RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033363
(121 letters)
>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 = 107 bits (268), Expect = 4e-31
Identities = 36/94 (38%), Positives = 54/94 (57%)
Query: 21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHG 80
V+ P A+ A D ++ +++ LGL RA I +FS EYL + W + +LHG
Sbjct: 52 VLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHG 111
Query: 81 VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114
+GKY D++ IFC +W +V P DH LN Y ++L
Sbjct: 112 IGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL 145
>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 = 37.3 bits (86), Expect = 6e-04
Identities = 25/145 (17%), Positives = 41/145 (28%), Gaps = 47/145 (32%)
Query: 10 KEIAILLKAGR---VIS----DLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKR 62
K++ I L G V+S L+ L + K + GL + R P +R
Sbjct: 364 KQVEISLVNGAKNLVVSGPPQSLYGLNL-----------TLRKAKAPSGLDQSRIPFSER 412
Query: 63 ---FSQE-----------YLGESWTHVTQ-LHGVG-KYAADAFAI--FCTGKWDRVRPTD 104
FS L + + + L + A I + T +R
Sbjct: 413 KLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLS 472
Query: 105 HMLNY-----------YWEFLVSTK 118
++ WE K
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFK 497
Score = 28.1 bits (62), Expect = 0.94
Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 25/101 (24%)
Query: 10 KEIAILL--KAGRVISD-----LFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIK- 61
+ I + G+ I + +F D K TE +EI + ++ + ++ +
Sbjct: 1670 VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT 1729
Query: 62 RFSQ-----------EYLGESWTHVTQL-----HGVGKYAA 86
+F+Q E L +S + H +G+YAA
Sbjct: 1730 QFTQPALTLMEKAAFEDL-KSKGLIPADATFAGHSLGEYAA 1769
>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 = 36.4 bits (85), Expect = 7e-04
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 12 IAILLKA-------GRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS 64
IA++L A +V LF V EE+E+ I ++GL + +A I++
Sbjct: 38 IAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLC 97
Query: 65 Q----EYLGE---SWTHVTQLHGVG 82
+Y GE + +L GVG
Sbjct: 98 AMLIDKYNGEVPRDRDELMKLPGVG 122
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 36.0 bits (84), Expect = 0.001
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 24 DLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGE---SWTHVT 76
L+ + E+ E ++ I T+GL +A I + + ++ GE +
Sbjct: 53 KLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALE 112
Query: 77 QLHGVG 82
L GVG
Sbjct: 113 ALPGVG 118
>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 = 32.4 bits (74), Expect = 0.017
Identities = 11/95 (11%), Positives = 28/95 (29%), Gaps = 18/95 (18%)
Query: 20 RVISDLFTLCPDAKTAT-------EVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYL 68
+ + +L ++ ++ + + G ++A + S ++
Sbjct: 50 KSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQ 109
Query: 69 GESWTHV-------TQLHGVGKYAADAFAIFCTGK 96
G+GK +ADA + K
Sbjct: 110 SFENFKQEVTREWLLDQKGIGKESADAILCYACAK 144
>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 = 30.9 bits (70), Expect = 0.081
Identities = 16/104 (15%), Positives = 34/104 (32%), Gaps = 13/104 (12%)
Query: 2 AQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIK 61
+ K + F P + + E + + GL +++A +I
Sbjct: 134 VVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRE----CGLSRRKAELIV 189
Query: 62 RFSQEYLGESWT---------HVTQLHGVGKYAADAFAIFCTGK 96
++E E ++T G+G++ A+ GK
Sbjct: 190 EIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALGK 233
>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 = 29.5 bits (65), Expect = 0.18
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 28/56 (50%)
Query: 39 DAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCT 94
+ + ++K+ ++L K A +S A A AI T
Sbjct: 18 EKQALKKLQASL---KLYAD-----------DS--------------APALAIKAT 45
Score = 29.5 bits (65), Expect = 0.20
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 10/36 (27%)
Query: 9 LKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIE 44
LK++ LK L+ D+ A + A +E
Sbjct: 22 LKKLQASLK-------LYA--DDSAPALAIKA-TME 47
>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 = 28.4 bits (63), Expect = 0.55
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 70 ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTD 104
E + + GVG AD +F K+ P D
Sbjct: 208 ECHEELKKFMGVGPQVADCIMLFSMQKYSAF-PVD 241
>1u2z_A Histone-lysine N-methyltransferase, H3 lysine-79 specific; histone
methyltransferase, nucleosome; HET: SAH; 2.20A
{Saccharomyces cerevisiae} SCOP: c.66.1.31
Length = 433
Score = 26.8 bits (58), Expect = 1.9
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 13/68 (19%)
Query: 8 RLKEIAILLKAG-RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66
++++I K G ++IS L +L + E I + +R+ +
Sbjct: 341 KVEKILQTAKVGCKIIS-LKSLRSLTYQINFYNVENIFNRLKV-----------QRYDLK 388
Query: 67 YLGESWTH 74
SWTH
Sbjct: 389 EDSVSWTH 396
>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 = 26.2 bits (58), Expect = 3.2
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 76 TQLHGVGKYAADAFAIFCTGKWD 98
TQ+ G+G++ + IF + D
Sbjct: 142 TQIKGIGRWTVEMLLIFSLNRDD 164
>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 = 25.8 bits (57), Expect = 4.3
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 18/94 (19%)
Query: 19 GRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWT----- 73
GRV + + V E + + G+ K++ I+ +
Sbjct: 74 GRVEQLVGGALEKPEQLYRVSDEALRQA----GVSKRKIEYIRHVCEHVESGRLDFTELE 129
Query: 74 ---------HVTQLHGVGKYAADAFAIFCTGKWD 98
+T + G+G++ A+ F +F G+ D
Sbjct: 130 GAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLD 163
>2iht_A Carboxyethylarginine synthase; thiamin diphosphate complex,
transferase; HET: MSE TPP; 2.00A {Streptomyces
clavuligerus} SCOP: c.31.1.3 c.36.1.5 c.36.1.9 PDB:
1upb_A* 1upc_A* 1upa_A* 2ihu_A* 2ihv_A*
Length = 573
Score = 25.6 bits (57), Expect = 4.8
Identities = 3/31 (9%), Positives = 9/31 (29%), Gaps = 1/31 (3%)
Query: 20 RVISDLFTLCPDAKTA-TEVDAEEIEKIIST 49
+ ++ + KT I ++
Sbjct: 301 DLRPSMWQKGIEKKTVRISPTVNPIPRVYRP 331
>1jmu_B Protein MU-1; protein-protein complex, jelly roll, zinc finger,
viral protein; HET: BOG; 2.80A {Reovirus SP} SCOP:
e.35.1.1 PDB: 2cse_A
Length = 666
Score = 25.6 bits (55), Expect = 5.3
Identities = 8/51 (15%), Positives = 14/51 (27%)
Query: 70 ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGN 120
E WT +Q+ + + L Y +E K +
Sbjct: 369 ELWTAASQIGQATVVNYVQLYAEDSSFTAQSIIATTSLAYNYEPEQLNKTD 419
>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 = 25.1 bits (55), Expect = 7.9
Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 16/81 (19%)
Query: 30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL--------GESWTHV----TQ 77
P + D + + LG+ KRA + + L
Sbjct: 156 PTPQRLAAADPQAL----KALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQT 211
Query: 78 LHGVGKYAADAFAIFCTGKWD 98
G+G++ A+ FA+ D
Sbjct: 212 FPGIGRWTANYFALRGWQAKD 232
>2j82_A TPPHA, protein serine-threonine phosphatase; PP2C family
phosphatase, hydrolase; 1.28A {Synechococcus elongatus}
PDB: 2j86_A 2y09_A 2xzv_A
Length = 240
Score = 24.9 bits (55), Expect = 8.9
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 24 DLFTLCPDAKTATEVDAEEIEKIISTLGLQKK 55
D LC D T E+ + I +S +QK
Sbjct: 186 DRLLLCSDGLTE-ELTDDVISIYLSEPNVQKA 216
>3cb6_A FACT complex subunit SPT16; peptidase homology domain, histone
binding module, histone H chaperone, PITA-bread fold;
1.84A {Schizosaccharomyces pombe} PDB: 3cb5_A
Length = 444
Score = 24.9 bits (54), Expect = 8.9
Identities = 10/72 (13%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 10 KEIAILLKAGRVISDLFTLCPDAKTATEVD----------AEEIEKIISTLGLQKKRAPM 59
+E+A + A RV + + + +T +D ++++E +I + ++
Sbjct: 181 QELANIKGASRVSVAVMSKYFVDELSTYIDQGKKITHSKFSDQMESLIDNEAFFQTKSLK 240
Query: 60 IKRFSQEYLGES 71
+ + L
Sbjct: 241 LGDIDLDQLEWC 252
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 24.8 bits (54), Expect = 9.1
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 4 IYSIRLKEIAILLKAGRVISDLFTLCPDAKTATE----VDAEEIEKI 46
+ IR KE+ + AGR+ LF + + + + E I+++
Sbjct: 602 VRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQL 648
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
0.322 0.136 0.412
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: 1,926,528
Number of extensions: 105823
Number of successful extensions: 293
Number of sequences better than 10.0: 1
Number of HSP's gapped: 293
Number of HSP's successfully gapped: 26
Length of query: 121
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 39
Effective length of database: 4,412,271
Effective search space: 172078569
Effective search space used: 172078569
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 (21.9 bits)
S2: 51 (23.6 bits)