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= 026900
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XB3|A Chain A, The Structure Of Cyanobacterial Psbp
Length = 165
Score = 68.2 bits (165), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 39/110 (35%), Positives = 63/110 (57%), Gaps = 9/110 (8%)
Query: 98 GFREYIDTFDGYSFKYPQNWIQVRGAG-ADIFYRDPYVLDENVSVELXXXXXXRYKSVED 156
G + Y+D++DGY F YP+ W+QV+ D+ + D ENVSV + KS+E+
Sbjct: 7 GLQAYVDSYDGYEFLYPRGWVQVQVEDPVDVVFHDIIETTENVSVVVNTVAST--KSLEE 64
Query: 157 LGPPKEAGRKVLRQYLTEFMSTRLGVRRESNILSTSSRVADDGRLYYLVE 206
LG P+E G ++LR + S R S +++ +S+ ADD + YY++E
Sbjct: 65 LGSPEEVGDRLLRNIIAPSESG-----RSSALIAATSQKADD-KTYYILE 108
>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
Synechocystis Sp. Pcc 6803
Length = 170
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 57/112 (50%), Gaps = 12/112 (10%)
Query: 99 FREYIDTFDGYSFKYPQNWI--QVRGA--GADIFYRDPYVLDENVSVELXXXXXXRYKSV 154
+ Y DT DGY F YP WI V+GA G D+ +RD DEN+SV + K++
Sbjct: 14 LQRYSDTKDGYEFLYPNGWIGVDVKGASPGVDVVFRDLIERDENLSVIISEIPSD--KTL 71
Query: 155 EDLGPPKEAGRKVLRQYLTEFMSTRLGVRRESNILSTSSRVADDGRLYYLVE 206
DLG + G + ++ R++ +++ +R +DG++YY +E
Sbjct: 72 TDLGTATDVGYRFMKTVNDASQGD-----RQAELINAEAR-DEDGQVYYTLE 117
>pdb|3KUX|A Chain A, Structure Of The Ypo2259 Putative Oxidoreductase From
Yersinia Pestis
Length = 352
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 83 SDFGFRNTALAQQSVGFREYIDT-FDGYSFKYPQNWIQVRGAGADIFYR-DPYVLDE 137
SDF T LA+ S+G Y ++ FD Y + Q W + GAG I+Y P++LD+
Sbjct: 131 SDFLTLKTLLAEGSLGNVVYFESHFDRYRPEIRQRWREQAGAGGGIWYDLGPHLLDQ 187
>pdb|3CSK|A Chain A, Structure Of Dpp Iii From Saccharomyces Cerevisiae
Length = 711
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 2 ARMVMMQ--HQTHPCFSILTSTLSGFNGASLHSQVRQQQQTPLPREALHVTASNEKKNPV 59
+R+VM Q H++ P F ++ + S NG + Q+QQT L E + SN
Sbjct: 44 SRVVMRQVSHESEPIFDLILAIHSKLNGKYPEDDITQKQQTGLYLEYVSQFLSNLGNFKS 103
Query: 60 MAATQFAVPR 69
T+F +PR
Sbjct: 104 FGDTKF-IPR 112
>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 = 30.4 bits (67), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 43/112 (38%), Gaps = 24/112 (21%)
Query: 48 HVTASNEKKNPV-------------MAATQFAVPRRNAMALILSSYIFSDFGF---RNTA 91
H+TAS KK P+ + QF + L+ S Y S G R
Sbjct: 192 HLTASEAKKLPIQEFHLSRILQELGLNQEQFV----DLCILLGSDYCESIRGIGPKRAVD 247
Query: 92 LAQQSVGFREYIDTFDGYSFKYPQNWIQVRGAGADIFYRDPYVLDENVSVEL 143
L Q+ E + D + P+NW+ A + +P VLD SVEL
Sbjct: 248 LIQKHKSIEEIVRRLDPNKYPVPENWLHKE---AHQLFLEPEVLDPE-SVEL 295
>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 = 30.4 bits (67), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 43/112 (38%), Gaps = 24/112 (21%)
Query: 48 HVTASNEKKNPV-------------MAATQFAVPRRNAMALILSSYIFSDFGF---RNTA 91
H+TAS KK P+ + QF + L+ S Y S G R
Sbjct: 192 HLTASEAKKLPIQEFHLSRILQELGLNQEQFV----DLCILLGSDYCESIRGIGPKRAVD 247
Query: 92 LAQQSVGFREYIDTFDGYSFKYPQNWIQVRGAGADIFYRDPYVLDENVSVEL 143
L Q+ E + D + P+NW+ A + +P VLD SVEL
Sbjct: 248 LIQKHKSIEEIVRRLDPNKYPVPENWLHKE---AHQLFLEPEVLDPE-SVEL 295
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 43/112 (38%), Gaps = 24/112 (21%)
Query: 48 HVTASNEKKNPV-------------MAATQFAVPRRNAMALILSSYIFSDFGF---RNTA 91
H+TAS KK P+ + QF + L+ S Y S G R
Sbjct: 192 HLTASEAKKLPIQEFHLSRILQELGLNQEQFV----DLCILLGSDYCESIRGIGPKRAVD 247
Query: 92 LAQQSVGFREYIDTFDGYSFKYPQNWIQVRGAGADIFYRDPYVLDENVSVEL 143
L Q+ E + D + P+NW+ A + +P VLD SVEL
Sbjct: 248 LIQKHKSIEEIVRRLDPNKYPVPENWLHKE---AHQLFLEPEVLDPE-SVEL 295
>pdb|2D1C|A Chain A, Crystal Structure Of Tt0538 Protein From Thermus
Thermophilus Hb8
pdb|2D1C|B Chain B, Crystal Structure Of Tt0538 Protein From Thermus
Thermophilus Hb8
Length = 496
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 44/116 (37%), Gaps = 23/116 (19%)
Query: 108 GYS-FKYPQNWIQVRGAGADIFYRDPYVLDENVSVELXXXXXXRYKSVEDLG-------- 158
GY F+ PQ V GA A I R V+ +V VE K++EDL
Sbjct: 366 GYKPFRLPQ----VDGAIAPIVPRSRRVVGVDVFVETNLLPEALGKALEDLAAGTPFRLK 421
Query: 159 ----------PPKEAGRKVLRQYLTEFMSTRLGVRRESNILSTSSRVADDGRLYYL 204
PP ++ Y F+ T G ++ IL SRVA R +L
Sbjct: 422 MISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVASRFRWMHL 477
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
0.323 0.135 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,929,330
Number of Sequences: 62578
Number of extensions: 214050
Number of successful extensions: 636
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 631
Number of HSP's gapped (non-prelim): 9
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)