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= 048138
(182 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 185 bits (469), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 92/182 (50%), Positives = 118/182 (64%), Gaps = 3/182 (1%)
Query: 2 KPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYV 61
+PL+VTYG+G +HD EGR++TAEF FFL++ YVPN+ GL RL YR T WD +Y+
Sbjct: 103 EPLNVTYGIGKEEHDKEGRVITAEFPDFFLVTAYVPNASRGLVRLDYRKT-WDVDFRAYL 161
Query: 62 KELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQ 121
L+ +KP++L GDLN AHQEID+ NP GNR++AGFT EER+ F L GF D+FR
Sbjct: 162 CGLDARKPLVLCGDLNVAHQEIDLKNPKGNRKNAGFTPEEREGF-TQLLEAGFTDSFREL 220
Query: 122 HRG-VVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLIL 180
+ YT+W Y R N GWRLDYF++S +L DS I GSDH PI L L
Sbjct: 221 YPDQAYAYTFWTYMMNARSKNVGWRLDYFVLSSALLPGLCDSKIRNTAMGSDHCPITLFL 280
Query: 181 KL 182
+
Sbjct: 281 AV 282
>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 = 184 bits (466), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 108 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 166
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 167 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 226
Query: 123 RGV-VGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 227 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 286
Query: 182 L 182
L
Sbjct: 287 L 287
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 184 bits (466), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 106 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 164
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 165 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 224
Query: 123 RGV-VGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 225 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 284
Query: 182 L 182
L
Sbjct: 285 L 285
>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 = 184 bits (466), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 139 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 197
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 198 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 257
Query: 123 RGVV-GYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 258 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 317
Query: 182 L 182
L
Sbjct: 318 L 318
>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 = 184 bits (466), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 97 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 155
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 156 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 215
Query: 123 RGV-VGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 216 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 275
Query: 182 L 182
L
Sbjct: 276 L 276
>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 = 183 bits (465), Expect = 4e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 100 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 158
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 159 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 218
Query: 123 RGV-VGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 219 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 278
Query: 182 L 182
L
Sbjct: 279 L 279
>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 = 183 bits (465), Expect = 4e-47, Method: Compositional matrix adjust.
Identities = 90/181 (49%), Positives = 115/181 (63%), Gaps = 2/181 (1%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVK 62
PL V+YG+G +HD EGR++ AEFDSF L++ YVPN+G GL RL YR WD + ++K
Sbjct: 138 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLK 196
Query: 63 ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRAQH 122
L +KP++L GDLN AH+EID+ NP GN+++AGFT +ERQ FG + D+FR +
Sbjct: 197 GLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLY 256
Query: 123 RGVV-GYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIGLILK 181
YT+W Y R N GWRLDYFL+S SL DS I GSDH PI L L
Sbjct: 257 PNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLA 316
Query: 182 L 182
L
Sbjct: 317 L 317
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 143 bits (360), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 73/177 (41%), Positives = 100/177 (56%), Gaps = 1/177 (0%)
Query: 1 IKPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSY 60
+ P S+ G G+ D+EGR+ A+FD F L + Y PN RL Y++ +D L
Sbjct: 77 VPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGAMSEERLKYKLEFYDAFLEDV 136
Query: 61 VKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRA 120
+E + + VI+ GD N AH+EID+ P N +GF ER ++ F+ G+VDTFR
Sbjct: 137 NRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVER-AWIDKFIENGYVDTFRM 195
Query: 121 QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIG 177
+ YT+W YR R+ N GWRLDYF V++ K S+IL DV GSDH PIG
Sbjct: 196 FNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIG 252
>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 = 142 bits (358), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 73/177 (41%), Positives = 100/177 (56%), Gaps = 1/177 (0%)
Query: 1 IKPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSY 60
+ P S+ G G+ D+EGR+ A+FD F L + Y PN RL Y++ +D L
Sbjct: 77 VPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDV 136
Query: 61 VKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRA 120
+E + + VI+ GD N AH+EID+ P N +GF ER ++ F+ G+VDTFR
Sbjct: 137 NRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVER-AWIDKFIENGYVDTFRM 195
Query: 121 QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIG 177
+ YT+W YR R+ N GWRLDYF V++ K S+IL DV GSDH PIG
Sbjct: 196 FNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIG 252
>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 = 140 bits (354), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 72/177 (40%), Positives = 100/177 (56%), Gaps = 1/177 (0%)
Query: 1 IKPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSY 60
+ P S+ G G+ D+EGR+ A+FD F L + Y PN RL Y++ +D L
Sbjct: 77 VPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDV 136
Query: 61 VKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRA 120
+E + + VI+ G+ N AH+EID+ P N +GF ER ++ F+ G+VDTFR
Sbjct: 137 NRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVER-AWIDKFIENGYVDTFRM 195
Query: 121 QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPIG 177
+ YT+W YR R+ N GWRLDYF V++ K S+IL DV GSDH PIG
Sbjct: 196 FNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIG 252
>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 = 111 bits (277), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 61/178 (34%), Positives = 99/178 (55%), Gaps = 6/178 (3%)
Query: 2 KPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPN--SGDGLRRLSYRITE-WDPSLS 58
KP +V G+GI + D EGR V +F ++S Y+P+ S + +++ YR + + P L
Sbjct: 76 KPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLE 135
Query: 59 SYVKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTF 118
+ E + +++ GD N AHQ ID+ N GN++++GF EER+ G G+ D +
Sbjct: 136 AMKNE---GRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMW 192
Query: 119 RAQHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPI 176
R + V GYT+W R + GWR+DY +V+ LA K +++ D SDH+P+
Sbjct: 193 RTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPL 250
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 109 bits (273), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 99/178 (55%), Gaps = 6/178 (3%)
Query: 2 KPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPN--SGDGLRRLSYRITE-WDPSLS 58
KP +V G+GI + D EGR V +F ++S Y+P+ S + +++ YR + + P L
Sbjct: 76 KPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLE 135
Query: 59 SYVKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTF 118
+ E + +++ G+ N AHQ ID+ N GN++++GF EER+ G G+ D +
Sbjct: 136 AMKNE---GRDIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMW 192
Query: 119 RAQHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPI 176
R + V GYT+W R + GWR+DY +V+ LA K +++ D SDH+P+
Sbjct: 193 RTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPL 250
>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 = 101 bits (252), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 72/201 (35%), Positives = 93/201 (46%), Gaps = 37/201 (18%)
Query: 16 DSEGRLVTA----------EFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSYVKELE 65
D EGR++T L++ YV NSG GL RL YR+ +DPS+ Y+ L+
Sbjct: 267 DEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLD 326
Query: 66 K-----------------KKP--VILTGDLNCAHQEIDIYNPAGNRRS----AGFTDEER 102
P I GDLN A ++ D Y AG +S +GF EER
Sbjct: 327 TWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYY-AGTFKSMQECSGFAPEER 385
Query: 103 QSFGANFLSKGFVDTFRA--QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFH 160
SF VD FR G V Y++W R GR N GWRLDYF+VS LA
Sbjct: 386 MSFRETMQRTNSVDIFRQLYPQAGPV-YSFWSQRINGRPRNLGWRLDYFVVSSRLASYVV 444
Query: 161 DSYILPDVTGSDHSPIGLILK 181
D + +P V GSDH P + ++
Sbjct: 445 DCFPMPTVMGSDHCPFQMWMR 465
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 77/176 (43%)
Query: 1 IKPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITEWDPSLSSY 60
++P +V GLG D GR + A+FD + + +P+ G L+ + D
Sbjct: 108 LQPKAVISGLGFETADRYGRYLQADFDKVSIATLLLPSGQSGDESLNQKFKFMDDFTHYL 167
Query: 61 VKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRA 120
K+ K++ I G L AHQ++D+ N ++ GF ER F + G+ D R
Sbjct: 168 SKQRRKRREYIYCGSLYVAHQKMDVKNWRECQQMPGFLAPERAWLDEVFGNLGYADALRE 227
Query: 121 QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTGSDHSPI 176
R +++W N GWR DY +++ L ++ + S H+P+
Sbjct: 228 VSREGDQFSWWPDSEQAEMLNLGWRFDYQVLTPGLRRFVRNAKLPRQPRFSQHAPL 283
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 50/180 (27%), Positives = 83/180 (46%), Gaps = 8/180 (4%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGDGLRRLSYRITE-WDPSLSSYV 61
P V +GL D + R++ A +++ Y N G+ L ++ E W +L+ +V
Sbjct: 73 PQDVHFGLPALPDDPQRRVIAATVSGVRVINVYCVN-GEALDSPKFKYKEQWFAALTEFV 131
Query: 62 K-ELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFRA 120
+ E+ + ++L GD N A + D Y+P + ERQ F N L G D+ R
Sbjct: 132 RDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWF-QNLLDLGLTDSLRQ 190
Query: 121 QHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVTG----SDHSPI 176
H YT++ YR + G R+D+ LVS ++A D + + SDH+P+
Sbjct: 191 VHPEGAFYTWFDYRGAMFQRKLGLRIDHILVSPAMAAALKDVRVDLETRALERPSDHAPV 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 = 69.3 bits (168), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 53/188 (28%), Positives = 92/188 (48%), Gaps = 10/188 (5%)
Query: 2 KPLSVTYGLGISDHDSEGRLVTAEFDSFFLLSCYVPNSGD-GLRRLSYRITEWDPSLSSY 60
+P V++GL S+ E RL+ A+ +++ YVP + Y++ +W L Y
Sbjct: 73 EPEDVSFGLD-SEPKDEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKL-QWLERLYHY 130
Query: 61 V-KELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFGANFLSKGFVDTFR 119
+ K ++ + + GD+N A + ID+++P + F ++ R+++ L GFVD R
Sbjct: 131 LQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVXFHEDARRAY-KKILELGFVDVLR 189
Query: 120 AQHRGVVGYTYWGYR-HGGRKTNRGWRLDYFLVSQSLADKFHDSY--ILPDVT--GSDHS 174
H YT++ YR G + GWR D L + LA++ D Y I P + SDH
Sbjct: 190 KIHPNERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDCYADIKPRLAEKPSDHL 249
Query: 175 PIGLILKL 182
P+ + +
Sbjct: 250 PLVAVFDV 257
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 53/191 (27%), Positives = 96/191 (50%), Gaps = 18/191 (9%)
Query: 3 PLSVTYGLGISDHDSEGRLVTAEFDSFF----LLSCYVPNSGDGLRRLSYRI-TEWDPSL 57
P++V G D +++ R++ AE S +++ Y P + + ++ +L
Sbjct: 73 PIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNL 132
Query: 58 SSYVK-ELEKKKPVILTGDLNCAHQEIDIYNPAGNRR------SAGFTDEERQSFGANFL 110
+Y++ EL++ PV++ GD+N + ++DI NR+ F EER+ + +
Sbjct: 133 QNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEERE-WMDRLM 191
Query: 111 SKGFVDTFR-AQHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILPDVT 169
S G VDTFR A + ++++ YR G NRG R+D L SQ LA+ ++ I ++
Sbjct: 192 SWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCVETGIDYEIR 251
Query: 170 G----SDHSPI 176
SDH+P+
Sbjct: 252 SMEKPSDHAPV 262
>pdb|3LPO|A Chain A, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|B Chain B, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|C Chain C, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|D Chain D, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPP|A Chain A, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|B Chain B, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|C Chain C, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|D Chain D, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
Length = 898
Score = 30.0 bits (66), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 130 YWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDSYILP------DVTGSDHSPIGLILKL 182
++ Y G ++ R R+D +L + + YI+P T S +P+GLI+ L
Sbjct: 729 WYDYESGAKRPWRKQRVDMYLPADKIGLHLRGGYIIPIQEPDVTTTASRKNPLGLIVAL 787
>pdb|3QAN|A Chain A, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Halodurans
pdb|3QAN|B Chain B, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Halodurans
pdb|3QAN|C Chain C, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Halodurans
Length = 538
Score = 26.6 bits (57), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 25/54 (46%)
Query: 53 WDPSLSSYVKELEKKKPVILTGDLNCAHQEIDIYNPAGNRRSAGFTDEERQSFG 106
++ +L KEL K+ P+I+ G+ +I +NPA + G + Q
Sbjct: 23 FEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLA 76
>pdb|1YQ2|A Chain A, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|B Chain B, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|C Chain C, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|D Chain D, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|E Chain E, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|F Chain F, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
Length = 1024
Score = 26.6 bits (57), Expect = 9.4, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 106 GANFLSKGFVDTFRAQHRGVVGYTYWGYRHGGRKTNRGWRLDYFLVSQSLADKFHDS-YI 164
GA + VD + H G V W +R G +T +++F + HDS ++
Sbjct: 532 GAMDQYEALVDKYPRLHGGFV----WEWRDHGIRTRTAEGMEFFAYGGDFGEVVHDSNFV 587
Query: 165 LPDVTGSDHSP 175
+ + SD +P
Sbjct: 588 MDGMVLSDSTP 598
>pdb|3P1T|A Chain A, Crystal Structure Of A Putative Aminotransferase
(Bpsl1724) From Burkholderia Pseudomallei K96243 At 2.60
A Resolution
pdb|3P1T|B Chain B, Crystal Structure Of A Putative Aminotransferase
(Bpsl1724) From Burkholderia Pseudomallei K96243 At 2.60
A Resolution
pdb|3P1T|C Chain C, Crystal Structure Of A Putative Aminotransferase
(Bpsl1724) From Burkholderia Pseudomallei K96243 At 2.60
A Resolution
pdb|3P1T|D Chain D, Crystal Structure Of A Putative Aminotransferase
(Bpsl1724) From Burkholderia Pseudomallei K96243 At 2.60
A Resolution
Length = 337
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 87 NPAGNRRSAGFTDEERQSFGANFLSKGFVD--TFRAQ 121
NP G SAG D+ RQ G + + +VD +FRA+
Sbjct: 146 NPTGQALSAGELDQLRQRAGKLLIDETYVDYSSFRAR 182
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 0.140 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,102,599
Number of Sequences: 62578
Number of extensions: 263206
Number of successful extensions: 492
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 448
Number of HSP's gapped (non-prelim): 21
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
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: 48 (23.1 bits)