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= 025911
(246 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 = 94.4 bits (233), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 46 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 101
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 102 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 156
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 157 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 204
>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 = 94.4 bits (233), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 103 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 157
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>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 = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+ R
Sbjct: 103 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 157
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>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 = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 155
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 156 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>pdb|3RZM|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 206
Score = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 155
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 156 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>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 = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 44 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 99
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 100 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 154
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 155 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 202
>pdb|3BTX|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna Through
Active Site Cross-Linking
Length = 204
Score = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 45 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 100
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+ R
Sbjct: 101 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 155
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 156 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>pdb|3BU0|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With
Cofactors
Length = 203
Score = 93.6 bits (231), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 44 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 99
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+ R
Sbjct: 100 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 154
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 155 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 202
>pdb|3BTZ|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna
Length = 202
Score = 93.6 bits (231), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 43 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 98
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+ R
Sbjct: 99 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 153
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 154 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 201
>pdb|3RZG|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 93.6 bits (231), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 64/177 (36%), Positives = 86/177 (48%), Gaps = 18/177 (10%)
Query: 69 IRVFGRSCLQPRDTCYVASEGVTQLIYSGYRPHPYSWDDFPPLKDILDIVLKVLPGSRFN 128
++VFG+ PR G+T +SG P W P L+ I D V V G FN
Sbjct: 47 VQVFGKWHSVPRKQATYGDAGLT-YTFSGLTLSPKPW--IPVLERIRDHVSGVT-GQTFN 102
Query: 129 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEP 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+ R
Sbjct: 103 FVLINRYKDGSDHICEHRDDERDLAPGSPIASVSFGASRDFVFRHKDSRGKSPSR----- 157
Query: 189 VSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 245
+ L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 ---------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>pdb|2IUW|A Chain A, Crystal Structure Of Human Abh3 In Complex With Iron Ion
And 2-Oxoglutarate
Length = 238
Score = 92.0 bits (227), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 67/212 (31%), Positives = 99/212 (46%), Gaps = 26/212 (12%)
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 GSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEPVSKRLKKKGNLDQHSFTLKHGSML 212
G P IAS+SFG R F ++ KP D +R+K L HG++L
Sbjct: 151 GRCPIIASLSFGATRTFEMRKKPPPE----ENGDYTYVERVK---------IPLDHGTLL 197
Query: 213 VMRGYTQRDWIHSVPRRAKAESTRINLTFRHV 244
+M G TQ DW H VP+ + R+NLTFR V
Sbjct: 198 IMEGATQADWQHRVPKEYHSREPRVNLTFRTV 229
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 0.138 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,078,278
Number of Sequences: 62578
Number of extensions: 359679
Number of successful extensions: 724
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 700
Number of HSP's gapped (non-prelim): 13
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
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: 50 (23.9 bits)