RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 016856
(381 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 = 71.7 bits (175), Expect = 5e-14
Identities = 28/135 (20%), Positives = 56/135 (41%), Gaps = 16/135 (11%)
Query: 252 FPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKL 311
FPS + LA + ++ LGYRA + AR I++ Q L L+ + +Y +
Sbjct: 196 FPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRES----SYEEA 251
Query: 312 AEQLSQINGFGPFTRNNV-LVCIGFYHVIPTDSETIRHLKQVHARNC-----------TS 359
+ L + G G + + L+ + +P + ++ ++ + T+
Sbjct: 252 HKALCILPGVGTCVADKICLMALDKPQAVPVNVHMWHIAQRDYSWHPTTSQAKGPSPQTN 311
Query: 360 KTVQMIAESIYGKYA 374
K + S++G YA
Sbjct: 312 KELGNFFRSLWGPYA 326
Score = 27.8 bits (61), Expect = 7.2
Identities = 14/92 (15%), Positives = 26/92 (28%), Gaps = 9/92 (9%)
Query: 61 PSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDFSG-RVFR 119
S + L V++ +L ++ + + F G R+ R
Sbjct: 97 KSQASRPTPDELEAVRKYFQLD-------VTLAQLYHHWGSVDSHFQEVAQKFQGVRLLR 149
Query: 120 SPTLFEDMVKCMLLCNCQWPRTLSMARALCEL 151
E + + N R M LC+
Sbjct: 150 QD-PIECLFSFICSSNNNIARITGMVERLCQA 180
>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 = 70.7 bits (173), Expect = 6e-14
Identities = 22/125 (17%), Positives = 52/125 (41%), Gaps = 10/125 (8%)
Query: 252 FPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKL 311
FP+ +L E + C G+RA + I +G++ L ++ + +
Sbjct: 158 FPTVDKLHEFTEKDF-EECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNE-------C 209
Query: 312 AEQLSQINGFGPFTRNNVLV-CIGFYHVIPTDSETIRHLKQVH-ARNCTSKTVQMIAESI 369
E+L + G GP + +++ + Y P D+ + + ++ A + + K ++
Sbjct: 210 HEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREK 269
Query: 370 YGKYA 374
+G +
Sbjct: 270 FGSLS 274
>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 = 52.7 bits (126), Expect = 1e-07
Identities = 44/236 (18%), Positives = 76/236 (32%), Gaps = 64/236 (27%)
Query: 8 DPLSRSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQ 67
+ + L + SL N V + P Q + L + +R + APS +Q
Sbjct: 354 NKTNSHLPAGKQVEISLVNG--AKNLV---VSGPPQSLYGLNLTLRKAK---APS-GLDQ 404
Query: 68 QDALLAQVK-----RMLR---------LSEADERNVRDFKRIVRQVAQEEGEESQYMTDF 113
++ K R L L A + +D + ++ + Y T F
Sbjct: 405 SRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT-F 463
Query: 114 SGRVFR--SPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQTP 171
G R S ++ E +V C++ +W T + H + DF P
Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVKWETTTQF---------KATHI---L--DFGPGGA 509
Query: 172 AGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDI 227
+G LT R + +++ AG L+ N P +D
Sbjct: 510 SG------------LGVLTHRNKDGTG-------VRVIVAGTLDIN-----PDDDY 541
>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 = 42.7 bits (101), Expect = 7e-05
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 9/82 (10%)
Query: 250 GNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAY 308
G P +L + + L ++ + R I + + G++ ELE
Sbjct: 82 GALEKPEQLYRVSDEAL-RQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATT----- 135
Query: 309 VKLAEQLSQINGFGPFTRNNVL 330
+ E+L+ I G G +T +
Sbjct: 136 --VIEKLTAIKGIGQWTAEMFM 155
>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 = 42.9 bits (101), Expect = 8e-05
Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 9/90 (10%)
Query: 241 DPPSARDRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMC 300
+ FP+P+ LA D L RA ++ LA ++G + + D+
Sbjct: 144 ERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDV- 202
Query: 301 NEASLTAYVKLAEQLSQINGFGPFTRNNVL 330
E + L G G +T N
Sbjct: 203 -EQ-------AMKTLQTFPGIGRWTANYFA 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 = 41.3 bits (97), Expect = 3e-04
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 252 FPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVK 310
FP+ + L + C L R A I+++A+ + L EL++ E
Sbjct: 161 FPTQEAILKAGVEGL-RECGLSRRKAELIVEIAK-----EENLEELKEWGEEE------- 207
Query: 311 LAEQLSQINGFGPFTRNNVL 330
E L+ G G +T VL
Sbjct: 208 AYEYLTSFKGIGRWTAELVL 227
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 40.4 bits (95), Expect = 4e-04
Identities = 16/76 (21%), Positives = 25/76 (32%), Gaps = 9/76 (11%)
Query: 251 NFPSPRELANLDESFLAKRCNL-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYV 309
P L + L + L + + A V GQI L +E
Sbjct: 91 GGVVPAALLKVSGDDL-RGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDEL------ 143
Query: 310 KLAEQLSQINGFGPFT 325
+ +L Q+ G G +T
Sbjct: 144 -VIAELVQLPGIGRWT 158
>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 = 37.8 bits (88), Expect = 0.003
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 250 GNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRE-LEDMCNEASLTA 307
G FP+P E+ ++D + + C R + +A + G I +E E + NE
Sbjct: 82 GQFPTPEEIRDMDFEIM-RACGFSARKIDSLKSIAEATISGLIPTKEEAERLSNEE---- 136
Query: 308 YVKLAEQLSQINGFGPFTRNNVL 330
L E+L+QI G G +T +L
Sbjct: 137 ---LIERLTQIKGIGRWTVEMLL 156
>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 = 34.6 bits (79), Expect = 0.031
Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 275 RAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCI 333
+A I+ + + +++ L D + + E+L I G G ++ L +
Sbjct: 85 KAKYIIMAREKVYGRLKEEIKPLADEDQQLAR-------ERLLNIKGIGMQEASHFLRNV 137
Query: 334 GFYHVIPTDSETIRHLK 350
G++ + D I ++
Sbjct: 138 GYFDLAIIDRHIIDFMR 154
>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 = 33.7 bits (76), Expect = 0.11
Identities = 36/185 (19%), Positives = 64/185 (34%), Gaps = 26/185 (14%)
Query: 154 ELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSR----IAESKASSEDYMNLKLD 209
E Q+ I F + K Q + K S L+ I SK +
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPK--SILSKEEIDHIIMSK-DAVSGTLRLFW 69
Query: 210 CAGVLEENVQPSFPQNDIESDLHGLNELSTTDP--PSARDRIGNFPSPRE-LANLDESFL 266
+E + F + + + L T+ PS R + R+ L N ++ F
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR--MYIEQRDRLYNDNQVF- 126
Query: 267 AKRCNLGYRAGRILKLARGIVDGQIQLRE-----LEDM--CNEASLTAYVKLAEQLSQIN 319
AK N+ R LKL + + ++LR ++ + + + V L+ ++
Sbjct: 127 AKY-NV-SRLQPYLKLRQAL----LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM 180
Query: 320 GFGPF 324
F F
Sbjct: 181 DFKIF 185
>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 = 0.19
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 10/30 (33%)
Query: 47 SLRIEVRNSASGSAPSLSQEQQDALLAQVK 76
SL++ A SAP+L A+ A ++
Sbjct: 28 SLKL----YADDSAPAL------AIKATME 47
Score = 28.8 bits (63), Expect = 2.1
Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 10/32 (31%)
Query: 12 RSLSRPLHLSNSL-----DNTDIPSVSVDVTI 38
++L + L SL D+ P++++ T+
Sbjct: 20 QALKK---LQASLKLYADDSA--PALAIKATM 46
Score = 27.2 bits (59), Expect = 6.7
Identities = 7/29 (24%), Positives = 13/29 (44%), Gaps = 6/29 (20%)
Query: 179 RQKVSKVASKLTSRIAES------KASSE 201
+Q + K+ + L +S KA+ E
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATME 47
>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 = 31.3 bits (71), Expect = 0.31
Identities = 16/113 (14%), Positives = 38/113 (33%), Gaps = 27/113 (23%)
Query: 249 IGNFPSPRELANLDESFLAKRCN-LGY---RAGRILKLARGIVDGQIQLRELEDMCNEAS 304
+ +PS D +++ LG RA I+K + + Q
Sbjct: 57 LEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQW------------- 103
Query: 305 LTAYVKLAEQLSQINGFGPFTRNNVLV-CIG-FYHVIPTDSETIRHLKQVHAR 355
+ +++G G + ++ + C+ + V P D + ++ +
Sbjct: 104 --------KYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWEN 148
>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 = 31.2 bits (71), Expect = 0.40
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 16/100 (16%)
Query: 253 PSPRELANLDESFLA---KRCNLGYR--AGRILKLARGIVDGQIQLRELEDMCNEASLTA 307
+ +++A ++ S LA + Y A R++ L+ I+ + E+ E +
Sbjct: 67 INLKKIAYIEFSKLAECVRPSGF-YNQKAKRLIDLSGNILK---DFQSFENFKQEVTR-- 120
Query: 308 YVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIPTDSETIR 347
E L G G + + +L V+ D +
Sbjct: 121 -----EWLLDQKGIGKESADAILCYACAKEVMVVDKYSYL 155
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.84
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 24/70 (34%)
Query: 40 QPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQV 99
+ Q+P S+R + R E+Q RL E D + ++ R+
Sbjct: 79 RLTQEPESIR-KWR------------EEQRK---------RLQELDAASKVM-EQEWREK 115
Query: 100 AQEEGEESQY 109
A+++ EE
Sbjct: 116 AKKDLEE-WN 124
>1hbn_B Methyl-coenzyme M reductase I beta subunit; methanogenesis,
biological methanogenesis, NI-enzyme, oxidoreductase;
HET: MHS AGM MGN F43 TP7; 1.16A
{Methanothermobacterthermautotrophicus} SCOP: a.89.1.1
d.58.31.2 PDB: 1hbm_B* 1hbo_B* 1hbu_B* 1mro_B* 3m1v_B*
3m2r_B* 3m2u_B* 3m2v_B* 3m30_B* 3m32_B* 3pot_B* 1e6v_B*
Length = 442
Score = 29.1 bits (65), Expect = 2.3
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 66 EQQDALLAQVKRMLRLSEADERNVRDF---KRIVRQV 99
+++ A K M++++E D+ NV KR + QV
Sbjct: 79 GNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQV 115
>3sqg_B Methyl-coenzyme M reductase, beta subunit; anaerobic methane
oxidation, transferase; HET: MHS 0AF TP7 M43 1PE PGE
P6G; 2.10A {Uncultured archaeon}
Length = 433
Score = 29.1 bits (65), Expect = 2.3
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 66 EQQDALLAQVKRMLRLSEADERNVRDF---KRIVRQV 99
++ + V+ MLR+ D+ NV KR++ Q
Sbjct: 77 DKAKEIAKAVEDMLRVESGDDTNVELIAGGKRMMVQP 113
>1e6y_B Methyl-coenzyme M reductase I beta subunit; biological
methanogenesis, NI-enzyme, oxidoreductase, NI ENZ; HET:
MHS AGM F43 TP7; 1.6A {Methanosarcina barkeri} SCOP:
a.89.1.1 d.58.31.2
Length = 433
Score = 29.1 bits (65), Expect = 2.4
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 66 EQQDALLAQVKRMLRLSEADERNVRDF---KRIVRQV 99
DA+ VK+++++ E D+ NV K ++ Q
Sbjct: 76 GNADAIAENVKKLVQVDEGDDTNVIKVKGGKSLLIQS 112
>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, nucleic acid binding
Pro RNA complex; 2.60A {Thermus thermophilus} PDB:
3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A
3hjf_A
Length = 685
Score = 28.4 bits (63), Expect = 4.3
Identities = 11/62 (17%), Positives = 17/62 (27%)
Query: 63 LSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDFSGRVFRSPT 122
L L + + L LS E R + I + + G + P
Sbjct: 261 LVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPK 320
Query: 123 LF 124
L
Sbjct: 321 LM 322
>3sp7_A BCL-2-like protein 1; apoptosis regulator-inhibitor complex; HET:
03B; 1.40A {Homo sapiens} PDB: 2lp8_A* 2lpc_A 1ysg_A*
1ysi_A* 1ysn_A* 2o1y_A* 2yxj_A* 3pl7_A 3qkd_A* 1g5j_A
4ehr_A* 3spf_A* 2pon_B 3r85_A 2p1l_A 4a1u_A* 2yj1_A
3fdm_A 3inq_A* 3io8_A ...
Length = 172
Score = 27.4 bits (60), Expect = 6.6
Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 2/91 (2%)
Query: 46 HSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLS--EADERNVRDFKRIVRQVAQEE 103
S + + S + ++ + VK+ LR + E + R R F + Q+
Sbjct: 20 LSQKGYSWSQFSDVEENRTEAPEGTESEAVKQALREAGDEFELRYRRAFSDLTSQLHITP 79
Query: 104 GEESQYMTDFSGRVFRSPTLFEDMVKCMLLC 134
G Q +FR + +V
Sbjct: 80 GTAYQSFEQVVNELFRDGVNWGRIVAFFSFG 110
>2d1s_A Luciferase, luciferin 4-monooxygenase; alpha/beta, beta barrel,
alpha+beta, riken structural genomics/proteomics
initiative, RSGI; HET: SLU; 1.30A {Luciola cruciata}
PDB: 2d1q_A* 2d1r_A* 2d1t_A*
Length = 548
Score = 27.9 bits (63), Expect = 6.9
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 165 DFIPQTPAGKESKR--RQKVSKVASKL 189
D +P+ GK R R+ + K +K+
Sbjct: 522 DEVPKGLTGKIDGRAIREILKKPVAKM 548
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
0.317 0.131 0.383
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: 5,529,698
Number of extensions: 319100
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 674
Number of HSP's successfully gapped: 26
Length of query: 381
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 286
Effective length of database: 4,049,298
Effective search space: 1158099228
Effective search space used: 1158099228
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 (21.7 bits)
S2: 58 (26.3 bits)