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= psy8013
(252 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GEJ|A Chain A, Crystal Structure Of Phosphatidylinositol
Mannosyltransferase (Pima) From Mycobacterium Smegmatis
In Complex With Gdp-Man
pdb|2GEK|A Chain A, Crystal Structure Of Phosphatidylinositol
Mannosyltransferase (Pima) From Mycobacterium Smegmatis
In Complex With Gdp
Length = 406
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 1 MVSDFFYPNVGGVEEHIFNLSQCLLQRGHKVIVLTHSYKDRVGIRYMTNGLKVYYCPIKT 60
MV + + GGV+ H+ L++ L GH+V VL + Y+ +G K P
Sbjct: 25 MVCPYSFDVPGGVQSHVLQLAEVLRDAGHEVSVLAPASPHVKLPDYVVSGGKAVPIP--- 81
Query: 61 FYNQSI 66
YN S+
Sbjct: 82 -YNGSV 86
>pdb|4GYZ|A Chain A, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|B Chain B, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|C Chain C, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|D Chain D, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|E Chain E, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|F Chain F, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|G Chain G, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|H Chain H, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|I Chain I, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GZ0|A Chain A, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|B Chain B, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|E Chain E, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|K Chain K, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|G Chain G, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|I Chain I, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ1|A Chain A, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
pdb|4GZ1|B Chain B, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
Length = 256
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 4/92 (4%)
Query: 115 FTDHSLFGFADSSAIVTNKCLEISLAGCNHCICVSHI--GKENTVLRARVNHYNVSVIPN 172
F + F ++ + C+ +SL G C+ SH+ +E++ R R + +
Sbjct: 87 FKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQE 146
Query: 173 AVDTT--VFVPDVSRRSHNETLIAGIESAISD 202
A D+T +F D + R G+ + D
Sbjct: 147 APDSTTVIFAGDTNLRDQEVIKCGGLPDNVFD 178
>pdb|4GZ2|A Chain A, Mus Musculus Tdp2 Excluded Ssdna Complex
pdb|4GZ2|B Chain B, Mus Musculus Tdp2 Excluded Ssdna Complex
Length = 255
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 4/92 (4%)
Query: 115 FTDHSLFGFADSSAIVTNKCLEISLAGCNHCICVSHI--GKENTVLRARVNHYNVSVIPN 172
F + F ++ + C+ +SL G C+ SH+ +E++ R R + +
Sbjct: 87 FKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQE 146
Query: 173 AVDTT--VFVPDVSRRSHNETLIAGIESAISD 202
A D+T +F D + R G+ + D
Sbjct: 147 APDSTTVIFAGDTNLRDQEVIKCGGLPDNVFD 178
>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 = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 4 DFFYPNVGGVEEHIFNLSQCLLQRGHKVIVLTHSY 38
+F VGG+ E + +S+ L GH+V+V T S+
Sbjct: 11 EFLPVKVGGLAEALTAISEALASLGHEVLVFTPSH 45
>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 = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 4 DFFYPNVGGVEEHIFNLSQCLLQRGHKVIVLTHSY 38
+F VGG+ E + +S+ L GH+V+V T S+
Sbjct: 12 EFLPVKVGGLAEALTAISEALASLGHEVLVFTPSH 46
>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 = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 4 DFFYPNVGGVEEHIFNLSQCLLQRGHKVIVLTHSY 38
+F VGG+ E + +S+ L GH+V+V T S+
Sbjct: 11 EFLPVKVGGLAEALTAISEALASLGHEVLVFTPSH 45
>pdb|3PRL|A Chain A, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125
pdb|3PRL|B Chain B, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125
pdb|3PRL|C Chain C, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125
pdb|3PRL|D Chain D, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125
pdb|3RHH|A Chain A, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125 Complexed With Nadp
pdb|3RHH|B Chain B, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125 Complexed With Nadp
pdb|3RHH|C Chain C, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125 Complexed With Nadp
pdb|3RHH|D Chain D, Crystal Structure Of Nadp-Dependent
Glyceraldehyde-3-Phosphate Dehydrogenase From Bacillus
Halodurans C-125 Complexed With Nadp
Length = 505
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 196 IESAISDLKNGRAISPFK-CHETVKSLYNWVD-VSERTEIVYKRVTQEETK 244
+ AI K+ + I + HE V LY W D + ER EI+ + + E K
Sbjct: 51 VNDAIQGAKDAQKIWKIRPIHERVDLLYAWADLLEERKEIIGELIMHEVAK 101
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 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,001,261
Number of Sequences: 62578
Number of extensions: 255062
Number of successful extensions: 467
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 462
Number of HSP's gapped (non-prelim): 10
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)