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= 016711
(384 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 = 410 bits (1054), Expect = e-115, Method: Compositional matrix adjust.
Identities = 203/369 (55%), Positives = 272/369 (73%), Gaps = 5/369 (1%)
Query: 2 GIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEV 61
GI+GL KL+AD AP +++E +SYFGRK+AIDASMSIYQFLI V R G ++L NE GE
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAV-RQGGDVLQNEEGET 59
Query: 62 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNK 121
TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L +A AG +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 122 EDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDM 181
+++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+VYA A+EDM
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 182 DSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRG 241
D LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G DYC+SIRG
Sbjct: 180 DCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG 239
Query: 242 IGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWS 301
IG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D E +++KWS
Sbjct: 240 IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-DPESVELKWS 298
Query: 302 APDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLESFFKPVANTSAPIKRKEP 361
P+EE LI F+ E F+ +R+ S+QGRL+ FFK V + + KRKEP
Sbjct: 299 EPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFK-VTGSLSSAKRKEP 357
Query: 362 ENTPKATTN 370
E PK +T
Sbjct: 358 E--PKGSTK 364
>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 = 386 bits (992), Expect = e-108, Method: Compositional matrix adjust.
Identities = 185/322 (57%), Positives = 249/322 (77%), Gaps = 2/322 (0%)
Query: 2 GIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEV 61
GI+GL KL+AD AP +++E +SYFGRK+AIDASMSIYQFLI V R G ++L NE GE
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAV-RQGGDVLQNEEGET 59
Query: 62 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNK 121
TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L +A AG +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 122 EDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDM 181
+++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+VYA A+EDM
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 182 DSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRG 241
D LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G DYC+SIRG
Sbjct: 180 DCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG 239
Query: 242 IGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWS 301
IG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D E +++KWS
Sbjct: 240 IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-DPESVELKWS 298
Query: 302 APDEEGLINFLVSENGFNSDRV 323
P+EE LI F+ E F+ +R+
Sbjct: 299 EPNEEELIKFMCGEKQFSEERI 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 = 384 bits (985), Expect = e-107, Method: Compositional matrix adjust.
Identities = 184/322 (57%), Positives = 248/322 (77%), Gaps = 2/322 (0%)
Query: 2 GIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEV 61
GI+GL KL+AD AP +++E +SYFGRK+AIDASMSIYQFLI V R G ++L NE GE
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAV-RQGGDVLQNEEGET 59
Query: 62 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNK 121
TSHL GMF RTIR++E G+KP+YVFDG+PP LK ELAKR +RA+A L +A AG +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 122 EDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDM 181
+++EKF+KR VKVTKQHND+CK LL LMG+P ++APSEAEA CAAL K+G+VYA A+EDM
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 182 DSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRG 241
LTFG+P +RHL ++K+P+ EF +++IL+EL L +QF+DLCIL G DYC+SIRG
Sbjct: 180 ACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG 239
Query: 242 IGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWS 301
IG + A+ LI++H SIE I+ ++ +Y +PE+W ++EA +LF EPEV+ D E +++KWS
Sbjct: 240 IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVL-DPESVELKWS 298
Query: 302 APDEEGLINFLVSENGFNSDRV 323
P+EE LI F+ E F+ +R+
Sbjct: 299 EPNEEELIKFMCGEKQFSEERI 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 = 239 bits (609), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 133/347 (38%), Positives = 194/347 (55%), Gaps = 23/347 (6%)
Query: 10 LADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMF 69
+ D P+ KE E+ +G+KIAIDA +IYQFL + + L + G +TSHL G+F
Sbjct: 5 IGDLVPR--KEIDLENLYGKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLF 62
Query: 70 TRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSK 129
RTI L+EAG+KP YVFDG+PP+ K++EL KR R +A EA+ GN E+ K+++
Sbjct: 63 YRTINLMEAGIKPAYVFDGKPPEFKRKELEKRREAREEAELKWKEALAKGNLEEARKYAQ 122
Query: 130 RTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAP 189
R KV + +D K+LL+LMG+P+++APSE EAQ A + G VYA AS+D DSL FGAP
Sbjct: 123 RATKVNEMLIEDAKKLLQLMGIPIIQAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAP 182
Query: 190 RFLRHLMDPSSRKIPVMEFEVA---------KILEELNLTMDQFIDLCILSGCDYC-DSI 239
R +R+L RK+P + V ++L+EL +T ++ I+L IL G DY +
Sbjct: 183 RLIRNLTITGKRKMPGKDVYVEIKPELVVLDEVLKELKITREKLIELAILVGTDYNPGGV 242
Query: 240 RGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIK 299
+GIG + AL+++R ++Q D + F P V + +
Sbjct: 243 KGIGPKKALEIVRYSRD--------PLAKFQRQSDVDLYAIKEFFLNPPVTN---EYSLS 291
Query: 300 WSAPDEEGLINFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLESFF 346
W PDEEG++ FL E+ F+ +RV Q LES+F
Sbjct: 292 WKEPDEEGILKFLCDEHNFSEERVKNGIERLKKAIKAGRQSTLESWF 338
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 234 bits (596), Expect = 9e-62, Method: Compositional matrix adjust.
Identities = 138/339 (40%), Positives = 194/339 (57%), Gaps = 21/339 (6%)
Query: 19 KEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEA 78
KE + E+ +G+KIAIDA +IYQFL + + L + G +TSHL G+F RTI L+EA
Sbjct: 12 KEIELENLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEA 71
Query: 79 GMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQH 138
G+KP+YVFDG+PP+ KK+EL KR R +A + EA+E G E+ K+++R +V +
Sbjct: 72 GIKPVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEARKYAQRATRVNEML 131
Query: 139 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDP 198
+D K+LL+LMG+P+V+APSE EAQ A + G VYA AS+D DSL FGAPR +R+L
Sbjct: 132 IEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTIT 191
Query: 199 SSRKIPVMEFEV---------AKILEELNLTMDQFIDLCILSGCDYC-DSIRGIGGQTAL 248
RK+P V ++L+EL LT ++ I+L IL G DY I+GIG + AL
Sbjct: 192 GKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKKAL 251
Query: 249 KLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGL 308
+++R ++Q D + F P VTD L W PDEEG+
Sbjct: 252 EIVRHSKD--------PLAKFQKQSDVDLYAIKEFFLNPP-VTDNYNLV--WRDPDEEGI 300
Query: 309 INFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLESFFK 347
+ FL E+ F+ +RV Q LES+FK
Sbjct: 301 LKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWFK 339
>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 = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 123/315 (39%), Positives = 189/315 (60%), Gaps = 19/315 (6%)
Query: 10 LADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMF 69
D PK++ FE G+K+AID ++YQFL + L N GE+TS G+F
Sbjct: 5 FGDFIPKNI--ISFEDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVF 62
Query: 70 TRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSK 129
+TI LLE + PI+VFDG+PP LK++ R + A + EA++ + E+ K++K
Sbjct: 63 YKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAK 122
Query: 130 RTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAP 189
R +T + ++CK LL LMG+P VEAPSE EAQ + + K G V+AV S+D D+L +GAP
Sbjct: 123 RVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAP 182
Query: 190 RFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYC-DSIRGIGGQTAL 248
R +R+L +++++P + E+ ++LE+L +++D ID+ I G DY ++GIG + A
Sbjct: 183 RVVRNLT--TTKEMPEL-IELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAY 239
Query: 249 KLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGL 308
+L+R + + + + + Y E +R+FKEP+ VTD L +K PD+EG+
Sbjct: 240 ELVRSGVAKDVLKKEVEY----------YDEIKRIFKEPK-VTDNYSLSLK--LPDKEGI 286
Query: 309 INFLVSENGFNSDRV 323
I FLV EN FN DRV
Sbjct: 287 IKFLVDENDFNYDRV 301
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 219 bits (557), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 123/317 (38%), Positives = 191/317 (60%), Gaps = 18/317 (5%)
Query: 19 KEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEA 78
+E F G++++ID ++YQFL + + L + G VTSHL G+F RTI +LE
Sbjct: 9 RELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEE 68
Query: 79 GMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQH 138
G+ PIYVFDG+PP+ K +EL +R + +A L A G E++ K+S+ ++++
Sbjct: 69 GVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELRKYSQAILRLSNIM 128
Query: 139 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDP 198
++ K+LL+ MG+P+V+APSE EA+ A L K G +A AS+D D++ FGA R +R+L
Sbjct: 129 VEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTIT 188
Query: 199 SSRKIP-----------VMEFEVAKILEELNLTMDQFIDLCILSGCDYC-DSIRGIGGQT 246
RK+P ++E E+ +L++L +T +Q ID+ IL G DY D IRGIG +
Sbjct: 189 GKRKLPNKDVYVEIKPELIETEI--LLKKLGITREQLIDIGILIGTDYNPDGIRGIGPER 246
Query: 247 ALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEE 306
ALK+I+++G IE +E + I ++ E R LF P+VV EE L + + P+ E
Sbjct: 247 ALKIIKKYGKIEKAMEYGEISKKDI--NFNIDEIRGLFLNPQVVKPEEALDL--NEPNGE 302
Query: 307 GLINFLVSENGFNSDRV 323
+IN LV E+ F+ +RV
Sbjct: 303 DIINILVYEHNFSEERV 319
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 214 bits (546), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 115/307 (37%), Positives = 182/307 (59%), Gaps = 17/307 (5%)
Query: 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFD 87
G+ I ID ++YQFL + + L + G +TSHL G+F RTI ++EAG+KP+YVFD
Sbjct: 35 GKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFD 94
Query: 88 GQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLK 147
G+PP+LK +E+ +R + + +A EAV++G+ E +++ + K+T++ D K LL
Sbjct: 95 GKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLD 154
Query: 148 LMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 207
MG+P V+AP+E EAQ A + K G YA AS+D DSL FG+P+ +R+L RK+P
Sbjct: 155 AMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKN 214
Query: 208 ---------FEVAKILEELNLTMDQFIDLCILSGCDYC-DSIRGIGGQTALKLIRQHGSI 257
E+ K+L +L +T++ ID+ IL G DY D GIG + AL+L++ +G I
Sbjct: 215 EYVEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGI 274
Query: 258 ETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENG 317
E I + I + P + ++ F +P+V + +I+W PD + + LV E+
Sbjct: 275 EKIPKPILKS----PIEVDVIAIKKYFLQPQVT---DNYRIEWHTPDPDAVKRILVDEHD 327
Query: 318 FNSDRVT 324
F+ DRV+
Sbjct: 328 FSIDRVS 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 = 199 bits (506), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 117/337 (34%), Positives = 182/337 (54%), Gaps = 21/337 (6%)
Query: 19 KEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEA 78
+E + E + G+KIA+DA ++YQF+ ++ + L + G +TSHL G+ R ++E
Sbjct: 12 EEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEV 71
Query: 79 GMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQH 138
G++P++VFDG+PP+ KK E+ +R +RA+A + A++AG+K D +K+++ +V +
Sbjct: 72 GIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDK-DAKKYAQAAGRVDEYI 130
Query: 139 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDP 198
D K LL MG+P V+APSE EAQ A + G V S+D DSL FG+PR R+L
Sbjct: 131 VDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAIT 190
Query: 199 SSRKIPVMEFEV---------AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALK 249
RK+P V L+ L LT +Q ID+ IL G DY + ++G+G + AL
Sbjct: 191 GKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALN 250
Query: 250 LIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLI 309
I+ +G I L+ + + +E R F P V D +I++ PD E I
Sbjct: 251 YIKTYGDIFRALKALKVNIDHV------EEIRNFFLNPPVTDD---YRIEFREPDFEKAI 301
Query: 310 NFLVSENGFNSDRVTXXXXXXXXXXXXSSQGRLESFF 346
FL E+ F+ +RV S+Q LE +F
Sbjct: 302 EFLCEEHDFSRERV--EKALEKLKALKSTQATLERWF 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 = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 82/284 (28%), Positives = 139/284 (48%), Gaps = 22/284 (7%)
Query: 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGE 60
MGI+GL + + + A + + +K++ G+ +A+D +++ I + GE
Sbjct: 1 MGIQGLLQFIKE-ASEPIHVRKYK---GQVVAVDTYCWLHKGAIACAEKLAK------GE 50
Query: 61 VTSHLQGMFTRTIR-LLEAGMKPIYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEA 118
T G + + LL G+KPI VFDG P K+ E ++R ++A+ E
Sbjct: 51 PTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREG 110
Query: 119 GNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVAS 178
E E F+ R++ +T + + GV + AP EA+AQ A L K+G V A+ +
Sbjct: 111 KVSEARECFT-RSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIIT 169
Query: 179 EDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELN--LTMDQFIDLCILSGCDYC 236
ED D L FG + + MD + + + + + +L T ++F +CILSGCDY
Sbjct: 170 EDSDLLAFGCKKVILK-MDQFGNGLEIDQARLG-MCRQLGDVFTEEKFRYMCILSGCDYL 227
Query: 237 DSIRGIGGQTALKLIR--QHGSIETILENIN---RERYQIPEDW 275
S+RGIG A K++R + I +++ I + +PED+
Sbjct: 228 SSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDY 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 = 82.4 bits (202), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 83/284 (29%), Positives = 139/284 (48%), Gaps = 22/284 (7%)
Query: 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGE 60
MGI+GL + + + A + + +K++ G+ +A+D +++ I E L GE
Sbjct: 1 MGIQGLLQFIKE-ASEPIHVRKYK---GQVVAVDTYCWLHKGAIAC----AEKLAK--GE 50
Query: 61 VTSHLQGMFTRTIR-LLEAGMKPIYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEA 118
T G + + LL G+KPI VFDG P K+ E ++R ++A+ E
Sbjct: 51 PTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREG 110
Query: 119 GNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVAS 178
E E F+ R++ +T + + GV + AP EA+AQ A L K+G V A+ +
Sbjct: 111 KVSEARECFT-RSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIIT 169
Query: 179 EDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELN--LTMDQFIDLCILSGCDYC 236
ED L FG + + MD + + + + + +L T ++F +CILSGCDY
Sbjct: 170 EDSALLAFGCKKVILK-MDQFGNGLEIDQARLG-MCRQLGDVFTEEKFRYMCILSGCDYL 227
Query: 237 DSIRGIGGQTALKLIR--QHGSIETILENIN---RERYQIPEDW 275
S+RGIG A K++R + I +++ I + +PED+
Sbjct: 228 SSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDY 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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 65/255 (25%), Positives = 106/255 (41%), Gaps = 45/255 (17%)
Query: 28 GRKIAIDASMSIYQ-FLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLL-EAGMKPIYV 85
GR + +D Y+ F + G LT GE + G ++ L E G I V
Sbjct: 12 GRVLLVDGHHLAYRTFHALKG------LTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVV 65
Query: 86 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 145
FD + P + + + RA +D F ++ + K L
Sbjct: 66 FDAKAPSFRHEAYGGYKAGRAPTPED---------------FPRQLALI--------KEL 102
Query: 146 LKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSS 200
+ L+G+ +E P EA+ A+L K G + + D D + R H++ P
Sbjct: 103 VDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRI--HVLHPEG 160
Query: 201 RKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIE 258
I A + E+ L DQ+ D L+G D ++GIG +TA KL+ + GS+E
Sbjct: 161 YLI-----TPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLE 215
Query: 259 TILENINRERYQIPE 273
+L+N++R + I E
Sbjct: 216 ALLKNLDRLKPAIRE 230
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 65/255 (25%), Positives = 106/255 (41%), Gaps = 45/255 (17%)
Query: 28 GRKIAIDASMSIYQ-FLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLL-EAGMKPIYV 85
GR + +D Y+ F + G LT GE + G ++ L E G I V
Sbjct: 12 GRVLLVDGHHLAYRTFHALKG------LTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVV 65
Query: 86 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 145
FD + P + + + RA +D F ++ + K L
Sbjct: 66 FDAKAPSFRHEAYGGYKAGRAPTPED---------------FPRQLALI--------KEL 102
Query: 146 LKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSS 200
+ L+G+ +E P EA+ A+L K G + + D D + R H++ P
Sbjct: 103 VDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRI--HVLHPEG 160
Query: 201 RKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIE 258
I A + E+ L DQ+ D L+G D ++GIG +TA KL+ + GS+E
Sbjct: 161 YLI-----TPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLE 215
Query: 259 TILENINRERYQIPE 273
+L+N++R + I E
Sbjct: 216 ALLKNLDRLKPAIRE 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 = 0.50, Method: Compositional matrix adjust.
Identities = 52/196 (26%), Positives = 87/196 (44%), Gaps = 40/196 (20%)
Query: 96 QELAKRYSKRADAT-DDLAEAV--------EAGNKEDIEKFSKRT----------VKVTK 136
Q LAK YS R D ++V AGN++ EK+++RT + K
Sbjct: 52 QSLAKSYSARTTIVLGDKGKSVFRLEHLPEYAGNRD--EKYAQRTEEEKALDEQFFEYLK 109
Query: 137 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS--GQVYAVASE-DMDSL-TFGAPRFL 192
+ CK + VEA A A L V+ ++++ D D+L T RF
Sbjct: 110 DAFELCKTTFPTFTIRGVEADDMA-AYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRF- 167
Query: 193 RHLMDPSSRKIPVMEFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTAL 248
++R+ E+ + + E N+ ++QFI L + G D D+IRG IG +
Sbjct: 168 ----SFTTRR----EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGY 218
Query: 249 KLIRQHGSIETILENI 264
+IR+ G++ I++ +
Sbjct: 219 NIIREFGNVLDIIDQL 234
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 121 KEDIEKFSKRTVKVTKQHNDDCKRLLKL 148
KEDI +F KR +K+T+++ D C + +
Sbjct: 162 KEDIAEFYKRQLKLTQEYTDHCVKWYNV 189
>pdb|1EXN|A Chain A, T5 5'-Exonuclease
pdb|1EXN|B Chain B, T5 5'-Exonuclease
Length = 290
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 51/196 (26%), Positives = 85/196 (43%), Gaps = 40/196 (20%)
Query: 96 QELAKRYSKRADAT-DDLAEAV--------EAGNKEDIEKFSKRT----------VKVTK 136
Q LAK YS R D ++V GN++ EK+++RT + K
Sbjct: 51 QSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRD--EKYAQRTEEEKALDEQFFEYLK 108
Query: 137 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS--GQVYAVASE-DMDSL-TFGAPRFL 192
+ CK + VEA A A L V+ ++++ D D+L T RF
Sbjct: 109 DAFELCKTTFPTFTIRGVEADDXA-AYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRF- 166
Query: 193 RHLMDPSSRKIPVMEFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTAL 248
++R+ E+ + E N+ ++QFI L + G D D+IRG IG +
Sbjct: 167 ----SFTTRR----EYHLRDXYEHHNVDDVEQFISLKAIXG-DLGDNIRGVEGIGAKRGY 217
Query: 249 KLIRQHGSIETILENI 264
+IR+ G++ I++ +
Sbjct: 218 NIIREFGNVLDIIDQL 233
>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 = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 207 EFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRG---IGGQTALKLIRQHGSIETILE 262
E+ + + E N+ ++QFI L + G D D+IRG IG + +IR+ G++ I++
Sbjct: 174 EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGYNIIREFGNVLDIID 232
Query: 263 NI 264
+
Sbjct: 233 QL 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: 111 DLAEAVEAGNKEDIEKFSK 129
DL EAV AGNKED++K+ K
Sbjct: 38 DLNEAVVAGNKEDVDKYIK 56
>pdb|3CNF|T Chain T, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus
By Cryo-Electron Microscopy
Length = 1057
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 16 KSMKEQKFESYFGRKIAIDAS-MSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIR 74
S ++Q FES FG I++ + S ++V +E + N E S L G+F T
Sbjct: 617 NSYEDQSFESMFGETISVVTTCASAATRVLVKINHPSEYMINSVIERLSQLGGVFYHTAL 676
Query: 75 LLEAGMKP 82
L A P
Sbjct: 677 LKTASQNP 684
>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 = 7.9, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 270 QIPEDWPYQEARRLFKEPEVVTDEEQL 296
++ E +P+ + R L EPE V+DEEQL
Sbjct: 687 RLEELFPHHKERLLTNEPEQVSDEEQL 713
>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 = 9.5, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 86 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 145
F +P DLK+ + +YS D TD A + G + R + +T Q +DD ++L
Sbjct: 87 FFREPTDLKQFKQDAKYSHGIDVTDLF--ATQPGLTSAVIDALPRNMVITCQGSDDIRKL 144
Query: 146 LKLMG 150
L+ G
Sbjct: 145 LESQG 149
>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 = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 86 FDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRL 145
F +P DLK+ + +YS D TD A + G + R + +T Q +DD ++L
Sbjct: 87 FFREPTDLKQFKQDAKYSHGIDVTDLF--ATQPGLTSAVIDALPRNMVITCQGSDDIRKL 144
Query: 146 LKLMG 150
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
0.316 0.133 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,195,518
Number of Sequences: 62578
Number of extensions: 399249
Number of successful extensions: 1221
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1180
Number of HSP's gapped (non-prelim): 24
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
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)