RI NR W P T + R+
Sbjct: 222 LCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPW--HPKTSRAKGPSPFARK 279
Query: 167 ALQRWLPKEEW 177
L + W
Sbjct: 280 ELGN-FFRSLW 289
>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or
apyrimidinic site) lyase (subfamily of ENDO3).
Length = 21
Score = 37.5 bits (88), Expect = 1e-04
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 191 ICTPLRPRCGMCTVSEYCPSA 211
ICT +PRC C + + CP+
Sbjct: 1 ICTARKPRCDECPLKDLCPAY 21
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 36.3 bits (84), Expect = 0.007
Identities = 31/123 (25%), Positives = 45/123 (36%), Gaps = 22/123 (17%)
Query: 26 FAVLLSALLSSLTKDKVADGALQRLLQ------NGLH---TAEAIDKADEATIKDLIYPV 76
F L+ A+LS A RL+ H T E + ADE ++
Sbjct: 106 FEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRCGLSG 165
Query: 77 AFYTRKACNMKKIAKICLTK-------YDGDIPSSLDELLALPGIGPKMANMVM--TLGW 127
RKA + +A+ +++EL AL GIGP A M + LG
Sbjct: 166 ----RKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGR 221
Query: 128 FNV 130
+V
Sbjct: 222 PDV 224
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 35.7 bits (83), Expect = 0.019
Identities = 30/109 (27%), Positives = 46/109 (42%), Gaps = 31/109 (28%)
Query: 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTR 81
E+ LL+A+ S K L RLL A I E T K+L F T
Sbjct: 475 GEKSAQNLLNAIEKSKEK------PLARLL-----FALGIRHVGEVTAKNLA--KHFGT- 520
Query: 82 KACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNV 130
+ K+ +SL+ELL++ G+GPK+A ++ +F+
Sbjct: 521 ----LDKLKA-----------ASLEELLSVEGVGPKVAESIVN--FFHD 552
>gnl|CDD|236671 PRK10308, PRK10308, 3-methyl-adenine DNA glycosylase II;
Provisional.
Length = 283
Score = 35.1 bits (81), Expect = 0.021
Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL-----TKYDGDIPSSLDELLAL 111
T E + AD +K L P+ ++A + +A L GD+ ++ L
Sbjct: 157 TPERLAAADPQALKALGMPL----KRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTF 212
Query: 112 PGIGPKMANMVMTLGW 127
PGIG AN GW
Sbjct: 213 PGIGRWTANYFALRGW 228
>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 = 34.9 bits (81), Expect = 0.025
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 16/76 (21%)
Query: 67 ATIKDLIYPVAFYTRKACNM----KKIAKIC--------LTKYD---GDIPSSLDELLAL 111
++ L P+ A + KKIA+ L K + D+P L LL +
Sbjct: 32 RALESLPEPIESLEE-AKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRV 90
Query: 112 PGIGPKMANMVMTLGW 127
PG+GPK A + LG
Sbjct: 91 PGVGPKTARKLYELGI 106
>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif. The HhH domain of
DisA, a bacterial checkpoint control protein, is a
DNA-binding domain.
Length = 64
Score = 31.7 bits (73), Expect = 0.035
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 7/47 (14%)
Query: 87 KKIAKICLTKYDGDI----PSSLDELLALPGIGPKMANMVMTLGWFN 129
+K AK+ L K+ G + +S++ELL + IGP +A ++ +F
Sbjct: 13 EKTAKL-LAKHFGSLDALANASVEELLEIDDIGPIVAQSIVE--FFA 56
>gnl|CDD|197622 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 30.3 bits (70), Expect = 0.052
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 106 DELLALPGIGPKMANMVM 123
+ELL +PGIGPK A ++
Sbjct: 1 EELLKVPGIGPKTAEKIL 18
>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 = 30.1 bits (69), Expect = 0.062
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 192 CTPLRPRCGMCTVSEYC 208
CT +P+C C +++ C
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|184390 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Provisional.
Length = 218
Score = 33.3 bits (76), Expect = 0.067
Identities = 27/114 (23%), Positives = 52/114 (45%), Gaps = 12/114 (10%)
Query: 21 PKERRFAVLLSALLSSLTKDKVADGALQRLLQNG-LHTAEAIDKADEATIK-----DLIY 74
P +F LL A+L+ TK + + +L+ L L + I+ A I+ + +
Sbjct: 26 PNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVR 85
Query: 75 PVAFYTRKACNMKKIAKICLTKYDGDIPS-----SLDELLALPGIGPKMANMVM 123
P FY +KA + +++ L + G + + + LL GIG + A+ ++
Sbjct: 86 PSGFYNQKAKRLIDLSENILKDF-GSFENFKQEVTREWLLDQKGIGKESADAIL 138
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 33.2 bits (77), Expect = 0.12
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 104 SLDELLALPGIGPKMANMVMTLGWFNVQGI 133
S +EL A+ G+G +A ++ +F V+
Sbjct: 541 SEEELAAVEGVGEVVAQSIVE--FFAVEEN 568
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 30.6 bits (70), Expect = 0.74
Identities = 27/119 (22%), Positives = 44/119 (36%), Gaps = 32/119 (26%)
Query: 13 DETDSSLPP-KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKD 71
+E SL E+ LL+A+ S + L R L A I E T K
Sbjct: 478 EEDLLSLEGFGEKSAENLLNAIEKSKKQP------LARFL-----YALGIRHVGETTAKS 526
Query: 72 LIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNV 130
L A + + + + +S +EL ++PGIG +A ++ +F
Sbjct: 527 L----------ARHFGTLEAL--------LAASEEELASIPGIGEVVARSIIE--FFAN 565
>gnl|CDD|224472 COG1555, ComEA, DNA uptake protein and related DNA-binding proteins
[DNA replication, recombination, and repair].
Length = 149
Score = 29.3 bits (66), Expect = 0.88
Identities = 29/115 (25%), Positives = 43/115 (37%), Gaps = 20/115 (17%)
Query: 16 DSSLPPKERRFAVLLSALLSSLTKD-KVADGALQRLLQNGLHTAEAIDKADEA------- 67
S P +E A L + SL KV + L + + A + +A
Sbjct: 5 AVSQPEEESVIAEKLEPEIESLLVTVKVYSARSKSRLADAIEKAGGLSDVADALAVNTAA 64
Query: 68 --TIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPS-SLDELLALPGIGPKMA 119
+ L Y VA + ++ +I + S +EL ALPGIGPK A
Sbjct: 65 KLADEKLSY-VAGSDPASSAEEEKKV--------NINTASAEELQALPGIGPKKA 110
>gnl|CDD|221191 pfam11731, Cdd1, Pathogenicity locus. Cdd1 is expressed as part of
the pathogenicity locus operon in several different
orders of bacteria. Many members of the family are
annotated as being putative mitomycin resistance
proteins but this could not be confirmed.
Length = 92
Score = 28.4 bits (64), Expect = 1.0
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGI 133
S+L EL LP IG A + LG + +
Sbjct: 8 RSALKELTDLPNIGKATAKDLRLLGINSPAQL 39
>gnl|CDD|178728 PLN03186, PLN03186, DNA repair protein RAD51 homolog;
Provisional.
Length = 342
Score = 30.1 bits (68), Expect = 1.1
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 34 LSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91
+ L +A +++L G+HT E++ A KDL+ K + + A
Sbjct: 28 IEQLQASGIAALDIKKLKDAGIHTVESLAY---APKKDLLQIKGISEAKVEKILEAAS 82
>gnl|CDD|205097 pfam12836, HHH_3, Helix-hairpin-helix motif. The HhH domain is a
short DNA-binding domain.
Length = 65
Score = 27.4 bits (62), Expect = 1.2
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 104 SLDELLALPGIGPKMAN 120
S + L +PGIGPK+A
Sbjct: 12 SAELLQRVPGIGPKLAK 28
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 29.7 bits (68), Expect = 1.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 104 SLDELLALPGIGPKMANMV 122
S++EL +PGI K+A +
Sbjct: 573 SVEELAKVPGISKKLAEAI 591
>gnl|CDD|217408 pfam03177, Nucleoporin_C, Non-repetitive/WGA-negative nucleoporin
C-terminal. This is the C-termainl half of a family of
nucleoporin proteins. Nucleoporins are the main
components of the nuclear pore complex in eukaryotic
cells, and mediate bidirectional nucleocytoplasmic
transport, especially of mRNA and proteins. Two
nucleoporin classes are known: one is characterized by
the FG repeat pfam03093; the other is represented by
this family, and lacks any repeats. RNA undergoing
nuclear export first encounters the basket of the
nuclear pore and many nucleoporins are accessible on the
basket side of the pore.
Length = 559
Score = 29.4 bits (66), Expect = 1.8
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 8 YSLGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEA 67
YSL ++E S +R +LL L++L + L LL E + + A
Sbjct: 380 YSLALEEASSFTITLSKRIELLLRK-LAALASENDGTPILSELLS------EIEELLEVA 432
Query: 68 TIKDLIY 74
I+ +
Sbjct: 433 KIQKDLL 439
>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 = 28.7 bits (65), Expect = 2.0
Identities = 8/16 (50%), Positives = 11/16 (68%), Gaps = 1/16 (6%)
Query: 133 IC-VDTHVHRICNRLG 147
I +DTH HR+ +LG
Sbjct: 174 IIPLDTHTHRVARKLG 189
>gnl|CDD|218638 pfam05559, DUF763, Protein of unknown function (DUF763). This
family consists of several uncharacterized bacterial and
archaeal proteins of unknown function.
Length = 319
Score = 28.0 bits (63), Expect = 4.4
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 85 NMKKIAKICLTKYDGDIPSSLDELLALPGIGPK 117
+++++ K+ Y+ + P +ELL L G+GP
Sbjct: 249 DLRRLWKVLRAAYERN-PEDFEELLLLKGVGPS 280
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 28.1 bits (63), Expect = 4.6
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 10 LGVDETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQ 52
+G+ ET L ER+++ L+ + + ++A+ LQRL++
Sbjct: 497 IGIQETRYLLDQMERKYSDLVKEVQRQIPLQRIAE-ILQRLVE 538
>gnl|CDD|214688 smart00483, POLXc, DNA polymerase X family. includes vertebrate
polymerase beta and terminal
deoxynucleotidyltransferases.
Length = 334
Score = 27.7 bits (62), Expect = 4.8
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMA 119
++ C+ + A L I +S+ +L LPGIG K+
Sbjct: 24 KRKCSYFRKAASVLKSLPFPI-NSMKDLKGLPGIGDKIK 61
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 27.9 bits (62), Expect = 5.1
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 59 EAIDKADEATIKDLI-YPVAFYTRKACNMKKIAKICLTKYDGDIP 102
I++ E I ++ F R +K+IAKIC + D+P
Sbjct: 146 TIIEEKGEEVILAVLSTTSCFAPRSPDRVKEIAKIC---AEYDVP 187
>gnl|CDD|213597 TIGR01259, comE, comEA protein. This model describes the ComEA
protein in bacteria. The com E locus is obligatory for
bacterial cell competence - the process of internalizing
the exogenous added DNA. Lesions in the loci has been
variously described for the appearance of
competence-related pheonotypes and impairment of
competence, suggesting their intimate functional role in
bacterial transformation [Cellular processes, DNA
transformation].
Length = 120
Score = 26.8 bits (59), Expect = 5.4
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 103 SSLDELLALPGIGPKMA 119
+SL+EL ALPGIGP A
Sbjct: 65 ASLEELQALPGIGPAKA 81
>gnl|CDD|221472 pfam12228, DUF3604, Protein of unknown function (DUF3604). This
family of proteins is found in bacteria. Proteins in
this family are typically between 621 and 693 amino
acids in length.
Length = 592
Score = 28.0 bits (63), Expect = 5.6
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 150 TQPGTKQKTSSPEQT---REALQRWLPKEEWVRINPLLVGF 187
G++ KT R AL+R L E+ + +NP GF
Sbjct: 284 NLCGSEPKTPDMLPGSYVRSALKRGLSLEQKLGVNPYKFGF 324
>gnl|CDD|130412 TIGR01345, malate_syn_G, malate synthase G. This model describes
the G isozyme of malate synthase. Isocitrate synthase
and malate synthase form the glyoxylate shunt, which
generates additional TCA cycle intermediates [Energy
metabolism, TCA cycle].
Length = 721
Score = 28.0 bits (62), Expect = 5.7
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 50 LLQNGLHTAEAID------KADEATIKDLIYPVAFYTRKAC 84
L NGLH ID K D A IKD++ A T C
Sbjct: 230 LKNNGLHIELQIDANHPIGKDDPAHIKDIVLESAITTIMDC 270
>gnl|CDD|233996 TIGR02750, TraN_Ftype, type-F conjugative transfer system
mating-pair stabilization protein TraN. TraN is a large
cysteine-rich outer membrane protein involved in the
mating-pair stabilization (adhesin) component of the
F-type conjugative plamid transfer system. TraN is
believed to interact with the core type IV secretion
system apparatus through the TraV protein.
Length = 572
Score = 27.5 bits (61), Expect = 6.6
Identities = 16/86 (18%), Positives = 26/86 (30%), Gaps = 22/86 (25%)
Query: 125 LGWFNVQGICVDTHVHRICNRLGW--VTQPGTKQKTSSPEQTREALQRWLPKEEWVRINP 182
L W C +T + G T P T ++ ++ E W
Sbjct: 235 LYWTKQWPTCTNTTLLVATINCGNGRTTVPLALTVTVHSKE-------YISDEYW----- 282
Query: 183 LLVGFGQTICTPLRPRCGMCTVSEYC 208
C P++ +C + SE C
Sbjct: 283 ------DNQCEPIQSKCFI--TSEQC 300
>gnl|CDD|221395 pfam12048, DUF3530, Protein of unknown function (DUF3530). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 272 to 336 amino acids in length.
These proteins are distantly related to alpa/beta
hydrolases so they may act as enzymes.
Length = 294
Score = 27.4 bits (61), Expect = 7.3
Identities = 8/32 (25%), Positives = 18/32 (56%)
Query: 150 TQPGTKQKTSSPEQTREALQRWLPKEEWVRIN 181
K + E+++E L+R+LP++E ++
Sbjct: 30 ATTAAAPKPALSERSQEDLERYLPEDEVKWLD 61
>gnl|CDD|201312 pfam00570, HRDC, HRDC domain. The HRDC (Helicase and RNase D
C-terminal) domain has a putative role in nucleic acid
binding. Mutations in the HRDC domain cause human
disease. It is interesting to note that the RecQ
helicase in Deinococcus radiodurans has three tandem
HRDC domains.
Length = 68
Score = 25.2 bits (56), Expect = 8.0
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 8/32 (25%)
Query: 86 MKKIAKICLTKYDGDIPSSLDELLALPGIGPK 117
+ +IA+ P +L+ELL +PG+GP+
Sbjct: 32 LLEIAEKL--------PRTLEELLRIPGVGPR 55
>gnl|CDD|176461 cd01334, Lyase_I, Lyase class I family; a group of proteins which
catalyze similar beta-elimination reactions. The Lyase
class I family contains class II fumarase, aspartase,
adenylosuccinate lyase (ASL), argininosuccinate lyase
(ASAL), prokaryotic-type 3-carboxy-cis,cis-muconate
cycloisomerase (pCMLE), and related proteins. It belongs
to the Lyase_I superfamily. Proteins of this family for
the most part catalyze similar beta-elimination
reactions in which a C-N or C-O bond is cleaved with the
release of fumarate as one of the products. These
proteins are active as tetramers. The four active sites
of the homotetrameric enzyme are each formed by residues
from three different subunits.
Length = 325
Score = 27.1 bits (61), Expect = 8.8
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 8/32 (25%)
Query: 137 THVHRICN--RL------GWVTQPGTKQKTSS 160
+ +I N RL G V P KQ SS
Sbjct: 220 VSLSKIANDLRLLSSGEFGEVELPDAKQPGSS 251
>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
Decarboxylases, and Related Enzymes. This family
includes eukaryotic ornithine decarboxylase (ODC, EC
4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
4.1.1.20), plant and prokaryotic biosynthetic arginine
decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
decarboxylase (CANSDC), and ODC-like enzymes from
diverse bacterial species. These proteins are fold type
III PLP-dependent enzymes that catalyze essential steps
in the biosynthesis of polyamine and lysine. ODC and
ADC participate in alternative pathways of the
biosynthesis of putrescine, which is the precursor of
aliphatic polyamines in many organisms. ODC catalyzes
the direct synthesis of putrescine from L-ornithine,
while ADC converts L-arginine to agmatine, which is
hydrolysed to putrescine by agmatinase in a pathway that
exists only in plants and bacteria. DapDC converts
meso-2,6-diaminoheptanedioate to L-lysine, which is the
final step of lysine biosynthesis. CANSDC catalyzes the
decarboxylation of carboxynorspermidine, which is the
last step in the synthesis of norspermidine. The
PLP-dependent decarboxylases in this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. Prokaryotic ornithine, lysine and
biodegradative arginine decarboxylases are fold type I
PLP-dependent enzymes and are not included in this
family.
Length = 368
Score = 26.9 bits (60), Expect = 9.4
Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 78 FYTRKACNMKKIAKICLTKYDG-DIPSSLDELLALPGIGPKMANMVMT 124
FY KA + + G D+ +S EL G ++ T
Sbjct: 29 FYAVKANPNPHVLRTLAEAGTGFDV-ASKGELALALAAGVPPERIIFT 75
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
0.317 0.132 0.395
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: 11,479,082
Number of extensions: 1030593
Number of successful extensions: 1228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1207
Number of HSP's successfully gapped: 52
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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: 57 (25.6 bits)