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= psy14291
(538 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 73/256 (28%), Positives = 113/256 (44%), Gaps = 61/256 (23%)
Query: 303 SLELGTDKKRRPYVSR-----KML--EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQ 355
+L G ++ R Y R +ML +A++LLQL G+P I AP E EAQ A +
Sbjct: 108 ALAKGNLEEARKYAQRATKVNEMLIEDAKKLLQLMGIPIIQAPSEGEAQAAYMASKGDVY 167
Query: 356 GVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYFEL----------------TR 399
+ D D LFGA + +N + + P Y E+ TR
Sbjct: 168 ASASQDYDSLLFGAPRLIRNL----TITGKRKMPGKDVYVEIKPELVVLDEVLKELKITR 223
Query: 400 EKLIQLALLVGSDYTPG-LQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKN 458
EKLI+LA+LVG+DY PG ++G+GP ALEI+ Y + + +F+
Sbjct: 224 EKLIELAILVGTDYNPGGVKGIGPKKALEIV-----------RYSRDPLAKFQR------ 266
Query: 459 KPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGW 518
D ++ E +L P + TN L+W PD +G+ +F ++ +
Sbjct: 267 ---------------QSDVDLYAIKEFFLNPPV-TNEYSLSWKEPDEEGILKFLCDEHNF 310
Query: 519 SQNRVDQTLIPIMKKI 534
S+ RV + + K I
Sbjct: 311 SEERVKNGIERLKKAI 326
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 77/256 (30%), Positives = 111/256 (43%), Gaps = 61/256 (23%)
Query: 303 SLELGTDKKRRPYVSR-----KML--EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQ 355
+LE G ++ R Y R +ML +A++LL+L G+P + AP E EAQ A +
Sbjct: 108 ALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVY 167
Query: 356 GVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYFE----------------LTR 399
+ D D LFGA + +N L P Y E LTR
Sbjct: 168 ASASQDYDSLLFGAPRLVRNLTITGKRKL----PGKNVYVEIKPELIILEEVLKELKLTR 223
Query: 400 EKLIQLALLVGSDYTP-GLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKN 458
EKLI+LA+LVG+DY P G++G+G ALEI +R K+ LAK
Sbjct: 224 EKLIELAILVGTDYNPGGIKGIGLKKALEI------------------VRHSKDPLAKFQ 265
Query: 459 KPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGW 518
K D ++ E +L P + N L W PD +G+ +F ++ +
Sbjct: 266 K--------------QSDVDLYAIKEFFLNPPVTDNYN-LVWRDPDEEGILKFLCDEHDF 310
Query: 519 SQNRVDQTLIPIMKKI 534
S+ RV L + K I
Sbjct: 311 SEERVKNGLERLKKAI 326
>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 = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 54/214 (25%), Positives = 95/214 (44%), Gaps = 44/214 (20%)
Query: 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF---D 378
E + LL L G+P++ AP EAEA CA+L T+D D FG+ + ++
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEA 198
Query: 379 KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSP 438
KK + + I L +E+ + L +L+GSDY ++G+GP A++++ K
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQK------- 251
Query: 439 NQNYIVESMRRF--------KNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPD 490
I E +RR +NWL K + H + +L+P+
Sbjct: 252 -HKSIEEIVRRLDPNKYPVPENWLHK----EAH--------------------QLFLEPE 286
Query: 491 I-NTNVQKLAWGTPDLDGLRRFAANKFGWSQNRV 523
+ + +L W P+ + L +F + +S+ R+
Sbjct: 287 VLDPESVELKWSEPNEEELIKFMCGEKQFSEERI 320
>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 = 75.9 bits (185), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 54/214 (25%), Positives = 95/214 (44%), Gaps = 44/214 (20%)
Query: 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF---D 378
E + LL L G+P++ AP EAEA CA+L T+D D FG+ + ++
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEA 198
Query: 379 KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSP 438
KK + + I L +E+ + L +L+GSDY ++G+GP A++++ K
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQK------- 251
Query: 439 NQNYIVESMRRF--------KNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPD 490
I E +RR +NWL K + H + +L+P+
Sbjct: 252 -HKSIEEIVRRLDPNKYPVPENWLHK----EAH--------------------QLFLEPE 286
Query: 491 I-NTNVQKLAWGTPDLDGLRRFAANKFGWSQNRV 523
+ + +L W P+ + L +F + +S+ R+
Sbjct: 287 VLDPESVELKWSEPNEEELIKFMCGEKQFSEERI 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 = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 53/214 (24%), Positives = 94/214 (43%), Gaps = 44/214 (20%)
Query: 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF---D 378
E + LL L G+P++ AP EAEA CA+L T+D FG+ + ++
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEA 198
Query: 379 KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSP 438
KK + + I L +E+ + L +L+GSDY ++G+GP A++++ K
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQK------- 251
Query: 439 NQNYIVESMRRF--------KNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPD 490
I E +RR +NWL K + H + +L+P+
Sbjct: 252 -HKSIEEIVRRLDPNKYPVPENWLHK----EAH--------------------QLFLEPE 286
Query: 491 I-NTNVQKLAWGTPDLDGLRRFAANKFGWSQNRV 523
+ + +L W P+ + L +F + +S+ R+
Sbjct: 287 VLDPESVELKWSEPNEEELIKFMCGEKQFSEERI 320
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 68.6 bits (166), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 41/129 (31%), Positives = 66/129 (51%), Gaps = 21/129 (16%)
Query: 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS 381
E+++LL+ G+P + AP E EA+ A L + + D D LFGA+ + +N
Sbjct: 131 ESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGK 190
Query: 382 HVLRYTAPDIRYYFE----------------LTREKLIQLALLVGSDYTP-GLQGVGPVT 424
L P+ Y E +TRE+LI + +L+G+DY P G++G+GP
Sbjct: 191 RKL----PNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPER 246
Query: 425 ALEILAKFS 433
AL+I+ K+
Sbjct: 247 ALKIIKKYG 255
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 63/254 (24%), Positives = 105/254 (41%), Gaps = 58/254 (22%)
Query: 296 EAEAQCASLELGTDKKRRPYVSRKMLE-----AQELLQLFGVPFIVAPGEAEAQCASLEL 350
E Q LEL +R +S K+ E A+ LL G+P++ AP E EAQ A +
Sbjct: 120 EEAVQSGDLELA---RRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVK 176
Query: 351 GNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYFE-------------- 396
+ D D LFG+ + +N + R P Y E
Sbjct: 177 KGDAYASASQDYDSLLFGSPKLVRNL----TISGRRKLPRKNEYVEVKPELIELDKLLVQ 232
Query: 397 --LTREKLIQLALLVGSDYTP-GLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNW 453
+T E LI + +L+G+DY P G +G+GP AL+++ +
Sbjct: 233 LGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYG-------------------G 273
Query: 454 LAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAA 513
+ K KP +K + +++ + +L+P + N ++ W TPD D ++R
Sbjct: 274 IEKIPKP---------ILKSPIEVDVIAIKKYFLQPQVTDNY-RIEWHTPDPDAVKRILV 323
Query: 514 NKFGWSQNRVDQTL 527
++ +S +RV L
Sbjct: 324 DEHDFSIDRVSTAL 337
>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 = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 59/219 (26%), Positives = 95/219 (43%), Gaps = 47/219 (21%)
Query: 323 AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKN------- 375
A+ LL G+PF+ AP E EAQ A + + + D D LFG+ + +N
Sbjct: 134 AKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKR 193
Query: 376 -------FFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEI 428
+ D K ++ + R LTRE+LI +A+LVG+DY G++GVG AL
Sbjct: 194 KLPGKNVYVDVKPEIIILESNLKR--LGLTREQLIDIAILVGTDYNEGVKGVGVKKAL-- 249
Query: 429 LAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLK 488
NYI K + R L+ +K+N D + +L
Sbjct: 250 ------------NYI---------------KTYGDIFRALKALKVNIDHVE-EIRNFFLN 281
Query: 489 PDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTL 527
P + T+ ++ + PD + F + +S+ RV++ L
Sbjct: 282 PPV-TDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKAL 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 = 65.5 bits (158), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 65/121 (53%), Gaps = 2/121 (1%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KR Y++ KM+E + LL L G+P++ AP E EAQ + + V++ D D L+GA
Sbjct: 122 KRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGA 181
Query: 370 RTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTP-GLQGVGPVTALEI 428
V +N K ++ ++ + LI +A+ +G+DY P G++G+G A E+
Sbjct: 182 PRVVRNLTTTKEMPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYEL 241
Query: 429 L 429
+
Sbjct: 242 V 242
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 39/128 (30%), Positives = 65/128 (50%), Gaps = 11/128 (8%)
Query: 331 GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPD 390
GV +VAP EA+AQ A L Q +IT+DSD+ FG + V D+ + L
Sbjct: 141 GVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILK-MDQFGNGLEIDQAR 199
Query: 391 IRYYFEL----TREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVES 446
+ +L T EK + +L G DY L+G+G A ++L +++P+ IV+
Sbjct: 200 LGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVL---RLANNPD---IVKV 253
Query: 447 MRRFKNWL 454
+++ ++L
Sbjct: 254 IKKIGHYL 261
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 64/128 (50%), Gaps = 11/128 (8%)
Query: 331 GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPD 390
GV +VAP EA+AQ A L Q +IT+DS + FG + V D+ + L
Sbjct: 141 GVDCLVAPYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILK-MDQFGNGLEIDQAR 199
Query: 391 IRYYFEL----TREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVES 446
+ +L T EK + +L G DY L+G+G A ++L +++P+ IV+
Sbjct: 200 LGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVL---RLANNPD---IVKV 253
Query: 447 MRRFKNWL 454
+++ ++L
Sbjct: 254 IKKIGHYL 261
>pdb|1ZQ1|C Chain C, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
pdb|1ZQ1|D Chain D, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
Length = 633
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 74 LPPPSVSREVDMFELPPAPAQTVQDEEEDTL-ENIYIMGVNG------LWKLLEASGKPV 126
LP V R V ++L + AQT+ D+E D L E + MGV L +L+ K V
Sbjct: 458 LPQAKVERYVKEYKLDRSLAQTLVDDERDELFEELVSMGVKPSLAASILVVVLKGLRKEV 517
Query: 127 PVETLENKVLAVGILYFTQGRAS 149
P+E + ++ + + +G+ +
Sbjct: 518 PIENVTDEHIREAFQLYLEGKIA 540
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 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,951,453
Number of Sequences: 62578
Number of extensions: 541196
Number of successful extensions: 1589
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1549
Number of HSP's gapped (non-prelim): 30
length of query: 538
length of database: 14,973,337
effective HSP length: 103
effective length of query: 435
effective length of database: 8,527,803
effective search space: 3709594305
effective search space used: 3709594305
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: 54 (25.4 bits)