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= 009898
(523 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 79.3 bits (194), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 46/130 (35%), Positives = 74/130 (56%), Gaps = 12/130 (9%)
Query: 59 SCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDI 118
+ M++E+K L ++G+P ++ E EA+ A LN L S D D LFGA+ + R++
Sbjct: 126 NIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNL 185
Query: 119 WL-GERG------YVVC----YEMDDIERKLGFGRNSLITLALLLGSDYS-QGVRGLGPE 166
+ G+R YV E + + +KLG R LI + +L+G+DY+ G+RG+GPE
Sbjct: 186 TITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPE 245
Query: 167 SACQIVKSVG 176
A +I+K G
Sbjct: 246 RALKIIKKYG 255
>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 = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 43/126 (34%), Positives = 71/126 (56%), Gaps = 12/126 (9%)
Query: 60 CMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIW 119
+I++AK L +G+P ++ E EAQ A + + S D D LFGA + R++
Sbjct: 130 MLIEDAKKLLQLMGIPIIQAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAPRLIRNLT 189
Query: 120 L-GER---GYVVCYE-------MDDIERKLGFGRNSLITLALLLGSDYSQ-GVRGLGPES 167
+ G+R G V E +D++ ++L R LI LA+L+G+DY+ GV+G+GP+
Sbjct: 190 ITGKRKMPGKDVYVEIKPELVVLDEVLKELKITREKLIELAILVGTDYNPGGVKGIGPKK 249
Query: 168 ACQIVK 173
A +IV+
Sbjct: 250 ALEIVR 255
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 41/128 (32%), Positives = 69/128 (53%), Gaps = 12/128 (9%)
Query: 61 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 120
M+++AK+L ++G+P ++ E EAQ A + + S D D LFG+ + R++ +
Sbjct: 145 MVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTI 204
Query: 121 GER-------GYVVC----YEMDDIERKLGFGRNSLITLALLLGSDYS-QGVRGLGPESA 168
R YV E+D + +LG +LI + +LLG+DY+ G G+GP+ A
Sbjct: 205 SGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKA 264
Query: 169 CQIVKSVG 176
Q+VK+ G
Sbjct: 265 LQLVKAYG 272
>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 = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 41/128 (32%), Positives = 71/128 (55%), Gaps = 11/128 (8%)
Query: 61 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 120
++ AK L +G+P ++ E EAQ A + + + S D D LFG+ + R++ +
Sbjct: 130 IVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAI 189
Query: 121 -------GERGYV-VCYEMDDIE---RKLGFGRNSLITLALLLGSDYSQGVRGLGPESAC 169
G+ YV V E+ +E ++LG R LI +A+L+G+DY++GV+G+G + A
Sbjct: 190 TGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKAL 249
Query: 170 QIVKSVGD 177
+K+ GD
Sbjct: 250 NYIKTYGD 257
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 41/130 (31%), Positives = 71/130 (54%), Gaps = 12/130 (9%)
Query: 60 CMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIW 119
+I++AK L +G+P ++ E EAQ A + + S D D LFGA + R++
Sbjct: 130 MLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLT 189
Query: 120 L-GER---GYVVCYE-------MDDIERKLGFGRNSLITLALLLGSDYSQ-GVRGLGPES 167
+ G+R G V E ++++ ++L R LI LA+L+G+DY+ G++G+G +
Sbjct: 190 ITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKK 249
Query: 168 ACQIVKSVGD 177
A +IV+ D
Sbjct: 250 ALEIVRHSKD 259
>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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 34/112 (30%), Positives = 56/112 (50%), Gaps = 2/112 (1%)
Query: 64 EAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER 123
E K L +G+P L+ EAEA CA L + D D FG+ + R + E
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEA 198
Query: 124 GYVVC--YEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVK 173
+ + + I ++LG + + L +LLGSDY + +RG+GP+ A +++
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQ 250
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 34/112 (30%), Positives = 56/112 (50%), Gaps = 2/112 (1%)
Query: 64 EAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER 123
E K L +G+P L+ EAEA CA L + D D FG+ + R + E
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEA 198
Query: 124 GYVVC--YEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVK 173
+ + + I ++LG + + L +LLGSDY + +RG+GP+ A +++
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQ 250
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 55/112 (49%), Gaps = 2/112 (1%)
Query: 64 EAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER 123
E K L +G+P L+ EAEA CA L + D FG+ + R + E
Sbjct: 139 ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEA 198
Query: 124 GYVVC--YEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVK 173
+ + + I ++LG + + L +LLGSDY + +RG+GP+ A +++
Sbjct: 199 KKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQ 250
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/115 (28%), Positives = 61/115 (53%), Gaps = 2/115 (1%)
Query: 61 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 120
M++ K L +G+P +E E EAQ + + + S D D L+GA V R++
Sbjct: 131 MVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNL-T 189
Query: 121 GERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQ-GVRGLGPESACQIVKS 174
+ E++++ L + LI +A+ +G+DY+ GV+G+G + A ++V+S
Sbjct: 190 TTKEMPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRS 244
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 2/120 (1%)
Query: 71 SLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 130
S GV CL EA+AQ A LN + + DSD+ FG + V + G +
Sbjct: 139 SQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQA 198
Query: 131 MDDIERKLG--FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEG 188
+ R+LG F + +L G DY +RG+G AC++++ + +++ I G
Sbjct: 199 RLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIG 258
>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 = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 54/120 (45%), Gaps = 2/120 (1%)
Query: 71 SLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 130
S GV CL EA+AQ A LN + + DS + FG + V + G +
Sbjct: 139 SQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQA 198
Query: 131 MDDIERKLG--FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEG 188
+ R+LG F + +L G DY +RG+G AC++++ + +++ I G
Sbjct: 199 RLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIG 258
>pdb|4BC5|A Chain A, Crystal Structure Of Human D-xylulokinase In Complex With
Inhibitor 5-deoxy-5-fluoro-d-xylulose
pdb|4BC5|B Chain B, Crystal Structure Of Human D-xylulokinase In Complex With
Inhibitor 5-deoxy-5-fluoro-d-xylulose
pdb|4BC5|C Chain C, Crystal Structure Of Human D-xylulokinase In Complex With
Inhibitor 5-deoxy-5-fluoro-d-xylulose
Length = 538
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 230 ETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPE 280
+ PFS+V+ NP+ + S +V L Q+A+L Q + PPE
Sbjct: 488 DVPFSEVVKLAPNPRLAATPSPGASQVYEALLPQYAKLEQRILSQTRGPPE 538
>pdb|4BC2|A Chain A, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose And Adenosine Diphosphate
pdb|4BC2|B Chain B, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose And Adenosine Diphosphate
pdb|4BC2|C Chain C, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose And Adenosine Diphosphate
pdb|4BC3|A Chain A, Crystal Structure Of Human D-xylulokinase
pdb|4BC3|B Chain B, Crystal Structure Of Human D-xylulokinase
pdb|4BC3|C Chain C, Crystal Structure Of Human D-xylulokinase
pdb|4BC4|A Chain A, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose
pdb|4BC4|B Chain B, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose
pdb|4BC4|C Chain C, Crystal Structure Of Human D-xylulokinase In Complex With
D- Xylulose
Length = 538
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 230 ETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPE 280
+ PFS+V+ NP+ + S +V L Q+A+L Q + PPE
Sbjct: 488 DVPFSEVVKLAPNPRLAATPSPGASQVYEALLPQYAKLEQRILSQTRGPPE 538
>pdb|2X9E|A Chain A, Human Mps1 In Complex With Nms-P715
Length = 317
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 164 GPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEIN 219
GP + C VK ++ L++I S G S V + N KK+ ++ K N EE+ NQ ++
Sbjct: 1 GPANECISVKGRIYSI-LKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLD 55
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 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,409,421
Number of Sequences: 62578
Number of extensions: 516409
Number of successful extensions: 1300
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1274
Number of HSP's gapped (non-prelim): 16
length of query: 523
length of database: 14,973,337
effective HSP length: 103
effective length of query: 420
effective length of database: 8,527,803
effective search space: 3581677260
effective search space used: 3581677260
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)