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= psy14294
(314 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 = 78.6 bits (192), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 49/171 (28%), Positives = 83/171 (48%), Gaps = 14/171 (8%)
Query: 139 NIVINKLLVDLISDVSIWLHQLTK--GTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVF 196
N+ K+ +D ++ + +L + + GT + +HL GL++R L+ IKP +
Sbjct: 18 NLYGKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAY 77
Query: 197 VFDGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQE 244
VFDG P+ K++ + + R++ L E K + A+ + E + +A++
Sbjct: 78 VFDGKPPEFKRKELEKRREAREEAELKWKEALAKGNLEEARKYAQRATKVNEMLIEDAKK 137
Query: 245 LLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNF 295
LLQL G+P I AP E EAQ A + + D D LFGA + +N
Sbjct: 138 LLQLMGIPIIQAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAPRLIRNL 188
>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 = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 41/134 (30%), Positives = 69/134 (51%), Gaps = 12/134 (8%)
Query: 174 NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERG-------- 225
+HL+G+++R +++ IKPV+VFDG PQLK ++ + R + +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 226 ----KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDS 281
K T+ +T+Q + E + LL L G+P++ AP EAEA CA+L T+D
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 282 DIWLFGARTVYKNF 295
D FG+ + ++
Sbjct: 180 DCLTFGSPVLMRHL 193
>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 = 3e-14, Method: Compositional matrix adjust.
Identities = 41/134 (30%), Positives = 69/134 (51%), Gaps = 12/134 (8%)
Query: 174 NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERG-------- 225
+HL+G+++R +++ IKPV+VFDG PQLK ++ + R + +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 226 ----KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDS 281
K T+ +T+Q + E + LL L G+P++ AP EAEA CA+L T+D
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 282 DIWLFGARTVYKNF 295
D FG+ + ++
Sbjct: 180 DCLTFGSPVLMRHL 193
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 75.1 bits (183), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 50/171 (29%), Positives = 86/171 (50%), Gaps = 14/171 (8%)
Query: 139 NIVINKLLVDLISDVSIWLHQLTK--GTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVF 196
N+ K+ +D ++ + +L + + GT + +HL GL++R L+ IKPV+
Sbjct: 18 NLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVY 77
Query: 197 VFDGGVPQLKKQTISTLEKDRDQLL------LERG------KQTRLASTITEQMSREAQE 244
VFDG P+ KK+ + + R++ LE+G K + A+ + E + +A++
Sbjct: 78 VFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEARKYAQRATRVNEMLIEDAKK 137
Query: 245 LLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNF 295
LL+L G+P + AP E EAQ A + + D D LFGA + +N
Sbjct: 138 LLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNL 188
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 70/135 (51%), Gaps = 14/135 (10%)
Query: 174 NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQ-------------L 220
+HL GL++R ++ IKPV+VFDG P+LK + I + +++ L
Sbjct: 69 TSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDL 128
Query: 221 LLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDD 280
L R + +++ +TE+M R+A+ LL G+P++ AP E EAQ A + + D
Sbjct: 129 ELAR-RYAMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQD 187
Query: 281 SDIWLFGARTVYKNF 295
D LFG+ + +N
Sbjct: 188 YDSLLFGSPKLVRNL 202
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 40/134 (29%), Positives = 68/134 (50%), Gaps = 12/134 (8%)
Query: 174 NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERG-------- 225
+HL+G+++R +++ IKPV+VFDG PQLK ++ + R + +
Sbjct: 60 TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE 119
Query: 226 ----KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDS 281
K T+ +T+Q + E + LL L G+P++ AP EAEA CA+L T+D
Sbjct: 120 QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM 179
Query: 282 DIWLFGARTVYKNF 295
FG+ + ++
Sbjct: 180 ACLTFGSPVLMRHL 193
>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 = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 42/133 (31%), Positives = 65/133 (48%), Gaps = 11/133 (8%)
Query: 174 NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQL------LLERG-- 225
+HL G+ +R+ ++ I+PVFVFDG P+ KK I +K R + L+ G
Sbjct: 55 TSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDK 114
Query: 226 ---KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSD 282
K + A + E + A+ LL G+PF+ AP E EAQ A + + + D D
Sbjct: 115 DAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYD 174
Query: 283 IWLFGARTVYKNF 295
LFG+ + +N
Sbjct: 175 SLLFGSPRLARNL 187
>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 = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 71/138 (51%), Gaps = 13/138 (9%)
Query: 170 GSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQT--ISTLEKDRDQLLL----- 222
G + +A+ G++++ LL I P++VFDG P+LK++T + K++ +L +
Sbjct: 52 GEITSAY-NGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIK 110
Query: 223 -----ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVI 277
E K + S +T +M + LL L G+P++ AP E EAQ + + V+
Sbjct: 111 KEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVV 170
Query: 278 TDDSDIWLFGARTVYKNF 295
+ D D L+GA V +N
Sbjct: 171 SQDYDALLYGAPRVVRNL 188
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 38/133 (28%), Positives = 67/133 (50%), Gaps = 12/133 (9%)
Query: 175 AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQL--LLERGKQ----- 227
+HL GL++R +L + P++VFDG P+ K + + K +++ LER K
Sbjct: 53 SHLSGLFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIE 112
Query: 228 -----TRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSD 282
++ ++ M E+++LL+ G+P + AP E EA+ A L + + D D
Sbjct: 113 ELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYD 172
Query: 283 IWLFGARTVYKNF 295
LFGA+ + +N
Sbjct: 173 AILFGAKRLVRNL 185
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 48/156 (30%), Positives = 70/156 (44%), Gaps = 19/156 (12%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLF-FKIKPVFVFDGG-VPQLKKQT 209
D WLH+ + P +G + +L IKP+ VFDG +P K+
Sbjct: 30 DTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVE 89
Query: 210 ISTLEKDRDQLLLERGKQ--------------TRLASTITEQMSREAQELLQLFGVPFIV 255
S E+ + LL +GKQ TR + IT M+ + + + GV +V
Sbjct: 90 RSRRERRQANLL--KGKQLLREGKVSEARECFTR-SINITHAMAHKVIKAARSQGVDCLV 146
Query: 256 APGEAEAQCASLELGNHTQGVITDDSDIWLFGARTV 291
AP EA+AQ A L Q +IT+DSD+ FG + V
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKV 182
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/156 (30%), Positives = 69/156 (44%), Gaps = 19/156 (12%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLF-FKIKPVFVFDGG-VPQLKKQT 209
D WLH+ + P +G + +L IKP+ VFDG +P K+
Sbjct: 30 DTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVE 89
Query: 210 ISTLEKDRDQLLLERGKQ--------------TRLASTITEQMSREAQELLQLFGVPFIV 255
S E+ + LL +GKQ TR + IT M+ + + + GV +V
Sbjct: 90 RSRRERRQANLL--KGKQLLREGKVSEARECFTR-SINITHAMAHKVIKAARSQGVDCLV 146
Query: 256 APGEAEAQCASLELGNHTQGVITDDSDIWLFGARTV 291
AP EA+AQ A L Q +IT+DS + FG + V
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKV 182
>pdb|1KWB|B Chain B, Crystal Structure Of The His145ala Mutant Of
2,3-Dihydroxybipheny Dioxygenase (Bphc)
pdb|1KWC|B Chain B, The His145ala Mutant Of 2,3-Dihydroxybiphenyl Dioxygenase
In Complex With 2,3-Dihydroxybiphenyl
Length = 292
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 38/140 (27%), Positives = 56/140 (40%), Gaps = 8/140 (5%)
Query: 150 ISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQT 209
+ DV W H LTK +A GS +A L R ++ ++P + D L+
Sbjct: 12 VKDVPAWDHFLTKSVGLMAAGSAGDAALYRADQRAWRI---AVQPGELDDLAYAGLEVDD 68
Query: 210 ISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQL---FGVPFIVAPGEAEAQCAS 266
+ LE+ D+L TR + +Q R+ LL L FG+P + G AE
Sbjct: 69 AAALERMADKLRQAGVAFTRGDEALMQQ--RKVMGLLCLQDPFGLPLEIYYGPAEIFHEP 126
Query: 267 LELGNHTQGVITDDSDIWLF 286
G +T D I F
Sbjct: 127 FLPSAPVSGFVTGDQGIGAF 146
>pdb|1EIQ|A Chain A, 2,3-dihydroxybiphenyl-1,2-dioxygenase
pdb|1EIR|A Chain A, 2,3-Dihydroxybiphenyl-1,2-Dioxygenase
pdb|1EIL|A Chain A, 2,3-Dihydroxybiphenyl-1,2-Dioxygenase
pdb|1KW3|B Chain B, Crystal Structure Of 2,3-Dihydroxybiphenyal Dioxygenase
(Bphc) At 1.45 A Resolution
pdb|1KW6|B Chain B, Crystal Structure Of 2,3-Dihydroxybiphenyl Dioxygenase
(Bphc) In Complex With 2,3-Dihydroxybiphenyl At 1.45 A
Resolution
pdb|1KW8|B Chain B, Crystal Structure Of Bphc-2,3-Dihydroxybiphenyl-No Complex
pdb|1KW9|B Chain B, Crystal Structure Of 2,3-Dihydroxybiphenyl Dioxygenase
(Bphc) In Complex With 2,3-Dihydroxybiphenyl At 2.0a
Resolution
pdb|1DHY|A Chain A, Kks102 Bphc Enzyme
Length = 292
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 38/140 (27%), Positives = 56/140 (40%), Gaps = 8/140 (5%)
Query: 150 ISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQT 209
+ DV W H LTK +A GS +A L R ++ ++P + D L+
Sbjct: 12 VKDVPAWDHFLTKSVGLMAAGSAGDAALYRADQRAWRI---AVQPGELDDLAYAGLEVDD 68
Query: 210 ISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQL---FGVPFIVAPGEAEAQCAS 266
+ LE+ D+L TR + +Q R+ LL L FG+P + G AE
Sbjct: 69 AAALERMADKLRQAGVAFTRGDEALMQQ--RKVMGLLCLQDPFGLPLEIYYGPAEIFHEP 126
Query: 267 LELGNHTQGVITDDSDIWLF 286
G +T D I F
Sbjct: 127 FLPSAPVSGFVTGDQGIGHF 146
>pdb|2A5Y|B Chain B, Structure Of A Ced-4CED-9 Complex
pdb|2A5Y|C Chain C, Structure Of A Ced-4CED-9 Complex
pdb|3LQQ|A Chain A, Structure Of The Ced-4 Apoptosome
pdb|3LQQ|B Chain B, Structure Of The Ced-4 Apoptosome
pdb|3LQR|A Chain A, Structure Of Ced-4:ced-3 Complex
pdb|3LQR|B Chain B, Structure Of Ced-4:ced-3 Complex
Length = 549
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 32/130 (24%), Positives = 53/130 (40%), Gaps = 10/130 (7%)
Query: 148 DLISDVSIWLHQLTKGTHDLAG-GSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQ-- 204
DL +D+ + L K DL SV + + L IC L + +FVFD V +
Sbjct: 202 DLFTDILLML----KSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEET 257
Query: 205 ---LKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAE 261
++ + L RD + QT +T E + L+ +G+P V E +
Sbjct: 258 IRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEED 317
Query: 262 AQCASLELGN 271
++EL +
Sbjct: 318 VLNKTIELSS 327
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 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,254,381
Number of Sequences: 62578
Number of extensions: 309119
Number of successful extensions: 853
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 831
Number of HSP's gapped (non-prelim): 14
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
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: 51 (24.3 bits)