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= psy17909
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QH3|A Chain A, Human Glyoxalase Ii With Cacodylate And Acetate Ions
Present In The Active Site
pdb|1QH3|B Chain B, Human Glyoxalase Ii With Cacodylate And Acetate Ions
Present In The Active Site
pdb|1QH5|A Chain A, Human Glyoxalase Ii With
S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione
pdb|1QH5|B Chain B, Human Glyoxalase Ii With
S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione
Length = 260
Score = 105 bits (262), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 50/82 (60%), Positives = 59/82 (71%)
Query: 28 SGDTLFVAGAGKFFEGDGAEMHHNLNVKLAKLPNETKVFCGHEYTVNNLYFSKHVEPNNT 87
+GDTLFVAG GKF+EG EM L L +LP +T+V+CGHEYT+NNL F++HVEP N
Sbjct: 132 TGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEYTINNLKFARHVEPGNA 191
Query: 88 RIAEKLKWAIEKRERKEPTVPS 109
I EKL WA EK EPTVPS
Sbjct: 192 AIREKLAWAKEKYSIGEPTVPS 213
>pdb|1XM8|A Chain A, X-Ray Structure Of Glyoxalase Ii From Arabidopsis Thaliana
Gene At2g31350
pdb|1XM8|B Chain B, X-Ray Structure Of Glyoxalase Ii From Arabidopsis Thaliana
Gene At2g31350
pdb|2Q42|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Glyoxalase Ii From Arabidopsis Thaliana Gene At2g31350
pdb|2Q42|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Glyoxalase Ii From Arabidopsis Thaliana Gene At2g31350
Length = 254
Score = 73.2 bits (178), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 37/95 (38%), Positives = 54/95 (56%), Gaps = 5/95 (5%)
Query: 15 FFEGDGAFVTSPLSGDTLFVAGAGKFFEGDGAEMHHNLNVKLAKLPNETKVFCGHEYTVN 74
+F G A T GDT+F GK FEG +M +L K+ LP++T ++CGHEYT++
Sbjct: 120 YFPGSRAIFT----GDTMFSLSCGKLFEGTPKQMLASLQ-KITSLPDDTSIYCGHEYTLS 174
Query: 75 NLYFSKHVEPNNTRIAEKLKWAIEKRERKEPTVPS 109
N F+ +EPNN + E R +K PT+P+
Sbjct: 175 NSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPT 209
>pdb|2QED|A Chain A, Crystal Structure Of Salmonella Thyphimurium Lt2
Glyoxalase Ii
Length = 258
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 28 SGDTLFVAGAGKFFEGDGAEMHHNLNVKLAKLPNETKVFCGHEYTVNNLYFSKHVEPNNT 87
GDTLF G G+ FEG ++M+ +L +K+ LP++T + C HEYT+ N+ F+ + P+++
Sbjct: 132 CGDTLFSGGCGRLFEGTPSQMYQSL-MKINSLPDDTLICCAHEYTLANIKFALSILPHDS 190
Query: 88 RIAEKLKWAIEKRERKEPTVP 108
I E + E R +K+ T+P
Sbjct: 191 FINEYYRKVKELRVKKQMTLP 211
>pdb|2P18|A Chain A, Crystal Structure Of The Leishmania Infantum Glyoxalase Ii
pdb|2P1E|A Chain A, Crystal Structure Of The Leishmania Infantum Glyoxalase Ii
With D- Lactate At The Active Site
Length = 311
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 32/97 (32%), Positives = 48/97 (49%), Gaps = 16/97 (16%)
Query: 27 LSGDTLFVAGAGKFFEGDGAEM-------HHNLNVKLAKLPNETKVFCGHEYTVNNLYFS 79
+GDT+F+AG G FFEGD +M +H L T +F GHEYT + FS
Sbjct: 177 FTGDTMFIAGIGAFFEGDEKDMCRAMEKVYHIHKGNDYALDKVTFIFPGHEYTSGFMTFS 236
Query: 80 KHVEPNNTRIAEKLKWAIEKRERK-------EPTVPS 109
+ P+ R ++ L + +R + +P+VPS
Sbjct: 237 EKTFPD--RASDDLAFIQAQRAKYAAAVKTGDPSVPS 271
>pdb|2GCU|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|B Chain B, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|C Chain C, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|D Chain D, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
Length = 245
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 10 AGAGKFFEGDGAFVTSP---LSGDTLFVAGAGK--FFEGDGAEMHHNLNVKLAKLPNETK 64
AG + G+GA P +GD + + G G+ F EG +++ +++ ++ LP +T
Sbjct: 119 AGCVTYVTGEGADQPQPRMAFTGDAVLIRGCGRTDFQEGSSDQLYESVHSQIFTLPKDTL 178
Query: 65 VFCGHEY 71
++ H+Y
Sbjct: 179 IYPAHDY 185
>pdb|4EFZ|A Chain A, Crystal Structure Of A Hypothetical Metallo-Beta-Lactamase
From Burkholderia Pseudomallei
pdb|4EFZ|B Chain B, Crystal Structure Of A Hypothetical Metallo-Beta-Lactamase
From Burkholderia Pseudomallei
Length = 298
Score = 30.4 bits (67), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 29 GDTLFVAGAG----KFFEGDGAEMHHNLNVKLAKLPNETKVFCGHEYTVNNLYFSKHVEP 84
GDTLF+ G F GD ++ ++ K+ LP T+++ H+Y N + ++
Sbjct: 173 GDTLFMPDYGTARCDFPGGDARSLYRSIR-KVLSLPPATRLYMCHDYQPNG----RAIQY 227
Query: 85 NNTRIAEKLKWAIEKRE 101
+T +A++L+ + RE
Sbjct: 228 AST-VADELRENVHIRE 243
>pdb|3FFC|D Chain D, Crystal Structure Of Cf34 Tcr In Complex With Hla-B8FLR
pdb|3FFC|I Chain I, Crystal Structure Of Cf34 Tcr In Complex With Hla-B8FLR
Length = 202
Score = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 12/65 (18%)
Query: 26 PLSGDTLFVAGAGKFFEGDGAEMHHNLN-----------VKLAKLPNETKVFCG-HEYTV 73
P SG+ +FV G + +G+ E ++LN + ++L + FC E T
Sbjct: 38 PSSGEMIFVIYQGSYDQGNATEGRYSLNFQKARKSANLVISASQLGDSAMYFCAMREDTG 97
Query: 74 NNLYF 78
N YF
Sbjct: 98 NQFYF 102
>pdb|2ZO9|B Chain B, Malonate-Bound Structure Of The Glycerophosphodiesterase
From Enterobacter Aerogenes (Gpdq) And Characterization
Of The Native Fe2+ Metal Ion Preference
pdb|2ZO9|C Chain C, Malonate-Bound Structure Of The Glycerophosphodiesterase
From Enterobacter Aerogenes (Gpdq) And Characterization
Of The Native Fe2+ Metal Ion Preference
pdb|2ZOA|A Chain A, Malonate-bound Structure Of The Glycerophosphodiesterase
From Enterobacter Aerogenes (gpdq) Collected At 1.280
Angstrom
pdb|2ZOA|B Chain B, Malonate-bound Structure Of The Glycerophosphodiesterase
From Enterobacter Aerogenes (gpdq) Collected At 1.280
Angstrom
pdb|3D03|A Chain A, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
pdb|3D03|B Chain B, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
pdb|3D03|C Chain C, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
pdb|3D03|D Chain D, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
pdb|3D03|E Chain E, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
pdb|3D03|F Chain F, 1.9a Structure Of Glycerophoshphodiesterase (Gpdq) From
Enterobacter Aerogenes
Length = 274
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 50 HNLNVKLAKLPNETKVFCGHEYTVNNLYFSK 80
H L + + P+ T++FCGH +++ + +
Sbjct: 176 HRLLALVERFPSLTRIFCGHNHSLTMTQYRQ 206
>pdb|2DXL|A Chain A, Glycerophosphodiesterase From Enterobacter Aerogenes
pdb|2DXL|B Chain B, Glycerophosphodiesterase From Enterobacter Aerogenes
pdb|2DXN|A Chain A, Glycerophosphodiesterase From Enterobacter Aerogenes
pdb|2DXN|B Chain B, Glycerophosphodiesterase From Enterobacter Aerogenes
Length = 274
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 50 HNLNVKLAKLPNETKVFCGHEYTVNNLYFSK 80
H L + + P+ T++FCGH +++ + +
Sbjct: 176 HRLLALVERFPSLTRIFCGHNHSLTMTQYRQ 206
>pdb|2ZKR|BB Chain b, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 403
Score = 25.8 bits (55), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 82 VEPNNTRIAEKLKWAIEKRERKEPTVP 108
V+ N +AEKL WA RER E VP
Sbjct: 183 VQVNGGTVAEKLDWA---RERLEQQVP 206
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
0.317 0.136 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,806,090
Number of Sequences: 62578
Number of extensions: 158207
Number of successful extensions: 275
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 257
Number of HSP's gapped (non-prelim): 16
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
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: 46 (22.3 bits)