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= 017876
(364 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Y Chain Y, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Z Chain Z, Crystal Structure Of The Human Fen1-Pcna Complex
Length = 379
Score = 335 bits (860), Expect = 2e-92, Method: Compositional matrix adjust.
Identities = 164/307 (53%), Positives = 224/307 (72%), Gaps = 2/307 (0%)
Query: 1 MLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60
+L NE GE TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L
Sbjct: 51 VLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQL 110
Query: 61 AEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQ 120
+A AG ++++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+
Sbjct: 111 QQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGK 170
Query: 121 VYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG 180
VYA A+EDMD LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G
Sbjct: 171 VYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLG 230
Query: 181 CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTD 240
DYC+SIRGIG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D
Sbjct: 231 SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-D 289
Query: 241 EEQLQIKWSAPDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLESFFKPVANT 300
E +++KWS P+EE LI F+ E F+ +R+ S+QGRL+ FFK V +
Sbjct: 290 PESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFK-VTGS 348
Query: 301 SAPIKRK 307
+ KRK
Sbjct: 349 LSSAKRK 355
>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Product 5'-Flap Dna, Sm3+, And K+
pdb|3Q8L|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Substrate 5'-Flap Dna, Sm3+, And K+
Length = 341
Score = 320 bits (820), Expect = 8e-88, Method: Compositional matrix adjust.
Identities = 152/271 (56%), Positives = 208/271 (76%), Gaps = 1/271 (0%)
Query: 1 MLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60
+L NE GE TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L
Sbjct: 51 VLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQL 110
Query: 61 AEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQ 120
+A AG ++++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+
Sbjct: 111 QQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGK 170
Query: 121 VYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG 180
VYA A+EDMD LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G
Sbjct: 171 VYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLG 230
Query: 181 CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTD 240
DYC+SIRGIG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D
Sbjct: 231 SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-D 289
Query: 241 EEQLQIKWSAPDEEGLINFLVSENGFNSDRV 271
E +++KWS P+EE LI F+ E F+ +R+
Sbjct: 290 PESVELKWSEPNEEELIKFMCGEKQFSEERI 320
>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
pdb|3Q8M|B Chain B, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
Length = 341
Score = 317 bits (813), Expect = 5e-87, Method: Compositional matrix adjust.
Identities = 151/271 (55%), Positives = 207/271 (76%), Gaps = 1/271 (0%)
Query: 1 MLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60
+L NE GE TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L
Sbjct: 51 VLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQL 110
Query: 61 AEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQ 120
+A AG ++++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+
Sbjct: 111 QQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGK 170
Query: 121 VYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG 180
VYA A+EDM LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G
Sbjct: 171 VYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLG 230
Query: 181 CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTD 240
DYC+SIRGIG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D
Sbjct: 231 SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-D 289
Query: 241 EEQLQIKWSAPDEEGLINFLVSENGFNSDRV 271
E +++KWS P+EE LI F+ E F+ +R+
Sbjct: 290 PESVELKWSEPNEEELIKFMCGEKQFSEERI 320
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
pdb|1MC8|B Chain B, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
Length = 343
Score = 213 bits (543), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 116/303 (38%), Positives = 169/303 (55%), Gaps = 21/303 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L + G +TSHL G+F RTI L+EAG+KP YVFDG+PP+ K++EL KR R +A
Sbjct: 47 LMDSKGRITSHLSGLFYRTINLMEAGIKPAYVFDGKPPEFKRKELEKRREAREEAELKWK 106
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
EA+ GN E+ K+++R KV + +D K+LL+LMG+P+++APSE EAQ A + G V
Sbjct: 107 EALAKGNLEEARKYAQRATKVNEMLIEDAKKLLQLMGIPIIQAPSEGEAQAAYMASKGDV 166
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVA---------KILEELNLTMDQF 172
YA AS+D DSL FGAPR +R+L RK+P + V ++L+EL +T ++
Sbjct: 167 YASASQDYDSLLFGAPRLIRNLTITGKRKMPGKDVYVEIKPELVVLDEVLKELKITREKL 226
Query: 173 IDLCILSGCDYC-DSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231
I+L IL G DY ++GIG + AL+++R ++Q D +
Sbjct: 227 IELAILVGTDYNPGGVKGIGPKKALEIVRYSRD--------PLAKFQRQSDVDLYAIKEF 278
Query: 232 FKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLE 291
F P V + + W PDEEG++ FL E+ F+ +RV Q LE
Sbjct: 279 FLNPPVTN---EYSLSWKEPDEEGILKFLCDEHNFSEERVKNGIERLKKAIKAGRQSTLE 335
Query: 292 SFF 294
S+F
Sbjct: 336 SWF 338
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 208 bits (530), Expect = 3e-54, Method: Compositional matrix adjust.
Identities = 123/304 (40%), Positives = 172/304 (56%), Gaps = 21/304 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L + G +TSHL G+F RTI L+EAG+KP+YVFDG+PP+ KK+EL KR R +A +
Sbjct: 47 LMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREAREEAEEKWR 106
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
EA+E G E+ K+++R +V + +D K+LL+LMG+P+V+APSE EAQ A + G V
Sbjct: 107 EALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSV 166
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV---------AKILEELNLTMDQF 172
YA AS+D DSL FGAPR +R+L RK+P V ++L+EL LT ++
Sbjct: 167 YASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKL 226
Query: 173 IDLCILSGCDYC-DSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231
I+L IL G DY I+GIG + AL+++R ++Q D +
Sbjct: 227 IELAILVGTDYNPGGIKGIGLKKALEIVRHSKD--------PLAKFQKQSDVDLYAIKEF 278
Query: 232 FKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLE 291
F P VTD L W PDEEG++ FL E+ F+ +RV Q LE
Sbjct: 279 FLNPP-VTDNYNLV--WRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLE 335
Query: 292 SFFK 295
S+FK
Sbjct: 336 SWFK 339
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 202 bits (513), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 114/282 (40%), Positives = 173/282 (61%), Gaps = 18/282 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L + G VTSHL G+F RTI +LE G+ PIYVFDG+PP+ K +EL +R + +A L
Sbjct: 44 LMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLE 103
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
A G E++ K+S+ ++++ ++ K+LL+ MG+P+V+APSE EA+ A L K G
Sbjct: 104 RAKSEGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLS 163
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIP-----------VMEFEVAKILEELNLTMD 170
+A AS+D D++ FGA R +R+L RK+P ++E E+ +L++L +T +
Sbjct: 164 WAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKPELIETEI--LLKKLGITRE 221
Query: 171 QFIDLCILSGCDYC-DSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEAR 229
Q ID+ IL G DY D IRGIG + ALK+I+++G IE +E + I ++ E R
Sbjct: 222 QLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKKDI--NFNIDEIR 279
Query: 230 RLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRV 271
LF P+VV EE L + + P+ E +IN LV E+ F+ +RV
Sbjct: 280 GLFLNPQVVKPEEALDL--NEPNGEDIINILVYEHNFSEERV 319
>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
pdb|1A77|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
Length = 326
Score = 201 bits (510), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 109/271 (40%), Positives = 168/271 (61%), Gaps = 17/271 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L N GE+TS G+F +TI LLE + PI+VFDG+PP LK++ R + A +
Sbjct: 47 LRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMK 106
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
EA++ + E+ K++KR +T + ++CK LL LMG+P VEAPSE EAQ + + K G V
Sbjct: 107 EAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDV 166
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGC 181
+AV S+D D+L +GAPR +R+L +++++P + E+ ++LE+L +++D ID+ I G
Sbjct: 167 WAVVSQDYDALLYGAPRVVRNLT--TTKEMPEL-IELNEVLEDLRISLDDLIDIAIFMGT 223
Query: 182 DYC-DSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTD 240
DY ++GIG + A +L+R + + + + + Y E +R+FKEP+ VTD
Sbjct: 224 DYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVEY----------YDEIKRIFKEPK-VTD 272
Query: 241 EEQLQIKWSAPDEEGLINFLVSENGFNSDRV 271
L +K PD+EG+I FLV EN FN DRV
Sbjct: 273 NYSLSLK--LPDKEGIIKFLVDENDFNYDRV 301
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 201 bits (510), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 107/281 (38%), Positives = 169/281 (60%), Gaps = 17/281 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L + G +TSHL G+F RTI ++EAG+KP+YVFDG+PP+LK +E+ +R + + +A
Sbjct: 61 LMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYE 120
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
EAV++G+ E +++ + K+T++ D K LL MG+P V+AP+E EAQ A + K G
Sbjct: 121 EAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDA 180
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME---------FEVAKILEELNLTMDQF 172
YA AS+D DSL FG+P+ +R+L RK+P E+ K+L +L +T++
Sbjct: 181 YASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENL 240
Query: 173 IDLCILSGCDYC-DSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231
ID+ IL G DY D GIG + AL+L++ +G IE I + I + P + ++
Sbjct: 241 IDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPILKS----PIEVDVIAIKKY 296
Query: 232 FKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVT 272
F +P+V + +I+W PD + + LV E+ F+ DRV+
Sbjct: 297 FLQPQVT---DNYRIEWHTPDPDAVKRILVDEHDFSIDRVS 334
>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
pdb|1RXV|B Chain B, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
pdb|1RXW|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
Length = 336
Score = 178 bits (452), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 106/302 (35%), Positives = 160/302 (52%), Gaps = 21/302 (6%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 61
L + G +TSHL G+ R ++E G++P++VFDG+PP+ KK E+ +R +RA+A +
Sbjct: 47 LKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWI 106
Query: 62 EAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQV 121
A++AG+K D +K+++ +V + D K LL MG+P V+APSE EAQ A + G V
Sbjct: 107 AALQAGDK-DAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDV 165
Query: 122 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV---------AKILEELNLTMDQF 172
S+D DSL FG+PR R+L RK+P V L+ L LT +Q
Sbjct: 166 EYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQL 225
Query: 173 IDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232
ID+ IL G DY + ++G+G + AL I+ +G I L+ + + +E R F
Sbjct: 226 IDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHV------EEIRNFF 279
Query: 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLES 292
P V D +I++ PD E I FL E+ F+ +RV S+Q LE
Sbjct: 280 LNPPVTDD---YRIEFREPDFEKAIEFLCEEHDFSRERV--EKALEKLKALKSTQATLER 334
Query: 293 FF 294
+F
Sbjct: 335 WF 336
>pdb|3QEA|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
Complex With Dna (Complex Ii)
pdb|3QEB|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
Complex With Dna And Mn2+ (Complex Iii)
Length = 352
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 71/226 (31%), Positives = 112/226 (49%), Gaps = 12/226 (5%)
Query: 7 GEVTSHLQGMFTRTIR-LLEAGMKPIYVFDG-QPPDLKKQELAKRYSKRADATDDLAEAV 64
GE T G + + LL G+KPI VFDG P K+ E ++R ++A+
Sbjct: 49 GEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLR 108
Query: 65 EAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAV 124
E E E F+ R++ +T + + GV + AP EA+AQ A L K+G V A+
Sbjct: 109 EGKVSEARECFT-RSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAI 167
Query: 125 ASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELN--LTMDQFIDLCILSGCD 182
+ED D L FG + + MD + + + + + +L T ++F +CILSGCD
Sbjct: 168 ITEDSDLLAFGCKKVILK-MDQFGNGLEIDQARLG-MCRQLGDVFTEEKFRYMCILSGCD 225
Query: 183 YCDSIRGIGGQTALKLIR--QHGSIETILENIN---RERYQIPEDW 223
Y S+RGIG A K++R + I +++ I + +PED+
Sbjct: 226 YLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDY 271
>pdb|3QE9|Y Chain Y, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
Complex With Dna (Complex I)
pdb|3QE9|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
Complex With Dna (Complex I)
Length = 352
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 70/226 (30%), Positives = 111/226 (49%), Gaps = 12/226 (5%)
Query: 7 GEVTSHLQGMFTRTIR-LLEAGMKPIYVFDG-QPPDLKKQELAKRYSKRADATDDLAEAV 64
GE T G + + LL G+KPI VFDG P K+ E ++R ++A+
Sbjct: 49 GEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLR 108
Query: 65 EAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAV 124
E E E F+ R++ +T + + GV + AP EA+AQ A L K+G V A+
Sbjct: 109 EGKVSEARECFT-RSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAI 167
Query: 125 ASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELN--LTMDQFIDLCILSGCD 182
+ED L FG + + MD + + + + + +L T ++F +CILSGCD
Sbjct: 168 ITEDSALLAFGCKKVILK-MDQFGNGLEIDQARLG-MCRQLGDVFTEEKFRYMCILSGCD 225
Query: 183 YCDSIRGIGGQTALKLIR--QHGSIETILENIN---RERYQIPEDW 223
Y S+RGIG A K++R + I +++ I + +PED+
Sbjct: 226 YLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDY 271
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 59/228 (25%), Positives = 96/228 (42%), Gaps = 38/228 (16%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLL-EAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60
LT GE + G ++ L E G I VFD + P + + + RA +D
Sbjct: 33 LTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPED- 91
Query: 61 AEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS- 118
F ++ + K L+ L+G+ +E P EA+ A+L K
Sbjct: 92 --------------FPRQLALI--------KELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 119 ---GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDL 175
G + + D D + R H++ P I A + E+ L DQ+ D
Sbjct: 130 EKEGYEVRILTADKDLYQLLSDRI--HVLHPEGYLI-----TPAWLWEKYGLRPDQWADY 182
Query: 176 CILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPE 221
L+G D ++GIG +TA KL+ + GS+E +L+N++R + I E
Sbjct: 183 RALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 59/228 (25%), Positives = 96/228 (42%), Gaps = 38/228 (16%)
Query: 2 LTNEAGEVTSHLQGMFTRTIRLL-EAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60
LT GE + G ++ L E G I VFD + P + + + RA +D
Sbjct: 33 LTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPED- 91
Query: 61 AEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS- 118
F ++ + K L+ L+G+ +E P EA+ A+L K
Sbjct: 92 --------------FPRQLALI--------KELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 119 ---GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDL 175
G + + D D + R H++ P I A + E+ L DQ+ D
Sbjct: 130 EKEGYEVRILTADKDLYQLLSDRI--HVLHPEGYLI-----TPAWLWEKYGLRPDQWADY 182
Query: 176 CILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPE 221
L+G D ++GIG +TA KL+ + GS+E +L+N++R + I E
Sbjct: 183 RALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a
pdb|1XO1|B Chain B, T5 5'-Exonuclease Mutant K83a
Length = 291
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 52/196 (26%), Positives = 87/196 (44%), Gaps = 40/196 (20%)
Query: 44 QELAKRYSKRADAT-DDLAEAV--------EAGNKEDIEKFSKRT----------VKVTK 84
Q LAK YS R D ++V AGN++ EK+++RT + K
Sbjct: 52 QSLAKSYSARTTIVLGDKGKSVFRLEHLPEYAGNRD--EKYAQRTEEEKALDEQFFEYLK 109
Query: 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS--GQVYAVASE-DMDSL-TFGAPRFL 140
+ CK + VEA A A L V+ ++++ D D+L T RF
Sbjct: 110 DAFELCKTTFPTFTIRGVEADDMA-AYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRF- 167
Query: 141 RHLMDPSSRKIPVMEFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTAL 196
++R+ E+ + + E N+ ++QFI L + G D D+IRG IG +
Sbjct: 168 ----SFTTRR----EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGY 218
Query: 197 KLIRQHGSIETILENI 212
+IR+ G++ I++ +
Sbjct: 219 NIIREFGNVLDIIDQL 234
>pdb|1EXN|A Chain A, T5 5'-Exonuclease
pdb|1EXN|B Chain B, T5 5'-Exonuclease
Length = 290
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 49/195 (25%), Positives = 84/195 (43%), Gaps = 38/195 (19%)
Query: 44 QELAKRYSKRADAT-DDLAEAV--------EAGNKEDIEKFSKRT----------VKVTK 84
Q LAK YS R D ++V GN++ EK+++RT + K
Sbjct: 51 QSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRD--EKYAQRTEEEKALDEQFFEYLK 108
Query: 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCK-SGQVYAVASE-DMDSL-TFGAPRFLR 141
+ CK + VEA A + V+ ++++ D D+L T RF
Sbjct: 109 DAFELCKTTFPTFTIRGVEADDXAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRF-- 166
Query: 142 HLMDPSSRKIPVMEFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTALK 197
++R+ E+ + E N+ ++QFI L + G D D+IRG IG +
Sbjct: 167 ---SFTTRR----EYHLRDXYEHHNVDDVEQFISLKAIXG-DLGDNIRGVEGIGAKRGYN 218
Query: 198 LIRQHGSIETILENI 212
+IR+ G++ I++ +
Sbjct: 219 IIREFGNVLDIIDQL 233
>pdb|1DLC|A Chain A, Crystal Structure Of Insecticidal Delta-Endotoxin From
Bacillus Thuringiensis At 2.5 Angstroms Resolution
Length = 584
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 69 KEDIEKFSKRTVKVTKQHNDDCKRLLKL 96
KEDI +F KR +K+T+++ D C + +
Sbjct: 162 KEDIAEFYKRQLKLTQEYTDHCVKWYNV 189
>pdb|1UT5|A Chain A, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT5|B Chain B, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT8|A Chain A, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
pdb|1UT8|B Chain B, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
Length = 291
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 51/196 (26%), Positives = 86/196 (43%), Gaps = 40/196 (20%)
Query: 44 QELAKRYSKRADAT-DDLAEAV--------EAGNKEDIEKFSKRT----------VKVTK 84
Q LAK YS R D ++V GN++ EK+++RT + K
Sbjct: 52 QSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRD--EKYAQRTEEEKALDEQFFEYLK 109
Query: 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS--GQVYAVASE-DMDSL-TFGAPRFL 140
+ CK + VEA A A L V+ ++++ D D+L T RF
Sbjct: 110 DAFELCKTTFPTFTIRGVEADDMA-AYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRF- 167
Query: 141 RHLMDPSSRKIPVMEFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTAL 196
++R+ E+ + + E N+ ++QFI L + G D D+IRG IG +
Sbjct: 168 ----SFTTRR----EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGY 218
Query: 197 KLIRQHGSIETILENI 212
+IR+ G++ I++ +
Sbjct: 219 NIIREFGNVLDIIDQL 234
>pdb|3FRY|A Chain A, Crystal Structure Of The Copa C-Terminal Metal Binding
Domain
pdb|3FRY|B Chain B, Crystal Structure Of The Copa C-Terminal Metal Binding
Domain
Length = 73
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 59 DLAEAVEAGNKEDIEKFSK 77
DL EAV AGNKED++K+ K
Sbjct: 38 DLNEAVVAGNKEDVDKYIK 56
>pdb|3U44|B Chain B, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|B Chain B, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1166
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 218 QIPEDWPYQEARRLFKEPEVVTDEEQL 244
++ E +P+ + R L EPE V+DEEQL
Sbjct: 687 RLEELFPHHKERLLTNEPEQVSDEEQL 713
>pdb|3Q7B|A Chain A, Exonuclease Domain Of Lassa Virus Nucleoprotein
pdb|3Q7C|A Chain A, Exonuclease Domain Of Lassa Virus Nucleoprotein Bound To
Manganese
Length = 243
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 34 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 93
F +P DLK+ + +YS D TD A + G + R + +T Q +DD ++L
Sbjct: 87 FFREPTDLKQFKQDAKYSHGIDVTDLF--ATQPGLTSAVIDALPRNMVITCQGSDDIRKL 144
Query: 94 LKLMG 98
L+ G
Sbjct: 145 LESQG 149
>pdb|4FVU|A Chain A, Structural Basis For The Dsrna Specificity Of The Lassa
Virus Np Exonuclease
Length = 243
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 34 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 93
F +P DLK+ + +YS D TD A + G + R + +T Q +DD ++L
Sbjct: 87 FFREPTDLKQFKQDAKYSHGIDVTDLF--ATQPGLTSAVIDALPRNMVITCQGSDDIRKL 144
Query: 94 LKLMG 98
L+ G
Sbjct: 145 LESQG 149
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
0.317 0.133 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,690,782
Number of Sequences: 62578
Number of extensions: 372435
Number of successful extensions: 1178
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: 1140
Number of HSP's gapped (non-prelim): 24
length of query: 364
length of database: 14,973,337
effective HSP length: 100
effective length of query: 264
effective length of database: 8,715,537
effective search space: 2300901768
effective search space used: 2300901768
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: 52 (24.6 bits)