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= 002141
(960 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ORN|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent
Intermediate: Estranged-Guanine Complex
pdb|1ORP|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent
Intermediate: Estranged-Adenine Complex
Length = 226
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 19/122 (15%)
Query: 491 DVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVXXXXXXXXX 550
+VP D+ + L+ G+G K+ V + A VDT+V R++ RLG+
Sbjct: 107 EVPRDR--DELMKLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEV 164
Query: 551 XXXXXXXXXVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGE 610
+++ I K W H++MI FG+ C P C +CP+
Sbjct: 165 EKT------LMKIIPKEEWS-----------ITHHRMIFFGRYHCKAQSPQCPSCPLLHL 207
Query: 611 CR 612
CR
Sbjct: 208 CR 209
>pdb|1P59|A Chain A, Structure Of A Non-Covalent Endonuclease Iii-Dna Complex
Length = 226
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 19/122 (15%)
Query: 491 DVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVXXXXXXXXX 550
+VP D+ + L+ G+G K+ V A VDT+V R++ RLG+
Sbjct: 107 EVPRDR--DELMKLPGVGRKTANVVVSTAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEV 164
Query: 551 XXXXXXXXXVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGE 610
+++ I K W H++MI FG+ C P C +CP+
Sbjct: 165 EKT------LMKIIPKEEWS-----------ITHHRMIFFGRYHCKAQSPQCPSCPLLHL 207
Query: 611 CR 612
CR
Sbjct: 208 CR 209
>pdb|3I0W|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA
CONTAINING CYTOSINE Opposite To 8-Oxog
Length = 290
Score = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 467 AGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLH-HLAF 525
A +KD ++R+ +G ++LE+++ + ++ E L F G+G + +C+ L ++ + AF
Sbjct: 181 AKYLKDTVDRIY--NGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAF 238
Query: 526 PVDTNVGRIAVRL 538
PVDT V + + L
Sbjct: 239 PVDTWVKKAMMSL 251
>pdb|3F10|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine Dna Glycosylase In Complex With
8-Oxoguanosine
Length = 292
Score = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 467 AGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLH-HLAF 525
A +KD ++R+ +G ++LE+++ + ++ E L F G+G + +C+ L ++ + AF
Sbjct: 181 AKYLKDTVDRIY--NGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAF 238
Query: 526 PVDTNVGRIAVRL 538
PVDT V + + L
Sbjct: 239 PVDTWVKKAMMSL 251
>pdb|3I0X|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA
CONTAINING ADENINE Opposite To 8-Oxog
Length = 291
Score = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 467 AGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLH-HLAF 525
A +KD ++R+ +G ++LE+++ + ++ E L F G+G + +C+ L ++ + AF
Sbjct: 181 AKYLKDTVDRIY--NGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAF 238
Query: 526 PVDTNVGRIAVRL 538
PVDT V + + L
Sbjct: 239 PVDTWVKKAMMSL 251
>pdb|3F0Z|A Chain A, Crystal Structure Of Clostridium Acetobutylicum
8-Oxoguanine GlycosylaseLYASE IN ITS APO-Form
Length = 292
Score = 39.7 bits (91), Expect = 0.008, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 467 AGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLH-HLAF 525
A +KD ++R+ +G ++LE+++ + ++ E L F G+G K +C+ L + + AF
Sbjct: 181 AKYLKDTVDRIY--NGELNLEYIKSLNDNECHEELKKFXGVGPKVADCIXLFSXQKYSAF 238
Query: 526 PVDTNVGR 533
PVDT V +
Sbjct: 239 PVDTWVKK 246
>pdb|1KEA|A Chain A, Structure Of A Thermostable Thymine-Dna Glycosylase
Length = 221
Score = 38.1 bits (87), Expect = 0.023, Method: Composition-based stats.
Identities = 53/239 (22%), Positives = 84/239 (35%), Gaps = 43/239 (17%)
Query: 394 IDDATSKSKSTRVS------KEKQNDFDWDSLR------------RQVEANGGKKERPEH 435
+DDAT+K + VS + DF W R R+ A KK +
Sbjct: 1 MDDATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKF 60
Query: 436 TKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPD 495
+E + ++IA IKE G++N A ++K+ ++ D+G VP
Sbjct: 61 FVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGG-------RVP-- 111
Query: 496 KAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVXXXXXXXXXXXXXX 555
+ ++ +L G+G + V L A VD N R+ R
Sbjct: 112 RNRKAILDLPGVGKYTCAAVMCLAFGKKAAMVDANFVRVINRY---------------FG 156
Query: 556 XXXXVLESIQKYLWPRLCKL-DQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRH 613
L K LW L + + ++ F + C KP C C M C +
Sbjct: 157 GSYENLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSY 215
>pdb|1KG5|A Chain A, Crystal Structure Of The K142q Mutant Of E.Coli Muty (Core
Fragment)
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1WEF|A Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant
pdb|1WEI|A Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant
Complexed To Adenine
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1KG4|A Chain A, Crystal Structure Of The K142a Mutant Of E. Coli Muty
(Core Fragment)
pdb|1WEG|A Chain A, Catalytic Domain Od Muty Form Escherichia Coli K142a
Mutant
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1KG6|A Chain A, Crystal Structure Of The K142r Mutant Of E.Coli Muty (Core
Fragment)
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1KG7|A Chain A, Crystal Structure Of The E161a Mutant Of E.coli Muty (core
Fragment)
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1MUY|A Chain A, Catalytic Domain Of Muty From Escherichia Coli
pdb|1KG2|A Chain A, Crystal Structure Of The Core Fragment Of Muty From E.Coli
At 1.2a Resolution
pdb|1KG3|A Chain A, Crystal Structure Of The Core Fragment Of Muty From E.Coli
At 1.55a Resolution
Length = 225
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1MUD|A Chain A, Catalytic Domain Of Muty From Escherichia Coli, D138n
Mutant Complexed To Adenine
pdb|1MUN|A Chain A, Catalytic Domain Of Muty From Escherichia Coli D138n
Mutant
Length = 225
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP C+ CP++ C
Sbjct: 184 MMDLGAMICTRSKPKCSLCPLQNGC 208
>pdb|1RN7|A Chain A, Structure Of Human Cystatin D
pdb|1ROA|A Chain A, Structure Of Human Cystatin D
Length = 122
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 584 HYQMITFGKVFCTKSKPNCNACPM 607
+Y + FG+ CTKS+PN + CP
Sbjct: 64 YYFNVKFGRTTCTKSQPNLDNCPF 87
>pdb|3HIL|A Chain A, Sam Domain Of Human Ephrin Type-A Receptor 1 (Epha1)
pdb|3HIL|B Chain B, Sam Domain Of Human Ephrin Type-A Receptor 1 (Epha1)
pdb|3KKA|A Chain A, Co-Crystal Structure Of The Sam Domains Of Epha1 And Epha2
pdb|3KKA|B Chain B, Co-Crystal Structure Of The Sam Domains Of Epha1 And Epha2
Length = 82
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 487 EWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHL 523
EWL + + K Y+L F GL ++ECV LT L
Sbjct: 28 EWLESI---RMKRYILHFHSAGLDTMECVLELTAEDL 61
>pdb|3T2U|A Chain A, Structure Of Wuchereria Bancrofti Pi-Class Glutathione
S-Transferase
pdb|3T2U|B Chain B, Structure Of Wuchereria Bancrofti Pi-Class Glutathione
S-Transferase
Length = 208
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 8/100 (8%)
Query: 699 DTFCEDPEEIPT--IKLNMKEFTQTLQNYMQENLELQEGDMSKALVALTAGAASIPAPKL 756
D FCE ++ T K+ + + +Y+++ L ++ K L G I K+
Sbjct: 88 DMFCEGVRDLHTKYTKMIYQAYDTEKDSYIKDILPVELAKFEKLLATRDDGKNFILGEKI 147
Query: 757 KNVSR-LRTEHQVYELPDSH-----PLLRGMEKREPDDPG 790
V L E ++++ D H PLL+ +R D PG
Sbjct: 148 SYVDFVLFEELDIHQILDPHCLDKFPLLKAYHQRMEDRPG 187
>pdb|1KQJ|A Chain A, Crystal Structure Of A Mutant Of Muty Catalytic Domain
Length = 225
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 587 MITFGKVFCTKSKPNCNACPMRGEC 611
M+ G + CT+SKP + CP++ C
Sbjct: 184 MMDLGAMICTRSKPKHSLCPLQNGC 208
>pdb|1PU6|A Chain A, Crystal Structure Of H.Pylori 3-Methyladenine Dna
Glycosylase (Magiii)
pdb|1PU6|B Chain B, Crystal Structure Of H.Pylori 3-Methyladenine Dna
Glycosylase (Magiii)
pdb|1PU7|A Chain A, Crystal Structure Of H.pylori 3-methyladenine Dna
Glycosylase (magiii) Bound To 3,9-dimethyladenine
pdb|1PU7|B Chain B, Crystal Structure Of H.pylori 3-methyladenine Dna
Glycosylase (magiii) Bound To 3,9-dimethyladenine
pdb|1PU8|A Chain A, Crystal Structure Of H.Pylori 3-Methyladenine Dna
Glycosylase (Magiii) Bound To 1,N6-Ethenoadenine
pdb|1PU8|B Chain B, Crystal Structure Of H.Pylori 3-Methyladenine Dna
Glycosylase (Magiii) Bound To 1,N6-Ethenoadenine
Length = 218
Score = 30.0 bits (66), Expect = 6.2, Method: Composition-based stats.
Identities = 16/78 (20%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKA 497
D ++ + + + +K+A ++ G N A R+ D +++D S + + +
Sbjct: 65 DEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFE-----NFKQEVT 119
Query: 498 KEYLLSFRGLGLKSVECV 515
+E+LL +G+G +S + +
Sbjct: 120 REWLLDQKGIGKESADAI 137
>pdb|2ABK|A Chain A, Refinement Of The Native Structure Of Endonuclease Iii To
A Resolution Of 1.85 Angstrom
Length = 211
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 38/164 (23%), Positives = 59/164 (35%), Gaps = 27/164 (16%)
Query: 450 VNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGL 509
V + IK G+ N A I L+ H +VP D+A L + G+G
Sbjct: 69 VEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG-------EVPEDRAA--LEALPGVGR 119
Query: 510 KSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVXXXXXXXXXXXXXXXXXXVLESIQKYLW 569
K+ V VDT++ R+ R + V E + K +
Sbjct: 120 KTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQ-----------VEEKLLKVV- 167
Query: 570 PRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRH 613
P K+D H+ +I G+ C KP C +C + C +
Sbjct: 168 PAEFKVD------CHHWLILHGRYTCIARKPRCGSCIIEDLCEY 205
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
0.315 0.131 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,034,571
Number of Sequences: 62578
Number of extensions: 979426
Number of successful extensions: 2212
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2196
Number of HSP's gapped (non-prelim): 23
length of query: 960
length of database: 14,973,337
effective HSP length: 108
effective length of query: 852
effective length of database: 8,214,913
effective search space: 6999105876
effective search space used: 6999105876
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)