BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 039703
(284 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3S6I|A Chain A, Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase
(Mag1) In Complex With Abasic-Dna.
pdb|3S6I|D Chain D, Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase
(Mag1) In Complex With Abasic-Dna
Length = 228
Score = 117 bits (294), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 62/199 (31%), Positives = 107/199 (53%), Gaps = 7/199 (3%)
Query: 68 EVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFV 127
+ +I L L + L L+ +RP + P+ L +++ QQL KAA +I+ RF
Sbjct: 17 KAEIHLSGLDENWKRLVKLVGNYRPNRSMEKKEPYEELIRAVASQQLHSKAANAIFNRFK 76
Query: 128 ALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGIL-SDESIVEMDDVT 186
++ N P+ + + + +R G S RK L+ +AE G++ + E + +
Sbjct: 77 SISNNGQFPTPEEIRDMDFEIMRACGFSARKIDSLKSIAEATISGLIPTKEEAERLSNEE 136
Query: 187 MFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPG---ALKME 243
+ + LT +KGIG W+V M +IFSL++ DV+P DL +R G + L+ L ++P LK
Sbjct: 137 LIERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRLPKIPTKMYVLKHS 196
Query: 244 EVCEKWKPYRSVGSWYMWR 262
E+C P+R+ +WY+W+
Sbjct: 197 EIC---APFRTAAAWYLWK 212
>pdb|2H56|A Chain A, Crystal Structure Of Dna-3-methyladenine Glycosidase
(10174367) From Bacillus Halodurans At 2.55 A Resolution
pdb|2H56|B Chain B, Crystal Structure Of Dna-3-methyladenine Glycosidase
(10174367) From Bacillus Halodurans At 2.55 A Resolution
pdb|2H56|C Chain C, Crystal Structure Of Dna-3-methyladenine Glycosidase
(10174367) From Bacillus Halodurans At 2.55 A Resolution
Length = 233
Score = 114 bits (284), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 63/163 (38%), Positives = 91/163 (55%), Gaps = 1/163 (0%)
Query: 100 SPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKA 159
+PF SL SI+ QQL+ KAA +IY R L G P+ + VS + LR+ GVS RK
Sbjct: 50 NPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALE-KPEQLYRVSDEALRQAGVSKRKI 108
Query: 160 SYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVG 219
Y+R + E G L + + T+ + LT++KGIG W+ F FSL + DVL VG
Sbjct: 109 EYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEXFXXFSLGRLDVLSVG 168
Query: 220 DLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGSWYMWR 262
D+G+++G + LYG E G + + W PY +V Y+W+
Sbjct: 169 DVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWK 211
>pdb|2YG9|A Chain A, Structure Of An Unusual 3-Methyladenine Dna Glycosylase Ii
( Alka) From Deinococcus Radiodurans
pdb|2YG9|B Chain B, Structure Of An Unusual 3-Methyladenine Dna Glycosylase Ii
( Alka) From Deinococcus Radiodurans
Length = 225
Score = 110 bits (275), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 70/206 (33%), Positives = 106/206 (51%), Gaps = 14/206 (6%)
Query: 57 PKIFKPLTFKGEVDIALRHLRDKDPLLATLID-AHRPPTFESSRSPFLSLAKSILYQQLA 115
P + PLT A+ HL +DP+LA + P + PF L +S+ QQL+
Sbjct: 20 PAVLPPLTDHAG---AVAHL-SRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLS 75
Query: 116 YKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILS 175
KAA++IY R L G ++P A+L VS LR +G+S+ K ++ A G +
Sbjct: 76 VKAAQAIYGRLEGLPGG---VVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQID 132
Query: 176 DESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235
+ D + L + GIG W+ MF++F+L +PDV GDL +R+G++ LY
Sbjct: 133 FAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLY---- 188
Query: 236 LPGALKMEEVCEKWKPYRSVGSWYMW 261
PG +V +W PYRS+ S Y+W
Sbjct: 189 -PGE-DWRDVTARWAPYRSLASRYLW 212
>pdb|2YG8|A Chain A, Structure Of An Unusual 3-Methyladenine Dna Glycosylase Ii
( Alka) From Deinococcus Radiodurans
pdb|2YG8|B Chain B, Structure Of An Unusual 3-Methyladenine Dna Glycosylase Ii
( Alka) From Deinococcus Radiodurans
Length = 225
Score = 108 bits (269), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 69/206 (33%), Positives = 105/206 (50%), Gaps = 14/206 (6%)
Query: 57 PKIFKPLTFKGEVDIALRHLRDKDPLLATLID-AHRPPTFESSRSPFLSLAKSILYQQLA 115
P + PLT A+ HL +DP+LA + P + PF L +S+ QQL+
Sbjct: 20 PAVLPPLTDHAG---AVAHL-SRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLS 75
Query: 116 YKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILS 175
KAA++IY R L G ++P A+L VS LR +G+S+ K ++ A G +
Sbjct: 76 VKAAQAIYGRLEGLPGG---VVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQID 132
Query: 176 DESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235
+ D + L + GIG W+ F++F+L +PDV GDL +R+G++ LY
Sbjct: 133 FAHLSGQPDELVIAELVQLPGIGRWTAEXFLLFALARPDVFSSGDLALRQGVERLY---- 188
Query: 236 LPGALKMEEVCEKWKPYRSVGSWYMW 261
PG +V +W PYRS+ S Y+W
Sbjct: 189 -PGE-DWRDVTARWAPYRSLASRYLW 212
>pdb|4HSB|A Chain A, S. Pombe 3-methyladenine Dna Glycosylase-like Protein Mag2
Bound To Damaged Dna
Length = 217
Score = 92.4 bits (228), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 49/196 (25%), Positives = 100/196 (51%), Gaps = 4/196 (2%)
Query: 72 ALRHLRDKDPLLATLIDAHRPPTF--ESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVAL 129
A +HL D ++L+ P T +P+ + ++I Q+L+ A SI +F
Sbjct: 14 AEKHLSSIDNKWSSLVKKVGPCTLTPHPEHAPYEGIIRAITSQKLSDAATNSIINKFCTQ 73
Query: 130 FNGEDNI-LPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVE-MDDVTM 187
+ D P ++ + L E G S K+ + +AE + + +S +E M + +
Sbjct: 74 CSDNDEFPTPKQIMETDVETLHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEEL 133
Query: 188 FKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCE 247
+ L+ +KG+ W++ M+ IF+L + D++P D ++ + +GL P ++E++ +
Sbjct: 134 MESLSKIKGVKRWTIEMYSIFTLGRLDIMPADDSTLKNEAKEFFGLSSKPQTEEVEKLTK 193
Query: 248 KWKPYRSVGSWYMWRL 263
KPYR++ +WY+W++
Sbjct: 194 PCKPYRTIAAWYLWQI 209
>pdb|4B21|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycosylase Homolog Mag2
pdb|4B22|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycosylase Homolog Mag2
pdb|4B23|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycoslase Homolog Mag2
pdb|4B24|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycoslase Homolog Mag2
Length = 232
Score = 92.0 bits (227), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 49/196 (25%), Positives = 100/196 (51%), Gaps = 4/196 (2%)
Query: 72 ALRHLRDKDPLLATLIDAHRPPTF--ESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVAL 129
A +HL D ++L+ P T +P+ + ++I Q+L+ A SI +F
Sbjct: 29 AEKHLSSIDNKWSSLVKKVGPCTLTPHPEHAPYEGIIRAITSQKLSDAATNSIINKFCTQ 88
Query: 130 FNGEDNI-LPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVE-MDDVTM 187
+ D P ++ + L E G S K+ + +AE + + +S +E M + +
Sbjct: 89 CSDNDEFPTPKQIMETDVETLHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEEL 148
Query: 188 FKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCE 247
+ L+ +KG+ W++ M+ IF+L + D++P D ++ + +GL P ++E++ +
Sbjct: 149 MESLSKIKGVKRWTIEMYSIFTLGRLDIMPADDSTLKNEAKEFFGLSSKPQTEEVEKLTK 208
Query: 248 KWKPYRSVGSWYMWRL 263
KPYR++ +WY+W++
Sbjct: 209 PCKPYRTIAAWYLWQI 224
>pdb|2JHN|A Chain A, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
pdb|2JHN|B Chain B, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
Length = 295
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 15/160 (9%)
Query: 98 SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED--NIL-------PDAVLAVSPQQ 148
S S F +AK+I+ QQ+++ A+ + + V F E N L +A+L +
Sbjct: 115 SMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEG 174
Query: 149 LREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208
LRE G+S RKA + ++A++ + E + E + ++ LTS KGIG W+ + +
Sbjct: 175 LRECGLSRRKAELIVEIAKE-----ENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSI 229
Query: 209 SLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEK 248
+L K +V P DLGVR+ + LY E+ A K+ E+ +
Sbjct: 230 ALGK-NVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARE 268
>pdb|2JHJ|A Chain A, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
pdb|2JHJ|B Chain B, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
Length = 295
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 15/160 (9%)
Query: 98 SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED--NIL-------PDAVLAVSPQQ 148
S S F +AK+I+ QQ+++ A+ + + V F E N L +A+L +
Sbjct: 115 SMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEG 174
Query: 149 LREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208
LRE G+S RKA + ++A++ + E + E + ++ LTS KGIG W+ + +
Sbjct: 175 LRECGLSRRKAELIVEIAKE-----ENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSM 229
Query: 209 SLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEK 248
+L K +V P DLGVR+ + LY E+ A K+ E+ +
Sbjct: 230 ALGK-NVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARE 268
>pdb|3OH6|A Chain A, Alka Undamaged Dna Complex: Interrogation Of A C:g Base
Pair
pdb|3OH9|A Chain A, Alka Undamaged Dna Complex: Interrogation Of A T:a Base
Pair
Length = 289
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 21/165 (12%)
Query: 107 KSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVL--------AVSPQQLREIGVSYRK 158
++IL Q ++ A + R L+ + P+ + A PQ L+ +G+ ++
Sbjct: 126 RAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKR 185
Query: 159 ASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPV 218
A L LA +G L + D K L + GIG W+ + F + DV
Sbjct: 186 AEALIHLANAALEGTLP--MTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLP 243
Query: 219 GDLGVRKGLQVLYGLKELPGAL--KMEEVCEKWKPYRSVGSWYMW 261
D +++ PG ++ E+WKP+RS ++W
Sbjct: 244 DDCLIKQ---------RFPGMTPAQIRRYAERWKPWRSYALLHIW 279
>pdb|3OGD|A Chain A, Alka Undamaged Dna Complex: Interrogation Of A G:c Base
Pair
Length = 289
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 21/165 (12%)
Query: 107 KSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVL--------AVSPQQLREIGVSYRK 158
++IL Q ++ A + R L+ + P+ + A PQ L+ +G+ ++
Sbjct: 126 RAILGQCVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKR 185
Query: 159 ASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPV 218
A L LA +G L + D K L + GIG W+ + F + DV
Sbjct: 186 AEALIHLANAALEGTLP--MTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLP 243
Query: 219 GDLGVRKGLQVLYGLKELPGAL--KMEEVCEKWKPYRSVGSWYMW 261
D +++ PG ++ E+WKP+RS ++W
Sbjct: 244 DDYLIKQ---------RFPGMTPAQIRRYAERWKPWRSYALLHIW 279
>pdb|1MPG|A Chain A, 3-Methyladenine Dna Glycosylase Ii From Escherichia Coli
pdb|1MPG|B Chain B, 3-Methyladenine Dna Glycosylase Ii From Escherichia Coli
pdb|1DIZ|A Chain A, Crystal Structure Of E. Coli 3-Methyladenine Dna
Glycosylase (Alka) Complexed With Dna
pdb|1DIZ|B Chain B, Crystal Structure Of E. Coli 3-Methyladenine Dna
Glycosylase (Alka) Complexed With Dna
pdb|1PVS|A Chain A, 3-Methyladenine Glcosylase Ii(Alka) Hypoxanthine Complex
pdb|1PVS|B Chain B, 3-Methyladenine Glcosylase Ii(Alka) Hypoxanthine Complex
pdb|3CVS|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:adenine Base Pair
pdb|3CVS|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:adenine Base Pair
pdb|3CVS|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:adenine Base Pair
pdb|3CVS|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:adenine Base Pair
pdb|3CVT|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CVT|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CVT|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CVT|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CW7|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CW7|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CW7|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CW7|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CWA|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CWA|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CWA|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CWA|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX
8oxoguanine:cytosine Base Pair
pdb|3CWS|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:thymine Base Pair
pdb|3CWS|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:thymine Base Pair
pdb|3CWS|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:thymine Base Pair
pdb|3CWS|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:thymine Base Pair
pdb|3CWT|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:adenine Base Pair
pdb|3CWT|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:adenine Base Pair
pdb|3CWT|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:adenine Base Pair
pdb|3CWT|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxyinosine:adenine Base Pair
pdb|3CWU|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxy-1,N6-Ethenoadenine:thymine Base Pair
pdb|3CWU|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxy-1,N6-Ethenoadenine:thymine Base Pair
pdb|3CWU|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxy-1,N6-Ethenoadenine:thymine Base Pair
pdb|3CWU|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX 2'-Fluoro-
2'-Deoxy-1,N6-Ethenoadenine:thymine Base Pair
pdb|3D4V|A Chain A, Crystal Structure Of An Alka HostGUEST COMPLEX
N7methylguanine:cytosine Base Pair
pdb|3D4V|B Chain B, Crystal Structure Of An Alka HostGUEST COMPLEX
N7methylguanine:cytosine Base Pair
pdb|3D4V|C Chain C, Crystal Structure Of An Alka HostGUEST COMPLEX
N7methylguanine:cytosine Base Pair
pdb|3D4V|D Chain D, Crystal Structure Of An Alka HostGUEST COMPLEX
N7methylguanine:cytosine Base Pair
Length = 282
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 21/165 (12%)
Query: 107 KSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVL--------AVSPQQLREIGVSYRK 158
++IL Q ++ A + R L+ + P+ + A PQ L+ +G+ ++
Sbjct: 119 RAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKR 178
Query: 159 ASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPV 218
A L LA +G L + D K L + GIG W+ + F + DV
Sbjct: 179 AEALIHLANAALEGTLP--MTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLP 236
Query: 219 GDLGVRKGLQVLYGLKELPGAL--KMEEVCEKWKPYRSVGSWYMW 261
D +++ PG ++ E+WKP+RS ++W
Sbjct: 237 DDYLIKQ---------RFPGMTPAQIRRYAERWKPWRSYALLHIW 272
>pdb|3I0W|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA
CONTAINING CYTOSINE Opposite To 8-Oxog
Length = 290
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 2/93 (2%)
Query: 139 DAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIG 198
D + + + E +R A YL+D ++ +G L+ E I ++D + L G+G
Sbjct: 162 DKLHEFTEKDFEECTAGFR-AKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVG 220
Query: 199 AWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLY 231
M+FS+ K PV D V+K + LY
Sbjct: 221 PQVADCIMLFSMQKYSAFPV-DTWVKKAMMSLY 252
>pdb|3I0X|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA
CONTAINING ADENINE Opposite To 8-Oxog
Length = 291
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 2/93 (2%)
Query: 139 DAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIG 198
D + + + E +R A YL+D ++ +G L+ E I ++D + L G+G
Sbjct: 162 DKLHEFTEKDFEECTAGFR-AKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVG 220
Query: 199 AWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLY 231
M+FS+ K PV D V+K + LY
Sbjct: 221 PQVADCIMLFSMQKYSAFPV-DTWVKKAMMSLY 252
>pdb|3F10|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine Dna Glycosylase In Complex With
8-Oxoguanosine
Length = 292
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 2/93 (2%)
Query: 139 DAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIG 198
D + + + E +R A YL+D ++ +G L+ E I ++D + L G+G
Sbjct: 162 DKLHEFTEKDFEECTAGFR-AKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVG 220
Query: 199 AWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLY 231
M+FS+ K PV D V+K + LY
Sbjct: 221 PQVADCIMLFSMQKYSAFPV-DTWVKKAMMSLY 252
>pdb|3F0Z|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN ITS APO-Form
Length = 292
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 2/93 (2%)
Query: 139 DAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIG 198
D + + + E +R A YL+D ++ +G L+ E I ++D + L G+G
Sbjct: 162 DKLHEFTEKDFEECTAGFR-AKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFXGVG 220
Query: 199 AWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLY 231
+FS K PV D V+K LY
Sbjct: 221 PKVADCIXLFSXQKYSAFPV-DTWVKKAXXSLY 252
>pdb|1KEA|A Chain A, Structure Of A Thermostable Thymine-Dna Glycosylase
Length = 221
Score = 34.7 bits (78), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 95 FESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNIL--PDAVLAVSPQQLREI 152
+ +R P++ L IL ++ K IY +F + ++IL P + +A + ++EI
Sbjct: 29 WRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIA---KDIKEI 85
Query: 153 GVSYRKASYLRDLAE 167
G+S ++A L++LA
Sbjct: 86 GLSNQRAEQLKELAR 100
>pdb|1IWG|A Chain A, Crystal Structure Of Bacterial Multidrug Efflux
Transporter Acrb
pdb|2DHH|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DHH|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DHH|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DR6|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|A Chain A, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|B Chain B, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|2DRD|C Chain C, Crystal Structure Of A Multidrug Transporter Reveal A
Functionally Rotating Mechanism
pdb|3AOA|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOA|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOA|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOB|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOC|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|A Chain A, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|B Chain B, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
pdb|3AOD|C Chain C, Structures Of The Multidrug Exporter Acrb Reveal A
Proximal Multisite Drug-Binding Pocket
Length = 1053
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2HQG|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|3NOC|A Chain A, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOC|B Chain B, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOC|C Chain C, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|A Chain A, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|B Chain B, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|C Chain C, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
Length = 1049
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2HQF|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2J8S|A Chain A, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
pdb|2J8S|B Chain B, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
pdb|2J8S|C Chain C, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By
Darpin Inhibitors
Length = 1055
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2GIF|A Chain A, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2GIF|B Chain B, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2GIF|C Chain C, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|A Chain A, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|B Chain B, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|C Chain C, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|D Chain D, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|E Chain E, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|2HRT|F Chain F, Asymmetric Structure Of Trimeric Acrb From Escherichia
Coli
pdb|4DX5|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX5|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX5|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX7|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
Length = 1057
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2HQD|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|2HQC|A Chain A, Conformation Of The Acrb Multidrug Efflux Pump In Mutants
Of The Putative Proton Relay Pathway
Length = 1053
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|4DX6|A Chain A, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX6|B Chain B, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
pdb|4DX6|C Chain C, Transport Of Drugs By The Multidrug Transporter Acrb
Involves An Access And A Deep Binding Pocket That Are
Separated By A Switch-Loop
Length = 1057
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|1T9T|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9U|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9V|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9W|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9X|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
pdb|1T9Y|A Chain A, Structural Basis Of Multidrug Transport By The Acrb
Multidrug Efflux Pump
Length = 1049
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|1OY6|A Chain A, Structural Basis Of The Multiple Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OY8|A Chain A, Structural Basis Of Multiple Drug Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OY9|A Chain A, Structural Basis Of Multiple Drug Binding Capacity Of The
Acrb Multidrug Efflux Pump
pdb|1OYD|A Chain A, Structural Basis Of Multiple Binding Capacity Of The Acrb
Multidrug Efflux Pump
pdb|1OYE|A Chain A, Structural Basis Of Multiple Binding Capacity Of The Acrb
Multidrug Efflux Pump
pdb|2I6W|A Chain A, Crystal Structure Of The Multidrug Efflux Transporter Acrb
pdb|2RDD|A Chain A, X-Ray Crystal Structure Of Acrb In Complex With A Novel
Transmembrane Helix.
pdb|3D9B|A Chain A, Symmetric Structure Of E. Coli Acrb
pdb|2W1B|A Chain A, The Structure Of The Efflux Pump Acrb In Complex With Bile
Acid
Length = 1049
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 146 PQQLREIGVSYRKAS--YLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203
PQ++++ GVS K+S +L + TDG ++ E I + M ++ G+G V
Sbjct: 119 PQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVG--DVQ 176
Query: 204 MF 205
+F
Sbjct: 177 LF 178
>pdb|1X7F|A Chain A, Crystal Structure Of An Uncharacterized B. Cereus Protein
Length = 385
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 120 KSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESI 179
+ I F + N + + +L V+P ++G+SY S+ +L DGI D
Sbjct: 70 EEIVAEFKEIINHAKDNNMEVILDVAPAVFDQLGISYSDLSFFAELG---ADGIRLD--- 123
Query: 180 VEMDDVTMFKMLTSVKGI 197
V D +T KM + G+
Sbjct: 124 VGFDGLTEAKMTNNPYGL 141
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,074,577
Number of Sequences: 62578
Number of extensions: 311278
Number of successful extensions: 748
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 719
Number of HSP's gapped (non-prelim): 29
length of query: 284
length of database: 14,973,337
effective HSP length: 98
effective length of query: 186
effective length of database: 8,840,693
effective search space: 1644368898
effective search space used: 1644368898
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)