RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8564
(341 letters)
>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 = 387 bits (997), Expect = e-135
Identities = 91/342 (26%), Positives = 165/342 (48%), Gaps = 15/342 (4%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
LPW+ ++ Y +W+SE+MLQQT+V TVIPY+++F+ +FP + +LA A + V++ W GLG
Sbjct: 31 LPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLG 90
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
YYSR RNLH K V +Y G P + L G+G T A+ AYG +DGNV
Sbjct: 91 YYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNV 150
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
R+L R+ + + K+ + +++ +N + + L++ G+++C +P C +
Sbjct: 151 MRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLL 210
Query: 182 CPLQLCCISYKTNKINNFLIKN-KKNIKNCSIIMFIVIDDD-YVLFQKRSNKGIWGGLLS 239
CP+Q C ++ +K K +K + + ++ DD+ VL +KR + G+ L
Sbjct: 211 CPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWE 270
Query: 240 FPEWILKDKIINFVDNNLKNLIELEIKKFISSFGF-IKNYLILPIISHKLTHLQFKIVPC 298
FP + + + E + +G ++ + H +HL +++
Sbjct: 271 FPS----------CETDGADGKEKLEQMVGEQYGLQVELTEPIVSFEHAFSHLVWQLTVF 320
Query: 299 HIFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340
L E + P ++K P +++ + +
Sbjct: 321 PGRLVHGGPVE--EPYRLAPEDELKAYAFPVSHQRVWREYKE 360
>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 = 332 bits (853), Expect = e-114
Identities = 79/249 (31%), Positives = 123/249 (49%), Gaps = 9/249 (3%)
Query: 2 LPWQNT--------KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENV 53
LPW+ + Y +W+SE+MLQQTQV TVI YY +++K+P + LA A LE V
Sbjct: 33 LPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINYYTGWMQKWPTLQDLASASLEEV 92
Query: 54 MELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLI-NLPGIGQSTASAIRVFAYGK 112
+LW+GLGYYSR R L A+ V + G P+ +L LPG+G+ TA AI A+G+
Sbjct: 93 NQLWAGLGYYSRGRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIAFGQ 152
Query: 113 RNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIIC 172
++DGNV R+L RV I + + ++LW A L+ + Q M+ G+ +C
Sbjct: 153 ATGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQQLVDPARPGDFNQAAMELGATVC 212
Query: 173 KKIKPKCKVCPLQLCCISYKTNKINNFLIKNKKNIKNCSIIMFIVIDDDYVLFQKRSNKG 232
+P C CP++ C + + + L + ++
Sbjct: 213 TPQRPLCSQCPVESLCRARQRVEQEQLLASGSLSGSPDVEECAPNTGQCHLCLPPSEPWD 272
Query: 233 IWGGLLSFP 241
G+++FP
Sbjct: 273 QTLGVVNFP 281
>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 = 329 bits (845), Expect = e-114
Identities = 97/204 (47%), Positives = 130/204 (63%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
LPWQ K Y +WLSE+MLQQTQV TVIPY++RF+ +FP + LA A L+ V+ LW+GLG
Sbjct: 22 LPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLG 81
Query: 62 YYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNV 121
YY+RARNLH A+ V + G FP+ F + LPG+G+STA AI + GK ILDGNV
Sbjct: 82 YYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNV 141
Query: 122 KRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKV 181
KR+L R ++ K +E KLW + + P +E + Q +MD G++IC + KPKC +
Sbjct: 142 KRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSL 201
Query: 182 CPLQLCCISYKTNKINNFLIKNKK 205
CPLQ CI+ N + K K
Sbjct: 202 CPLQNGCIAAANNSWALYPGKKPK 225
>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 = 311 bits (799), Expect = e-107
Identities = 60/195 (30%), Positives = 103/195 (52%), Gaps = 2/195 (1%)
Query: 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG 61
PW++T++ Y I ++EI+L++T V Y +F K+ + + + + +G
Sbjct: 27 FPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIG 86
Query: 62 YYS-RARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGN 120
+ RA L A++V Y G P+N ++++LPG+G+ T +A+ A+GK+ A++D N
Sbjct: 87 LSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFGKKAAMVDAN 146
Query: 121 VKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCK 180
R++ R G + N+ + K LW A L+P + GLMDF +IIC KPKC+
Sbjct: 147 FVRVINRYFGGSYE-NLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKCE 205
Query: 181 VCPLQLCCISYKTNK 195
C + C Y+
Sbjct: 206 KCGMSKLCSYYEKCS 220
>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 = 141 bits (358), Expect = 1e-41
Identities = 29/142 (20%), Positives = 56/142 (39%), Gaps = 10/142 (7%)
Query: 1 MLPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGL 60
++ + + + ++ I L +T IP +FL+K+P+ A +V EL L
Sbjct: 22 LVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPL 81
Query: 61 GYYS-RARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYG--KRNAIL 117
G Y RA+ + + K + I L GIG+ + R+F K+
Sbjct: 82 GLYDLRAKTIVKFSD-------EYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPE 134
Query: 118 DGNVKRILIRVLGINCSLNIKF 139
D + + + + L++
Sbjct: 135 DHKLNKYHDWLWENHEKLSLSH 156
>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 = 80.0 bits (198), Expect = 1e-17
Identities = 49/174 (28%), Positives = 81/174 (46%), Gaps = 10/174 (5%)
Query: 25 VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGI 83
VN V R +K+ LE + + +G Y ++ARN+ ++ KYNG
Sbjct: 51 VNKVTK---RLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGE 107
Query: 84 FPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGI-NCSLNIKFIEK 142
P++ L+ LPG+G+ TA+ + A+G +D +V+R+ R LG ++ +EK
Sbjct: 108 VPRDRDELMKLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKR-LGFCRWDDSVLEVEK 166
Query: 143 KLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKI 196
L + ++PK+ I ++ FG CK P+C CPL C K
Sbjct: 167 TLMK----IIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMR 216
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 77.6 bits (192), Expect = 5e-17
Identities = 38/174 (21%), Positives = 76/174 (43%), Gaps = 9/174 (5%)
Query: 24 QVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNG 82
VN + ++ + +E V +G Y S+A N+ +++ ++NG
Sbjct: 46 SVNKATA---KLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG 102
Query: 83 IFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEK 142
P++ +L LPG+G+ TA+ + A+G +D ++ R+ R N++ +E+
Sbjct: 103 EVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNR-TQFAPGKNVEQVEE 161
Query: 143 KLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKI 196
KL + ++P + L+ G C KP+C C ++ C + I
Sbjct: 162 KLLK----VVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEKVDI 211
>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 = 66.7 bits (163), Expect = 4e-13
Identities = 33/194 (17%), Positives = 60/194 (30%), Gaps = 24/194 (12%)
Query: 4 WQNTKNTYYIWLSEIMLQQT---QVNTVIP----YYQRFLKKFPNIMSLAQAKLENVMEL 56
W + L ++ Q T V + + N+ +A + + E
Sbjct: 24 WWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAEC 83
Query: 57 WSGLGYY-SRARNLHICAKLVFFKYNGIF----PKNFISLINLPGIGQSTASAIRVFAYG 111
G+Y +A+ L + + + L++ GIG+ +A AI +A
Sbjct: 84 VRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACA 143
Query: 112 KRNAILDGNVKRILIRVLGINCSLNIK---FIEKKLWRYAIDLLPKKNIEIYTQGLM--- 165
K ++D L + LGI + F EK + L I L
Sbjct: 144 KEVMVVDKYSYLFLKK-LGIEIEDYDELQHFFEKGVQENLNSALALYENTISLAQLYARF 202
Query: 166 -----DFGSIICKK 174
+F +
Sbjct: 203 HGKIVEFSKQKLEL 216
>1x51_A A/G-specific adenine DNA glycosylase; nudix domain, DNA repair,
alpha-3 isoform, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.113.1.3
Length = 155
Score = 64.4 bits (157), Expect = 9e-13
Identities = 18/137 (13%), Positives = 41/137 (29%), Gaps = 11/137 (8%)
Query: 204 KKNIKNCSIIMFIVID----DDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFVDNNLKN 259
+K + S ++ +L +R N G+ GL FP + L+
Sbjct: 13 RKPPREESSATCVLEQPGALGAQILLVQRPNSGLLAGLWEFPSVTWEPSEQLQRKALLQE 72
Query: 260 LIELEIKKFISSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKN-NFIWYP 318
L + L + H +H++ + L+ W
Sbjct: 73 LQRWAGPLPATHLRH------LGEVVHTFSHIKLTYQVYGLALEGQTPVTTVPPGARWLT 126
Query: 319 IKKIKNSPIPAPVRKIL 335
++ + + ++K+
Sbjct: 127 QEEFHTAAVSTAMKKVF 143
>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 = 50.8 bits (121), Expect = 1e-07
Identities = 21/117 (17%), Positives = 44/117 (37%), Gaps = 9/117 (7%)
Query: 39 FPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFIS-------- 90
I + ++ N+++ Y +A+ + + + V+ +
Sbjct: 59 GQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKEEIKPLADEDQQLARER 118
Query: 91 LINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRY 147
L+N+ GIG AS AI+D ++ + R +G N+K + K L+
Sbjct: 119 LLNIKGIGMQEASHFLRNVGYFDLAIIDRHIIDFMRR-IGAIGETNVKQLSKSLYIS 174
>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 = 42.9 bits (100), Expect = 1e-04
Identities = 39/304 (12%), Positives = 84/304 (27%), Gaps = 72/304 (23%)
Query: 42 IMSLAQAKLENVME---LWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIG 98
+ K++ M+ W L + + + + ++ + + N+
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227
Query: 99 QSTASAIRVFAYGKRNA----ILDGNV--KRILIRVLGINCSLNIKFIEKKLW--RYA-- 148
S + +R K +L NV + ++C K L R+
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLL-NVQNAKA-WNAFNLSC--------KILLTTRFKQV 277
Query: 149 IDLLPKKNIEIYTQGLMDFG-------SIICKKIKPKCKVCPLQLCCISYKTNKINNFLI 201
D L + S++ K + + + P ++ N +
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL-------TTNPRRL 330
Query: 202 KNKKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEW--ILKDKIINFVDNNLKN 259
SII + D W W + DK+ ++++L
Sbjct: 331 ---------SIIAESIRDG----------LATWD------NWKHVNCDKLTTIIESSLNV 365
Query: 260 LIELEIKKFISSFG-FIKNYLI----LPII-SHKLTHLQFKIVPCHIFLKKCFLKENKNN 313
L E +K F + I L +I + +V + K +++
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV--NKLHKYSLVEKQPKE 423
Query: 314 FIWY 317
Sbjct: 424 STIS 427
Score = 42.5 bits (99), Expect = 2e-04
Identities = 54/383 (14%), Positives = 112/383 (29%), Gaps = 108/383 (28%)
Query: 10 TYYI-WLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARN 68
T + W ++ +Q ++ Q+F+++ L N L S + R +
Sbjct: 64 TLRLFWT--LLSKQEEM------VQKFVEE-----VLRI----NYKFLMSPIKTEQRQPS 106
Query: 69 L----HICAKLVFFKYNGIFPKNFIS----LINLPGIGQSTASAIRVFAYGKRNAILDGN 120
+ +I + + N +F K +S + L A V G + G+
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG-----VLGS 161
Query: 121 VKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCK 180
K + + ++ + K K W ++L + E + L +I P
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFW---LNLKNCNSPETVLEMLQKL----LYQIDPNWT 214
Query: 181 VCPLQLCCISYKTNKINNF---LIKNKKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGG- 236
I + + I L+K+K +NC +V+ + V N W
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPY-ENC----LLVLLN--V-----QNAKAWNAF 262
Query: 237 ------LLSFPEWILKDK-IINFVDNNLKNLIELEIKKFISSFG-------FIKNYLILP 282
LL + K + +F+ I L+ + +K L
Sbjct: 263 NLSCKILL-----TTRFKQVTDFLSAATTTHISLD--HHSMTLTPDEVKSLLLK---YLD 312
Query: 283 IISHKLTHLQFKIVPCHIFLKKCFLKENKN---NFIWYPIKKI----------------- 322
L P + + +++ N+ K+
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 323 ----------KNSPIPAPVRKIL 335
++ IP + ++
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLI 395
Score = 34.4 bits (78), Expect = 0.053
Identities = 46/278 (16%), Positives = 85/278 (30%), Gaps = 95/278 (34%)
Query: 4 WQNTKNTYYIWLSEIMLQQTQVNTVIPYYQR--F--LKKFP---NIMSLAQAKLENVME- 55
W N K+ L+ I+ ++ +N + P R F L FP +I ++
Sbjct: 344 WDNWKHVNCDKLTTII--ESSLNVLEPAEYRKMFDRLSVFPPSAHIP-------TILLSL 394
Query: 56 LWSGL------------------------GYYS-------------RARNLHICAKLVFF 78
+W + S LH +V
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH--RSIVD- 451
Query: 79 KYNGI--FPKNFISLINLPG-----IGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGI 131
YN F + + L IG + +N + L R++
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIG-----------HHLKNIEHPERMT--LFRMV-- 496
Query: 132 NCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISY 191
L+ +F+E+K+ + +I Q L + IC P
Sbjct: 497 --FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDN-------DPK----YER 543
Query: 192 KTNKINNFLIKNKKNI---KNCSIIMFIVIDDDYVLFQ 226
N I +FL K ++N+ K ++ ++ +D +F+
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFE 581
>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 = 41.1 bits (96), Expect = 3e-04
Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 18/106 (16%)
Query: 36 LKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFIS----- 90
FP + L + ++ E G+ RA+ L + YNG +I
Sbjct: 155 YYAFPTVDKLHEFTEKDFEEC--TAGF--RAKYLKDTVDRI---YNGELNLEYIKSLNDN 207
Query: 91 -----LINLPGIGQSTASAIRVFAYGKRNAI-LDGNVKRILIRVLG 130
L G+G A I +F+ K +A +D VK+ ++ +
Sbjct: 208 ECHEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYV 253
>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 = 40.5 bits (94), Expect = 4e-04
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 14/106 (13%)
Query: 39 FPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFIS-------- 90
FP++ +LA ++E + GLGY RAR + A+ + + G+ +
Sbjct: 196 FPSLQALAGPEVEAHLRK-LGLGY--RARYVSASARAILEEQGGLAWLQQLRESSYEEAH 252
Query: 91 --LINLPGIGQSTASAIRVFAYGKRNAI-LDGNVKRILIRVLGINC 133
L LPG+G A I + A K A+ ++ ++ I R +
Sbjct: 253 KALCILPGVGTCVADKICLMALDKPQAVPVNVHMWHIAQRDYSWHP 298
>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 = 38.5 bits (89), Expect = 0.002
Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 5/92 (5%)
Query: 41 NIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFIS-----LINLP 95
++L + +LE ++ Y RA + + + K +N + N+
Sbjct: 72 GFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIK 131
Query: 96 GIGQSTASAIRVFAYGKRNAILDGNVKRILIR 127
GIG AS AI+D ++ R L
Sbjct: 132 GIGYKEASHFLRNVGYDDVAIIDRHILRELYE 163
>1k2e_A Nudix homolog; nudix/MUTT-like fold, mixed alpha/beta, dimer,
putative NUDI hydrolase, structural genomics, unknown
function; 1.80A {Pyrobaculum aerophilum} SCOP: d.113.1.1
PDB: 1jrk_A 1k26_A
Length = 156
Score = 37.6 bits (87), Expect = 0.002
Identities = 20/132 (15%), Positives = 41/132 (31%), Gaps = 21/132 (15%)
Query: 216 IVIDDDYVLFQKRSNKGIW---GGLLSFPEWILKDKIINFVDNNLKNL-----IELEIKK 267
+++++ VL K G++ GG + E + + + I +E
Sbjct: 7 VLVENGKVLLVKHKRLGVYIYPGGHVEHNETPI--------EAVKREFEEETGIVVEPIG 58
Query: 268 FISSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNN----FIWYPIKKIK 323
F P+ L + HI +L + W +++I
Sbjct: 59 FTYGIIDENAVER-PMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREID 117
Query: 324 NSPIPAPVRKIL 335
VRK++
Sbjct: 118 RIETFPNVRKVV 129
>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 = 37.3 bits (86), Expect = 0.003
Identities = 23/131 (17%), Positives = 44/131 (33%), Gaps = 12/131 (9%)
Query: 32 YQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFIS- 90
+ + + L +L + RA + + + + K + +
Sbjct: 69 IRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFI-VENRKLLGKLKNLVKGDPFQS 127
Query: 91 ----LINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIR---VLGINCSLNIKF---I 140
+ N GIG AS + AILD +V R++ R + I + K +
Sbjct: 128 REFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYV 187
Query: 141 EKKLWRYAIDL 151
E+ L + A
Sbjct: 188 EEILRKVAEAF 198
>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 = 36.2 bits (83), Expect = 0.016
Identities = 35/144 (24%), Positives = 50/144 (34%), Gaps = 54/144 (37%)
Query: 34 RFLKKFPNIMSLAQAKLENVMELWSGLGYYS---RARNLHICA--KLVFFKYNGIFPKN- 87
R + +PN SL + LE+ +E + G S NL V K N P
Sbjct: 309 RCYEAYPNT-SLPPSILEDSLE--NNEGVPSPMLSISNLTQEQVQDYVN-KTNSHLPAGK 364
Query: 88 --FISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVL-GINCSL--------- 135
ISL+N G +N ++ G + L G+N +L
Sbjct: 365 QVEISLVN-----------------GAKNLVVSGPP-----QSLYGLNLTLRKAKAPSGL 402
Query: 136 ---NIKFIEKKL---WRYAIDLLP 153
I F E+KL R+ LP
Sbjct: 403 DQSRIPFSERKLKFSNRF----LP 422
Score = 28.5 bits (63), Expect = 4.7
Identities = 7/35 (20%), Positives = 10/35 (28%), Gaps = 12/35 (34%)
Query: 307 LKENKNNFIWYPIKKIKNSPIPA-----PVRKILF 336
L K ++KI + V LF
Sbjct: 1869 LNFIK-------LQKIDIIELQKSLSLEEVEGHLF 1896
>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 = 34.0 bits (78), Expect = 0.049
Identities = 25/148 (16%), Positives = 50/148 (33%), Gaps = 23/148 (15%)
Query: 29 IPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLH-ICAKLVFFKYNGIFPKN 87
+ + FP ++ +A +E + E GL +A + I + + +
Sbjct: 151 VEWNGLKFYGFPTQEAILKAGVEGLREC--GLSR-RKAELIVEIAKEENLEELKEWGEEE 207
Query: 88 FIS-LINLPGIGQSTASAIRVFAYGKRNA--ILDGNVKRILIRVLGINCSLNIKFIEKK- 143
L + GIG+ TA + A G +N D V+R + R+ + + + +
Sbjct: 208 AYEYLTSFKGIGRWTAELVLSIALG-KNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIA 266
Query: 144 --------------LWRYAIDLLPKKNI 157
L+ Y K +
Sbjct: 267 RERFGRFARDILFYLFLYDRFFSKKTEL 294
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.8 bits (71), Expect = 0.16
Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 4/27 (14%)
Query: 136 NIKFIEKKLWRYAIDLLP----KKNIE 158
+K ++ L YA D P K +E
Sbjct: 21 ALKKLQASLKLYADDSAPALAIKATME 47
Score = 28.8 bits (63), Expect = 1.6
Identities = 6/21 (28%), Positives = 9/21 (42%), Gaps = 5/21 (23%)
Query: 319 IKKIKNS-----PIPAPVRKI 334
+KK++ S AP I
Sbjct: 22 LKKLQASLKLYADDSAPALAI 42
>3oga_A Nucleoside triphosphatase NUDI; salmonella enterica subsp. enterica
serovar typhimurium STR. unknown function; HET: PO4;
1.75A {Salmonella enterica subsp} PDB: 3n77_A
Length = 165
Score = 31.4 bits (71), Expect = 0.21
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 204 KKNIKNCSIIMFIVIDDDYVLFQKRS-NKGIWGGLLSFP 241
++ +I+ ++ +D L K + N+G++ G +
Sbjct: 22 SNAMRQRTIVCPLIQNDGCYLLCKMADNRGVFPGQWALS 60
>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 = 30.5 bits (69), Expect = 0.69
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 91 LINLPGIGQSTASAIRVFAYGKRNAILDG 119
L PGIG+ TA+ + + ++ L
Sbjct: 209 LQTFPGIGRWTANYFALRGWQAKDVFLPD 237
>3edu_A Beta-I spectrin, spectrin beta chain, erythrocyte; ankyrin,
ankyrin-binding domain, actin capping, AC binding,
cytoskeleton, disease mutation; 2.10A {Homo sapiens}
PDB: 3f57_A
Length = 218
Score = 29.6 bits (66), Expect = 1.3
Identities = 13/66 (19%), Positives = 19/66 (28%), Gaps = 1/66 (1%)
Query: 15 LSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLA-QAKLENVMELWSGLGYYSRARNLHICA 73
E+ L QV R + + A Q K + V W L R +
Sbjct: 153 ERELHLLGVQVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDACAGRRTQLVD 212
Query: 74 KLVFFK 79
F+
Sbjct: 213 TADKFR 218
>3ees_A Probable pyrophosphohydrolase; nudix, RNA pyrophosphohydrolase;
1.90A {Bdellovibrio bacteriovorus} PDB: 3eeu_A 3ef5_A*
3ffu_A*
Length = 153
Score = 28.4 bits (64), Expect = 1.8
Identities = 6/26 (23%), Positives = 9/26 (34%)
Query: 216 IVIDDDYVLFQKRSNKGIWGGLLSFP 241
+ D +L +R G FP
Sbjct: 28 FLRKDGKILVGQRPENNSLAGQWEFP 53
>2duy_A Competence protein comea-related protein; helix-hairpin-helix,
structural genomics, NPPSFA; 1.75A {Thermus
thermophilus} SCOP: a.60.2.7
Length = 75
Score = 27.3 bits (61), Expect = 1.8
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 91 LINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGI 131
L+ LPGIG A I + D L++V GI
Sbjct: 29 LMALPGIGPVLARRIV--EGRPYARVED------LLKVKGI 61
>3hhj_A Mutator MUTT protein; niaid, ssgcid, decode, UW, SBRI, infectious
diseases, hydrol structural genomics; 2.10A {Bartonella
henselae}
Length = 158
Score = 28.5 bits (64), Expect = 2.1
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 216 IVIDDDYVLFQKRSNKGIWGGLLSFP 241
++ D+ VL +R GL FP
Sbjct: 36 LLDQDNRVLLTQRPEGKSLAGLWEFP 61
>3fk9_A Mutator MUTT protein; structural genomics, hydrolase, PSI-2,
protein structure initiative; 2.50A {Bacillus
halodurans}
Length = 188
Score = 28.5 bits (64), Expect = 2.2
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 216 IVIDDDYVLFQKRSNKGIWGG 236
IV+D D VL ++ +G W
Sbjct: 10 IVVDHDQVLLLQKPRRGWWVA 30
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix
turn helix motif, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.60.2.7
Length = 98
Score = 27.1 bits (60), Expect = 2.9
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 91 LINLPGIGQSTASAIRVFAYGKRNAILDGNVKRI--LIRVLGI 131
L +L IG A I + + + G ++ L RV GI
Sbjct: 42 LRSLQRIGPKKAQLI--VGWRELH----GPFSQVEDLERVEGI 78
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination,
branch migration, DNA BIND oligomerization, acidic PIN;
2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A
2h5x_A 1bvs_A
Length = 212
Score = 28.0 bits (63), Expect = 3.3
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 88 FISLINLPGIGQSTASAI--RVFAYGKRNAILDGNVKRILIRVLGI 131
F++L+++ G+G A A A R + DGNV L RV GI
Sbjct: 87 FLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAA-LTRVPGI 131
>2rrk_A ORF135, CTP pyrophosphohydrolase; NMR {Escherichia coli}
Length = 140
Score = 27.6 bits (62), Expect = 3.7
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 216 IVIDDDYVLFQKRSNKGIWGGLLSFP 241
I+ D +L +R + GL F
Sbjct: 15 IIERDGKILLAQRPAQSDQAGLWEFA 40
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1
a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Length = 203
Score = 28.1 bits (63), Expect = 3.9
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 88 FISLINLPGIGQSTASAI--RVFAYGKRNAILDGNVKRILIRVLGI 131
F LI G+G A AI + A NA+ V L+++ GI
Sbjct: 72 FKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGA-LVKLPGI 116
>1mut_A MUTT, nucleoside triphosphate pyrophosphohydrolase; DNA repair; NMR
{Escherichia coli} SCOP: d.113.1.1 PDB: 1ppx_A* 1pun_A*
1puq_A* 1pus_A* 1tum_A* 3a6s_A* 3a6t_A* 3a6u_A* 3a6v_A*
Length = 129
Score = 26.7 bits (60), Expect = 5.2
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 216 IVIDDDYVLFQKRSNKGIWGGLLSFP 241
I +++ + +R+ L FP
Sbjct: 11 IRNENNEIFITRRAADAHMANKLEFP 36
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 27.2 bits (61), Expect = 6.1
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 88 FISLINLPGIGQSTASAI--RVFAYGKRNAILDGNVKRILIRVLGI 131
F L+++ G+G A A+ + A+L+G+ + L G+
Sbjct: 71 FELLLSVSGVGPKVALALLSALPPRLLARALLEGDARL-LTSASGV 115
>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A
{Xanthomonas campestris}
Length = 129
Score = 26.6 bits (59), Expect = 6.8
Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 9 NTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPN 41
N Y WL E ++ + ++P
Sbjct: 40 NALY-WLGESYYATRNFQLAEAQFRDLVSRYPT 71
>2q8t_A CCL14; common CC chemokine fold, cytokine; 2.23A {Homo sapiens}
Length = 74
Score = 25.5 bits (56), Expect = 7.0
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 187 CCISYKTNKINNFLIKN-KKNIKNCSI--IMFI 216
CC +Y T KI I + + CS I+FI
Sbjct: 16 CCFTYTTYKIPRQRIMDYYETNSQCSKPGIVFI 48
>3r03_A Nudix hydrolase; structural genomics, PSI2, protein structure INIT
NEW YORK SGX research center for structural genomics,
nysgx; HET: ADP; 2.49A {Rhodospirillum rubrum}
Length = 144
Score = 26.9 bits (60), Expect = 7.0
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 216 IVIDDDYVLFQKRSNKGIWGGLLSFP 241
++ D VL +R GL FP
Sbjct: 15 LIDPDGRVLLAQRPPGKSLAGLWEFP 40
>3sso_A Methyltransferase; macrolide, natural product, rossman fold; HET:
SAH; 1.90A {Micromonospora griseorubida} PDB: 3ssn_A*
3ssm_A*
Length = 419
Score = 27.2 bits (59), Expect = 8.4
Identities = 23/168 (13%), Positives = 48/168 (28%), Gaps = 23/168 (13%)
Query: 136 NIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNK 195
++ +E + Y ++ ++ G I I K V L++ I N
Sbjct: 217 QVRVLEIGVGGYKHPEWGGGSLRMWKS-FFPRGQIYGLDIMDKSHVDELRIRTIQGDQND 275
Query: 196 INNFLIKNKKNIKNCSIIMFIVIDDDYVL------FQKRSNKGIWGGLL----------- 238
+ + ++ D ++ F GGL
Sbjct: 276 AEFL----DRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWP 331
Query: 239 SFPEWILKDKIINFVDNNLKNLIE-LEIKKFISSFGFIKNYLILPIIS 285
F + LK+LI+ ++ ++ S Y+ I+
Sbjct: 332 GFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVG 379
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
0.327 0.144 0.449
Gapped
Lambda K H
0.267 0.0570 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,269,281
Number of extensions: 315245
Number of successful extensions: 1000
Number of sequences better than 10.0: 1
Number of HSP's gapped: 977
Number of HSP's successfully gapped: 65
Length of query: 341
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,077,219
Effective search space: 1007073093
Effective search space used: 1007073093
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.5 bits)