RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 020295
(328 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 = 233 bits (594), Expect = 1e-74
Identities = 104/333 (31%), Positives = 156/333 (46%), Gaps = 31/333 (9%)
Query: 6 NSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSLPLTFPTGQTFRWKKT 65
+S P P P + P+ W + +SEL L L P+GQ+FRW++
Sbjct: 9 HSQDPNSMPARALLPRRMGHRT---LASTPALWASIPCPRSELRLDLVLPSGQSFRWREQ 65
Query: 66 GPLQYTGPIGPHLISLKHLQNGDVCYHIHT-----SPSEPAAKSALLDFLNMGISLGELW 120
P ++G + + +L + C S P A+ + + ++L +L+
Sbjct: 66 SPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLY 125
Query: 121 EGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLAS-LGSHL 179
+ + D F E+A+ G R+LRQDP+ECL F+CSSNNNIARIT MV+ L G L
Sbjct: 126 HHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRL 185
Query: 180 GNVEGFEFHEFPSLERLSLVS-EVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVD 238
++ +H FPSL+ L+ E LR G GYR A+Y++ +
Sbjct: 186 IQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYR-----------------ARYVSASAR 228
Query: 239 VLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVW 298
+ + GG WL LR+ +EA ALC LPGVG VA I L +LD+ A+PV+ H+W
Sbjct: 229 AILEEQ-GGLAWLQQLRESSYEEAHKALCILPGVGTCVADKICLMALDKPQAVPVNVHMW 287
Query: 299 KIATRYLLPELAGVR---LTPKLCSRVAEAFCE 328
IA R + +P+ + F
Sbjct: 288 HIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRS 320
>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 = 219 bits (560), Expect = 2e-70
Identities = 71/263 (26%), Positives = 117/263 (44%), Gaps = 26/263 (9%)
Query: 46 SELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSPSEPAAKSA 105
L F GQ FRW + Y G ++ ++ + V Y+I +E K+
Sbjct: 19 ENFELKDIFDCGQCFRWHRQENGNYIGIAFEKVVEVQKIGEDVVIYNI----NEEEFKNV 74
Query: 106 LLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARI 165
++ ++ GE+ + S D + + G R+LRQDP E LL F+ S+NN I I
Sbjct: 75 WSEYFDLYRDYGEIKKELSR-DPLLKKSVDFGEGIRILRQDPFEILLSFIISANNRIPMI 133
Query: 166 TKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRR 225
K ++ ++ +G ++ FP++++L +E + G+R
Sbjct: 134 KKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEECTAGFR------------- 180
Query: 226 SFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 285
AKY+ TVD + + G L ++ L+ E + L GVGP+VA CI LFS+
Sbjct: 181 ----AKYLKDTVDRIYN----GELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSM 232
Query: 286 DQHHAIPVDTHVWKIATRYLLPE 308
++ A PVDT V K +
Sbjct: 233 QKYSAFPVDTWVKKAMMSLYVAP 255
>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 = 87.5 bits (217), Expect = 5e-20
Identities = 26/167 (15%), Positives = 50/167 (29%), Gaps = 30/167 (17%)
Query: 123 FSASDCRFAELAKYLAGARV---LRQDPVECLLQFLCSSNNNIARITKMVD-FLASLGSH 178
F D + L G + E + + + + K+ + G
Sbjct: 91 FMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDE 150
Query: 179 LGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVD 238
+ G +F+ FP+ E + LR G R +A+ I
Sbjct: 151 V-EWNGLKFYGFPTQEAILKAGVEGLRECGLSRR----------------KAELIVEIAK 193
Query: 239 VLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 285
+ L++ +EA + L + G+G A + +L
Sbjct: 194 EENLE---------ELKEWGEEEAYEYLTSFKGIGRWTAELVLSIAL 231
>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 = 61.5 bits (149), Expect = 2e-11
Identities = 24/127 (18%), Positives = 42/127 (33%), Gaps = 7/127 (5%)
Query: 203 ELRNAGFGYRSAPQSSLLFSVRRSFKQ--AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQ 260
L + ++L S + F AKYI + + + + L D Q
Sbjct: 57 CLGQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKE---EIKPLADEDQQ 113
Query: 261 EAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRY-LLPELAGVRLTPKLC 319
A + L + G+G + A+ AI +D H+ R + E +L+ L
Sbjct: 114 LARERLLNIKGIGMQEASHFLRNVGYFDLAI-IDRHIIDFMRRIGAIGETNVKQLSKSLY 172
Query: 320 SRVAEAF 326
Sbjct: 173 ISFENIL 179
>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 = 59.0 bits (143), Expect = 2e-10
Identities = 9/74 (12%), Positives = 22/74 (29%), Gaps = 8/74 (10%)
Query: 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 289
AK + + + + L G+G + A I ++ +
Sbjct: 94 AKRLIDLSGNILKDFQS-------FENFKQEVTREWLLDQKGIGKESADAILCYACAK-E 145
Query: 290 AIPVDTHVWKIATR 303
+ VD + + +
Sbjct: 146 VMVVDKYSYLFLKK 159
>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 = 51.3 bits (123), Expect = 1e-07
Identities = 36/204 (17%), Positives = 63/204 (30%), Gaps = 35/204 (17%)
Query: 125 ASDCRFAELAKYLAGARV-LRQDPVECLLQFLCSSNNNIARITKMVD-FLASLGSHLGNV 182
+ L G R+ D E ++ + ++A K+ G L
Sbjct: 90 IVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLD-- 147
Query: 183 EGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQS 242
+ E+ FP+ +RL+ L+ G K+A+ + +
Sbjct: 148 DFPEYICFPTPQRLAAADPQALKALGM----------------PLKRAEALIHLANAALE 191
Query: 243 KHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIAT 302
L D+++A+ L T PG+G A AL D ++ K
Sbjct: 192 GT------LPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF 245
Query: 303 RYLLPELAGVRLTPKLCSRVAEAF 326
+TP R AE +
Sbjct: 246 PG---------MTPAQIRRYAERW 260
>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 = 48.3 bits (114), Expect = 2e-06
Identities = 48/297 (16%), Positives = 86/297 (28%), Gaps = 73/297 (24%)
Query: 64 KTGPLQYT-GPIGPHLISLKHLQNGDVCYHIHTSPSEPAAKSALLDFLNMGISLGELWEG 122
+TG QY I + N D C + P +K + + ++
Sbjct: 10 ETGEHQYQYKDILSVFED-AFVDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 123 FSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSS--NNNIARITKMVDFLASLGSHLG 180
F + E+ + VLR + +FL S ++
Sbjct: 68 FWTLLSKQEEMVQKFVEE-VLRIN-----YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 181 NVEGFEFHEFPSLERLSLVSEV-----ELRN---------AGFGYRSAPQSSLLFSVRRS 226
+ + F + ++ RL ++ ELR G G ++ + V S
Sbjct: 122 DNQVFAKY---NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG-----KTWVALDVCLS 173
Query: 227 FKQAKYITGTVDVLQSKHSGGAEWLLSLRKL----DLQEAIDALCTLPGVGPKVAACIAL 282
+K +Q K WL +L+ + E + L + P +
Sbjct: 174 YK-----------VQCKMDFKIFWL-NLKNCNSPETVLEMLQKLLYQ--IDPNWTS---- 215
Query: 283 FSLDQHHAIPVDTHVWKIATRYLLPE---------LAGVRLTPKLCSRVAEAF---C 327
D I + H + R LL L V+ ++ AF C
Sbjct: 216 -RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ-----NAKAWNAFNLSC 266
Score = 38.7 bits (89), Expect = 0.002
Identities = 25/151 (16%), Positives = 46/151 (30%), Gaps = 41/151 (27%)
Query: 69 QYTGPIG--PHLISLKHLQNGDVCY---HI--HTSPSEPAAKSALLD--FLNMG------ 113
Y P + +L Y HI H E + L FL+
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQ----YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507
Query: 114 ISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITK-MVDFL 172
W + +L Y ++C ++ R+ ++DFL
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYK---------------PYICDNDPKYERLVNAILDFL 552
Query: 173 ASLGSHLGNVEGFEFHEFPSLERLSLVSEVE 203
+ +L ++ L R++L++E E
Sbjct: 553 PKIEENLIC------SKYTDLLRIALMAEDE 577
>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 = 45.4 bits (107), Expect = 8e-06
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 10/89 (11%)
Query: 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCT-LPGVGPKVAACIALFSLDQH 288
A++I +L L +L K D ++ + L G+G K A+ + +
Sbjct: 103 AEFIVENRKLLGK--------LKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVED 154
Query: 289 HAIPVDTHVWKIATRYLLPELAGVRLTPK 317
AI +D HV ++ R+ L + + K
Sbjct: 155 LAI-LDKHVLRLMKRHGLIQEIPKGWSKK 182
>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 = 45.4 bits (107), Expect = 2e-05
Identities = 61/355 (17%), Positives = 100/355 (28%), Gaps = 134/355 (37%)
Query: 40 PLNLTQSELSLPLTFPTGQTF-------RWKKTGPLQYTGPIG-------PHLIS--LKH 83
PL L+ L L PT F ++ K P G L+ L +
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY 67
Query: 84 LQNGDVCYHIHTSPSEPAAKSALLDFLNMGISLGELWEGF-----------------SAS 126
+ +S EP+ LN + L E + +
Sbjct: 68 V----------SSLVEPSKVGQFDQVLN--LCLTEFENCYLEGNDIHALAAKLLQENDTT 115
Query: 127 DCRFAELAK-YLAGARVLRQDPVE-----CLLQFLCSSNNNIARITKMVDFLASLGSHLG 180
+ EL K Y+ AR++ + P + L + + A++ + F G G
Sbjct: 116 LVKTKELIKNYIT-ARIMAKRPFDKKSNSALFR---AVGEGNAQL--VAIF----GGQ-G 164
Query: 181 NVEG-FE-----FHEFPSL---------ERL-SLVSEVE---------------LRNAGF 209
N + FE + + L E L L+ L N
Sbjct: 165 NTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS- 223
Query: 210 GYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQ--EAIDALC 267
+ P L S+ S I V+Q H ++++ + L E L
Sbjct: 224 ---NTPDKDYLLSIPISCPL---IG----VIQLAH-----YVVTAKLLGFTPGELRSYLK 268
Query: 268 TLPGVGPKV--AACIALFSLDQHHAIPVDTHVW----KIATRYLLPELA---GVR 313
G + A IA D+ W + + + GVR
Sbjct: 269 GATGHSQGLVTAVAIAE----------TDS--WESFFVSVRKAI--TVLFFIGVR 309
Score = 42.7 bits (100), Expect = 2e-04
Identities = 62/373 (16%), Positives = 111/373 (29%), Gaps = 140/373 (37%)
Query: 15 RLTPQPPPTPPNPQTL---------TTNKP-SKWTPLNLTQS----ELSLPLTFPTGQTF 60
+L + T + L +P K + L ++ L F GQ
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG-GQ-- 163
Query: 61 RWKKTGP-------LQ-----YTGPIGPHLISL--KHLQNGDVCYHIHTSPSEPAAKSAL 106
G L+ Y +G LI + L + A+
Sbjct: 164 -----GNTDDYFEELRDLYQTYHVLVGD-LIKFSAETLSE--------LIRTTLDAEK-- 207
Query: 107 LDFLNMGISLGELW---------EGFSASDCRFA-------ELAKYLAGARVLRQDPVEC 150
G+++ E W + + S + +LA Y+ A++L P E
Sbjct: 208 --VFTQGLNILE-WLENPSNTPDKDYLLS-IPISCPLIGVIQLAHYVVTAKLLGFTPGE- 262
Query: 151 LLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGF- 209
L +L + + + V +A S F + ++++ F
Sbjct: 263 LRSYLKGATGHSQGLVTAV-AIAETDS------WESFFVS-VRKAITVL---------FF 305
Query: 210 -GYRS---APQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLD---LQEA 262
G R P +SL S+ +++ + G +LS+ L +Q+
Sbjct: 306 IGVRCYEAYPNTSLPPSILED---------SLENNE----GVPSPMLSISNLTQEQVQDY 352
Query: 263 IDALCT-LPGVGPKVAACIALF-------------SL----------------DQHHAIP 292
++ + LP G +V I+L SL DQ IP
Sbjct: 353 VNKTNSHLPA-GKQVE--ISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR-IP 408
Query: 293 VDTHVWKIATRYL 305
K + R+L
Sbjct: 409 FSERKLKFSNRFL 421
Score = 37.3 bits (86), Expect = 0.006
Identities = 48/258 (18%), Positives = 88/258 (34%), Gaps = 86/258 (33%)
Query: 2 QSLKN---SPSP------LKRPRLTPQPPPT----PPNPQ---TLTTNKPSKW----TPL 41
SL+N PSP L + ++ T P Q +L N P
Sbjct: 326 DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV-NGAKNLVVSGPPQ 384
Query: 42 NLTQSELSL-PLTFPTG--QT---FRWKK-TGPLQYTGPIG-PHLISLKHLQNGDVCYHI 93
+L L+L P+G Q+ F +K ++ P+ P +H
Sbjct: 385 SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF-LPVASP--------------FH- 428
Query: 94 HTSPS-EPAAKSALLDFLNMGISL--GEL----WEGFSASDCRFAELAKYLAG--ARVLR 144
S PA+ D + +S ++ ++ F SD R L+ ++ +
Sbjct: 429 --SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR--VLSGSISERIVDCII 484
Query: 145 QDPV--ECLLQFLCSSNNNIARITKMVDF-------LASLGSHLGNVEGFEFHEFPSLER 195
+ PV E QF + T ++DF L L N +G + R
Sbjct: 485 RLPVKWETTTQF---------KATHILDFGPGGASGLGVLTHR--NKDG-------TGVR 526
Query: 196 LSLVSEVEL-RNAGFGYR 212
+ + +++ + +G++
Sbjct: 527 VIVAGTLDINPDDDYGFK 544
Score = 30.4 bits (68), Expect = 1.0
Identities = 22/122 (18%), Positives = 39/122 (31%), Gaps = 40/122 (32%)
Query: 47 ELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQ--NGDVCYHIHTSPSE----- 99
L++ G+ R + + + + L + K + N + S
Sbjct: 1671 NLTIHFGGEKGKRIR-ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT 1729
Query: 100 ----PA----AKSALLDFLNMGI----------SLGELWEGFSASDCRFAELAKYLAGAR 141
PA K+A D + G+ SLGE ++A LA + A
Sbjct: 1730 QFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGE----YAA-------LA---SLAD 1775
Query: 142 VL 143
V+
Sbjct: 1776 VM 1777
>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 = 42.4 bits (100), Expect = 8e-05
Identities = 22/106 (20%), Positives = 35/106 (33%), Gaps = 20/106 (18%)
Query: 189 EFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGA 248
E+L VS+ LR AG S ++ +YI + G
Sbjct: 83 ALEKPEQLYRVSDEALRQAGV----------------SKRKIEYIRH----VCEHVESGR 122
Query: 249 EWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVD 294
L + I+ L + G+G A +FSL + + V
Sbjct: 123 LDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVG 168
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 42.3 bits (100), Expect = 9e-05
Identities = 20/107 (18%), Positives = 29/107 (27%), Gaps = 20/107 (18%)
Query: 188 HEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGG 247
L VS +LR G S+ + + + S G
Sbjct: 90 PGGVVPAALLKVSGDDLRGVGL----------------SWAKVRTVQAAAAAAVS----G 129
Query: 248 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVD 294
L + I L LPG+G A LF+L +
Sbjct: 130 QIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSG 176
>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 = 42.0 bits (99), Expect = 1e-04
Identities = 18/97 (18%), Positives = 34/97 (35%), Gaps = 19/97 (19%)
Query: 189 EFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGA 248
+FP+ E + + +R GF S ++ + + S
Sbjct: 83 QFPTPEEIRDMDFEIMRACGF----------------SARKIDSLKSIAEATISGLIPTK 126
Query: 249 EWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 285
E +L +E I+ L + G+G + +FSL
Sbjct: 127 E---EAERLSNEELIERLTQIKGIGRWTVEMLLIFSL 160
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 38.7 bits (91), Expect = 0.001
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 18/77 (23%)
Query: 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ-- 287
A+ I T +L +H+G ++ E AL LPGVG K A + L+
Sbjct: 86 AENIIKTCRILLEQHNG-----------EVPEDRAALEALPGVGRKTANVV----LNTAF 130
Query: 288 -HHAIPVDTHVWKIATR 303
I VDTH++++ R
Sbjct: 131 GWPTIAVDTHIFRVCNR 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 = 38.7 bits (91), Expect = 0.001
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ-- 287
A+ I +L K++G ++ D L LPGVG K A + +
Sbjct: 90 ARNIQKLCAMLIDKYNG-----------EVPRDRDELMKLPGVGRKTANVV----VSVAF 134
Query: 288 -HHAIPVDTHVWKIATR 303
AI VDTHV +++ R
Sbjct: 135 GVPAIAVDTHVERVSKR 151
>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 = 38.7 bits (91), Expect = 0.001
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 259 LQEAIDALCTLPGVGPKVAACIALFSLDQ 287
L I L LPG+GPK A +A +Q
Sbjct: 7 LVSLIRELSRLPGIGPKSAQRLAFHLFEQ 35
>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 = 37.7 bits (87), Expect = 0.002
Identities = 18/118 (15%), Positives = 37/118 (31%), Gaps = 11/118 (9%)
Query: 203 ELRNAGFGYRSAPQSSLLFSVRRSFKQ--AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQ 260
E+ + L ++ F + A+YI K + + +
Sbjct: 68 EIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESF-------ENEK 120
Query: 261 EAIDALC-TLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPK 317
A + L + G+G K A+ AI +D H+ + + L+ +
Sbjct: 121 VAREFLVRNIKGIGYKEASHFLRNVGYDDVAI-IDRHILRELYENNYIDEIPKTLSRR 177
>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 = 37.9 bits (89), Expect = 0.002
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
A+ LPGVG A + + + A+ VD + ++ RY
Sbjct: 115 KAILDLPGVGKYTCAAVMCLAFGKKAAM-VDANFVRVINRYF 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 = 37.5 bits (88), Expect = 0.003
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
+ + LPGVG A I SL +H I +D +V ++ R
Sbjct: 109 EEVAALPGVGRSTAGAILSLSLGKHFPI-LDGNVKRVLARCY 149
>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 = 36.5 bits (85), Expect = 0.009
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
D L GVGP + + VD +V ++ +R
Sbjct: 118 DEFSRLKGVGPYTVGAVLSLAYGVPEPA-VDGNVMRVLSRLF 158
>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 = 31.7 bits (72), Expect = 0.15
Identities = 6/42 (14%), Positives = 14/42 (33%), Gaps = 3/42 (7%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
L G+G +F +++ + + H +Y
Sbjct: 104 KYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLN---KYH 142
>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 = 32.3 bits (74), Expect = 0.16
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 268 TLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
LPGVG A IA + Q + VD +V ++ R
Sbjct: 133 LLPGVGRYTAGAIASIAFGQATGV-VDGNVARVLCRVR 169
>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 = 29.2 bits (66), Expect = 0.30
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 256 KLDLQEA-IDALCTLPGVGPKVAACI 280
+ L EA ++ L LPG+GP +A I
Sbjct: 18 PVSLNEASLEELMALPGIGPVLARRI 43
>1mv3_A MYC box dependent interacting protein 1; tumor suppressor,
endocytosis/exocytosis complex; NMR {Homo sapiens}
SCOP: b.34.2.1
Length = 213
Score = 30.0 bits (66), Expect = 0.79
Identities = 10/53 (18%), Positives = 20/53 (37%)
Query: 7 SPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSLPLTFPTGQT 59
+ K P + PP PP P+ + + + L+L + ++ T
Sbjct: 25 GATLPKSPSQLRKGPPVPPPPKHTPSKEVKQEQILSLFEDTFVPEISVTTPSQ 77
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 30.6 bits (70), Expect = 0.87
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 259 LQEA-IDALCTLPGVGPKVAACIALFSLDQHH 289
L EA ++ L + VG A I D
Sbjct: 533 LLEASLEELIEVEEVGELTARAILETLKDPAF 564
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 30.2 bits (69), Expect = 1.1
Identities = 16/139 (11%), Positives = 35/139 (25%), Gaps = 41/139 (29%)
Query: 132 ELAKYLAGARVLRQ----DPVECLLQFLCSSNNNIARI--------TKMV-DF--LA--S 174
++ + R D + +F+ + I ++V + A
Sbjct: 342 QICQRRGEWRHNHALVFKDRPDY--RFILGEKGEVLDIVAEPRRIANRIVEEAMIAANIC 399
Query: 175 LGSHLGNVEG---FEFHEFPSLERLSLVSEVELRNAGFGYRSA----------------- 214
L + G + H ++ + L+ G +
Sbjct: 400 AARVLRDKLGFGIYNVHMGFDPANADALAAL-LKTHGLHVDAEEVLTLDGFCKLRRELDA 458
Query: 215 -PQSSLLFSVRRSFKQAKY 232
P L +RR A+
Sbjct: 459 QPTGFLDSRIRRFQSFAEI 477
>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 = 28.2 bits (63), Expect = 1.3
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 264 DALCTLPGVGPKVAACI 280
L +L +GPK A I
Sbjct: 40 RDLRSLQRIGPKKAQLI 56
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 29.8 bits (68), Expect = 1.4
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 248 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 289
A + +L L +I+ L +P VG VA+ + F ++ +
Sbjct: 529 AAYFGTLEAL-EAASIEELQKVPDVGIVVASHVHNFFAEESN 569
>1zlg_A Anosmin 1; insulin-like growth factor receptor Cys-rich fold, WHEY
acidic protein fold, fibronectin type III fold, hormone-
growth factor complex; NMR {Homo sapiens}
Length = 680
Score = 29.5 bits (65), Expect = 1.7
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 17 TPQPPPTPPNPQTLTTNKPSKWTP 40
TP+ PP+ + L P + P
Sbjct: 629 TPELPPSSAHRSHLKHRHPHHYKP 652
>2jll_A NCAM2, neural cell adhesion molecule 2; immunoglobulin domain,
immunoglobulin superfamily, transmembrane,
phosphoprotein, membrane, glycoprotein; HET: NAG; 2.30A
{Homo sapiens} PDB: 2xyc_A* 2jlk_A* 2doc_A
Length = 389
Score = 29.4 bits (66), Expect = 1.7
Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 8 PSPLKRPRLTPQPPPTPPNPQTLTTNKPS---KWTP 40
S ++ + P P+PP+ ++ S T
Sbjct: 280 YSKIEIFQTLPVREPSPPSIHGQPSSGKSFKLSITK 315
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis,
oxygen-evolving, tetra- manganese, membrane; HET: CL1
PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus
elongatus}
Length = 134
Score = 28.1 bits (62), Expect = 1.9
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 256 KLDLQEA-IDALCTLPGVGPKVAACI 280
K+DL I A G+ P +A I
Sbjct: 54 KIDLNNTNIAAFIQYRGLYPTLAKLI 79
>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein
complex, transmembrane alpha-helix, E transport,
photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT
HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus}
PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U*
3a0b_U* 3a0h_U*
Length = 97
Score = 27.6 bits (61), Expect = 2.2
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 256 KLDLQEA-IDALCTLPGVGPKVAACI 280
K+DL I A G+ P +A I
Sbjct: 17 KIDLNNTNIAAFIQYRGLYPTLAKLI 42
>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 = 27.9 bits (63), Expect = 3.2
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 5/25 (20%)
Query: 258 DLQEAI-----DALCTLPGVGPKVA 277
L A+ L + GVG ++A
Sbjct: 96 LLARALLEGDARLLTSASGVGRRLA 120
>1h8l_A Carboxypeptidase GP180 residues 503-882; hydrolase, zinc-dependent
protease; HET: NAG BMA NDG GEM; 2.6A {Lophonetta
specularioides} SCOP: b.3.2.1 c.56.5.1 PDB: 1qmu_A*
Length = 380
Score = 28.3 bits (63), Expect = 3.6
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 151 LLQFLCSSNNNIARITKMVD-----FLASLGSHLGNVEGFEF 187
L+++LC + +T +V + S+ N +G+E
Sbjct: 84 LIEYLCKNFGTDPEVTDLVQSTRIHIMPSM-----NPDGYEK 120
>3dcp_A Histidinol-phosphatase; HISK, histidine biosynthesis, NESG, LMR141,
structural genomics, PSI-2, protein structure
initiative; 2.10A {Listeria monocytogenes str}
Length = 283
Score = 28.0 bits (62), Expect = 3.7
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 91 YHIHTSPSEPAAKSALLDFLNMGISLG 117
H HT + + + I L
Sbjct: 5 GHTHTEFCPHGTHDDVEEMVLKAIELD 31
>2v5y_A Receptor-type tyrosine-protein phosphatase MU; membrane, hydrolase,
glycoprotein, receptor protei tyrosine phosphatase, cell
adhesion; HET: NAG; 3.10A {Homo sapiens}
Length = 731
Score = 28.6 bits (63), Expect = 3.8
Identities = 7/34 (20%), Positives = 9/34 (26%)
Query: 7 SPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTP 40
+ P P QT T K +K
Sbjct: 695 DCVQVATKGAATPKPVPEPEKQTDHTVKGTKHHH 728
>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2
related L recognition, receptor, innate immunity,
glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus
musculus} PDB: 3b2d_A* 3rg1_A*
Length = 606
Score = 28.4 bits (64), Expect = 4.1
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 152 LQFLCSSNNNIARITKMVDFLASL------GSHLGNVEGFEFHEFPSLERLSL 198
LQ L + +++ + + L++L + N+ FPSL LS+
Sbjct: 280 LQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSI 332
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 28.3 bits (64), Expect = 4.3
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 259 LQEA-IDALCTLPGVGPKVAACIALFSLDQHH 289
+ A D L + GVGP +AA + + H
Sbjct: 555 IAAASTDQLAAVEGVGPTIAAAVTEWFAVDWH 586
>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 = 27.7 bits (62), Expect = 4.6
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 5/25 (20%)
Query: 258 DLQEAI-----DALCTLPGVGPKVA 277
A+ AL LPG+G K A
Sbjct: 97 QFVNAVEREEVGALVKLPGIGKKTA 121
>3ghp_A Cellulosomal scaffoldin adaptor protein B; linker segments, beta
barrel, alpha helix, beta flaps, structural protein;
2.49A {Acetivibrio cellulolyticus}
Length = 227
Score = 27.5 bits (60), Expect = 4.7
Identities = 6/30 (20%), Positives = 7/30 (23%)
Query: 8 PSPLKRPRLTPQPPPTPPNPQTLTTNKPSK 37
S + LTP P T
Sbjct: 190 ASTMPTVTLTPTPTATTTTTIPTAVPTTES 219
>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 = 27.6 bits (62), Expect = 4.9
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 258 DLQEAI-----DALCTLPGVGPKVA 277
L++ + AL +PG+G + A
Sbjct: 112 ALRQVLADGNVAALTRVPGIGKRGA 136
>3mn8_A LP15968P; catalytic domain of alpha/beta-hydrolase fold,
C-terminal, A transthyretin-like domain, hydrolase; HET:
NAG GEM; 2.70A {Drosophila melanogaster}
Length = 435
Score = 27.6 bits (61), Expect = 5.9
Identities = 6/42 (14%), Positives = 20/42 (47%), Gaps = 10/42 (23%)
Query: 151 LLQFLCSSNNNIARITKMVD-----FLASLGSHLGNVEGFEF 187
+ Q+L ++ I+ + ++V+ + ++ N +G+
Sbjct: 114 MAQYLLGNHERISDLGQLVNSTDIYLVPTM-----NPDGYAL 150
>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 = 26.8 bits (58), Expect = 6.2
Identities = 7/32 (21%), Positives = 10/32 (31%), Gaps = 8/32 (25%)
Query: 2 QSLKNSPSPLKRPRLTPQPPPTPPNPQTLTTN 33
Q+LK + LK + P L
Sbjct: 20 QALKKLQASLK-----LYADDSAP---ALAIK 43
>1xx7_A Oxetanocin-like protein; PSI, secsg, protein structure initiative,
southeast collaboratory for structural genomics; 2.26A
{Pyrococcus furiosus} SCOP: a.211.1.1
Length = 184
Score = 27.0 bits (59), Expect = 7.1
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 12/68 (17%)
Query: 87 GDV-CYHIHTSPSEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQ 145
D+ E A AL D L EL+E +S + +L K
Sbjct: 83 TDLPLSAQKYLNKEEAEAKALKDVLPE---YTELFEEYSKALTLEGQLVKIA-------- 131
Query: 146 DPVECLLQ 153
D ++ ++Q
Sbjct: 132 DKLDMIIQ 139
>1nnl_A L-3-phosphoserine phosphatase; PSP, HPSP, phospho-aspartyl,
hydrolase; 1.53A {Homo sapiens} SCOP: c.108.1.4 PDB:
1l8l_A* 1l8o_A
Length = 225
Score = 26.8 bits (60), Expect = 8.3
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 260 QEAIDALCTLPGVGPKVAA 278
+E ID L + GV V+
Sbjct: 28 EEGIDELAKICGVEDAVSE 46
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
0.319 0.135 0.415
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,995,061
Number of extensions: 288181
Number of successful extensions: 951
Number of sequences better than 10.0: 1
Number of HSP's gapped: 925
Number of HSP's successfully gapped: 73
Length of query: 328
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 234
Effective length of database: 4,077,219
Effective search space: 954069246
Effective search space used: 954069246
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: 57 (25.9 bits)