RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 039604
(373 letters)
>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 = 261 bits (669), Expect = 6e-87
Identities = 63/196 (32%), Positives = 100/196 (51%), Gaps = 1/196 (0%)
Query: 129 EAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIAL 188
++ + D +L I+I + PF +L SI+ QQL+ KA ++IY R L
Sbjct: 20 SPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQL 79
Query: 189 CGGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFT 248
GG PE + ++ + LRQ GVS RK Y+ + ++G L + + + ++
Sbjct: 80 VGGAL-EKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIE 138
Query: 249 MLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKW 308
LT + GIG W+ MFM+FSL R DVL + D+G+++G + LY E + + W
Sbjct: 139 KLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAW 198
Query: 309 RPYRSVASWYLWRFVE 324
PY +VA YLW+
Sbjct: 199 APYETVACLYLWKAAG 214
>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 = 254 bits (651), Expect = 3e-84
Identities = 59/203 (29%), Positives = 99/203 (48%), Gaps = 4/203 (1%)
Query: 129 EAAIRHLRNADRQLASLIDI---HPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRF 185
A HL D L+ + + P P+ L R++ QQL KA +I+ RF
Sbjct: 16 TKAEIHLSGLDENWKRLVKLVGNYRPNRSMEKKEPYEELIRAVASQQLHSKAANAIFNRF 75
Query: 186 IALCGGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGIL-SDSAIVNMDDK 244
++ PE + + + +R G S RK L +A +G++ + + ++
Sbjct: 76 KSISNNGQFPTPEEIRDMDFEIMRACGFSARKIDSLKSIAEATISGLIPTKEEAERLSNE 135
Query: 245 SLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQL 304
L LT + GIG W+V M +IFSL+R DV+P +DL +R G + L+ L ++P + +
Sbjct: 136 ELIERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRLPKIPTKMYVLKH 195
Query: 305 CEKWRPYRSVASWYLWRFVEAKG 327
E P+R+ A+WYLW+ +
Sbjct: 196 SEICAPFRTAAAWYLWKTSKLAD 218
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 237 bits (606), Expect = 2e-77
Identities = 73/233 (31%), Positives = 111/233 (47%), Gaps = 14/233 (6%)
Query: 101 KSRAIQQQQQTLTVPRIIARPLSSEGEVEAAIRHLRNADRQLASLIDIHPP-PTFDSFHT 159
+ A+ Q ++ + L + A+ HL D LA + + P
Sbjct: 2 RGGALHQNRRVTLPSVPLPAVLPPLTDHAGAVAHLS-RDPVLAQVTSLCGELPVLAPTPD 60
Query: 160 PFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQIGVSGRKAS 219
PF L RS+ QQL+ KA +IY R L GG VVP +L ++ LR +G+S K
Sbjct: 61 PFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGG---VVPAALLKVSGDDLRGVGLSWAKVR 117
Query: 220 YLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPIND 279
+ A +G + + + D+ + L + GIG W+ MF++F+L RPDV D
Sbjct: 118 TVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGD 177
Query: 280 LGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRF---VEAKGAP 329
L +R+GV+ LY E+ + +W PYRS+AS YLW ++A GAP
Sbjct: 178 LALRQGVERLYPGEDWRD------VTARWAPYRSLASRYLWANSARMQAGGAP 224
>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 = 198 bits (505), Expect = 2e-61
Identities = 42/214 (19%), Positives = 89/214 (41%), Gaps = 18/214 (8%)
Query: 131 AIRHLRNADRQLASLIDIHPPPTFDSFHT--PFLALTRSILYQQLAFKAGTSIYTRFIAL 188
+ + D +L L + + F + ++I+ QQ++F + + +
Sbjct: 87 ELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGR 146
Query: 189 CGGEAGVV---------PETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIV 239
G E E +L + LR+ G+S RKA + ++A++ L +
Sbjct: 147 FGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKE---- 202
Query: 240 NMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPS 299
++ + LT GIG W+ + + +L + +V P +DLGVR+ V LY E+
Sbjct: 203 -WGEEEAYEYLTSFKGIGRWTAELVLSIALGK-NVFPADDLGVRRAVSRLYFNGEIQSAE 260
Query: 300 QMDQLC-EKWRPYRSVASWYLWRFVEAKGAPSSA 332
++ ++ E++ + +YL+ + +
Sbjct: 261 KVREIARERFGRFARDILFYLFLYDRFFSKKTEL 294
>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 = 190 bits (483), Expect = 2e-58
Identities = 46/226 (20%), Positives = 80/226 (35%), Gaps = 24/226 (10%)
Query: 116 RIIARPLSSEGEVEAAIRHL-------RNADRQLASLIDIHPPPTFDSFHTPFLALTRSI 168
+ A E A + L + + L L P F R+I
Sbjct: 62 NLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAI 121
Query: 169 LYQQLAFKAGTSIYTRFIALCGGEAG--------VVPETVLALTPQQLRQIGVSGRKASY 220
L Q ++ + R L G P+ + A PQ L+ +G+ ++A
Sbjct: 122 LGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEA 181
Query: 221 LHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDL 280
L LA G L + D + L GIG W+ + F + DV +D
Sbjct: 182 LIHLANAALEGTLPMTI--PGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDY 239
Query: 281 GVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRFVEAK 326
+++ + P+Q+ + E+W+P+RS A ++W +
Sbjct: 240 LIKQRFPGMT-------PAQIRRYAERWKPWRSYALLHIWYTEGWQ 278
>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 = 157 bits (399), Expect = 7e-46
Identities = 38/200 (19%), Positives = 66/200 (33%), Gaps = 12/200 (6%)
Query: 132 IRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGG 191
I+ + D L +D PF L I+ G
Sbjct: 88 IKKELSRDPLLKKSVDFGEGIRILRQD-PFEILLSFIISANNRIPMIKKCINNISEKAGK 146
Query: 192 EAGVV---------PETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMD 242
+ + + T + + +G +A YL D + NG L+ I +++
Sbjct: 147 KLEYKGKIYYAFPTVDKLHEFTEKDFEECT-AGFRAKYLKDTVDRIYNGELNLEYIKSLN 205
Query: 243 DKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMD 302
D L G+G M+FS+ + P+ D V+K + LY ++ D
Sbjct: 206 DNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPV-DTWVKKAMMSLYVAPDVSLKKIRD 264
Query: 303 QLCEKWRPYRSVASWYLWRF 322
EK+ A YL+ +
Sbjct: 265 FGREKFGSLSGFAQQYLFYY 284
>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 = 110 bits (277), Expect = 1e-27
Identities = 27/216 (12%), Positives = 56/216 (25%), Gaps = 25/216 (11%)
Query: 129 EAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIAL 188
H + D + P L I T + R
Sbjct: 122 AQLYHHWGSVDSHFQEVAQKFQGVRLLRQD-PIECLFSFICSSNNNIARITGMVERLCQA 180
Query: 189 CGGEAGVV----------PETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSA- 237
G + + + + + G +A Y+ AR +
Sbjct: 181 FGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWL 240
Query: 238 --IVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295
+ + L ++ G+G+ + +L +P +P+ ++ + Q YS
Sbjct: 241 QQLRESSYEEAHKALCILPGVGTCVADKICLMALDKPQAVPV-NVHMWHIAQRDYSWHPT 299
Query: 296 PRPSQM----------DQLCEKWRPYRSVASWYLWR 321
++ + W PY A L+
Sbjct: 300 TSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFS 335
>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 = 65.3 bits (158), Expect = 1e-11
Identities = 67/464 (14%), Positives = 134/464 (28%), Gaps = 140/464 (30%)
Query: 31 TALAVIPVQTETANNATITHANVTPQTSSPPSKIPL-RPRKIRKL-------SPDNGV-- 80
+ + Q I + + +K + R + KL P V
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 81 ------------DQASSSQPTESSKA------TSAKSTKSRAIQQQQQTLTV---PRIIA 119
S + + + Q L P +
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215
Query: 120 RPLSSEG---EVEAAIRHLRN--ADRQLA-SLI---DIHPPPTFDSF--HTPFLALTRSI 168
R S + + LR + L+ ++ +++F L TR
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR-- 273
Query: 169 LYQQLAFKAGTSIYTRF-----------------IALC-GGEAGVVPETVLALTPQQLRQ 210
++Q+ + T + +P VL P++L
Sbjct: 274 -FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI 332
Query: 211 IGVSGRKAS-----YLHDLARKYQNGILSDSAIVNMDD---KSLFTMLTM----VNGIGS 258
I S R + H K I +S++ ++ + +F L++ + I +
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTII--ESSLNVLEPAEYRKMFDRLSVFPPSAH-IPT 389
Query: 259 ------WS-----VHMFMIFSLHR---------PDVLPINDLGVRKGVQL--LYSLE--- 293
W M ++ LH+ + I + + V+L Y+L
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Query: 294 ----ELPR--------PSQMD--------------QLCEKWRPYRSVASWYL-WRFVEAK 326
+P+ P +D + E+ +R +L +RF+E K
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM---VFLDFRFLEQK 506
Query: 327 GAPSSAAAVAAGAALPQPQQEEQQQPQLLDQ-------INSLIN 363
S A A+G+ L QQ + +P + D +N++++
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550
>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 = 57.4 bits (138), Expect = 5e-09
Identities = 70/420 (16%), Positives = 124/420 (29%), Gaps = 115/420 (27%)
Query: 3 EQTQSQ-TQNQPEPQP------EPETQP---------------PPNQDSTTALAVIPVQT 40
Q Q Q + PEP EP T P + + +
Sbjct: 31 SQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE 90
Query: 41 -ETA----NNATITHANVTPQTSSPPSKIPLRPRKIRKLSPDNGVDQASSSQPTESS--K 93
E N+ I HA + + I+ + + + + S+ +
Sbjct: 91 FENCYLEGND--I-HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR 147
Query: 94 ATSAKSTKSRAI---Q-------QQQQTL-TVPRIIARPL--SSEGEVEAAIRHLRNADR 140
A + + AI Q ++ + L ++ L S + IR +A++
Sbjct: 148 AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK 207
Query: 141 QLASLIDIH-------PPPTFD-------SFHTPFLALTRSILYQQLAFKAGTS---IYT 183
++I P D S P + + + Y A G + + +
Sbjct: 208 VFTQGLNILEWLENPSNTPDKDYLLSIPISC--PLIGVIQLAHYVVTAKLLGFTPGELRS 265
Query: 184 RFIALCGGEAGVVPETVLALTP-------------QQLRQIGVSGRKASYLHDLARKYQN 230
G G+V +A T L IGV +A L
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPS--- 322
Query: 231 GILSDS------------AIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLH---RPDVL 275
IL DS +I N+ + + + N + + SL + V+
Sbjct: 323 -ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI--SLVNGAKNLVV 379
Query: 276 --PINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWR-PYRSVASWYLWRFVEAKGAPSSA 332
P L G+ L +L + PS +DQ R P+ + RF+ P ++
Sbjct: 380 SGPPQSL---YGLNL--TLRKAKAPSGLDQ----SRIPFSERKLKFSNRFL-----PVAS 425
Score = 53.9 bits (129), Expect = 6e-08
Identities = 66/434 (15%), Positives = 121/434 (27%), Gaps = 177/434 (40%)
Query: 47 TITHANVTPQTSSPPSKIP----LRPRKIRKLSPDNGVDQ--ASSSQPTESSKATSAKST 100
T++H ++ P + L+ +Q +PTE
Sbjct: 10 TLSHGSLEHVLLVPTASFFIASQLQ-------------EQFNKILPEPTE---------- 46
Query: 101 KSRAIQQQQQTLTVPRIIARPL---------SSEGEVEAAIRH-LRNADRQLASLIDIH- 149
+ T ++ + L S G+ + + L + DIH
Sbjct: 47 ---GFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHA 103
Query: 150 -------PPPT------------FDSFHT---PFLALTRSILYQQLAFKAGTSIYTRFIA 187
T + PF + S L++ A G + +A
Sbjct: 104 LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR--AVGEGN---AQLVA 158
Query: 188 LCGGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLF 247
+ GG+ G + ++LR + + + DL + LS+ +D + +F
Sbjct: 159 IFGGQ-G-NTDDYF----EELRDLYQTYH--VLVGDLIKFSAE-TLSELIRTTLDAEKVF 209
Query: 248 TMLTMVNG--IGSWSVHMFMIFSLHRPDVLPIND-----------LGVRKGVQLL-Y--S 291
T G I W L P P D +GV +QL Y +
Sbjct: 210 T-----QGLNILEW---------LENPSNTPDKDYLLSIPISCPLIGV---IQLAHYVVT 252
Query: 292 LEEL-PRPSQM-DQL-----CEK-------------WRPYRSVASWYL-------WRFVE 324
+ L P ++ L + W + + R E
Sbjct: 253 AKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYE 312
Query: 325 A------------------KGAPSSAAAVAAGAALPQPQQEEQQQPQLLDQIN------- 359
A +G PS ++ + L Q Q ++ +++ N
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLSI---SNLTQEQVQD-----YVNKTNSHLPAGK 364
Query: 360 ----SLINIGYNDF 369
SL+N G +
Sbjct: 365 QVEISLVN-GAKNL 377
Score = 43.1 bits (101), Expect = 1e-04
Identities = 50/281 (17%), Positives = 81/281 (28%), Gaps = 108/281 (38%)
Query: 19 PETQPPPN--QDS--------TTALAVIPVQTETANNATITHANVTPQTSSPPSK---IP 65
P T PP+ +DS + L++ + E + N + P K I
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ-DYVNKTN----SHLPAGKQVEIS 369
Query: 66 LRPRKIRKLSPDNGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRIIARPLSSE 125
L NG S P +S + K++A Q+ RI P S
Sbjct: 370 LV----------NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS----RI---PFSE- 411
Query: 126 GEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRF 185
R L+ ++R L P FH+ L ++ + L
Sbjct: 412 -------RKLKFSNRFL---------PVASPFHSHLLVPASDLINKDLVKNN-------- 447
Query: 186 IALCGGEAGVVPETVLALTPQQLRQIGV----SGRKASYLHDLARKYQNGILSDSAIVNM 241
++ + ++ I V G DL R I IV+
Sbjct: 448 ---------------VSFNAKDIQ-IPVYDTFDGS------DL-RVLSGSISER--IVDC 482
Query: 242 DDKSLFTMLTMVNGIGSW-SVHMFMIFSLHRPDVLPINDLG 281
+ + V W + F + H +L D G
Sbjct: 483 ----IIRL--PVK----WETTTQFK--ATH---IL---DFG 505
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 38.8 bits (89), Expect = 0.003
Identities = 18/165 (10%), Positives = 44/165 (26%)
Query: 3 EQTQSQTQNQPEPQPEPETQPPPNQDSTTALAVIPVQTETANNATITHANVTPQTSSPPS 62
E + E++ N+ + + + A+ T +S +
Sbjct: 23 ETAVPENSGANTELVSGESEHSTNEADKQNEGEHARENKLEKAEGVATASETASPASNEA 82
Query: 63 KIPLRPRKIRKLSPDNGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRIIARPL 122
P+ + + P+ +K S K T+++ Q + P A
Sbjct: 83 ATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEATNQGDESKPAAEANKT 142
Query: 123 SSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRS 167
E + + + + ++ A+ R
Sbjct: 143 EKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGAREDDAINRG 187
>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 = 33.9 bits (78), Expect = 0.049
Identities = 25/137 (18%), Positives = 48/137 (35%), Gaps = 15/137 (10%)
Query: 145 LIDIHPPPTFDSFHTPFLALTRSILYQQ----LAFKAGTSIYTRFIALCGGEAGVVPETV 200
+ + P + F AL ++L Q K+ ++ F + + + + +
Sbjct: 15 DLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAF--ILENDDEINLKKI 72
Query: 201 LALTPQQL----RQIGVSGRKASYLHDLARKYQNGILSD-SAIVNMDDKSLFTMLTMVNG 255
+ +L R G +KA L DL+ IL D + N + L G
Sbjct: 73 AYIEFSKLAECVRPSGFYNQKAKRLIDLSGN----ILKDFQSFENFKQEVTREWLLDQKG 128
Query: 256 IGSWSVHMFMIFSLHRP 272
IG S + ++ +
Sbjct: 129 IGKESADAILCYACAKE 145
>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 = 32.2 bits (72), Expect = 0.14
Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 136 RNADRQLASLIDIHPPPTFDSFHTPFLALTRSI 168
+ A ++L + + ++ DS P LA+ ++
Sbjct: 19 KQALKKLQASLKLYAD---DS--APALAIKATM 46
Score = 29.9 bits (66), Expect = 0.83
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 16/42 (38%)
Query: 300 QMDQLCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAAL 341
+ +L + Y A SA A+A A +
Sbjct: 21 ALKKLQASLKLY----------------ADDSAPALAIKATM 46
Score = 29.1 bits (64), Expect = 1.3
Identities = 7/24 (29%), Positives = 9/24 (37%), Gaps = 11/24 (45%)
Query: 25 PNQDSTTALAVIPVQTETANNATI 48
DS ALA+ AT+
Sbjct: 34 D--DSAPALAI---------KATM 46
Score = 28.4 bits (62), Expect = 2.6
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 15/34 (44%)
Query: 69 RKIRKL-------SPDNGVDQASSSQPTESSKAT 95
+ ++KL + D S P + KAT
Sbjct: 20 QALKKLQASLKLYADD--------SAPALAIKAT 45
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex,
inter-protein beta sheet, protein-protein, metal
transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A
{Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Length = 229
Score = 28.1 bits (62), Expect = 3.9
Identities = 17/76 (22%), Positives = 32/76 (42%)
Query: 2 VEQTQSQTQNQPEPQPEPETQPPPNQDSTTALAVIPVQTETANNATITHANVTPQTSSPP 61
V + + + +P+P+P + Q P +D + E A +T + T TS P
Sbjct: 77 VVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPV 136
Query: 62 SKIPLRPRKIRKLSPD 77
+ + PR + + P
Sbjct: 137 TSVASGPRALSRNQPQ 152
>2c2j_A DNA-binding stress response protein; DNA-binding protein, DPS;
2.05A {Deinococcus radiodurans} PDB: 2c6r_A
Length = 211
Score = 27.9 bits (62), Expect = 4.0
Identities = 11/72 (15%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 78 NGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRIIARPLSSEGEVEAAIRHLRN 137
NGV + + P ++ ++A++T + + + T+P +++ +++ L+
Sbjct: 1 NGVPSTNVNTPAPNTGQSTAQNTNTASPLPYNRATTLPAA------GTEDLKKSVQALQ- 53
Query: 138 ADRQLASLIDIH 149
L L +
Sbjct: 54 --NTLTELQALQ 63
>2wvr_C DNA replication factor CDT1; DNA replication license, DNA
replication inhibitor, phosphoprotein, UBL conjugation,
DNA-binding, polymorphism; HET: DNA; 3.30A {Homo
sapiens} PDB: 2klo_A*
Length = 546
Score = 28.5 bits (62), Expect = 4.3
Identities = 20/148 (13%), Positives = 35/148 (23%)
Query: 13 PEPQPEPETQPPPNQDSTTALAVIPVQTETANNATITHANVTPQTSSPPSKIPLRPRKIR 72
+P P PP T P A+ + + P + + R+
Sbjct: 11 ARRRPGPPRIAPPKLACRTPSPARPALRAPASATSGSRKRARPPAAPGRDQARPPARRRL 70
Query: 73 KLSPDNGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRIIARPLSSEGEVEAAI 132
+LS D ++ P + + + K Q +S
Sbjct: 71 RLSVDEVSSPSTPEAPDIPACPSPGQKIKKSTPAAGQPPHLTSAQDQDTISELASCLQRA 130
Query: 133 RHLRNADRQLASLIDIHPPPTFDSFHTP 160
R L R L +
Sbjct: 131 RELGARVRALKASAQDAGESCTPEAEGR 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 = 27.4 bits (61), Expect = 4.7
Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 157 FHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGE---AGVVPETVLALTPQQLRQIGV 213
FH P+ L +I + + K + +F+ V L L+ +G+
Sbjct: 28 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSEL----LKPLGL 83
Query: 214 SGRKASYLHDLARKY 228
+A + + +Y
Sbjct: 84 YDLRAKTIVKFSDEY 98
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 253
Score = 28.1 bits (62), Expect = 4.8
Identities = 17/124 (13%), Positives = 38/124 (30%), Gaps = 14/124 (11%)
Query: 5 TQSQTQNQPEPQPEPETQPPPNQDSTTALAVIPVQTETANNATITHANVTPQTSSPPSKI 64
TQ+ + P P P P + P Q + Q + +
Sbjct: 6 TQTFYGRRWRPAPVQRYIPQPQPPAPPRRRRGPSQLQ--------------QLVAALGAL 51
Query: 65 PLRPRKIRKLSPDNGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRIIARPLSS 124
L+P++ +K + + KS+ ++ + + + P+
Sbjct: 52 ALQPKQKQKRAQKKPKKTPPPKPKKTQKPKKPTQKKKSKPGKRMRNCMKIENDCIFPVML 111
Query: 125 EGEV 128
+G+V
Sbjct: 112 DGKV 115
>1nth_A Monomethylamine methyltransferase MTMB1; TIM barrel; HET: BGX;
1.55A {Methanosarcina barkeri} SCOP: c.1.25.1 PDB:
1l2q_A* 1tv2_A* 1tv3_A* 1tv4_A*
Length = 458
Score = 28.2 bits (62), Expect = 5.4
Identities = 24/153 (15%), Positives = 44/153 (28%), Gaps = 19/153 (12%)
Query: 77 DNGVDQASSSQPTESSKATSAKSTKSRAIQQQQQTLTVPRI------IARPLSSEGEVEA 130
NGV + + + K+ + R LS++G + A
Sbjct: 157 VNGVMTSVRGKSPIPKSPYEVLAAKTETRLIKNACAMAGRPGMGVKGPETSLSAQGNISA 216
Query: 131 AIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCG 190
D H + A++ Y+ I + + G
Sbjct: 217 DCTGGMTCT-------DSHEVSQLNELKIDLDAISVIAHYKGN----SDIIMDEQMPIFG 265
Query: 191 GEAGVVPETVLALTPQQLRQIGVSGRKASYLHD 223
G AG + ET + + + +S AS+ D
Sbjct: 266 GYAGGIEETTIVDVATHINAVLMSS--ASWHLD 296
>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 = 27.3 bits (61), Expect = 6.4
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 240 NMDDKSLFTMLTMVNGIG 257
N +++LF L NG+G
Sbjct: 65 NKQERTLFKELIKTNGVG 82
>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 = 8.1
Identities = 6/18 (33%), Positives = 13/18 (72%)
Query: 240 NMDDKSLFTMLTMVNGIG 257
+ ++ +LF +L V+G+G
Sbjct: 64 DEENLALFELLLSVSGVG 81
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 27.6 bits (61), Expect = 8.2
Identities = 7/73 (9%), Positives = 16/73 (21%), Gaps = 6/73 (8%)
Query: 13 PEPQPEPETQPPPNQDSTTALAVIPVQTETANNATITHANVTPQTSSPPSKIPLRPRKIR 72
P T PP + P+ + + + +R
Sbjct: 18 QAANGGPATPAPPALGAAPT------GDPKPKKNKKPKNPTPPRPAGDNATVAAGHATLR 71
Query: 73 KLSPDNGVDQASS 85
+ D + +
Sbjct: 72 EHLRDIKAENTDA 84
>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 = 26.8 bits (60), Expect = 9.7
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 240 NMDDKSLFTMLTMVNGIG 257
+ + + LF L V+G+G
Sbjct: 80 DGETRDLFLTLLSVSGVG 97
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 0.129 0.370
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: 5,385,289
Number of extensions: 312648
Number of successful extensions: 873
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 42
Length of query: 373
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 278
Effective length of database: 4,049,298
Effective search space: 1125704844
Effective search space used: 1125704844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.3 bits)