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= 003536
(812 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 92.8 bits (229), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 54/165 (32%), Positives = 84/165 (50%), Gaps = 13/165 (7%)
Query: 638 GKQPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQGTAPAKELASCGLDV 697
G +PD++H HDWQ A + P+Y + S T HN +QG A + L
Sbjct: 128 GWRPDMVHAHDWQAA-MTPVYMRYAETPEIPS---LLTIHNIAFQGQFGANIFSKLALPA 183
Query: 698 QQLNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQE-----GGQGLHSTLNFHSK 752
M+ ++ ++ LKG + + ++TVSPSYA+E G GL + +
Sbjct: 184 HAFG----MEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGMGLEGVIGSRAH 239
Query: 753 KFVGILNGIDTDAWNPATDTFLKVQYNANDLQGKAENKESIRKHL 797
GI+NGID D WNPATD + Y+A +L+ +A NK+++ +H
Sbjct: 240 VLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHF 284
>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 = 89.7 bits (221), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 92/346 (26%), Positives = 143/346 (41%), Gaps = 69/346 (19%)
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-NSARVCFTCHNFEYQGTAPAKELASCGLDVQQLNRPDRMQDN----SAHD--- 713
Y P G+ +A+V F HN YQG + D +LN +R + + +D
Sbjct: 175 YQPNGIYRNAKVAFCIHNISYQGRFAFE-------DYPELNLSERFRSSFDFIDGYDTPV 227
Query: 714 ---RINPLKGAIVFSNIVTTVSPSYAQEGGQGLHSTLNFHS----KKFVGILNGIDTDAW 766
+IN +K I+ ++ V TVSP YA+E G+ + GI+NG+D W
Sbjct: 228 EGRKINWMKAGILEADRVLTVSPYYAEELISGIARGCELDNIMRLTGITGIVNGMDVSEW 287
Query: 767 NPATDTFLKVQYNAND-LQGKAENKESIRKHLGLSSADARKPLVKF 811
+P+ D ++ +Y+A ++ KA NKE+++ GL D + PL+ F
Sbjct: 288 DPSKDKYITAKYDATTAIEAKALNKEALQAEAGL-PVDRKIPLIAF 332
>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 = 87.0 bits (214), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 53/165 (32%), Positives = 81/165 (49%), Gaps = 13/165 (7%)
Query: 638 GKQPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQGTAPAKELASCGLDV 697
G +PD +H HDWQ A P+Y + S T HN +QG A + L
Sbjct: 128 GWRPDXVHAHDWQAAXT-PVYXRYAETPEIPS---LLTIHNIAFQGQFGANIFSKLALPA 183
Query: 698 QQLNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQE-----GGQGLHSTLNFHSK 752
+ ++ ++ LKG + + ++TVSPSYA+E G GL + +
Sbjct: 184 HAFG----XEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGXGLEGVIGSRAH 239
Query: 753 KFVGILNGIDTDAWNPATDTFLKVQYNANDLQGKAENKESIRKHL 797
GI+NGID D WNPATD + Y+A +L+ +A NK+++ +H
Sbjct: 240 VLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHF 284
>pdb|3D1J|A Chain A, Crystal Structure Of E.Coli Gs Mutant Dmgs(C7s;c408s)
Length = 477
Score = 83.6 bits (205), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 57/177 (32%), Positives = 88/177 (49%), Gaps = 19/177 (10%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQGTAPAKELASCGLDVQQ 699
+PD++H HDW A +AP Y +G A+ FT HN YQG A + L
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQGMFYAHHMNDIQLPWSF 183
Query: 700 LNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQE--------GGQGLHSTLNFHS 751
N + + +I+ LK + +++ +T VSP+YA+E G +GL +
Sbjct: 184 FN----IHGLEFNGQISFLKAGLYYADHITAVSPTYAREITEPQFAYGMEGLLQQRH-RE 238
Query: 752 KKFVGILNGIDTDAWNPATDTFLKVQYNANDLQGKAENKESIRKHLGLSSADARKPL 808
+ G+LNG+D W+P TD L +Y + L+ KAENK ++ +GL D + PL
Sbjct: 239 GRLSGVLNGVDEKIWSPETDLLLASRYTRDTLEDKAENKRQLQIAMGL-KVDDKVPL 294
>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 = 83.2 bits (204), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 57/177 (32%), Positives = 88/177 (49%), Gaps = 19/177 (10%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQGTAPAKELASCGLDVQQ 699
+PD++H HDW A +AP Y +G A+ FT HN YQG A + L
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQGMFYAHHMNDIQLPWSF 183
Query: 700 LNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQE--------GGQGLHSTLNFHS 751
N + + +I+ LK + +++ +T VSP+YA+E G +GL +
Sbjct: 184 FN----IHGLEFNGQISFLKAGLYYADHITAVSPTYAREITEPQFAYGMEGLLQQRH-RE 238
Query: 752 KKFVGILNGIDTDAWNPATDTFLKVQYNANDLQGKAENKESIRKHLGLSSADARKPL 808
+ G+LNG+D W+P TD L +Y + L+ KAENK ++ +GL D + PL
Sbjct: 239 GRLSGVLNGVDEKIWSPETDLLLASRYTRDTLEDKAENKRQLQIAMGL-KVDDKVPL 294
>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 = 83.2 bits (204), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 57/177 (32%), Positives = 88/177 (49%), Gaps = 19/177 (10%)
Query: 640 QPDIIHCHDWQTAFVAPLYWDLYVPKGLNSARVCFTCHNFEYQGTAPAKELASCGLDVQQ 699
+PD++H HDW A +AP Y +G A+ FT HN YQG A + L
Sbjct: 129 RPDVVHAHDWH-AGLAPAY---LAARG-RPAKSVFTVHNLAYQGMFYAHHMNDIQLPWSF 183
Query: 700 LNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQE--------GGQGLHSTLNFHS 751
N + + +I+ LK + +++ +T VSP+YA+E G +GL +
Sbjct: 184 FN----IHGLEFNGQISFLKAGLYYADHITAVSPTYAREITEPQFAYGMEGLLQQRH-RE 238
Query: 752 KKFVGILNGIDTDAWNPATDTFLKVQYNANDLQGKAENKESIRKHLGLSSADARKPL 808
+ G+LNG+D W+P TD L +Y + L+ KAENK ++ +GL D + PL
Sbjct: 239 GRLSGVLNGVDEKIWSPETDLLLASRYTRDTLEDKAENKRQLQIAMGL-KVDDKVPL 294
>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 = 42.7 bits (99), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 40/135 (29%), Positives = 52/135 (38%), Gaps = 24/135 (17%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPLYWDLY-VPKGLNSARVCFTCHNFEYQGTAPAKELAS 692
LL+ PD++H HDW T F L + +P FT H + PA
Sbjct: 116 LLREEPLPDVVHFHDWHTVFAGALIKKYFKIP-------AVFTIHRLN-KSKLPAFYFHE 167
Query: 693 CGLDVQQLNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQEGGQGLHSTLNFHSK 752
GL + PD I+P ++IVTTVS Y + G NF
Sbjct: 168 AGLS-ELAPYPD----------IDPEHTGGYIADIVTTVSRGYLID-EWGFFR--NFEG- 212
Query: 753 KFVGILNGIDTDAWN 767
K + NGID WN
Sbjct: 213 KITYVFNGIDCSFWN 227
>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 = 42.7 bits (99), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 52/136 (38%), Gaps = 26/136 (19%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPLYWDLY-VPKGLNSARVCFTCHNFEYQGTAPAKELAS 692
LL+ PD++H HDW T F L + +P FT H + PA
Sbjct: 116 LLREEPLPDVVHFHDWHTVFAGALIKKYFKIP-------AVFTIHRLN-KSKLPAFYFHE 167
Query: 693 CGLDVQQLNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSY-AQEGGQGLHSTLNFHS 751
GL + PD I+P ++IVTTVS Y E G NF
Sbjct: 168 AGLS-ELAPYPD----------IDPEHTGGYIADIVTTVSRGYLIDEWG----FFRNFEG 212
Query: 752 KKFVGILNGIDTDAWN 767
K + NGID WN
Sbjct: 213 -KITYVFNGIDCSFWN 227
>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 = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 40/135 (29%), Positives = 52/135 (38%), Gaps = 24/135 (17%)
Query: 634 LLQAGKQPDIIHCHDWQTAFVAPLYWDLY-VPKGLNSARVCFTCHNFEYQGTAPAKELAS 692
LL+ PD++H HDW T F L + +P FT H + PA
Sbjct: 117 LLREEPLPDVVHFHDWHTVFAGALIKKYFKIP-------AVFTIHRLN-KSKLPAFYFHE 168
Query: 693 CGLDVQQLNRPDRMQDNSAHDRINPLKGAIVFSNIVTTVSPSYAQEGGQGLHSTLNFHSK 752
GL + PD I+P ++IVTTVS Y + G NF
Sbjct: 169 AGLS-ELAPYPD----------IDPEHTGGYIADIVTTVSRGYLID-EWGFFR--NFEG- 213
Query: 753 KFVGILNGIDTDAWN 767
K + NGID WN
Sbjct: 214 KITYVFNGIDCSFWN 228
>pdb|1JR9|A Chain A, Crystal Structure Of Manganese Superoxide Dismutases From
Bacillus Halodenitrificans
Length = 202
Score = 30.0 bits (66), Expect = 5.8, 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 = 30.0 bits (66), Expect = 6.0, 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 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,641,584
Number of Sequences: 62578
Number of extensions: 872982
Number of successful extensions: 2863
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 52
Number of HSP's that attempted gapping in prelim test: 2792
Number of HSP's gapped (non-prelim): 96
length of query: 812
length of database: 14,973,337
effective HSP length: 107
effective length of query: 705
effective length of database: 8,277,491
effective search space: 5835631155
effective search space used: 5835631155
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 56 (26.2 bits)