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= 026782
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DE8|B Chain B, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
Abasic Dna
pdb|1DE8|A Chain A, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
Abasic Dna
pdb|1DE9|A Chain A, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
pdb|1DE9|B Chain B, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
Length = 276
Score = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 108 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 165
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 166 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 210
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 211 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 263
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 264 GSDHCPI 270
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 96.3 bits (238), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 117 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 174
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 175 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 219
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 220 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 272
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 273 GSDHCPI 279
>pdb|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna
pdb|1DEW|B Chain B, Crystal Structure Of Human Ape1 Bound To Abasic Dna
Length = 279
Score = 96.3 bits (238), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 111 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 168
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 169 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 213
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 214 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 266
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 267 GSDHCPI 273
>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease
Hap1 Suggests The Recognition Of Extra-Helical
Deoxyribose At Dna Abasic Sites
Length = 287
Score = 96.3 bits (238), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 119 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 176
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 177 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 221
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 222 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 274
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 275 GSDHCPI 281
>pdb|1E9N|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|1E9N|B Chain B, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|1HD7|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIDINIMIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|3U8U|A Chain A, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|B Chain B, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|C Chain C, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|D Chain D, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|E Chain E, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|F Chain F, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
Length = 318
Score = 95.5 bits (236), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 150 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 207
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 208 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 252
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 253 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 305
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 306 GSDHCPI 312
>pdb|2ISI|A Chain A, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|2ISI|B Chain B, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|2ISI|C Chain C, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|4IEM|A Chain A, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|B Chain B, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|C Chain C, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|D Chain D, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
Length = 317
Score = 95.5 bits (236), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 61/187 (32%), Positives = 101/187 (54%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+
Sbjct: 149 EHDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVL 206
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D+
Sbjct: 207 CGDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADS 251
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ F W+ + + R+DYF++S L + +++ +
Sbjct: 252 FRHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------ 304
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 305 GSDHCPI 311
>pdb|2O3C|A Chain A, Crystal Structure Of Zebrafish Ape
pdb|2O3C|B Chain B, Crystal Structure Of Zebrafish Ape
pdb|2O3C|C Chain C, Crystal Structure Of Zebrafish Ape
Length = 282
Score = 82.0 bits (201), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 55/187 (29%), Positives = 91/187 (48%), Gaps = 26/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIW 85
+++ +GRVI AEF F+L+ Y PN R+ WD + ++ KPL+
Sbjct: 115 EHDKEGRVITAEFPDFFLVTAYVPNAS--RGLVRLDYRKTWDVDFRAYLCGLDARKPLVL 172
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGDLNV+H+EID+ +P K + GFT ER+ F +L+ G D+
Sbjct: 173 CGDLNVAHQEIDLKNP---------------KGNRKNAGFTPEEREGFTQLLEAG-FTDS 216
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R L+ ++ F W+ + + R+DYF++S L + +++ +
Sbjct: 217 FRELYPDQAYAYTF-WTYMMNARSKNVGWRLDYFVLSSALLPGLCDSKIRNTAM------ 269
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 270 GSDHCPI 276
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 52/187 (27%), Positives = 86/187 (45%), Gaps = 26/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIW 85
+++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I
Sbjct: 90 RFDTEGRIQIADFDDFLLYNIYFPNGAMSEERLKY-KLEFYDAFLEDVNRERDSGRNVII 148
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGD N +H EID++ P KE+ GF ER ++ G +D
Sbjct: 149 CGDFNTAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDT 192
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R + + WS + R R+DYF V+EE K ++ + L
Sbjct: 193 FRMFNSDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVM 244
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 245 GSDHCPI 251
>pdb|3FZI|A Chain A, 1.9 Angstrom Structure Of The Thermophilic Exonuclease Iii
Homologue Mth0212
pdb|3G0A|A Chain A, Mth0212 With Two Bound Manganese Ions
pdb|3G1K|A Chain A, Mth0212 (Wt) Crystallized In A Monoclinic Space Group
pdb|3G1K|B Chain B, Mth0212 (Wt) Crystallized In A Monoclinic Space Group
pdb|3G2C|A Chain A, Mth0212 In Complex With A Short Ssdna (Cgta)
pdb|3G2C|B Chain B, Mth0212 In Complex With A Short Ssdna (Cgta)
pdb|3G3C|A Chain A, Mth0212 (Wt) In Complex With A 6bp Dsdna Containing A
Single One Nucleotide Long 3'-Overhang
pdb|3G3C|B Chain B, Mth0212 (Wt) In Complex With A 6bp Dsdna Containing A
Single One Nucleotide Long 3'-Overhang
pdb|3G3Y|A Chain A, Mth0212 In Complex With Ssdna In Space Group P32
pdb|3G3Y|B Chain B, Mth0212 In Complex With Ssdna In Space Group P32
pdb|3G4T|A Chain A, Mth0212 (Wt) In Complex With A 7bp Dsdna
pdb|3G4T|B Chain B, Mth0212 (Wt) In Complex With A 7bp Dsdna
Length = 265
Score = 71.2 bits (173), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 52/187 (27%), Positives = 86/187 (45%), Gaps = 26/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIW 85
+++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I
Sbjct: 90 RFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVII 148
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CGD N +H EID++ P KE+ GF ER ++ G +D
Sbjct: 149 CGDFNTAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDT 192
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R + + WS + R R+DYF V+EE K ++ + L
Sbjct: 193 FRMFNSDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVM 244
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 245 GSDHCPI 251
>pdb|3G00|A Chain A, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7
Angstrom
pdb|3G00|B Chain B, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7
Angstrom
pdb|3G0R|A Chain A, Complex Of Mth0212 And An 8bp Dsdna With Distorted Ends
pdb|3G0R|B Chain B, Complex Of Mth0212 And An 8bp Dsdna With Distorted Ends
pdb|3G2D|A Chain A, Complex Of Mth0212 And A 4 Bp Dsdna With 3'-Overhang
pdb|3G2D|B Chain B, Complex Of Mth0212 And A 4 Bp Dsdna With 3'-Overhang
pdb|3G38|A Chain A, The Catalytically Inactive Mutant Mth0212 (D151n) In
Complex With An 8 Bp Dsdna
pdb|3G8V|A Chain A, The Rationally Designed Catalytically Inactive Mutant
Mth0212(D151n)
pdb|3GA6|A Chain A, Mth0212 In Complex With Two Dna Helices
pdb|3GA6|B Chain B, Mth0212 In Complex With Two Dna Helices
Length = 265
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 51/187 (27%), Positives = 86/187 (45%), Gaps = 26/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIW 85
+++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I
Sbjct: 90 RFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVII 148
Query: 86 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDA 145
CG+ N +H EID++ P KE+ GF ER ++ G +D
Sbjct: 149 CGNFNTAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDT 192
Query: 146 YRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
+R + + WS + R R+DYF V+EE K ++ + L
Sbjct: 193 FRMFNSDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVM 244
Query: 206 GSDHCPV 212
GSDHCP+
Sbjct: 245 GSDHCPI 251
>pdb|2J63|A Chain A, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
Major
pdb|2J63|B Chain B, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
Major
Length = 467
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 38/187 (20%)
Query: 44 LLNTYAPNNGWKEEENSFQRR------RKWDKRIQEFVLQCSGKP-------------LI 84
L+NTY N+G ++ + R++ R+ + + + P I
Sbjct: 292 LVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFI 351
Query: 85 WCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLID 144
W GDLNV+ + D + F + + GF ER F ++ +D
Sbjct: 352 WAGDLNVAERDYDRYYAGTFKSMQECS------------GFAPEERMSFRETMQRTNSVD 399
Query: 145 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 204
+R L+ + F WS G+ R R+DYF+VS L ++ C +
Sbjct: 400 IFRQLYPQAGPVYSF-WSQRINGRPRNLGWRLDYFVVSSRLASYVVDC------FPMPTV 452
Query: 205 YGSDHCP 211
GSDHCP
Sbjct: 453 MGSDHCP 459
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 53/199 (26%), Positives = 84/199 (42%), Gaps = 31/199 (15%)
Query: 20 HFLLSALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFV---L 76
HF L AL +P RVI A ++N Y NG + F+ + +W + EFV +
Sbjct: 77 HFGLPALPDDPQRRVIAATVSGVRVINVYC-VNGEALDSPKFKYKEQWFAALTEFVRDEM 135
Query: 77 QCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGF-TIAERKRFGA 135
GK L+ GD N++ + D P E W + + ER+ F
Sbjct: 136 TRHGK-LVLLGDFNIAPADADCYDP----------------EKWHEKIHCSSVERQWFQN 178
Query: 136 ILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRI--IACE 193
+L G L D+ R +H E F + G + G +RID+ +VS + + + +
Sbjct: 179 LLDLG-LTDSLRQVHPEGAFYTWFDYRGAMFQRKLG--LRIDHILVSPAMAAALKDVRVD 235
Query: 194 MQGHGIELEGFYGSDHCPV 212
++ +E SDH PV
Sbjct: 236 LETRALE----RPSDHAPV 250
>pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
pdb|2VOA|B Chain B, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
Length = 257
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 44/172 (25%), Positives = 78/172 (45%), Gaps = 22/172 (12%)
Query: 25 ALKYEP--DGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG-- 80
L EP + R+I A+ ++NTY P G+K + +Q + +W +R+ ++ +
Sbjct: 80 GLDSEPKDEDRLIRAKIAGIDVINTYVPQ-GFKIDSEKYQYKLQWLERLYHYLQKTVDFR 138
Query: 81 KPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEG 140
+WCGD+NV+ E IDV P+ KL +V F R+ + IL+ G
Sbjct: 139 SFAVWCGDMNVAPEPIDVHSPD-----KLKNHV----------XFHEDARRAYKKILELG 183
Query: 141 RLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIAC 192
+D R +H + + + + + RG R D + + L +R + C
Sbjct: 184 -FVDVLRKIHPNERIYTFYDYRVKGAIE-RGLGWRGDAILATPPLAERCVDC 233
>pdb|2JC5|A Chain A, Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From
Neisseria Meningitidis
pdb|4B5F|A Chain A, Substrate Bound Neisseria Ap Endonuclease In Absence Of
Metal Ions (Crystal Form 1)
pdb|4B5G|A Chain A, Substrate Bound Neisseria Ap Endonuclease In Absence Of
Metal Ions (Crystal Form 2)
pdb|4B5G|B Chain B, Substrate Bound Neisseria Ap Endonuclease In Absence Of
Metal Ions (Crystal Form 2)
pdb|4B5G|C Chain C, Substrate Bound Neisseria Ap Endonuclease In Absence Of
Metal Ions (Crystal Form 2)
pdb|4B5I|A Chain A, Product Complex Of Neisseria Ap Endonuclease In Presence
Of Metal Ions
pdb|4B5J|A Chain A, Neisseria Ap Endonuclease Bound To The Substrate With An
Orphan Adenine Base
pdb|4B5M|A Chain A, Neisseria Ap Endonuclease Bound To The Substrate With A
Cytosine Orphan Base
pdb|4B5M|B Chain B, Neisseria Ap Endonuclease Bound To The Substrate With A
Cytosine Orphan Base
pdb|4B5M|C Chain C, Neisseria Ap Endonuclease Bound To The Substrate With A
Cytosine Orphan Base
Length = 259
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 43/187 (22%), Positives = 85/187 (45%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWC 86
+++ +GR + +F +++ Y P+ EE + R ++ G+ ++ C
Sbjct: 88 EFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVC 147
Query: 87 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAY 146
GD N++H+ ID+ + + K +G++P ER+ G ++ + D +
Sbjct: 148 GDWNIAHQNIDLKN--WKGNQKNSGFLPE-------------EREWIGKVIHKLGWTDMW 192
Query: 147 RFLHKEKDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
R L+ + G++W N Y + RIDY +V+ EL + ++ H + E F
Sbjct: 193 RTLYPDVP---GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSA----HVYKDEKF- 244
Query: 206 GSDHCPV 212
SDH P+
Sbjct: 245 -SDHAPL 250
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/187 (22%), Positives = 85/187 (45%), Gaps = 25/187 (13%)
Query: 27 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWC 86
+++ +GR + +F +++ Y P+ EE + R ++ G+ ++ C
Sbjct: 88 EFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVC 147
Query: 87 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAY 146
G+ N++H+ ID+ + + K +G++P ER+ G ++ + D +
Sbjct: 148 GNWNIAHQNIDLKN--WKGNQKNSGFLPE-------------EREWIGKVIHKLGWTDMW 192
Query: 147 RFLHKEKDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFY 205
R L+ + G++W N Y + RIDY +V+ EL + ++ H + E F
Sbjct: 193 RTLYPDVP---GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSA----HVYKDEKF- 244
Query: 206 GSDHCPV 212
SDH P+
Sbjct: 245 -SDHAPL 250
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 47/196 (23%), Positives = 82/196 (41%), Gaps = 31/196 (15%)
Query: 29 EPDGRVILAEFETFY----LLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGK--- 81
E R+I+AE + ++N Y P ++ F + ++ + +Q + L+ K
Sbjct: 86 EAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNY-LETELKRDN 144
Query: 82 PLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDW---GQPGFTIAERKRFGAILK 138
P++ GD+N+S ++D+ G N++ W G+ F ER+ ++
Sbjct: 145 PVLIMGDMNISPTDLDI------------GIGEENRKRWLRTGKCSFLPEEREWMDRLMS 192
Query: 139 EGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKR-MRIDYFIVSEELKDRIIACEMQGH 197
G L+D +R H FSW + R +RID + S+ L + C G
Sbjct: 193 WG-LVDTFR--HANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAE---CCVETGI 246
Query: 198 GIELEGF-YGSDHCPV 212
E+ SDH PV
Sbjct: 247 DYEIRSMEKPSDHAPV 262
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 136 ILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKD 187
I+KE LI A +KEKD++ F++ G P +YR DY+ E L+D
Sbjct: 194 IIKEA-LIRARDRANKEKDIEVKFTYQGAP--RYRIDITAPDYYKAEEVLED 242
>pdb|1FWK|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWL|A Chain A, Crystal Structure Of Homoserine Kinase
pdb|1FWL|B Chain B, Crystal Structure Of Homoserine Kinase
pdb|1FWL|C Chain C, Crystal Structure Of Homoserine Kinase
pdb|1FWL|D Chain D, Crystal Structure Of Homoserine Kinase
pdb|1H72|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Hse
pdb|1H74|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H73|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With
Threonine
Length = 296
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 145 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 204
Y +K+K + + S I RGK + +YF + EE+KD++ + G G + F
Sbjct: 206 VYALYNKDKSLFGRYMMSDKVIEPVRGKLIP-NYFKIKEEVKDKVYGITISGSGPSIIAF 264
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/145 (22%), Positives = 59/145 (40%), Gaps = 25/145 (17%)
Query: 22 LLSALKYEPD---GRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC 78
++S L +E GR + A+F+ + P+ + + S ++ K+ ++ +
Sbjct: 113 VISGLGFETADRYGRYLQADFDKVSIATLLLPSG--QSGDESLNQKFKFMDDFTHYLSKQ 170
Query: 79 SGK--PLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAI 136
K I+CG L V+H+++DV + +E PGF ER +
Sbjct: 171 RRKRREYIYCGSLYVAHQKMDVKN---------------WRECQQMPGFLAPERAWLDEV 215
Query: 137 LKEGRLIDAYRFLHKEKDMDCGFSW 161
DA R + +E D FSW
Sbjct: 216 FGNLGYADALREVSREGDQ---FSW 237
>pdb|3RFZ|B Chain B, Crystal Structure Of The Fimd Usher Bound To Its Cognate
Fimc:fimh Substrate
pdb|3RFZ|E Chain E, Crystal Structure Of The Fimd Usher Bound To Its Cognate
Fimc:fimh Substrate
Length = 843
Score = 28.1 bits (61), Expect = 4.1, Method: Composition-based stats.
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 89 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWG 121
L+V + ++++ P+ F + + GY+PP D G
Sbjct: 104 LDVGQQRLNLTIPQAFMSNRARGYIPPELWDPG 136
>pdb|1ZDV|A Chain A, Solution Structure Of The Type 1 Pilus Assembly Platform
Fimd(25-139)
Length = 115
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 89 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWG 121
L+V + ++++ P+ F + + GY+PP D G
Sbjct: 80 LDVGQQRLNLTIPQAFMSNRARGYIPPELWDPG 112
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
0.323 0.142 0.458
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,307,922
Number of Sequences: 62578
Number of extensions: 318552
Number of successful extensions: 560
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 511
Number of HSP's gapped (non-prelim): 23
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)