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= 026231
(241 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 = 95.5 bits (236), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 157
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>pdb|3BTZ|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna
Length = 202
Score = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K +R + S+R+
Sbjct: 99 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 155
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 156 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 201
>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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 102 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 158
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 159 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 103 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 159
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 160 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 100 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 156
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 157 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 202
>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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 101 FVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 157
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>pdb|3BU0|A Chain A, Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With
Cofactors
Length = 203
Score = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K +R + S+R+
Sbjct: 100 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 156
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 157 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 202
>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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K +R + S+R+
Sbjct: 103 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 159
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 160 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>pdb|3BTX|A Chain A, X-Ray Structure Of Human Abh2 Bound To Dsdna Through
Active Site Cross-Linking
Length = 204
Score = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++G H DD + IASVSFG RDF+ + K +R + S+R+
Sbjct: 101 FVLINRYKDGSDHIGEHRDDCRELAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 157
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 158 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 203
>pdb|3RZG|A Chain A, Duplex Interrogation By A Direct Dna Repair Protein In The
Search Of Damage
Length = 209
Score = 94.7 bits (234), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 13/172 (7%)
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 SLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSKRL 188
+L+NRYK G+D++ H DDE+ IASVSFG RDF+ + K +R + S+R+
Sbjct: 103 FVLINRYKDGSDHICEHRDDERDLAPGSPIASVSFGASRDFVFRHKDSR---GKSPSRRV 159
Query: 189 KKKGNLDQHSFTLKHGSMLVMRGYTQRDWIHSVPRRAKAESTRINLTFRHVL 240
L HGS+L+M T W HS+P R K + R+NLTFR +L
Sbjct: 160 AVV------RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKIL 205
>pdb|2IUW|A Chain A, Crystal Structure Of Human Abh3 In Complex With Iron Ion
And 2-Oxoglutarate
Length = 238
Score = 93.2 bits (230), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 67/208 (32%), Positives = 99/208 (47%), Gaps = 23/208 (11%)
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 GSTPEIASVSFGCERDFLLKIK-PNRRTDDEPVSKRLKKKGNLDQHSFTLKHGSMLVMRG 211
G P IAS+SFG R F ++ K P D +R+K L HG++L+M G
Sbjct: 151 GRCPIIASLSFGATRTFEMRKKPPPEENGDYTYVERVK---------IPLDHGTLLIMEG 201
Query: 212 YTQRDWIHSVPRRAKAESTRINLTFRHV 239
TQ DW H VP+ + R+NLTFR V
Sbjct: 202 ATQADWQHRVPKEYHSREPRVNLTFRTV 229
>pdb|2H7O|A Chain A, Crystal Structure Of The Rho-Gtpase Binding Domain Of Ypka
pdb|2H7V|C Chain C, Co-crystal Structure Of Ypka-rac1
pdb|2H7V|D Chain D, Co-crystal Structure Of Ypka-rac1
Length = 303
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 15/75 (20%)
Query: 127 FNSLLLNRYKGGNDYVGWHADDEKLYGSTPEIASVSFGCERDFLLKIKPNRRTDDEPVSK 186
FNSL+L Y+ DYV D K S+ E VS +F+L I EP +
Sbjct: 68 FNSLILKTYRVIEDYVKGREGDTK--NSSTE---VSPYHRSNFMLSIV-------EPSLQ 115
Query: 187 RLKKKGNLDQ-HSFT 200
R++K +LDQ HSF+
Sbjct: 116 RIQK--HLDQTHSFS 128
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 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,944,188
Number of Sequences: 62578
Number of extensions: 353190
Number of successful extensions: 672
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 648
Number of HSP's gapped (non-prelim): 14
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
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)