BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 030096
(183 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RZL|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
pdb|3RZL|D Chain D, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 208
Score = 67.0 bits (162), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 46 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 101
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 102 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 150
>pdb|3RZM|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 206
Score = 67.0 bits (162), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 149
>pdb|3RZH|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
pdb|3RZJ|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
pdb|3RZK|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 103 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|3S57|A Chain A, Abh2 Cross-Linked With Undamaged Dsdna-1 Containing
Cofactors
pdb|3S5A|A Chain A, Abh2 Cross-Linked To Undamaged Dsdna-2 With Cofactors
Length = 204
Score = 66.6 bits (161), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 149
>pdb|3BTY|A Chain A, Crystal Structure Of Human Abh2 Bound To Dsdna Containing
1mea Through Cross-Linking Away From Active Site
pdb|3BUC|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna With Mn(Ii)
And 2kg
Length = 203
Score = 66.6 bits (161), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 44 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 99
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 100 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 148
>pdb|3H8O|A Chain A, Structure Determination Of Dna Methylation Lesions N1-mea
And N3-mec In Duplex Dna Using A Cross-linked Host-guest
System
pdb|3H8R|A Chain A, Structure Determination Of Dna Methylation Lesions N1-Mea
And N3-Mec In Duplex Dna Using A Cross-Linked Host-Guest
System
pdb|3H8X|A Chain A, Structure Determination Of Dna Methylation Lesions N1-Mea
And N3-Mec In Duplex Dna Using A Cross-Linked Host-Guest
System
Length = 209
Score = 66.6 bits (161), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 103 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|3BTZ|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna
Length = 202
Score = 66.6 bits (161), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 43 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 98
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 99 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 147
>pdb|3BTX|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna Through
Active Site Cross-Linking
Length = 204
Score = 66.6 bits (161), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 101 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 149
>pdb|3BU0|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With
Cofactors
Length = 203
Score = 66.6 bits (161), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 44 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 99
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 100 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 148
>pdb|3RZG|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 66.2 bits (160), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 58/109 (53%), Gaps = 4/109 (3%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGV-TGQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 177
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 103 FVLINRYKDGSDHICEHRDDERDLAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|2IUW|A Chain A, Crystal Structure Of Human Abh3 In Complex With Iron Ion
And 2-Oxoglutarate
Length = 238
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 69/149 (46%), Gaps = 13/149 (8%)
Query: 37 SEVIYFPRIIKMEDSWKFFDYLNNRIPWNRPTIRVFGRSCLQPRDTCYVASEGVTQLIYS 96
S V +P + ++++ + L +PW + T + QPR T + +L Y+
Sbjct: 40 SRVCLYPGFVDVKEADWILEQLCQDVPWKQRTGIREDITYQQPRLTAWYG-----ELPYT 94
Query: 97 GYR----PHPYSWDDFPPLKDILDIVLKVLPGSRFNSLLLNRYKGGNDYVGWHADDEKLY 152
R P+P+ + P+ L ++ G FNSL N Y+ D V WH+DDE
Sbjct: 95 YSRITMEPNPH----WHPVLRTLKNRIEENTGHTFNSLXCNLYRNEKDSVDWHSDDEPSL 150
Query: 153 GSTPEIASVSFGCERDFLLKIKPSKSYQG 181
G P IAS+SFG R F ++ KP G
Sbjct: 151 GRCPIIASLSFGATRTFEMRKKPPPEENG 179
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.140 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,346,061
Number of Sequences: 62578
Number of extensions: 285400
Number of successful extensions: 511
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 497
Number of HSP's gapped (non-prelim): 15
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)