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= psy1209
(61 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 = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 37/62 (59%), Positives = 46/62 (74%), Gaps = 7/62 (11%)
Query: 2 GILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
GI GLAKL+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE T
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 55 RY 56
+
Sbjct: 61 SH 62
>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 = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 37/62 (59%), Positives = 46/62 (74%), Gaps = 7/62 (11%)
Query: 2 GILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
GI GLAKL+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE T
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 55 RY 56
+
Sbjct: 61 SH 62
>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 = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 37/62 (59%), Positives = 46/62 (74%), Gaps = 7/62 (11%)
Query: 2 GILGLAKLVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT 54
GI GLAKL+ADVAPS+IRE+ RK+ IDASMS+YQFLIAVR G+ L + +GE T
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60
Query: 55 RY 56
+
Sbjct: 61 SH 62
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 22 RKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTRY 56
+KI IDA ++YQFL +R E G LM G T +
Sbjct: 22 KKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSH 57
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 28.9 bits (63), Expect = 0.84, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 20 ESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTRY 56
+ +++ ID +LYQFL A+R +G LM G T +
Sbjct: 17 KGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSH 54
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
pdb|1B43|B Chain B, Fen-1 From P. Furiosus
Length = 340
Score = 28.5 bits (62), Expect = 0.96, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 22 RKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTRY 56
+KI IDA ++YQFL +R +G LM G T +
Sbjct: 22 KKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSH 57
>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 = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 20 ESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPT 54
+ +K+ ID +LYQFL ++R +G+ L + GE T
Sbjct: 20 KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEIT 55
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
Length = 363
Score = 28.1 bits (61), Expect = 1.4, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 18 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTRY 56
I + I ID +LYQFL A+R +G LM +G T +
Sbjct: 32 ILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSH 71
>pdb|1Y7U|A Chain A, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
pdb|1Y7U|B Chain B, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
pdb|1Y7U|C Chain C, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
Length = 174
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 3 ILGLAKLVADVAPSSIRESRKICIDASMSLYQFLIAVRS 41
IL VA ++ S R SRK C+ AS FL VRS
Sbjct: 42 ILSEXDXVASISAS--RHSRKECVTASXDWVDFLHPVRS 78
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 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,504,303
Number of Sequences: 62578
Number of extensions: 37183
Number of successful extensions: 101
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 93
Number of HSP's gapped (non-prelim): 11
length of query: 61
length of database: 14,973,337
effective HSP length: 32
effective length of query: 29
effective length of database: 12,970,841
effective search space: 376154389
effective search space used: 376154389
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: 45 (21.9 bits)