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= psy1206
(531 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 = 213 bits (542), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 94/142 (66%), Positives = 120/142 (84%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
+ L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
L+KEA +LF PEV DPE++E
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295
Score = 133 bits (335), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 64/99 (64%), Positives = 80/99 (80%), Gaps = 7/99 (7%)
Query: 304 ELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGT 356
+L+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE TSHLMG
Sbjct: 7 KLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGM 66
Query: 357 FYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
FYRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 67 FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105
Score = 115 bits (289), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 48/74 (64%), Positives = 63/74 (85%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE WL+KEA +L
Sbjct: 222 FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 281
Query: 292 FRHPEIADPETIEL 305
F PE+ DPE++EL
Sbjct: 282 FLEPEVLDPESVEL 295
Score = 75.1 bits (183), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 33/63 (52%), Positives = 47/63 (74%), Gaps = 3/63 (4%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIR---REEKR 59
LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +TQGRLD FF + KR
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKR 354
Query: 60 KAP 62
K P
Sbjct: 355 KEP 357
Score = 74.3 bits (181), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 30/55 (54%), Positives = 45/55 (81%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTI 459
E +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +TQGRLD FF +
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKV 345
>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 = 212 bits (540), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 94/142 (66%), Positives = 120/142 (84%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
+ L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
L+KEA +LF PEV DPE++E
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295
Score = 133 bits (334), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 64/98 (65%), Positives = 79/98 (80%), Gaps = 7/98 (7%)
Query: 305 LVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTF 357
L+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE TSHLMG F
Sbjct: 8 LIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMF 67
Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
YRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 68 YRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105
Score = 115 bits (288), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 48/74 (64%), Positives = 63/74 (85%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE WL+KEA +L
Sbjct: 222 FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 281
Query: 292 FRHPEIADPETIEL 305
F PE+ DPE++EL
Sbjct: 282 FLEPEVLDPESVEL 295
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 37/45 (82%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
E +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +T
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 35/41 (85%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTT 43
LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +T
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
>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 = 209 bits (533), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 93/142 (65%), Positives = 119/142 (83%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP EAEA CAA+VKAGKVYA ATEDM LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
+ L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
L+KEA +LF PEV DPE++E
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295
Score = 133 bits (334), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 64/98 (65%), Positives = 79/98 (80%), Gaps = 7/98 (7%)
Query: 305 LVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTF 357
L+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE TSHLMG F
Sbjct: 8 LIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMF 67
Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
YRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 68 YRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105
Score = 115 bits (288), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 48/74 (64%), Positives = 63/74 (85%)
Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+ +D KY VPE WL+KEA +L
Sbjct: 222 FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 281
Query: 292 FRHPEIADPETIEL 305
F PE+ DPE++EL
Sbjct: 282 FLEPEVLDPESVEL 295
Score = 58.5 bits (140), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 37/45 (82%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
E +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +T
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 35/41 (85%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTT 43
LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R +T
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 101 bits (252), Expect = 9e-22, Method: Compositional matrix adjust.
Identities = 61/166 (36%), Positives = 99/166 (59%), Gaps = 14/166 (8%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHL---- 115
+AP E EA+ A + K G +A A++D DA+ FG+ L+R++T + RKLP ++ ++
Sbjct: 145 QAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKP 204
Query: 116 -----EKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENI 169
E +L+ + ++ E+ ID+ IL+G DY D IRGIGP+RA+++IK++ IEK +E
Sbjct: 205 ELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYG 264
Query: 170 DTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCD 215
+ K + + E R LF +P+V PE E +DL G D +
Sbjct: 265 EISKKDI--NFNIDEIRGLFLNPQVVKPE--EALDLNEPNGEDIIN 306
Score = 97.4 bits (241), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
+++ ID +LYQFL A+R +G LM G TSHL G FYRTI ++E G+ PIYVFD
Sbjct: 18 GKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFD 77
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
GKPP KS EL +R + +E+A++ L +A+ +GK+
Sbjct: 78 GKPPEQKSEELERRRKAKEEAERKLERAKSEGKI 111
Score = 55.5 bits (132), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 3/72 (4%)
Query: 231 SFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 289
ID+ IL+G DY D IRGIGP+RA+++IK++ IEK +E + K + + E R
Sbjct: 222 QLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKKDI--NFNIDEIR 279
Query: 290 ELFRHPEIADPE 301
LF +P++ PE
Sbjct: 280 GLFLNPQVVKPE 291
Score = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 2 TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLK----ARSSTTQGRLDSFF 51
L ++P+ + ++ L + NF+E+R++NG ++L K A+ ++ Q LD +F
Sbjct: 293 ALDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 346
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 32/53 (60%), Gaps = 4/53 (7%)
Query: 409 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLK----ARSTTTQGRLDSFF 457
L ++P+ + ++ L + NF+E+R++NG ++L K A+ + Q LD +F
Sbjct: 294 LDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 346
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 97.8 bits (242), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 60/153 (39%), Positives = 86/153 (56%), Gaps = 14/153 (9%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE------- 112
+AP E EAQ A +VK G YA+A++D D+L FGS L+R++T S RKLP +
Sbjct: 162 QAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKP 221
Query: 113 --FHLEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENI 169
L+K+L + ++ E ID+ ILLG DY D GIGPK+A++L+K + IEKI + I
Sbjct: 222 ELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPI 281
Query: 170 DTKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
V ++ F P+V D IE+
Sbjct: 282 LKSPIEVD----VIAIKKYFLQPQVTDNYRIEW 310
Score = 97.1 bits (240), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 56/132 (42%), Positives = 77/132 (58%), Gaps = 9/132 (6%)
Query: 314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIY 372
I + I ID +LYQFL A+R +G LM +G TSHL G FYRTI +VE G+KP+Y
Sbjct: 32 ILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVY 91
Query: 373 VFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAED 432
VFDGKPP LK+ E+ +R +E+A K +A + G L+ + +Y E+
Sbjct: 92 VFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELAR-------RYAMMSAKLTEE 144
Query: 433 RIRNGAKKLLKA 444
+R+ AK LL A
Sbjct: 145 MVRD-AKSLLDA 155
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 45/90 (50%), Gaps = 19/90 (21%)
Query: 186 RELFRHPEVAD--PETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDY 243
R+L R E + PE IE L + LG L + ID+ ILLG DY
Sbjct: 208 RKLPRKNEYVEVKPELIELDKLLVQLGI----------------TLENLIDIGILLGTDY 251
Query: 244 C-DSIRGIGPKRAIELIKEHRSIEKILENI 272
D GIGPK+A++L+K + IEKI + I
Sbjct: 252 NPDGFEGIGPKKALQLVKAYGGIEKIPKPI 281
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 24/44 (54%)
Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQG 451
+++W PD D + + L + +F+ DR+ ++ +KA +G
Sbjct: 307 RIEWHTPDPDAVKRILVDEHDFSIDRVSTALERYVKAFKENIRG 350
Score = 29.6 bits (65), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 23/43 (53%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQG 45
++W PD D + + L + +F+ DR+ ++ +KA +G
Sbjct: 308 IEWHTPDPDAVKRILVDEHDFSIDRVSTALERYVKAFKENIRG 350
>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 = 95.5 bits (236), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 50/94 (53%), Positives = 60/94 (63%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
+KI IDA ++YQFL +R E G LM G TSHL G FYRTI L+E G+KP YVFD
Sbjct: 21 GKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAYVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
GKPP K EL KR E RE+A+ +A +G L
Sbjct: 81 GKPPEFKRKELEKRREAREEAELKWKEALAKGNL 114
Score = 91.7 bits (226), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 50/148 (33%), Positives = 86/148 (58%), Gaps = 20/148 (13%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLE--- 116
+AP E EAQ A M G VYA+A++D D+L FG+ L+R++T + RK+P ++ ++E
Sbjct: 148 QAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAPRLIRNLTITGKRKMPGKDVYVEIKP 207
Query: 117 ------KVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHR-SIEKILEN 168
+VL+ ++++ E+ I+L IL+G DY ++GIGPK+A+E+++ R + K
Sbjct: 208 ELVVLDEVLKELKITREKLIELAILVGTDYNPGGVKGIGPKKALEIVRYSRDPLAKFQRQ 267
Query: 169 IDTKKYTVPEGWLYKEARELFRHPEVAD 196
D Y + +E F +P V +
Sbjct: 268 SDVDLYAI---------KEFFLNPPVTN 286
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 40/54 (74%)
Query: 2 TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRR 55
+L W +PDE+G++K+LC + NF+E+R++NG ++L KA + Q L+S+F ++
Sbjct: 289 SLSWKEPDEEGILKFLCDEHNFSEERVKNGIERLKKAIKAGRQSTLESWFVKKK 342
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 38/53 (71%)
Query: 409 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRR 461
L W +PDE+G++K+LC + NF+E+R++NG ++L KA Q L+S+F ++
Sbjct: 290 LSWKEPDEEGILKFLCDEHNFSEERVKNGIERLKKAIKAGRQSTLESWFVKKK 342
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHR-SIEKILENIDTKKYTVPEGWL 284
I+L IL+G DY ++GIGPK+A+E+++ R + K D Y + E +L
Sbjct: 226 LIELAILVGTDYNPGGVKGIGPKKALEIVRYSRDPLAKFQRQSDVDLYAIKEFFL 280
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 23/30 (76%), Gaps = 1/30 (3%)
Query: 201 EFIDLCILLGCDYC-DSIRGIGPKRAIELL 229
+ I+L IL+G DY ++GIGPK+A+E++
Sbjct: 225 KLIELAILVGTDYNPGGVKGIGPKKALEIV 254
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 91.3 bits (225), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 53/148 (35%), Positives = 85/148 (57%), Gaps = 20/148 (13%)
Query: 60 KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH----- 114
+AP E EAQ A M G VYA+A++D D+L FG+ L+R++T + RKLP + +
Sbjct: 148 QAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKP 207
Query: 115 ----LEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRS-IEKILEN 168
LE+VL+ ++L+ E+ I+L IL+G DY I+GIG K+A+E+++ + + K +
Sbjct: 208 ELIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQ 267
Query: 169 IDTKKYTVPEGWLYKEARELFRHPEVAD 196
D Y + +E F +P V D
Sbjct: 268 SDVDLYAI---------KEFFLNPPVTD 286
Score = 82.4 bits (202), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 48/94 (51%), Positives = 64/94 (68%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
+KI IDA ++YQFL +R +G LM G TSHL G FYRTI L+E G+KP+YVFD
Sbjct: 21 GKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
G+PP K EL KR E RE+A++ +A E+G++
Sbjct: 81 GEPPEFKKKELEKRREAREEAEEKWREALEKGEI 114
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 37/50 (74%)
Query: 2 TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
L W DPDE+G++K+LC + +F+E+R++NG ++L KA S Q L+S+F
Sbjct: 289 NLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWF 338
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 33/103 (32%), Positives = 53/103 (51%), Gaps = 20/103 (19%)
Query: 375 DGKPPTLKSGELNKRMEKREDAQKALAKAQEQG--------------------KLKWSDP 414
D P +K L K +E ++ LAK Q+Q L W DP
Sbjct: 236 DYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVDLYAIKEFFLNPPVTDNYNLVWRDP 295
Query: 415 DEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
DE+G++K+LC + +F+E+R++NG ++L KA + Q L+S+F
Sbjct: 296 DEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWF 338
Score = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 11/70 (15%)
Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRS-IEKILENIDTKKYTVPEGWLYKEAR 289
I+L IL+G DY I+GIG K+A+E+++ + + K + D Y + +
Sbjct: 226 LIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVDLYAI---------K 276
Query: 290 ELFRHPEIAD 299
E F +P + D
Sbjct: 277 EFFLNPPVTD 286
>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 = 88.2 bits (217), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 54/155 (34%), Positives = 81/155 (52%), Gaps = 23/155 (14%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH------ 114
AP E EAQ A M G V T ++D D+L FGS L R++ + RKLP + +
Sbjct: 148 APSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPE 207
Query: 115 ---LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH----RSIEKILE 167
LE L+ + L+ E+ ID+ IL+G DY + ++G+G K+A+ IK + R+++ +
Sbjct: 208 IIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKV 267
Query: 168 NIDTKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
NID +E R F +P V D IEF
Sbjct: 268 NIDH----------VEEIRNFFLNPPVTDDYRIEF 292
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/92 (39%), Positives = 56/92 (60%), Gaps = 1/92 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
+KI +DA +LYQF+ +R +G L G TSHL G YR +VE G++P++VFD
Sbjct: 21 GKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
G+PP K E+ +R ++R +A++ A + G
Sbjct: 81 GEPPEFKKAEIEERKKRRAEAEEMWIAALQAG 112
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 14/79 (17%)
Query: 231 SFIDLCILLGCDYCDSIRGIGPKRAIELIKEH----RSIEKILENIDTKKYTVPEGWLYK 286
ID+ IL+G DY + ++G+G K+A+ IK + R+++ + NID +
Sbjct: 224 QLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDH----------VE 273
Query: 287 EARELFRHPEIADPETIEL 305
E R F +P + D IE
Sbjct: 274 EIRNFFLNPPVTDDYRIEF 292
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDL-----CILLGCDYCDSIRGI 250
+ ID+ IL+G DY + ++G+G K+A+ + ++ D+ + + D+ + IR
Sbjct: 224 QLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNF 278
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
++++ +PD + +++LC + +F+ +R+ +KL +S TQ L+ +F
Sbjct: 289 RIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKS--TQATLERWF 336
Score = 28.9 bits (63), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 3 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
+++ +PD + +++LC + +F+ +R+ +KL +S TQ L+ +F
Sbjct: 290 IEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKS--TQATLERWF 336
>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 = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 44/137 (32%), Positives = 80/137 (58%), Gaps = 14/137 (10%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
AP E EAQ + M K G V+A ++D DAL +G+ ++R++T + +++P + L +VLE
Sbjct: 149 APSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTT--KEMP-ELIELNEVLE 205
Query: 121 GMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
+ +S ++ ID+ I +G DY ++GIG KRA EL++ + + + + ++
Sbjct: 206 DLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVE--------- 256
Query: 180 WLYKEARELFRHPEVAD 196
Y E + +F+ P+V D
Sbjct: 257 -YYDEIKRIFKEPKVTD 272
Score = 72.4 bits (176), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 37/89 (41%), Positives = 56/89 (62%), Gaps = 1/89 (1%)
Query: 316 ESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF 374
+ +K+ ID +LYQFL ++R +G+ L + GE TS G FY+TI L+E+ + PI+VF
Sbjct: 20 KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVF 79
Query: 375 DGKPPTLKSGELNKRMEKREDAQKALAKA 403
DG+PP LK R E +E A+ + +A
Sbjct: 80 DGEPPKLKEKTRKVRREMKEKAELKMKEA 108
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 11/75 (14%)
Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
ID+ I +G DY ++GIG KRA EL++ + + + + ++ Y E +
Sbjct: 214 LIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVE----------YYDEIKR 263
Query: 291 LFRHPEIADPETIEL 305
+F+ P++ D ++ L
Sbjct: 264 IFKEPKVTDNYSLSL 278
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 183 KEARELFRHPEVADPETI---EFIDLCILLGCDYC-DSIRGIGPKRAIELLYSFIDLCIL 238
KE EL EV + I + ID+ I +G DY ++GIG KRA EL+ S + +L
Sbjct: 192 KEMPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVL 251
Query: 239 LG-CDYCDSIRGI 250
+Y D I+ I
Sbjct: 252 KKEVEYYDEIKRI 264
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 52/238 (21%), Positives = 90/238 (37%), Gaps = 48/238 (20%)
Query: 231 SFIDLCILLGCDYCDSIRGI--------GPKRAIELIKEHRSIEKILENIDTKKYTVPEG 282
S++ ++ C Y S+ GI G +A + K+ + ++ D Y P
Sbjct: 125 SYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAP-- 182
Query: 283 WLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQL 342
+ R L E+ PE IEL + + E +I +D + + F
Sbjct: 183 ---RVVRNLTTTKEM--PELIEL------NEVLEDLRISLDDLIDIAIF----------- 220
Query: 343 MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKAL-- 400
M D P F R LV G+ L K +E ++ ++
Sbjct: 221 MGTDYNPGGVKGIGFKRAYELVRSGVA-------------KDVLKKEVEYYDEIKRIFKE 267
Query: 401 AKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLK-ARSTTTQGRLDSFF 457
K + L PD++G++K+L + +F DR++ KL + T Q LD++F
Sbjct: 268 PKVTDNYSLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKTKQKTLDAWF 325
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 8 PDEDGLVKYLCGDKNFAEDRIRNGAKKLLK-ARSSTTQGRLDSFF 51
PD++G++K+L + +F DR++ KL + T Q LD++F
Sbjct: 281 PDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKTKQKTLDAWF 325
>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 = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 50/145 (34%), Positives = 76/145 (52%), Gaps = 9/145 (6%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFG-SNILLRHMTFSEARKLPVQEFHLEKVL 119
AP EA+AQ A + KAG V A TED D L FG ++L+ F ++ + + L
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQL 206
Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIK--EHRSIEKILENID---TKKY 174
G + E+F +CIL GCDY S+RGIG +A ++++ + I K+++ I
Sbjct: 207 -GDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNI 265
Query: 175 TVPEGWL--YKEARELFRHPEVADP 197
TVPE ++ + A F + V DP
Sbjct: 266 TVPEDYINGFIRANNTFLYQLVFDP 290
Score = 35.0 bits (79), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 48/114 (42%), Gaps = 6/114 (5%)
Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIK 260
+F +CIL GCDY S+RGIG +A ++L + D I+ IG + +
Sbjct: 214 KFRYMCILSGCDYLSSLRGIGLAKACKVLR------LANNPDIVKVIKKIGHYLKMNITV 267
Query: 261 EHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSI 314
I + +T Y + + ++ L + + DPET+ SI
Sbjct: 268 PEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSI 321
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 347 GEPTSHLMGTFYRTIR-LVEHGLKPIYVFDG 376
GEPT +G + + L+ HG+KPI VFDG
Sbjct: 49 GEPTDRYVGFCMKFVNMLLSHGIKPILVFDG 79
>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 = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 49/145 (33%), Positives = 75/145 (51%), Gaps = 9/145 (6%)
Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFG-SNILLRHMTFSEARKLPVQEFHLEKVL 119
AP EA+AQ A + KAG V A TED L FG ++L+ F ++ + + L
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQL 206
Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIK--EHRSIEKILENID---TKKY 174
G + E+F +CIL GCDY S+RGIG +A ++++ + I K+++ I
Sbjct: 207 -GDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNI 265
Query: 175 TVPEGWL--YKEARELFRHPEVADP 197
TVPE ++ + A F + V DP
Sbjct: 266 TVPEDYINGFIRANNTFLYQLVFDP 290
Score = 35.0 bits (79), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 48/114 (42%), Gaps = 6/114 (5%)
Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIK 260
+F +CIL GCDY S+RGIG +A ++L + D I+ IG + +
Sbjct: 214 KFRYMCILSGCDYLSSLRGIGLAKACKVLR------LANNPDIVKVIKKIGHYLKMNITV 267
Query: 261 EHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSI 314
I + +T Y + + ++ L + + DPET+ SI
Sbjct: 268 PEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSI 321
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 347 GEPTSHLMGTFYRTIR-LVEHGLKPIYVFDG 376
GEPT +G + + L+ HG+KPI VFDG
Sbjct: 49 GEPTDRYVGFCMKFVNMLLSHGIKPILVFDG 79
>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 = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 61/127 (48%), Gaps = 22/127 (17%)
Query: 51 FTIRREEKRKAPCEAEAQCAAMVK-AGKVYATA---TEDMDALTFGSNILLRHMTFSEAR 106
FTIR EA+ A +VK G +Y + D D T ++ + R +F+ R
Sbjct: 122 FTIR-------GVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSR-FSFTTRR 173
Query: 107 KLPVQEFHLEKVLEGMELSH-EEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSI 162
E+HL + E + E+FI L ++G D D+IRG IG KR +I+E ++
Sbjct: 174 -----EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGYNIIREFGNV 227
Query: 163 EKILENI 169
I++ +
Sbjct: 228 LDIIDQL 234
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a
pdb|1XO1|B Chain B, T5 5'-Exonuclease Mutant K83a
Length = 291
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 61/127 (48%), Gaps = 22/127 (17%)
Query: 51 FTIRREEKRKAPCEAEAQCAAMVK-AGKVYATA---TEDMDALTFGSNILLRHMTFSEAR 106
FTIR EA+ A +VK G +Y + D D T ++ + R +F+ R
Sbjct: 122 FTIR-------GVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSR-FSFTTRR 173
Query: 107 KLPVQEFHLEKVLEGMELSH-EEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSI 162
E+HL + E + E+FI L ++G D D+IRG IG KR +I+E ++
Sbjct: 174 -----EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGYNIIREFGNV 227
Query: 163 EKILENI 169
I++ +
Sbjct: 228 LDIIDQL 234
>pdb|1EXN|A Chain A, T5 5'-Exonuclease
pdb|1EXN|B Chain B, T5 5'-Exonuclease
Length = 290
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 22/127 (17%)
Query: 51 FTIRREEKRKAPCEAEAQCAAMVK-AGKVYATA---TEDMDALTFGSNILLRHMTFSEAR 106
FTIR EA+ A +VK G +Y + D D T ++ + R +F+ R
Sbjct: 121 FTIR-------GVEADDXAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSR-FSFTTRR 172
Query: 107 KLPVQEFHLEKVLEGMELSH-EEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSI 162
E+HL E + E+FI L + G D D+IRG IG KR +I+E ++
Sbjct: 173 -----EYHLRDXYEHHNVDDVEQFISLKAIXG-DLGDNIRGVEGIGAKRGYNIIREFGNV 226
Query: 163 EKILENI 169
I++ +
Sbjct: 227 LDIIDQL 233
>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 = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 124 LSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPE 178
L +++ D L G D ++GIG K A +L++E S+E +L+N+D K + E
Sbjct: 174 LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 241 CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPE 281
D ++GIG K A +L++E S+E +L+N+D K + E
Sbjct: 190 SDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 124 LSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPE 178
L +++ D L G D ++GIG K A +L++E S+E +L+N+D K + E
Sbjct: 174 LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 241 CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPE 281
D ++GIG K A +L++E S+E +L+N+D K + E
Sbjct: 190 SDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIRE 230
>pdb|4F7A|A Chain A, Crystal Structure Of A Susd Homolog (Bvu_2203) From
Bacteroides Vulgatus Atcc 8482 At 1.85 A Resolution
Length = 511
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 19 GDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRR-----EEKRKAPCEAEAQCAAMV 73
G + +AE R R G KL K +++ + G +D+ IRR ++ +K P + + C A+
Sbjct: 435 GXEAWAEQR-RTGYPKLFKVQTNNSNGTIDTDIXIRRLPFSQDDAKKDPEQYKNLCTALG 493
Query: 74 KA 75
A
Sbjct: 494 GA 495
>pdb|1K8K|A Chain A, Crystal Structure Of Arp23 COMPLEX
pdb|1TYQ|A Chain A, Crystal Structure Of Arp23 COMPLEX WITH BOUND ATP AND
Calcium
pdb|1U2V|A Chain A, Crystal Structure Of Arp23 COMPLEX WITH BOUND ADP AND
Calcium
pdb|2P9I|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp And Crosslinked With Gluteraldehyde
pdb|2P9K|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Atp And Crosslinked With Glutaraldehyde
pdb|2P9L|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX
pdb|2P9N|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9P|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9S|A Chain A, Structure Of Bovine Arp23 COMPLEX CO-Crystallized With
AtpMG2+
pdb|2P9U|A Chain A, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Amp-Pnp And Calcium
pdb|3DXK|A Chain A, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0944636
pdb|3DXM|A Chain A, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0993548
pdb|3RSE|A Chain A, Structural And Biochemical Characterization Of Two Binding
Sites For Nucleation Promoting Factor Wasp-Vca On Arp23
COMPLEX
pdb|3UKR|A Chain A, Crystal Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-666
pdb|3UKU|A Chain A, Structure Of Arp2/3 Complex With Bound Inhibitor Ck-869
pdb|3ULE|A Chain A, Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-869 And Atp
Length = 418
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 269 LENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSL 328
+ I K++++ G+ E+F HPE A+P+ + +++V I+ ID L
Sbjct: 259 INAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCP---IDVRRPL 315
Query: 329 YQFLI 333
Y+ ++
Sbjct: 316 YKNIV 320
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 0.138 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,924,667
Number of Sequences: 62578
Number of extensions: 573873
Number of successful extensions: 1963
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1862
Number of HSP's gapped (non-prelim): 79
length of query: 531
length of database: 14,973,337
effective HSP length: 103
effective length of query: 428
effective length of database: 8,527,803
effective search space: 3649899684
effective search space used: 3649899684
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: 54 (25.4 bits)