RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 002448
(921 letters)
>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 = 100 bits (252), Expect = 3e-24
Identities = 27/170 (15%), Positives = 62/170 (36%), Gaps = 10/170 (5%)
Query: 421 KQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEW 480
K + D ++ + + +++E ++ G N A+R+ D ++++ S
Sbjct: 56 KNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQS----- 110
Query: 481 LRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPE 540
+ + +++LL +G+G +S + + VD +LG +
Sbjct: 111 FENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEI--EDYD 168
Query: 541 SLQLHLLELYPVLESIQKYLWPRLCKLDQRTLY-ELHYQLITFGKVFCTK 589
LQ + E++ L + LY H +++ F K
Sbjct: 169 ELQHFFEKGVQ--ENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216
>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 = 72.3 bits (178), Expect = 2e-14
Identities = 37/172 (21%), Positives = 71/172 (41%), Gaps = 26/172 (15%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
++E+ + I+ G+ A ++ L+ ++ +VP D+ + L+
Sbjct: 66 HDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNG-------EVPRDRDE--LM 116
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLE 554
+ G+G K+ V + A VDT+V R++ RLG+ ++ L+++ P
Sbjct: 117 KLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIP--- 173
Query: 555 SIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHF 606
K W H+++I FG+ C P C +CP+ CR
Sbjct: 174 ---KEEWSIT-----------HHRMIFFGRYHCKAQSPQCPSCPLLHLCREG 211
>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 = 69.6 bits (170), Expect = 2e-13
Identities = 24/137 (17%), Positives = 56/137 (40%), Gaps = 3/137 (2%)
Query: 434 YEALRCANVKEISEAIKERGMN--NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKD 491
+ + AN +EI +K N+ A+ + ++ +++ L D A++
Sbjct: 59 GQKIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKVYGRLKE-EIKPLADEDQQLARE 117
Query: 492 YLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 551
LL+I+G+G++ + +D ++ R+G + + + + +
Sbjct: 118 RLLNIKGIGMQEASHFLRNVGYFDLAIIDRHIIDFMRRIGAIGETNVKQLSKSLYISFEN 177
Query: 552 VLESIQKYLWPRLCKLD 568
+L+SI L + LD
Sbjct: 178 ILKSIASNLNMSVGILD 194
>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 = 73.3 bits (179), Expect = 2e-13
Identities = 83/532 (15%), Positives = 158/532 (29%), Gaps = 149/532 (28%)
Query: 329 HHTDL-AKEQNVPSGSMLAEKTRNLGDDISV-----------ANKLSDNKLIEPNSVEQV 376
HH D E +L+ D+ + + D+ ++ ++V
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 377 LSAHKVYD--ETNPNISKSKKRKADGEKKNAIDW--ESLRKEVQRNSGKQER---SRDRM 429
L +++ + +K + + N + ++ E ++ S RDR+
Sbjct: 65 L---RLFWTLLSKQE-EMVQKFVEEVLRIN-YKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 430 DS-----LDYEALRCANVKEISEAIKE-RGMNNMLAERMKDFLNRLVREHG--SIDLEWL 481
+ Y R ++ +A+ E R N+L + + G + L+
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS--------GKTWVALDVC 171
Query: 482 RDVPPDKAKD---YLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPL 538
D + L+++ L L + P T+ + + L
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI------KL 225
Query: 539 P-ESLQLHLLEL-----YP----VLESIQ-KYLWPRL---CKLDQRTLYELHYQLITFGK 584
S+Q L L Y VL ++Q W CK+ L+T
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKI-----------LLT--- 271
Query: 585 VFCTKSKPNCNACPMRGECR----HFASAFASARLALPGPEEKSIVSSTMPTMAERNPSV 640
T+ K + H + E KS++ + + P
Sbjct: 272 ---TRFKQVTDFLSAATTTHISLDHHSMTLTP-------DEVKSLLLKYLDCRPQDLPRE 321
Query: 641 V--INPMPLPSPEKSSLAEVRREIGKCEPIIEEPATPEQ-------ECTEITESDIED-- 689
V NP L S+ I E I + AT + + T I ES +
Sbjct: 322 VLTTNPRRL------SI------IA--ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367
Query: 690 -----AFYED----PDE--IPTIKLNIEEFTVNLQSYMQEKMELQECDMSKALVALNPDA 738
++ P IPTI L++ ++ + + + +LV P
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILLSL--IWFDVIKSDVMVV-VNKL-HKYSLVEKQPKE 423
Query: 739 ASIPAPKL-----KNVSRLRTEHQV----YELPDSHPLLEGMDRREPDDPSP 781
++I P + + H+ Y +P + DD P
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD---------SDDLIP 466
Score = 51.4 bits (122), Expect = 1e-06
Identities = 67/487 (13%), Positives = 134/487 (27%), Gaps = 152/487 (31%)
Query: 68 MSGVGKTSLPEPHGIGLEEEIISSQDSLSSTILQS--NGGI-----RSCSGSNSEAED-- 118
+ G GKT + + D S +Q + I ++C+ + E
Sbjct: 158 VLGSGKTWV--------------ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203
Query: 119 ------SPPGCKLDNGSANFQQVGNATLFQDFYSCINDSSLFQEGYHRFKQA---EDGGN 169
P + S+N + ++ Q L + ++ N
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHS--IQA-----ELRRLLKS--KPYENCLLVLL--N 252
Query: 170 FQQESGLESIDNLGSSLTFT----QLLNFNSPQNQVGFSSDYEPHMTSYSELLEAEGSEI 225
Q + + L + T Q+ +F S S D+ L E +
Sbjct: 253 VQNAKAWNAFN-LSCKILLTTRFKQVTDFLSAATTTHISLDHHS-----MTLTPDEVKSL 306
Query: 226 YNGECSSWPSISSESSKAKNESYARAQQPAEDIGETMVQQNGLSTPEKMLSASPYV--LL 283
+ +D+ P ++L+ +P ++
Sbjct: 307 ----LLKYLDCR-----------------PQDL------------PREVLTTNPRRLSII 333
Query: 284 KKPTMQQPNASQTRSPPKYDQSCCDIYQHERRTFQCESISIAEQMHH-TDLA---KEQNV 339
+ + CD + + AE L+ ++
Sbjct: 334 AESIRDGLATWDN-----WKHVNCDKLTTIIESS-LNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 340 PSG--SML-AEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKR 396
P+ S++ + ++ D + V NKL L+E E +S +Y E K
Sbjct: 388 PTILLSLIWFDVIKS--DVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL--------KV 437
Query: 397 KADGEK---KNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG 453
K + E ++ +D ++ K + + +D Y + G
Sbjct: 438 KLENEYALHRSIVDHYNIPKTFDSD----DLIPPYLDQYFYSHI---------------G 478
Query: 454 --MNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL- 510
+ N+ + +D +L + K IR +L
Sbjct: 479 HHLKNIEHPERMTLFRMVF-----LDFRFL------EQK-----IRHDSTAWNASGSILN 522
Query: 511 TLHHLAF 517
TL L F
Sbjct: 523 TLQQLKF 529
Score = 37.1 bits (85), Expect = 0.027
Identities = 34/241 (14%), Positives = 72/241 (29%), Gaps = 73/241 (30%)
Query: 665 CEPIIEEPATPEQ-----ECTEITESDIEDAFYEDPDEI------PTIKLNIEEFTVNLQ 713
+ II + ++ F E+ I IK + ++ +
Sbjct: 51 IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR 110
Query: 714 SYMQEKMELQECDMSKALVALNPDAASIPAPKLKNVSRLRTEHQV----YEL-PDSHPLL 768
Y++++ L D N K NVSRL+ ++ EL P + L+
Sbjct: 111 MYIEQRDRLYN-D--------NQ-----VFAKY-NVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 769 EGMDRREPDDPSPYLLAIWTPGETANSIQLPESRCRSKESGKLCDEKTCFSCN----SMR 824
+G+ G + + + C S + + +++
Sbjct: 156 DGV-----------------LG-SGKTW-VALDVCLSYK------VQCKMDFKIFWLNLK 190
Query: 825 ETNSQTVRGTLLIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLNPIDVPREWLWNLPRRM 884
NS T+L L +Q++ + + I + + RR+
Sbjct: 191 NCNSP---ETVLEM----------LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 885 V 885
+
Sbjct: 238 L 238
Score = 30.2 bits (67), Expect = 3.9
Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 28/82 (34%)
Query: 44 LRHPGSSQSS-----------------ITPHEPTEHQRVREMSGVGKTSLPEPHGIGLEE 86
+RH ++ ++ I ++P + V + LP+ EE
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI----LDFLPKI-----EE 557
Query: 87 EIISSQ--DSLSSTILQSNGGI 106
+I S+ D L ++ + I
Sbjct: 558 NLICSKYTDLLRIALMAEDEAI 579
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 66.8 bits (164), Expect = 1e-12
Identities = 38/172 (22%), Positives = 64/172 (37%), Gaps = 27/172 (15%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
A+ V+ + IK G+ N AE + L+ +H +VP D+ L
Sbjct: 62 AAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG-------EVPEDR--AALE 112
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLE 554
++ G+G K+ V VDT++ R+ R + P E ++ LL++ P
Sbjct: 113 ALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAP-GKNVEQVEEKLLKVVP--- 168
Query: 555 SIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHF 606
H+ LI G+ C KP C +C + C +
Sbjct: 169 ---AEFKVDC-----------HHWLILHGRYTCIARKPRCGSCIIEDLCEYK 206
>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 = 66.5 bits (162), Expect = 6e-12
Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 3/90 (3%)
Query: 474 GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGW 532
G ++LE+++ + ++ + L G+G + +C+ L ++ AFPVDT V + + L
Sbjct: 194 GELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYV 253
Query: 533 VPLQPLPESLQLHLLELYPVLESI-QKYLW 561
P + ++ E + L Q+YL+
Sbjct: 254 AP-DVSLKKIRDFGREKFGSLSGFAQQYLF 282
>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 = 66.2 bits (161), Expect = 5e-11
Identities = 100/582 (17%), Positives = 166/582 (28%), Gaps = 220/582 (37%)
Query: 286 PTMQQPNASQTRS------PPKYDQSCCDIYQHERRTFQCESISIAEQ----MHHTDLAK 335
PT ASQ + P + D E + AE + +
Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAADD----------EPTTPAELVGKFLGYVSSLV 72
Query: 336 EQNVPS------GSMLAEKTRNL--GDDI-SVANKLSDNKLIEPNSVEQVL----SAHKV 382
E + L E G+DI ++A KL ++++ +A +
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 383 YDETNPNISKSK--KRKADGEKK---------NAID-WESLRKEVQRNSGKQERSRDRMD 430
S S + +G + N D +E LR
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD----------------- 175
Query: 431 SL--DYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVRE---------HGSIDL- 478
L Y L V + L + + L+ L+R G +++
Sbjct: 176 -LYQTYHVL----VGD-------------LIKFSAETLSELIRTTLDAEKVFTQG-LNIL 216
Query: 479 EWLRDVPPDKA--KDYLLSIRGLGLKSVECVRLLTLHHLA-FPVDTNVGRIAVRLGWVP- 534
EWL + P KDYLLSI + C L+ + LA + V + LG+ P
Sbjct: 217 EWLEN--PSNTPDKDYLLSI------PISCP-LIGVIQLAHYVVTAKL------LGFTPG 261
Query: 535 -LQPLPESLQLHLLELYPVL-----ESIQKYLWPRLCKLDQRTLYELHYQLITFGKVF-- 586
L+ + H L + +S W + + + IT +F
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDS-----WE--------SFFVSVRKAITV--LFFI 306
Query: 587 ---CTKSKPNCN----------------ACPM---RGECRHFASAFASARLALPGPEEKS 624
C ++ PN + PM + + + P K
Sbjct: 307 GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV-NKTNSHLPAGKQ 365
Query: 625 IVSSTMPTMAERN-PS--VVINPMPLPSPEKSSLAEVRREIGKCEPIIEEPATPEQECTE 681
+ ++ N VV P P+ SL + + K + P+ +Q +
Sbjct: 366 VE------ISLVNGAKNLVVSGP-----PQ--SLYGLNLTLRK----AKAPSGLDQ--SR 406
Query: 682 ITESD----IEDAFYEDPDEIPTIKLNIEEF-TVNLQSYMQEKMELQECDMSKALVALNP 736
I S+ + F P P F + + +L D+ K V+ N
Sbjct: 407 IPFSERKLKFSNRF--LPVASP--------FHS----HLLVPASDLINKDLVKNNVSFNA 452
Query: 737 DAASIPAPKLKNVSRLRTEHQVYELPDSHPLLEGMDRREPDD 778
IP VY+ D G D R
Sbjct: 453 KDIQIP---------------VYDTFD------GSDLRVLSG 473
Score = 59.3 bits (143), Expect = 5e-09
Identities = 79/470 (16%), Positives = 134/470 (28%), Gaps = 168/470 (35%)
Query: 61 EHQRVREMSGVGKTSLPEPHGIGLEEEIISSQD--SLSSTILQSNGG--------IRS-- 108
E +V + V L E E + D +L++ +LQ N I++
Sbjct: 73 EPSKVGQFDQVLNLCLTE-----FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYI 127
Query: 109 --CSGSNSEAEDSPPGCKLDNGSANFQQV--GNATLF----------------QDFY--- 145
+ + SA F+ V GNA L +D Y
Sbjct: 128 TARIMAKRPFDKKSN-------SALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTY 180
Query: 146 -SCIND---------SSLFQEGYHRFKQAEDGGNFQQ----ESGLESIDNLGSS------ 185
+ D S L + K G N + S D L S
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL 240
Query: 186 LTFTQLLNFNSPQNQVGFS-SDYEPHM---TSYSE-LLEAEGSEIYNGECSSWPSISSES 240
+ QL ++ +GF+ + ++ T +S+ L+ A + E SW S
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA----VAIAETDSWESFFVSV 296
Query: 241 SKAKNESY---ARAQQ--PAEDIGETMVQQ---NGLSTPEKMLSAS--PYVLLKK----- 285
KA + R + P + ++++ N P MLS S ++
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 286 ----PTMQQ----------------PNAS---------QTRSPPKYDQSCCDIYQHERRT 316
P +Q P S + ++P DQS I ER+
Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS--RIPFSERKL 414
Query: 317 ------------FQCESISIAEQMHHTDLAKEQNVPSGSMLA---EKTRNLGDDISVANK 361
F + A + + DL K + + T + G D+
Sbjct: 415 KFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLR---V 470
Query: 362 LSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESL 411
LS + I V+ ++ + WE+
Sbjct: 471 LSGS--ISERIVDCIIRLP-------------------------VKWETT 493
Score = 37.0 bits (85), Expect = 0.034
Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 75/238 (31%)
Query: 361 KLSDN--KLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGE---KKN----------A 405
++ +N +I V+ L K++ E N + + R G + A
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA 1742
Query: 406 IDWESLRKE--VQRNS---GKQERSRDRMDSL-DYEALRC-ANVKEISEAIK---ERG-- 453
+E L+ + + ++ G SL +Y AL A+V I ++ RG
Sbjct: 1743 A-FEDLKSKGLIPADATFAGH---------SLGEYAALASLADVMSIESLVEVVFYRGMT 1792
Query: 454 MNNMLAERMKDFLNRLV------REHGSIDLEWLRDVPPD--KAKDYLLSI-----RGL- 499
M + N + R S E L+ V K +L+ I
Sbjct: 1793 MQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQ 1852
Query: 500 ----G-LKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQL-----HLL 547
G L++++ V + L+ + + +I + L +SL L HL
Sbjct: 1853 YVAAGDLRALDTVTNV-LNFI------KLQKI-------DIIELQKSLSLEEVEGHLF 1896
Score = 36.2 bits (83), Expect = 0.063
Identities = 47/259 (18%), Positives = 81/259 (31%), Gaps = 91/259 (35%)
Query: 156 EGY--HRFKQAEDGGNFQQESGLESIDNLGSSLTF---TQLLNFNSPQN-QVGFSSDYEP 209
E Y F+ DG + E + I+ +S TF LL ++ Q Q P
Sbjct: 1686 ENYSAMIFETIVDG-KLKTEKIFKEINEHSTSYTFRSEKGLL--SATQFTQ--------P 1734
Query: 210 HM--TSYS--ELLEAEGSEIYN--------GECSSWPSISSESSKAKNESY----ARAQQ 253
+ + E L+++G + GE Y + A
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADATFAGHSLGE------------------YAALASLADV 1776
Query: 254 -PAEDIGETMVQQNGLST----PEKMLSASPYVLLKKPTMQQPNASQTRSPPKYDQSCCD 308
E + E +V G++ P L S Y M N P + S
Sbjct: 1777 MSIESLVE-VVFYRGMTMQVAVPRDELGRSNY------GMIAIN------PGRVAASFSQ 1823
Query: 309 IYQHERRTFQCESISIAEQMHHTD---------LAKEQNVPSGSMLA-EKTRNLGDDISV 358
E + E + T + +Q V +G + A + N+ + I +
Sbjct: 1824 ----EALQYVVERVG-----KRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKL 1874
Query: 359 AN-KLSDNKLIEPNSVEQV 376
+ +L + S+E+V
Sbjct: 1875 QKIDII--ELQKSLSLEEV 1891
Score = 33.5 bits (76), Expect = 0.37
Identities = 32/191 (16%), Positives = 60/191 (31%), Gaps = 43/191 (22%)
Query: 740 SIPAPKLKNVSRLRTEHQVYELPDSHPLLEGMDRREPDDPSPYLLAIWTPGETANSIQLP 799
+P S+L+ + LP+ D EP P+ L+ + G ++ ++ P
Sbjct: 21 LVPTASFFIASQLQEQFNK-ILPEPTEGFAADD--EPTTPAE-LVGKFL-GYVSSLVE-P 74
Query: 800 ESRCRSKESGKLCDEKTCFSCNSMRETNSQTVRGTLLIPCRTAMRGSFPLNGTYFQVNEV 859
+ + LC T F + + + LL T + + L Y +
Sbjct: 75 SKVGQFDQVLNLC--LTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 860 FADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGLSTEGIQF--CFWKG-----KN 912
+ P D S++F+ + Q F G +
Sbjct: 133 ------AKRPFDKKSN----------------SALFRAVGEGNAQLVAIF--GGQGNTDD 168
Query: 913 Y--EIPVQSLY 921
Y E+ + LY
Sbjct: 169 YFEEL--RDLY 177
>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 = 62.8 bits (152), Expect = 2e-10
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 6/98 (6%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYL 493
+AL V EA + A + ++ E G + L+ LR+ ++A L
Sbjct: 200 QALAGPEV----EAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKAL 255
Query: 494 LSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL 530
+ G+G + + L+ L A PV+ ++ IA R
Sbjct: 256 CILPGVGTCVADKICLMALDKPQAVPVNVHMWHIAQRD 293
>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 = 51.6 bits (123), Expect = 2e-07
Identities = 26/155 (16%), Positives = 54/155 (34%), Gaps = 14/155 (9%)
Query: 434 YEALRCANVKEISEAIKERGMN--NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKD 491
+ ++E++E ++E G AE + + L + + + P +
Sbjct: 76 GKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGD-----PFQSREF 130
Query: 492 YLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 551
+ + +G+G K T +D +V R+ R G + P + L +
Sbjct: 131 LVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIP-KGWSKKRYLYVEE 189
Query: 552 VLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVF 586
+L + + K D L+ + GKV
Sbjct: 190 ILRKVAEAFGESPGKFD------LYLWYLVKGKVD 218
>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 = 49.4 bits (118), Expect = 3e-06
Identities = 29/117 (24%), Positives = 52/117 (44%), Gaps = 9/117 (7%)
Query: 447 EAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVEC 506
E ++E G++ AE + + + +E +LE L++ ++A +YL S +G+G + E
Sbjct: 173 EGLRECGLSRRKAELIVE----IAKE---ENLEELKEWGEEEAYEYLTSFKGIGRWTAEL 225
Query: 507 VRLLTLHHLAFPV-DTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESI-QKYLW 561
V + L FP D V R RL + E ++ E + YL+
Sbjct: 226 VLSIALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLF 282
>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 = 41.6 bits (98), Expect = 5e-04
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 5/78 (6%)
Query: 474 GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGW 532
G +D L + L +I+G+G + E + +L L VG + ++ G
Sbjct: 121 GRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLS----VGDVGLQRGA 176
Query: 533 VPLQPLPESLQLHLLELY 550
L E LL +
Sbjct: 177 KWLYGNGEGDGKKLLIYH 194
>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 = 39.8 bits (94), Expect = 0.002
Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 20/107 (18%)
Query: 519 VDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQ 578
+D NV R+ R + + +P + ++ LW ++ E Q
Sbjct: 137 LDGNVKRVLARC--------------YAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQ 182
Query: 579 -LITFGKVFCTKSKPNCNACPMRGECRHFASAFASARLA-LPGPEEK 623
++ G + CT+SKP C+ CP++ C A A+ A PG + K
Sbjct: 183 AMMDLGAMICTRSKPKCSLCPLQNGCI----AAANNSWALYPGKKPK 225
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 39.6 bits (93), Expect = 0.002
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 474 GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGW 532
G ID L P + L+ + G+G + E L L F G +A+R G
Sbjct: 129 GQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFS----SGDLALRQGV 184
>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 = 38.9 bits (90), Expect = 0.003
Identities = 24/132 (18%), Positives = 49/132 (37%), Gaps = 9/132 (6%)
Query: 440 ANVKEISEAIKERGMN--NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL-SI 496
+E+ E +K G AE + R +I A+++L+ +I
Sbjct: 76 LPREELEEKLKNLGHRFYRKRAEYIVL-----ARRFKNIKDIVESFENEKVAREFLVRNI 130
Query: 497 RGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESI 556
+G+G K + +D ++ R ++ P + LE+ +L I
Sbjct: 131 KGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIP-KTLSRRKYLEIENILRDI 189
Query: 557 QKYLWPRLCKLD 568
+ + +L +LD
Sbjct: 190 GEEVNLKLSELD 201
>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 = 39.2 bits (92), Expect = 0.004
Identities = 11/43 (25%), Positives = 14/43 (32%), Gaps = 5/43 (11%)
Query: 582 FGKVFCTKSKPNCNACPMRGECRHFASAFASARLA-LPGPEEK 623
G CT +P C+ CP+ CR A L
Sbjct: 207 LGATVCTPQRPLCSQCPVESLCR----ARQRVEQEQLLASGSL 245
>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 = 38.3 bits (90), Expect = 0.005
Identities = 20/90 (22%), Positives = 25/90 (27%), Gaps = 16/90 (17%)
Query: 519 VDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQ 578
VD N R+ R Y L K LW L
Sbjct: 143 VDANFVRVINRY--------------FGGS-YENLNYNHKALWELAETLVPGGKCRDFNL 187
Query: 579 -LITFGKVFCTKSKPNCNACPMRGECRHFA 607
L+ F + C KP C C M C ++
Sbjct: 188 GLMDFSAIICAPRKPKCEKCGMSKLCSYYE 217
>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 = 38.1 bits (89), Expect = 0.011
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 582 FGKVFCTKSKPNCNACPMRGECRHFASAFASARLA-LPGPEEK 623
G + CT +P+C CP++ C+ AFA LP +K
Sbjct: 196 LGALVCTPRRPSCLLCPVQAYCQ----AFAEGVAEELPVKMKK 234
>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 = 35.8 bits (83), Expect = 0.042
Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 6/79 (7%)
Query: 474 GSIDL-EWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLG 531
G I E + ++ + L I+G+G +VE + + +L+ P +++R G
Sbjct: 121 GLIPTKEEAERLSNEELIERLTQIKGIGRWTVEMLLIFSLNRDDVMP----ADDLSIRNG 176
Query: 532 WVPLQPLPESLQLHLLELY 550
+ L LP+ + +
Sbjct: 177 YRYLHRLPKIPTKMYVLKH 195
>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 = 34.2 bits (77), Expect = 0.070
Identities = 6/22 (27%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 747 KNVSRLRTEHQVYELPDSHPLL 768
+ + +L+ ++Y DS P L
Sbjct: 20 QALKKLQASLKLYA-DDSAPAL 40
Score = 33.8 bits (76), Expect = 0.10
Identities = 5/33 (15%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 676 EQECTEITESDIEDAFYEDPDEIPTIKLN--IE 706
+Q ++ ++ ++ Y D P + + +E
Sbjct: 19 KQALKKL-QASLK--LYA-DDSAPALAIKATME 47
Score = 29.5 bits (65), Expect = 3.3
Identities = 5/24 (20%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 369 EPNSVEQVLSAHKVY-DETNPNIS 391
E +++++ ++ K+Y D++ P ++
Sbjct: 18 EKQALKKLQASLKLYADDSAPALA 41
>3kfu_F Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; ASPRS, gatcab,
ATP-binding, aminoacyl-tRNA synthetase, ligas
nucleotide-binding, protein biosynthesis, ligase-RNA
comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Length = 466
Score = 32.9 bits (76), Expect = 0.55
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 20/52 (38%)
Query: 574 ELHYQLITFGKVFCTKS------KPNCNACPMRGECRHFASAFASARLALPG 619
E+H L T K+FC +PN + CP+ C L LPG
Sbjct: 9 EVHLHLKTRTKMFCGCRADYFGAEPNTHTCPV---C-----------LGLPG 46
>3h0l_B Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; multi
protein complex, ligase, protein biosynthesis; HET: ADP;
2.30A {Aquifex aeolicus} PDB: 3h0m_B 3h0r_B*
Length = 478
Score = 30.9 bits (71), Expect = 2.3
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 19/51 (37%)
Query: 574 ELHYQLITFGKVFCTKS-----KPNCNACPMRGECRHFASAFASARLALPG 619
E+H Q+ T K+FC +PN N CP+ C L +PG
Sbjct: 12 EIHVQMDTKTKMFCGCKVEFGAEPNTNVCPV---C-----------LGMPG 48
>3ip4_B Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; multi protein
complex, ligase, ATP-binding, nucleotide-bindi protein
biosynthesis; 1.90A {Staphylococcus aureus subsp} PDB:
2df4_B 2dqn_B* 2g5h_B 2g5i_B* 2f2a_B
Length = 483
Score = 30.9 bits (71), Expect = 2.4
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 19/51 (37%)
Query: 574 ELHYQLITFGKVFCTKS-----KPNCNACPMRGECRHFASAFASARLALPG 619
E+H +L T K+F +PN N + LA PG
Sbjct: 10 EVHVELKTDSKMFSPSPAHFGAEPNSNTNVI---D-----------LAYPG 46
>3al0_B Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; protein-RNA
complex, ligase-RNA complex; HET: GSU; 3.37A {Thermotoga
maritima}
Length = 482
Score = 30.5 bits (70), Expect = 2.6
Identities = 15/52 (28%), Positives = 18/52 (34%), Gaps = 20/52 (38%)
Query: 574 ELHYQLITFGKVFCTKS------KPNCNACPMRGECRHFASAFASARLALPG 619
E+H QL T K FC+ PN CP+ C PG
Sbjct: 10 EIHVQLSTKTKAFCSCPADVFELPPNTAICPV---C-----------TGQPG 47
>3gjx_B Snurportin-1; transport, cytoplasm, nucleus, RNA-binding,
acetylation, GTP-binding, HOST-virus interaction,
nucleotide-binding, phosphoprotein; HET: GTP; 2.50A
{Homo sapiens} PDB: 3nby_B* 3nbz_B* 3nc0_B* 3gb8_B
2qna_B
Length = 365
Score = 30.2 bits (67), Expect = 3.7
Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 13/109 (11%)
Query: 392 KSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKE 451
KSK + ++ L + + +R L + +E ++ E
Sbjct: 37 KSKYSSLEQSERRR---RLLELQKSKRLDYVNHAR----RLAEDDWTGMESEEENKKDDE 89
Query: 452 RGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLG 500
+ + + K + N+L+ EWL DVP D +++++ + +G
Sbjct: 90 EMDIDTVKKLPKHYANQLMLS------EWLIDVPSDLGQEWIVVVCPVG 132
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 29.2 bits (66), Expect = 8.3
Identities = 9/68 (13%), Positives = 22/68 (32%), Gaps = 4/68 (5%)
Query: 729 KALVALNPDAASIPAPKLKNVSRLRTE---HQVYELPDSHPLLEGMDRREPDDPSPYLLA 785
+ + +L++ + + + + +L + P E + D+
Sbjct: 162 HTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNV-YGDNMGFLAKI 220
Query: 786 IWTPGETA 793
W GET
Sbjct: 221 NWRGGETQ 228
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
0.314 0.130 0.384
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,569,271
Number of extensions: 801720
Number of successful extensions: 1423
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1407
Number of HSP's successfully gapped: 41
Length of query: 921
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 819
Effective length of database: 3,853,851
Effective search space: 3156303969
Effective search space used: 3156303969
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 62 (27.6 bits)