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= 026678
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KHC|A Chain A, Crystal Structure Of Escherichia Coli Alkb In Complex With
Ssdna Containing A 1-Methylguanine Lesion
pdb|3KHC|B Chain B, Crystal Structure Of Escherichia Coli Alkb In Complex With
Ssdna Containing A 1-Methylguanine Lesion
Length = 219
Score = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 70 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 127
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 128 GAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 187
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 188 FYHGIQPLKAGF 199
>pdb|3BKZ|A Chain A, X-Ray Structure Of E Coli Alkb Crosslinked To Dsdna In The
Active Site
Length = 201
Score = 67.4 bits (163), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 54 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 111
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 112 GAKLSLHQDKCEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 171
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 172 FYHGIQPLKAGF 183
>pdb|2FD8|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDF|A Chain A, Crystal Structure Of Alkb In Complex With Co(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDG|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
Succinate, And Methylated Trinucleotide T-Mea-T
pdb|2FDH|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDI|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
(Air 3 Hours)
pdb|2FDJ|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii) And
Succinate
pdb|2FDK|A Chain A, Crystal Structure Of Alkb In Complex With Fe(ii),
2-oxoglutarate, And Methylated Trinucleotide T-mea-t
(air 9 Days)
pdb|3I2O|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mea-T
pdb|3I3M|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mec-T
pdb|3I3Q|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii) And
2-Oxoglutarate
pdb|3I3Q|B Chain B, Crystal Structure Of Alkb In Complex With Mn(Ii) And
2-Oxoglutarate
pdb|3I49|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mec-T
Length = 211
Score = 67.0 bits (162), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 57 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 114
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 115 GAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 174
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 175 FYHGIQPLKAGF 186
>pdb|3T3Y|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Iii) And
2-(3- Hydroxypicolinomido)acetic Acid
pdb|3T4H|B Chain B, Crystal Structure Of Alkb In Complex With Fe(Iii) And
N-Oxalyl-S-(3- Nitrobenzyl)-L-Cysteine
pdb|3T4V|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Iii) And
N-Oxalyl-S-(2- Napthalenemethyl)-L-Cysteine
Length = 206
Score = 67.0 bits (162), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 57 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 114
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 115 GAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 174
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 175 FYHGIQPLKAGF 186
>pdb|3KHB|A Chain A, Crystal Structure Of Escherichia Coli Alkb With Co(Ii) And
2-Og
pdb|3KHB|B Chain B, Crystal Structure Of Escherichia Coli Alkb With Co(Ii) And
2-Og
Length = 219
Score = 67.0 bits (162), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 70 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 127
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 128 GAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 187
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 188 FYHGIQPLKAGF 199
>pdb|3BI3|A Chain A, X-Ray Structure Of Alkb Protein Bound To Dsdna Containing
1meaA WITH Cofactors
Length = 201
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 55 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 112
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 113 GAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 172
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 173 FYHGIQPLKAGF 184
>pdb|3BIE|A Chain A, X-Ray Structure Of E Coli Alkb Bound To Dsdna Containing
1meaT WITH Mn And 2kg
Length = 202
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 55 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 112
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 113 GAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 172
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 173 FYHGIQPLKAGF 184
>pdb|3O1M|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1O|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1P|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1R|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1S|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1T|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1U|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1V|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
Length = 206
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 60/132 (45%), Gaps = 2/132 (1%)
Query: 97 LRWCTLGLQFDWSKRNYNVSLPHKKIPDALCQLAKRLAAPAMPIGEEFQPEAAIVNYFXX 156
L W T + +S + + P +P + L +R A A +FQP+A ++N +
Sbjct: 57 LGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG--YPDFQPDACLINRYAP 114
Query: 157 XXXXXXXXXXMEADWSKPIVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEARE 216
E D PIVS+SLG AIF GG R DP + L GD V+ GE+R
Sbjct: 115 GAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRL 174
Query: 217 CFHGECVLPGNF 228
+HG L F
Sbjct: 175 FYHGIQPLKAGF 186
>pdb|2QDE|A Chain A, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|B Chain B, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|C Chain C, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|D Chain D, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|E Chain E, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|F Chain F, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|G Chain G, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
pdb|2QDE|H Chain H, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING FAMILY Protein From Azoarcus Sp. Ebn1
Length = 397
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 175 IVSMSLGCKAIFLLGGKSREDPPLAMFLRSGDAVLMAGEA----RECFH 219
+V G LLGGK+ E PL + L +G+ +A EA RE FH
Sbjct: 114 LVGKRFGVPVYQLLGGKTIERIPLGLVLGAGEPEAVAEEALAVLREGFH 162
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
0.322 0.136 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,565,949
Number of Sequences: 62578
Number of extensions: 219017
Number of successful extensions: 352
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 341
Number of HSP's gapped (non-prelim): 11
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)