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= 025478
(252 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 = 91.3 bits (225), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 97 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 155
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 156 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 201
Query: 249 HVL 251
+L
Sbjct: 202 KIL 204
>pdb|3RZM|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 206
Score = 90.9 bits (224), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 154
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 155 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 200
Query: 249 HVL 251
+L
Sbjct: 201 KIL 203
>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 = 90.9 bits (224), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 156
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 157 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 202
Query: 249 HVL 251
+L
Sbjct: 203 KIL 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 = 90.9 bits (224), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 156
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 157 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 202
Query: 249 HVL 251
+L
Sbjct: 203 KIL 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 = 90.9 bits (224), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 154
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 155 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 200
Query: 249 HVL 251
+L
Sbjct: 201 KIL 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 = 90.9 bits (224), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 95 -GQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 153
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 154 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 199
Query: 249 HVL 251
+L
Sbjct: 200 KIL 202
>pdb|3BTX|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna Through
Active Site Cross-Linking
Length = 204
Score = 90.9 bits (224), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 96 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 154
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 155 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 200
Query: 249 HVL 251
+L
Sbjct: 201 KIL 203
>pdb|3BTZ|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna
Length = 202
Score = 90.9 bits (224), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 94 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 152
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 153 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 198
Query: 249 HVL 251
+L
Sbjct: 199 KIL 201
>pdb|3BU0|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With
Cofactors
Length = 203
Score = 90.5 bits (223), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++G H DD + IASVSFG RDF+ + K S+
Sbjct: 95 -GQTFNFVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSRGKSPS 153
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 154 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 199
Query: 249 HVL 251
+L
Sbjct: 200 KIL 202
>pdb|3RZG|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 90.5 bits (223), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 87/183 (47%), Gaps = 24/183 (13%)
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 PGSRFNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDR 188
G FN +L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K S+
Sbjct: 98 -GQTFNFVLINRYKDGSDHICEHRDDERDLAPGSPIASVSFGASRDFVFRHKDSRGKSPS 156
Query: 189 RTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFR 248
R + L HGS+L+M T W HS+P R K + R+NLTFR
Sbjct: 157 R--------------RVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFR 202
Query: 249 HVL 251
+L
Sbjct: 203 KIL 205
>pdb|2IUW|A Chain A, Crystal Structure Of Human Abh3 In Complex With Iron Ion
And 2-Oxoglutarate
Length = 238
Score = 87.8 bits (216), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 66/218 (30%), Positives = 98/218 (44%), Gaps = 32/218 (14%)
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 DDEKLYGSTPEIASVSFGCERDFLLKIKPSKSYQDRRTDDEPVSKRLKKKGNLDQHSFTL 212
DDE G P IAS+SFG R F ++ KP D +R+K L
Sbjct: 145 DDEPSLGRCPIIASLSFGATRTFEMRKKPPPE----ENGDYTYVERVK---------IPL 191
Query: 213 KHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHV 250
HG++L+M G TQ DW H VP+ + R+NLTFR V
Sbjct: 192 DHGTLLIMEGATQADWQHRVPKEYHSREPRVNLTFRTV 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 0.137 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,221,509
Number of Sequences: 62578
Number of extensions: 361343
Number of successful extensions: 718
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: 694
Number of HSP's gapped (non-prelim): 13
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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)