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= 027282
(225 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 = 70.1 bits (170), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 39/115 (33%), Positives = 66/115 (57%), Gaps = 9/115 (7%)
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 LGPPKEAGRKVLRQYLTEFMSTRLGVRRESNILSTSSRVADDGRLYYLVEHVLKI 211
LG P+E G ++LR + S R S +++ +S+ ADD + YY++E+ + +
Sbjct: 65 LGSPEEVGDRLLRNIIAPSES-----GRSSALIAATSQKADD-KTYYILEYAVTL 113
>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
Synechocystis Sp. Pcc 6803
Length = 170
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/113 (30%), Positives = 60/113 (53%), Gaps = 12/113 (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 EDLGPPKEAGRKVLRQYLTEFMSTRLGVRRESNILSTSSRVADDGRLYYLVEH 207
DLG + G + ++ ++ R++ +++ +R +DG++YY +E+
Sbjct: 72 TDLGTATDVGYRFMKT-----VNDASQGDRQAELINAEAR-DEDGQVYYTLEY 118
>pdb|3KUX|A Chain A, Structure Of The Ypo2259 Putative Oxidoreductase From
Yersinia Pestis
Length = 352
Score = 33.5 bits (75), Expect = 0.11, 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 = 32.7 bits (73), Expect = 0.19, 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 = 0.91, 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 = 30.0 bits (66), Expect = 0.98, 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 = 30.0 bits (66), Expect = 1.1, 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|1UYQ|A Chain A, Mutated B-Glucosidase A From Paenibacillus Polymyxa
Showing Increased Stability
Length = 447
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 154 VEDLGPPKEA-GRKVLRQYLTEFMSTRLGVRRESNILS---TSSRVADDGRLYYLVEHVL 209
V D+G P E+ G + YL ++ + + + ++ + +V DD R+ Y+ +H++
Sbjct: 320 VTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLV 379
Query: 210 KIH 212
++H
Sbjct: 380 QVH 382
>pdb|1BGG|A Chain A, Glucosidase A From Bacillus Polymyxa Complexed With
Gluconate
pdb|1BGG|B Chain B, Glucosidase A From Bacillus Polymyxa Complexed With
Gluconate
pdb|1BGG|C Chain C, Glucosidase A From Bacillus Polymyxa Complexed With
Gluconate
pdb|1BGG|D Chain D, Glucosidase A From Bacillus Polymyxa Complexed With
Gluconate
Length = 448
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 154 VEDLGPPKEA-GRKVLRQYLTEFMSTRLGVRRESNILS---TSSRVADDGRLYYLVEHVL 209
V D+G P E+ G + YL ++ + + + ++ + +V DD R+ Y+ +H++
Sbjct: 321 VTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLV 380
Query: 210 KIH 212
++H
Sbjct: 381 QVH 383
>pdb|1E4I|A Chain A, 2-Deoxy-2-Fluoro-Beta-D-GlucosylENZYME INTERMEDIATE
Complex Of The Beta-Glucosidase From Bacillus Polymyxa
Length = 447
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 154 VEDLGPPKEA-GRKVLRQYLTEFMSTRLGVRRESNILS---TSSRVADDGRLYYLVEHVL 209
V D+G P E+ G + YL ++ + + + ++ + +V DD R+ Y+ +H++
Sbjct: 320 VTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLV 379
Query: 210 KIH 212
++H
Sbjct: 380 QVH 382
>pdb|1BGA|A Chain A, Beta-Glucosidase A From Bacillus Polymyxa
pdb|1BGA|B Chain B, Beta-Glucosidase A From Bacillus Polymyxa
pdb|1BGA|C Chain C, Beta-Glucosidase A From Bacillus Polymyxa
pdb|1BGA|D Chain D, Beta-Glucosidase A From Bacillus Polymyxa
Length = 447
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 154 VEDLGPPKEA-GRKVLRQYLTEFMSTRLGVRRESNILS---TSSRVADDGRLYYLVEHVL 209
V D+G P E+ G + YL ++ + + + ++ + +V DD R+ Y+ +H++
Sbjct: 320 VTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLV 379
Query: 210 KIH 212
++H
Sbjct: 380 QVH 382
>pdb|1TR1|A Chain A, Crystal Structure Of E96k Mutated Beta-glucosidase A From
Bacillus Polymyxa, An Enzyme With Increased
Thermoresistance
pdb|1TR1|B Chain B, Crystal Structure Of E96k Mutated Beta-glucosidase A From
Bacillus Polymyxa, An Enzyme With Increased
Thermoresistance
pdb|1TR1|C Chain C, Crystal Structure Of E96k Mutated Beta-glucosidase A From
Bacillus Polymyxa, An Enzyme With Increased
Thermoresistance
pdb|1TR1|D Chain D, Crystal Structure Of E96k Mutated Beta-glucosidase A From
Bacillus Polymyxa, An Enzyme With Increased
Thermoresistance
Length = 447
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 154 VEDLGPPKEA-GRKVLRQYLTEFMSTRLGVRRESNILS---TSSRVADDGRLYYLVEHVL 209
V D+G P E+ G + YL ++ + + + ++ + +V DD R+ Y+ +H++
Sbjct: 320 VTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLV 379
Query: 210 KIH 212
++H
Sbjct: 380 QVH 382
>pdb|4HA3|A Chain A, Structure Of Beta-Glycosidase From Acidilobus
Saccharovorans In Complex With Tris
pdb|4HA4|A Chain A, Structure Of Beta-Glycosidase From Acidilobus
Saccharovorans In Complex With Glycerol
Length = 489
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 188 ILSTSSRVADDG---RLYYLVEHVLKIH 212
+L T + +AD+G R YYLV HV ++H
Sbjct: 380 LLVTENGIADEGDYQRPYYLVSHVYQVH 407
>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 = 28.1 bits (61), Expect = 4.3, 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
0.321 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,049,821
Number of Sequences: 62578
Number of extensions: 220370
Number of successful extensions: 547
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 542
Number of HSP's gapped (non-prelim): 15
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)