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= 043903
(146 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2UVE|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVE|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVF|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
pdb|2UVF|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
Length = 608
Score = 47.8 bits (112), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 11/97 (11%)
Query: 48 AEGALFNPATCVAGLPGDQYLPKRKVVMSIKDFG-VGDGTTSTTEVFRKAVRYVQAFGDK 106
A+G+L VA P + +++++DFG + DG T T+ ++A+ K
Sbjct: 135 ADGSL-----SVASKPITAKTSAKPQIVNVRDFGAIDDGKTLNTKAIQQAIDSC-----K 184
Query: 107 GGTQLNVPEGLWLTGSFILTSNFTLFLQKGAVILGSQ 143
G ++ +P G + +G+ L S+ TL LQ GA++LGS+
Sbjct: 185 PGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSE 221
>pdb|3JUR|A Chain A, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|B Chain B, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|C Chain C, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|D Chain D, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
Length = 448
Score = 47.4 bits (111), Expect = 3e-06, Method: Composition-based stats.
Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 7/72 (9%)
Query: 68 LPKRKVVMSIKDFGV-GDGTTSTTEVFRKAVRYVQAFGDKGGTQLNVPEGLWLTGSFILT 126
+P R+V ++ DFG GDG T +E F++A+ + +GG +L VPEG++LTG L
Sbjct: 23 IPDREV--NLLDFGARGDGRTDCSESFKRAI---EELSKQGGGRLIVPEGVFLTGPIHLK 77
Query: 127 SNFTLFLQKGAV 138
SN L + KG +
Sbjct: 78 SNIELHV-KGTI 88
>pdb|3B0H|A Chain A, Assimilatory Nitrite Reductase (Nii4) From Tobbaco Root
pdb|3B0H|B Chain B, Assimilatory Nitrite Reductase (Nii4) From Tobbaco Root
Length = 588
Score = 29.6 bits (65), Expect = 0.69, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 42 RVGFSGAEGALFNPATCVAGLPGDQYLPKRKVV 74
R GF+ G F+P C +P D ++P VV
Sbjct: 280 RFGFNLLVGGFFSPKRCAEAVPLDAWVPADDVV 312
>pdb|2ZC5|B Chain B, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
(Biapenem) From Streptococcus Pneumoniae
pdb|2ZC5|D Chain D, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
(Biapenem) From Streptococcus Pneumoniae
pdb|2ZC6|B Chain B, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
(Tebipenem) From Streptococcus Pneumoniae
pdb|2ZC6|D Chain D, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
(Tebipenem) From Streptococcus Pneumoniae
Length = 390
Score = 29.3 bits (64), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 82 VGDGTTSTTEVFRKAVRYVQAFGDKGGTQLNVPEGLWLTGSFIL 125
VG+G T +V+R + Y+ + N+PEGL+ G F+
Sbjct: 344 VGNGLTVAAKVYRSMMTYLSEGSNP--EDWNIPEGLYRNGEFVF 385
>pdb|2C5W|B Chain B, Penicillin-Binding Protein 1a (Pbp-1a) Acyl-Enzyme Complex
(Cefotaxime) From Streptococcus Pneumoniae
Length = 385
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 82 VGDGTTSTTEVFRKAVRYVQAFGDKGGTQLNVPEGLWLTGSFIL 125
VG+G T +V+R + Y+ + N+PEGL+ G F+
Sbjct: 342 VGNGLTVAAKVYRSMMTYLSEGSNP--EDWNIPEGLYRNGEFVF 383
>pdb|2C6W|B Chain B, Penicillin-Binding Protein 1a (Pbp-1a) From Streptococcus
Pneumoniae
Length = 384
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 82 VGDGTTSTTEVFRKAVRYVQAFGDKGGTQLNVPEGLWLTGSFIL 125
VG+G T +V+R + Y+ + N+PEGL+ G F+
Sbjct: 341 VGNGLTVAAKVYRSMMTYLSEGSNP--EDWNIPEGLYRNGEFVF 382
>pdb|2V2F|F Chain F, Crystal Structure Of Pbp1a From Drug-resistant Strain 5204
From Streptococcus Pneumoniae
Length = 390
Score = 29.3 bits (64), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 82 VGDGTTSTTEVFRKAVRYVQAFGDKGGTQLNVPEGLWLTGSFIL 125
VGDG +V+R + Y+ + N+PEGL+ G F+
Sbjct: 344 VGDGFLVAAKVYRSMITYLSEGSNP--EDWNIPEGLYRNGEFVF 385
>pdb|3P9D|B Chain B, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9D|J Chain J, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|BB Chain b, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|JJ Chain j, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|4D8Q|B Chain B, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8Q|J Chain J, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|BB Chain b, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|JJ Chain j, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
Length = 527
Score = 26.9 bits (58), Expect = 3.7, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 56 ATCVAGLPGDQYLPKRKVVMSI---KDFGVGDGTTSTT----EVFRKAVRYV 100
AT + +P D P KV+++I +D VGDGTTS T E+ R+A + +
Sbjct: 61 ATILKSIPLDN--PAAKVLVNISKVQDDEVGDGTTSVTVLSAELLREAEKLI 110
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
0.320 0.138 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,279,274
Number of Sequences: 62578
Number of extensions: 168645
Number of successful extensions: 363
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 13
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)