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= 005005
(720 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VUE|A Chain A, Crystal Structure Of Rice Granule Bound Starch Synthase I
Catalytic Domain
pdb|3VUF|A Chain A, Crystal Structure Of Rice Granule Bound Starch Synthase I
Catalytic Domain In Complex With Adp
Length = 536
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 53/203 (26%), Positives = 75/203 (36%), Gaps = 46/203 (22%)
Query: 512 LHVIHIAAEMAPXXXXXXXXXXXXXXXXXXQKKGHLVEIVLPKYDCMQY----------- 560
++V+ + AEMAP GH V ++ P+YD QY
Sbjct: 10 MNVVFVGAEMAPWSKTGGLGDVLGGLPPAMAANGHRVMVISPRYD--QYKDAWDTSVVAE 67
Query: 561 ----DRIDDLRALDV----VVESYFDGRLFKNKVWVSTIEGLPVYFIEPHHPDKFFWRGQ 612
DR + +R V + D F KVW T E + + PD G
Sbjct: 68 IKVADRYERVRFFHCYKRGVDRVFIDHPSFLEKVWGKTGEKI-------YGPDT----GV 116
Query: 613 FYGEHDDXXXXXXXXXAALEL--LLQAGKQP--------DIIH-CHDWQTAFVAPLYWDL 661
Y D+ AALE +L P D++ C+DW T +A +
Sbjct: 117 DY--KDNQMRFSLLCQAALEAPRILNLNNNPYFKGTYGEDVVFVCNDWHTGPLASYLKNN 174
Query: 662 YVPKGL-NSARVCFTCHNFEYQG 683
Y P G+ +A+V F HN YQG
Sbjct: 175 YQPNGIYRNAKVAFCIHNISYQG 197
>pdb|3D1J|A Chain A, Crystal Structure Of E.Coli Gs Mutant Dmgs(C7s;c408s)
Length = 477
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQG 683
+PD++H HDW A +AP Y +G A+ FT HN YQG
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQG 167
>pdb|3COP|A Chain A, Crystal Structure Of E.Coli Gs Mutant E377a In Complex
With Adp And Acceptor Analogue Heppso
pdb|3CX4|A Chain A, Crystal Structure Of E.Coli Gs Mutant E377a In Complex
With Adp And Oligosaccharides
Length = 485
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQG 683
+PD++H HDW A +AP Y +G A+ FT HN YQG
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQG 167
>pdb|2QZS|A Chain A, Crystal Structure Of Wild-Type E.Coli Gs In Complex With
Adp And Glucose(Wtgsb)
pdb|2R4T|A Chain A, Crystal Structure Of Wild-Type E.Coli Gs In Complex With
Adp And Glucose(Wtgsc)
pdb|2R4U|A Chain A, Crystal Structure Of Wild-Type E.Coli Gs In Complex With
Adp And Glucose(Wtgsd)
pdb|3GUH|A Chain A, Crystal Structure Of Wild-Type E.Coli Gs In Complex With
Adp And Dgm
Length = 485
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQG 683
+PD++H HDW A +AP Y +G A+ FT HN YQG
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQG 167
>pdb|1RZU|A Chain A, Crystal Structure Of The Glycogen Synthase From A.
Tumefaciens In Complex With Adp
pdb|1RZU|B Chain B, Crystal Structure Of The Glycogen Synthase From A.
Tumefaciens In Complex With Adp
Length = 485
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 638 GKQPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQG 683
G +PD++H HDWQ A + P+Y + S T HN +QG
Sbjct: 128 GWRPDMVHAHDWQAA-MTPVYMRYAETPEIPS---LLTIHNIAFQG 169
>pdb|1RZV|A Chain A, Crystal Structure Of The Glycogen Synthase From
Agrobacterium Tumefaciens (Non-Complexed Form)
pdb|1RZV|B Chain B, Crystal Structure Of The Glycogen Synthase From
Agrobacterium Tumefaciens (Non-Complexed Form)
Length = 485
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 638 GKQPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQG 683
G +PD +H HDWQ A P+Y + S T HN +QG
Sbjct: 128 GWRPDXVHAHDWQAAXT-PVYXRYAETPEIPS---LLTIHNIAFQG 169
>pdb|3FRO|A Chain A, Crystal Structure Of Pyrococcus Abyssi Glycogen Synthase
With Open And Closed Conformations
pdb|3FRO|B Chain B, Crystal Structure Of Pyrococcus Abyssi Glycogen Synthase
With Open And Closed Conformations
pdb|3FRO|C Chain C, Crystal Structure Of Pyrococcus Abyssi Glycogen Synthase
With Open And Closed Conformations
Length = 439
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPL 657
LL+ PD++H HDW T F L
Sbjct: 116 LLREEPLPDVVHFHDWHTVFAGAL 139
>pdb|2BIS|A Chain A, Structure Of Glycogen Synthase From Pyrococcus Abyssi
pdb|2BIS|B Chain B, Structure Of Glycogen Synthase From Pyrococcus Abyssi
pdb|2BIS|C Chain C, Structure Of Glycogen Synthase From Pyrococcus Abyssi
Length = 440
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPL 657
LL+ PD++H HDW T F L
Sbjct: 117 LLREEPLPDVVHFHDWHTVFAGAL 140
>pdb|3L01|A Chain A, Crystal Structure Of Monomeric Glycogen Synthase From
Pyrococcus Abyssi
pdb|3L01|B Chain B, Crystal Structure Of Monomeric Glycogen Synthase From
Pyrococcus Abyssi
Length = 428
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPL 657
LL+ PD++H HDW T F L
Sbjct: 116 LLREEPLPDVVHFHDWHTVFAGAL 139
>pdb|1JR9|A Chain A, Crystal Structure Of Manganese Superoxide Dismutases From
Bacillus Halodenitrificans
Length = 202
Score = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 91 IDREPIDVEHTEEQNLGSVFVPELKESLVLNCDGGEELSTSQLDNLISMIRNAEKNI 147
ID+E +++ HT+ N +V +L +L +G E+L L++LIS + +NI
Sbjct: 19 IDKETMNIHHTKHHN---TYVTKLNGAL----EGHEDLKNKSLNDLISNLDAVPENI 68
>pdb|1NOZ|A Chain A, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOZ|B Chain B, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOY|A Chain A, Dna Polymerase (e.c.2.7.7.7)/dna Complex
pdb|1NOY|B Chain B, Dna Polymerase (e.c.2.7.7.7)/dna Complex
Length = 388
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 107 GSVFVPELKESLVLNCDGGEELSTSQLDNLISMIRNAEKNILL 149
GSV + K + L+C+GG+E+ LD +I M + E+++L+
Sbjct: 154 GSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLM 196
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
0.315 0.131 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,858,662
Number of Sequences: 62578
Number of extensions: 741665
Number of successful extensions: 2630
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 58
Number of HSP's that attempted gapping in prelim test: 2581
Number of HSP's gapped (non-prelim): 95
length of query: 720
length of database: 14,973,337
effective HSP length: 106
effective length of query: 614
effective length of database: 8,340,069
effective search space: 5120802366
effective search space used: 5120802366
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)