RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4725
(457 letters)
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 191 bits (487), Expect = 4e-57
Identities = 99/258 (38%), Positives = 141/258 (54%), Gaps = 32/258 (12%)
Query: 12 GKILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFKECVWTLWADPSYLHYQV 71
I CP EL L L L GQSFRW++ + + GV + VWTL LH V
Sbjct: 39 ASIPCPRSELRLDLVLPSGQSFRWREQS------PAHWSGVLADQVWTLTQTEEQLHCTV 92
Query: 72 FSQHKLNANSVET----MLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDL 127
+ K A+ +++YF+LD L +LY W + D+ F++ F G+R+L QD
Sbjct: 93 YRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDP 152
Query: 128 TENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVT 187
E +FSF+CSSNNNIARI+GM++++C+ +G + LD
Sbjct: 153 IECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDV--------------------- 191
Query: 188 KFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQG-GGESWLERLGGKSYEEA 246
+ FPS+ ALA P VEA LR+LG GYRA+++ SA I++ GG +WL++L SYEEA
Sbjct: 192 TYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEA 251
Query: 247 REELQRLPGIGAKVGDGV 264
+ L LPG+G V D +
Sbjct: 252 HKALCILPGVGTCVADKI 269
Score = 103 bits (258), Expect = 1e-24
Identities = 35/96 (36%), Positives = 52/96 (54%), Gaps = 2/96 (2%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQK--STSKTLTPAVYNQIRAFFADK 384
G VAD ICLM+L QAVPV+ H++ IA Y + S +K +P ++ FF
Sbjct: 262 GTCVADKICLMALDKPQAVPVNVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSL 321
Query: 385 FGKYAGWAHSILFCADLKKFQAKPGEEKVGKRESGT 420
+G YAGWA ++LF ADL++ + ++ S
Sbjct: 322 WGPYAGWAQAVLFSADLRQSRHAQEPPAKRRKGSKG 357
Score = 48.6 bits (115), Expect = 2e-06
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 263 GVFKEHVWTLWADPSYLHYQVY----SQHKLNTNSVETMLKEYFRLDENLPELYAEWSNR 318
GV + VWTL LH VY SQ T +++YF+LD L +LY W +
Sbjct: 72 GVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSV 131
Query: 319 DAFFR 323
D+ F+
Sbjct: 132 DSHFQ 136
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG,
glycosylase, cytosine, hydrolase,lyase/DNA complex; HET:
8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A*
3f10_A* 3f0z_A
Length = 290
Score = 173 bits (441), Expect = 4e-51
Identities = 61/262 (23%), Positives = 104/262 (39%), Gaps = 37/262 (14%)
Query: 1 MSLGNTVHHLSGKILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFKECVWTL 60
M I+ L GQ FRW + + + G+ E V +
Sbjct: 1 MDFDMIEEKKDSVIVRNVENFELKDIFDCGQCFRWHRQENGN------YIGIAFEKVVEV 54
Query: 61 WADPSYLHYQVFSQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGI 120
+ + +N + + EYF L + E+ E S RD +++ GI
Sbjct: 55 QKIGEDVVI-----YNINEEEFKNVWSEYFDLYRDYGEIKKELS-RDPLLKKSVDFGEGI 108
Query: 121 RMLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHA 180
R+L QD E + SF+ S+NN I I I+ + ++ G + + G
Sbjct: 109 RILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKL---EYKGK------------ 153
Query: 181 KSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGGGESWLERLGG 240
++AFP++D L E + G+RAK+++ + + I GE LE +
Sbjct: 154 -------IYYAFPTVDKLHE-FTEKDFEECTAGFRAKYLKDTVDRIYN--GELNLEYIKS 203
Query: 241 KSYEEAREELQRLPGIGAKVGD 262
+ E EEL++ G+G +V D
Sbjct: 204 LNDNECHEELKKFMGVGPQVAD 225
Score = 76.1 bits (187), Expect = 1e-15
Identities = 25/72 (34%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFG 386
G VADCI L S+ A PVDT V + + Y +IR F +KFG
Sbjct: 220 GPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYV--------APDVSLKKIRDFGREKFG 271
Query: 387 KYAGWAHSILFC 398
+G+A LF
Sbjct: 272 SLSGFAQQYLFY 283
Score = 43.4 bits (102), Expect = 9e-05
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 263 GVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFF 322
G+ E V + + + +N + + EYF L + E+ E S RD
Sbjct: 45 GIAFEKVVEVQKIGEDVVI-----YNINEEEFKNVWSEYFDLYRDYGEIKKELS-RDPLL 98
Query: 323 RQ 324
++
Sbjct: 99 KK 100
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair,
N1-methyladenine, N3-methylcytosine, hyperthermophiles,
hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus}
PDB: 2jhj_A
Length = 295
Score = 70.6 bits (173), Expect = 1e-13
Identities = 41/205 (20%), Positives = 67/205 (32%), Gaps = 34/205 (16%)
Query: 59 TLWADPSYLHYQVFSQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFR---QTCG 115
+ + + +V L EY L PE + + D R
Sbjct: 49 MAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQN--PEELYRFMDGDEKLRMLKNRFY 106
Query: 116 DFVGIRMLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEK 175
F +++ + E I + + + K+ +G + + +G
Sbjct: 107 GFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEV---EWNGL------- 156
Query: 176 GRSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGGGESWL 235
KF+ FP+ +A+ + VE LR+ G R AE I++ E L
Sbjct: 157 ------------KFYGFPTQEAILKAGVEG-LRECGLSRRK------AELIVEIAKEENL 197
Query: 236 ERLGGKSYEEAREELQRLPGIGAKV 260
E L EEA E L GIG
Sbjct: 198 EELKEWGEEEAYEYLTSFKGIGRWT 222
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 59.5 bits (143), Expect = 2e-09
Identities = 74/509 (14%), Positives = 142/509 (27%), Gaps = 174/509 (34%)
Query: 6 TVHHL--SGK-ILCPAIELSLTLTLLGGQSFR--W---KQLTSDEKKLGNRFQGVFKECV 57
+ + SGK + A+++ L+ + F+ W K S E L E +
Sbjct: 154 LIDGVLGSGKTWV--ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL---------EML 202
Query: 58 WTLW--ADPSYLHYQVFSQH-KLNANSVETMLKEYFRLDENLPELYAE--------WSNR 106
L DP++ S + KL +S++ L+ + + Y + +
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS-----KPYENCLLVLLNVQNAK 257
Query: 107 --DAFFRQTCGDFVGIRMLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLD 164
+AF +L+ CK L+ T
Sbjct: 258 AWNAF----------------NLS------------------------CK---ILLTTRF 274
Query: 165 SDGNLVGDCEKG--RSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKS 222
V D +H S+D + +++ L K+
Sbjct: 275 KQ---VTDFLSAATTTH-------------ISLDHHSMTLTPDEVKSL-L---LKY---- 310
Query: 223 AEYIIQGGGESWLERLGGKSYEEAREELQRLP----GIGAKVGDGVFKEHVWTLWADPSY 278
L + + RE L P I + DG+ W W
Sbjct: 311 ---------------LDCRPQDLPREVLTTNPRRLSIIAESIRDGL---ATWDNW----- 347
Query: 279 LHYQVYSQHKLNTNSVETM----LKEY------FRLDENLPE--LYAEWSNRDAFFRQTC 326
H + +S+ + ++ F ++P L W + +
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI---KSDV 404
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAV---YNQIRAFFAD 383
V SL Q + I + L ++ YN + F +D
Sbjct: 405 MVVVNKL-HKYSLVEKQPKESTISIPSIYL-ELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 384 KFGK-----YAGWAHSI---LFCADL-KKFQAKPG--------EEKVGKRESGTITETPG 426
Y + I L + ++ E+K+ R T G
Sbjct: 463 DLIPPYLDQY--FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI--RHDSTAWNASG 518
Query: 427 AVIEKSGKVIEAKPKIDEDKRKSEIILQS 455
+++ ++ KP I ++ K E ++ +
Sbjct: 519 SILNTLQQLKFYKPYICDNDPKYERLVNA 547
Score = 54.9 bits (131), Expect = 4e-08
Identities = 46/289 (15%), Positives = 79/289 (27%), Gaps = 93/289 (32%)
Query: 9 HLSGKILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQ--GVFKECVW-------T 59
H++ L IE SL L E + F VF
Sbjct: 349 HVNCDKLTTIIESSL------------NVLEPAEYR--KMFDRLSVFPPSAHIPTILLSL 394
Query: 60 LWADPSYLHYQVFSQHKLNANSVETMLKE--------YFRL---DENLPELYAEWSNRDA 108
+W D V + VE KE Y L EN L+ +
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454
Query: 109 FFRQTCGD-------------FVGIRMLNQDLTENI---------FSFLCSSNNNIARIS 146
+ D +G + N + E + F FL
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ--------- 505
Query: 147 GMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSH-AKSCPAVTKFFAFPSIDALAR--PAV 203
K+ + T S N + + + + + P + ++A+ P +
Sbjct: 506 ----KIRHD-STAWNASGSILNTLQQLKFYKPYICDNDPKYERL-----VNAILDFLPKI 555
Query: 204 EAKLRQLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQR 252
E L +K+ +++ L +EEA +++QR
Sbjct: 556 EENL------ICSKYTD-----LLRIA----LMAEDEAIFEEAHKQVQR 589
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 58.5 bits (141), Expect = 3e-09
Identities = 71/435 (16%), Positives = 119/435 (27%), Gaps = 165/435 (37%)
Query: 55 ECVWTLWADPSYLHYQVFSQHKLN-ANSVETMLKEYFRLDE--NLPELYAEWSNRDAF-- 109
E V + P+ + + SQ + + + + DE EL + F
Sbjct: 17 EHVLLV---PTASFF-IASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK------FLG 66
Query: 110 F------RQTCGDFVGIRMLNQDLTENIF--SFLCSSNNNIARISGMIDKMCKEYGTLIC 161
+ G F + LN LTE F +L N+I L
Sbjct: 67 YVSSLVEPSKVGQFDQV--LNLCLTE--FENCYL--EGNDIH--------------ALAA 106
Query: 162 TLDSDGNLVGDCEKG--RSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFI 219
L + + K +++ + + F S AL R AV A+
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR-AVGEG--------NAQL- 156
Query: 220 QKSAEYII---QGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADP 276
I QG + + EEL+ L
Sbjct: 157 -----VAIFGGQGNTDDYF------------EELRDL----------------------- 176
Query: 277 SYLHYQVYSQHKLNTNSVETMLKEYF-RLDENLPELYAEWSNRDAFFRQTC--------- 326
YQ Y ++ + E L EL + + F Q
Sbjct: 177 ----YQTY----------HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
Query: 327 -----GDFVADC------ICLMSLSHLQAVPVDTHVYQIACNHYHFQ----KSTSKTLTP 371
D++ I ++ L+H Y + F +S K T
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVIQLAH----------YVVTAKLLGFTPGELRSYLKGATG 272
Query: 372 AVYNQIRA-FFA-----DKFGKYAGWAHSILFCADLKKFQAKPGEEKVGKRESGTITETP 425
+ A A + F A ++LF ++ ++A P T P
Sbjct: 273 HSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYP------------NTSLP 320
Query: 426 GAVIEKSGKVIEAKP 440
+++E S + E P
Sbjct: 321 PSILEDSLENNEGVP 335
Score = 32.7 bits (74), Expect = 0.32
Identities = 29/162 (17%), Positives = 48/162 (29%), Gaps = 56/162 (34%)
Query: 98 ELYAE-------WSNRDAFFRQTCG----------------DFVGIRMLNQDLTENIFSF 134
+LY W+ D F+ T G F G + + + EN +
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEK--GKRIRENYSAM 1691
Query: 135 LCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPS 194
+ + + + I K E+ T G L + T+ F P
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL---------------SATQ-FTQP- 1734
Query: 195 IDALARPAVE-AKLRQLGFGYRAKFIQKSAEYIIQGG---GE 232
AL +E A L ++K + + G GE
Sbjct: 1735 --ALT--LMEKAAFEDL----KSKGLIPADATFA--GHSLGE 1766
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
Length = 207
Score = 44.2 bits (104), Expect = 3e-05
Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 4/76 (5%)
Query: 192 FPSIDALARPAVEAKLRQLGFGY---RAKFIQKSAEYIIQGGGESWLERLGGKSYEEARE 248
I + L+ + + +AK+I + E + E ++ L + + ARE
Sbjct: 59 GQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKE-EIKPLADEDQQLARE 117
Query: 249 ELQRLPGIGAKVGDGV 264
L + GIG +
Sbjct: 118 RLLNIKGIGMQEASHF 133
Score = 40.0 bits (93), Expect = 7e-04
Identities = 11/80 (13%), Positives = 24/80 (30%), Gaps = 5/80 (6%)
Query: 331 ADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAG 390
A L ++ + +D H+ ++ K L+ ++Y
Sbjct: 130 ASHF-LRNVGYFDLAIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENIL-KSIASNLN 187
Query: 391 WAHSILFCADLKKFQAKPGE 410
+ IL DL + +
Sbjct: 188 MSVGIL---DLFIWYKETNT 204
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base
excision, methylation, ALK hydrolase; 1.80A {Escherichia
coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A*
3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A*
3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A*
Length = 282
Score = 44.0 bits (104), Expect = 4e-05
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 179 HAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGF-GYRAKFIQKSAEYIIQGGGESWLER 237
+ + ++ FP+ LA +A L+ LG RA+ + A ++G L
Sbjct: 142 YGERLDDFPEYICFPTPQRLAAADPQA-LKALGMPLKRAEALIHLANAALEGT----LPM 196
Query: 238 LGGKSYEEAREELQRLPGIG 257
E+A + LQ PGIG
Sbjct: 197 TIPGDVEQAMKTLQTFPGIG 216
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
DNA mismatch, methylation; 2.00A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: a.96.1.2
Length = 221
Score = 41.0 bits (97), Expect = 3e-04
Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 188 KFFA-FPSIDALARPAVEAKLRQL--GFGY---RAKFIQKSAEYIIQGGGESWLERLGGK 241
KFF + + + + ++++ + G RA+ +++ A +I GG+
Sbjct: 59 KFFVKYKCFEDILK-TPKSEIAKDIKEIGLSNQRAEQLKELARVVI--------NDYGGR 109
Query: 242 SYEEAREELQRLPGIG 257
R+ + LPG+G
Sbjct: 110 -VPRNRKAILDLPGVG 124
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 40.8 bits (96), Expect = 4e-04
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 186 VTKFFAFPSIDALARPAVEAKLRQLGF-GYRAKFIQKSAEYIIQGGGESWLERLGGKSYE 244
+ AL + + + LR +G + + +Q +A + G + L G+ E
Sbjct: 86 LEGLPGGVVPAALLKVSGDD-LRGVGLSWAKVRTVQAAAAAAVSG--QIDFAHLSGQPDE 142
Query: 245 EAREELQRLPGIG 257
EL +LPGIG
Sbjct: 143 LVIAELVQLPGIG 155
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 40.6 bits (96), Expect = 4e-04
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 14/71 (19%)
Query: 191 AFPSIDALARPAVEAKLRQL--GFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEA 246
FP++ LA A ++ L G GY RA+ + K+A+ + GGK + E
Sbjct: 58 RFPTVTDLAN-APLDEVLHLWTGLGYYARARNLHKAAQQVA--------TLHGGK-FPET 107
Query: 247 REELQRLPGIG 257
EE+ LPG+G
Sbjct: 108 FEEVAALPGVG 118
>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family,
hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo
sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A*
1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A
Length = 161
Score = 39.8 bits (93), Expect = 4e-04
Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 21/79 (26%)
Query: 184 PAVTKFFA-FPSIDALAR---PAVEAKLRQLGFGY-RAKFIQKSAEYIIQGGGESWLERL 238
P + KF +PS + V L+ LG RAK I K ++ +
Sbjct: 51 PVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYL----------- 99
Query: 239 GGKSYEEAREELQRLPGIG 257
+ + L GIG
Sbjct: 100 -----TKQWKYPIELHGIG 113
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 40.0 bits (94), Expect = 0.001
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 14/71 (19%)
Query: 191 AFPSIDALARPAVEAKLRQL--GFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEA 246
FP+++ALA A E ++ + G GY R + + + + + R GGK +
Sbjct: 67 RFPTLEALAD-ADEDEVLKAWEGLGYYSRVRNLHAAVKEVK--------TRYGGK-VPDD 116
Query: 247 REELQRLPGIG 257
+E RL G+G
Sbjct: 117 PDEFSRLKGVG 127
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision
repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori}
SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
Length = 218
Score = 38.2 bits (89), Expect = 0.003
Identities = 15/71 (21%), Positives = 23/71 (32%), Gaps = 14/71 (19%)
Query: 194 SIDALARPAVEAKLRQLGFGYR--AKFIQKSAEYIIQGGGESWLERLGGKSY---EEARE 248
I + + +R GF Y AK + + I+ + E RE
Sbjct: 71 KIAYIEFSKLAECVRPSGF-YNQKAKRLIDLSGNIL--------KDFQSFENFKQEVTRE 121
Query: 249 ELQRLPGIGAK 259
L GIG +
Sbjct: 122 WLLDQKGIGKE 132
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 38.4 bits (90), Expect = 0.003
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 13/71 (18%)
Query: 191 AFPSIDALARPAVEAKLRQL--GFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEA 246
+P++ LA A ++ QL G GY R + +Q+ A ++ E LGG A
Sbjct: 77 KWPTLQDLAS-ASLEEVNQLWAGLGYYSRGRRLQEGARKVV--------EELGGHMPRTA 127
Query: 247 REELQRLPGIG 257
Q LPG+G
Sbjct: 128 ETLQQLLPGVG 138
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc
genomics, PSI-2, protein structure initiative, joint
center structural genomics; 2.55A {Bacillus halodurans}
Length = 233
Score = 37.3 bits (87), Expect = 0.005
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 4/67 (5%)
Query: 192 FPSIDALARPAVEAKLRQLGFGYR-AKFIQKSAEYIIQGGGESWLERLGGKSYEEAREEL 250
+ L R + E LRQ G R ++I+ E++ G L G E+L
Sbjct: 84 LEKPEQLYRVSDE-ALRQAGVSKRKIEYIRHVCEHVESG--RLDFTELEGAEATTVIEKL 140
Query: 251 QRLPGIG 257
+ GIG
Sbjct: 141 TAIKGIG 147
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster,
iron-sulfur cluster, hydrolase/DNA complex; HET: PED;
1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1
PDB: 1orp_A* 1p59_A*
Length = 226
Score = 34.5 bits (80), Expect = 0.040
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 17/81 (20%)
Query: 186 VTK--FFAFPSIDALA---RPAVEAKLRQLGFGYR--AKFIQKSAEYIIQGGGESWLERL 238
VTK F + + +E +R +G YR A+ IQK +I ++
Sbjct: 54 VTKRLFEKYRTPHDYIAVPLEELEQDIRSIGL-YRNKARNIQKLCAMLI--------DKY 104
Query: 239 GGKSYEEAREELQRLPGIGAK 259
G+ R+EL +LPG+G K
Sbjct: 105 NGE-VPRDRDELMKLPGVGRK 124
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair,
helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF);
HET: 3DR; 2.28A {Schizosaccharomyces pombe}
Length = 228
Score = 34.3 bits (79), Expect = 0.058
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 204 EAKLRQLGFGYR-AKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIG 257
+R GF R ++ AE I G + E S EE E L ++ GIG
Sbjct: 95 FEIMRACGFSARKIDSLKSIAEATISGLIPTK-EEAERLSNEELIERLTQIKGIG 148
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 33.3 bits (77), Expect = 0.11
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 17/81 (20%)
Query: 186 VTK--FFAFPSIDALA---RPAVEAKLRQLGFGYR--AKFIQKSAEYIIQGGGESWLERL 238
T + + A+ V+ ++ +G Y A+ I K+ ++ E+
Sbjct: 50 ATAKLYPVANTPAAMLELGVEGVKTYIKTIGL-YNSKAENIIKTCRILL--------EQH 100
Query: 239 GGKSYEEAREELQRLPGIGAK 259
G+ E+ R L+ LPG+G K
Sbjct: 101 NGEVPED-RAALEALPGVGRK 120
>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA
repair, 8-oxoguanine, base EX repair, PSI-2, protein
structure initiative; 1.50A {Thermotoga maritima}
Length = 219
Score = 30.4 bits (68), Expect = 1.0
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 10/77 (12%)
Query: 192 FPSIDALARPAVEAKLRQLGFGY---RAKFIQKSAEYIIQGGGESWLERLGGKSYEEARE 248
L + KLR++G Y RA+FI ++ + + + L+ L ++RE
Sbjct: 76 GKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGK------LKNLVKGDPFQSRE 129
Query: 249 EL-QRLPGIGAKVGDGV 264
L + GIG K
Sbjct: 130 FLVRNAKGIGWKEASHF 146
>3cih_A Putative alpha-rhamnosidase; structural genomics, protein structure
initiative II, NYSGXRC, (alpha/alpha)6 barrel domain;
2.33A {Bacteroides thetaiotaomicron vpi-5482}
Length = 739
Score = 30.0 bits (67), Expect = 1.8
Identities = 4/44 (9%), Positives = 10/44 (22%), Gaps = 2/44 (4%)
Query: 257 GAKVGDGVFKEHVWT-LWADPS-YLHYQVYSQHKLNTNSVETML 298
+ + W S Y+ + L+ +
Sbjct: 33 NQMNNRRTERGAFFPPFWKTDSHYVVVEFSKVLNLSEPEEVFIA 76
>2o3e_A Neurolysin; thermolysin-like domain, substrate-binding channel,
hydrolase; 2.20A {Rattus norvegicus} PDB: 1i1i_P
Length = 678
Score = 29.9 bits (68), Expect = 2.2
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 14/77 (18%)
Query: 235 LERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTL--WADPSYLHYQVYS----QHK 288
L+ L K E + + + K + E+ + W D Y Y + K
Sbjct: 296 LDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAW-DLHY-----YMTQTEELK 349
Query: 289 LNTNSVETMLKEYFRLD 305
+ + + LKEYF ++
Sbjct: 350 YSVD--QESLKEYFPIE 364
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB:
3knt_A*
Length = 214
Score = 28.9 bits (64), Expect = 2.7
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 198 LARPAVEAKLRQLGFGY---RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREEL-QRL 253
L R +E KL+ LG + RA++I + + ++ + ARE L + +
Sbjct: 76 LPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESF-----ENEKVAREFLVRNI 130
Query: 254 PGIGAKVGD 262
GIG K
Sbjct: 131 KGIGYKEAS 139
>3m5u_A Phosphoserine aminotransferase; alpha-beta half sandwich, csgid,
amino-acid biosynthesis, cytoplasm, pyridoxal phosphate;
HET: MES; 2.15A {Campylobacter jejuni}
Length = 361
Score = 29.4 bits (67), Expect = 2.9
Identities = 17/106 (16%), Positives = 29/106 (27%), Gaps = 43/106 (40%)
Query: 204 EAKLRQL---GFGYRAKFIQ-----------------KSAEYIIQGGGESWLERLGGKSY 243
+ K ++L Y F+Q EY G W K+
Sbjct: 56 QEKAKKLYELNDDYEVLFLQGGASLQFAMIPMNLALNGVCEYANTG---VW----TKKAI 108
Query: 244 EEAREELQRLPGIGAKV------GDGVFKEHV--WTLWADPSYLHY 281
+EA+ +G V + F H+ + Y +
Sbjct: 109 KEAQI-------LGVNVKTVASSEESNFD-HIPRVEFSDNADYAYI 146
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 28.9 bits (65), Expect = 2.9
Identities = 9/42 (21%), Positives = 20/42 (47%)
Query: 190 FAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGGG 231
++ P A V+A+L ++G ++K+ + I+ G
Sbjct: 4 YSLPPEVLAALERVKARLNKVGEELEPISLRKAVRHYIETPG 45
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 28.7 bits (65), Expect = 3.7
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 244 EEAREELQRLPGIGAK 259
EL RLPGIG K
Sbjct: 8 VSLIRELSRLPGIGPK 23
>1ap8_A Translation initiation factor EIF4E; RNA CAP; HET: M7G; NMR
{Saccharomyces cerevisiae} SCOP: d.86.1.1 PDB: 1rf8_A*
Length = 213
Score = 27.8 bits (61), Expect = 6.6
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 267 EHVWTLWAD-PSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFF 322
WTLW P+ + +S S +T ++E++ + +N+PE + D
Sbjct: 40 NTKWTLWYTKPAVDKSESWSDLLRPVTSFQT-VEEFWAIIQNIPEPHELPLKSDYHV 95
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 28.1 bits (63), Expect = 7.1
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 200 RPAVEAKLRQLGFGYRAKFIQKSAEYIIQGGG 231
VE L + A+ +++ Y ++ GG
Sbjct: 14 GAEVEKALVRYLSIGLAEDFREAVLYQVKTGG 45
>2zze_A Alanyl-tRNA synthetase; ligase, hydrolase; HET: MLY; 2.16A
{Pyrococcus horikoshii} PDB: 2zzf_A 2zzg_A*
Length = 752
Score = 28.1 bits (61), Expect = 7.7
Identities = 8/48 (16%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 356 CNHYHF--QKSTSKTLTPAVYNQIRAFFADKFGKYAGWAHSILFCADL 401
C+ Y F + + T +++R F F + + H + +
Sbjct: 42 CDEYQFIGKPGIPRXYT---LDEMREXFLRFFEXHEIYPHGRVXRYPV 86
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 28.1 bits (62), Expect = 7.9
Identities = 7/58 (12%), Positives = 21/58 (36%), Gaps = 10/58 (17%)
Query: 214 YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWT 271
++++ + +A + E L ++ E E +P +G + + +
Sbjct: 32 FKSRAYRSAARSL---------EELNEETPELLAREFTGIPKVGKGIAA-ELSDFARS 79
>2c0r_A PSAT, phosphoserine aminotransferase; pyridoxal-5'-phosphate,
pyridine serine biosynthesis, amino-acid biosynthesis,
pyridoxal phosphate; HET: PLP; 1.2A {Bacillus circulans}
SCOP: c.67.1.4 PDB: 1bt4_A* 1w3u_A*
Length = 362
Score = 27.8 bits (63), Expect = 8.6
Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 34/103 (33%)
Query: 204 EAKLRQL---GFGYRAKFIQ------------------KSAEYIIQGGGESWLERLGGKS 242
+A+L L GY+ FIQ ++A Y++ G SW K+
Sbjct: 55 QARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTG---SW----ASKA 107
Query: 243 YEEAREELQRLPGIGAKVGDGVF----KEHVWTLWADPSYLHY 281
+EA+ + A + K L + +YLH
Sbjct: 108 LKEAKLIGD--THVAASSEASNYMTLPKLQEIQLQDNAAYLHL 148
>2o36_A ThiMet oligopeptidase; thermolysin-like domain, substrate-binding
channel, hydrolase; 1.95A {Homo sapiens} PDB: 1s4b_P
Length = 674
Score = 27.6 bits (62), Expect = 9.8
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 14/77 (18%)
Query: 235 LERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTL--WADPSYLHYQVYS----QHK 288
L+ L K +E + + + + W D Y Y + +
Sbjct: 280 LDELAQKLKPLGEQERAVILELKRAECERRGLPFDGRIRAW-DMRY-----YMNQVEETR 333
Query: 289 LNTNSVETMLKEYFRLD 305
+ + +LKEYF +
Sbjct: 334 YCVD--QNLLKEYFPVQ 348
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.135 0.417
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,185,751
Number of extensions: 431675
Number of successful extensions: 1181
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1163
Number of HSP's successfully gapped: 43
Length of query: 457
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 360
Effective length of database: 3,993,456
Effective search space: 1437644160
Effective search space used: 1437644160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)