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= 029450
(193 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RZM|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 206
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 45 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 95
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 149
>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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 46 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 96
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 97 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 150
>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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 45 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 95
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 47 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 97
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|3BTX|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna Through
Active Site Cross-Linking
Length = 204
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 45 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 95
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 44 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 94
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 95 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR 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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 47 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 97
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|3BTZ|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna
Length = 202
Score = 63.9 bits (154), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 43 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 93
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 94 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 147
>pdb|3BU0|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With
Cofactors
Length = 203
Score = 63.9 bits (154), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 44 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 94
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 95 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR 148
>pdb|3RZG|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 63.9 bits (154), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 69 IRVFGRSCLQVACISTPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVL 128
++VFG+ S PR G+T +SG P W P L+ I D V V
Sbjct: 47 VQVFGK------WHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT 97
Query: 129 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSK 183
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHICEHRDDERDLAPGSPIASVSFGASRDFVFRHKDSR 151
>pdb|2IUW|A Chain A, Crystal Structure Of Human Abh3 In Complex With Iron Ion
And 2-Oxoglutarate
Length = 238
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/149 (28%), Positives = 67/149 (44%), Gaps = 19/149 (12%)
Query: 37 SEVIYFPRIIKMEDSWKFFDYLNNRIPWNRPTIRVFGRSCLQVACISTPRDTCYVASEGV 96
S V +P + ++++ + L +PW + T + PR T +
Sbjct: 40 SRVCLYPGFVDVKEADWILEQLCQDVPWKQRT------GIREDITYQQPRLTAWYG---- 89
Query: 97 TQLIYSGYR----PHPYSWDDFPPLKDILDIVLKVLPGSRFNSLLLNRYKGGNDYVGWHA 152
+L Y+ R P+P+ + P+ L ++ G FNSL N Y+ D V WH+
Sbjct: 90 -ELPYTYSRITMEPNPH----WHPVLRTLKNRIEENTGHTFNSLXCNLYRNEKDSVDWHS 144
Query: 153 DDEKLYGSTPEIASVSFGCERDFLLKIKP 181
DDE G P IAS+SFG R F ++ KP
Sbjct: 145 DDEPSLGRCPIIASLSFGATRTFEMRKKP 173
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 0.139 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,524,808
Number of Sequences: 62578
Number of extensions: 289877
Number of successful extensions: 527
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: 513
Number of HSP's gapped (non-prelim): 15
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)