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= psy10937
(131 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2TMK|A Chain A, Yeast Thymidylate Kinase Complexed With 3'-Azido-3'-
Deoxythymidine Monophosphate (Azt-Mp)
pdb|2TMK|B Chain B, Yeast Thymidylate Kinase Complexed With 3'-Azido-3'-
Deoxythymidine Monophosphate (Azt-Mp)
pdb|1TMK|A Chain A, Yeast Thymidylate Kinase Complexed With Thymidine
Monophosphate (Dtmp)
pdb|1TMK|B Chain B, Yeast Thymidylate Kinase Complexed With Thymidine
Monophosphate (Dtmp)
pdb|3TMK|A Chain A, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|B Chain B, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|C Chain C, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|D Chain D, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|E Chain E, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|F Chain F, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|G Chain G, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
pdb|3TMK|H Chain H, Crystal Structure Of Yeast Thymidylate Kinase Complexed
With The Bisubstrate Inhibitor Tp5a At 2.0 A Resolution:
Implications For Catalysis And Azt Activation
Length = 216
Score = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 15/53 (28%)
Query: 70 VKLNWNAKPKVGSL-------------DNATHKPGGGDKKIESVKLDFKDKAK 109
+ L+W +P VG L DN K G GD++ E+VK F++K K
Sbjct: 111 MDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVK--FQEKVK 161
>pdb|1W8W|A Chain A, Cbm29-2 Mutant Y46a: Probing The Mechanism Of Ligand
Recognition By Family 29 Carbohydrate Binding Modules
pdb|1W8W|B Chain B, Cbm29-2 Mutant Y46a: Probing The Mechanism Of Ligand
Recognition By Family 29 Carbohydrate Binding Modules
Length = 149
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 48/106 (45%), Gaps = 7/106 (6%)
Query: 5 QVGAAPSPNLKKVTSKI--GSLQNAHYKPGGGKVKIENRKLEWKAEPRIAAKNDEYVPGG 62
Q G A + +LK+ + GSL+ G K+ +EN + + K E + +DEYV
Sbjct: 42 QEGKAGAVSLKRNSGSFRGGSLRFDMKNEGKVKILVENSEADEKFEVETISPSDEYVTYI 101
Query: 63 GDKKIEV--VKLNWNAKPKVGS---LDNATHKPGGGDKKIESVKLD 103
D ++ ++++ P G + N H G D ++ + L+
Sbjct: 102 LDVDFDLPFDRIDFQDAPGNGDRIWIKNLVHSTGSADDFVDPINLE 147
>pdb|1DXF|A Chain A, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
Coli In Complex With Pyruvate
pdb|1DXF|B Chain B, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
Coli In Complex With Pyruvate
Length = 256
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 5 QVGAAPSPNLKKVTSKIGSLQNAHYKPGGGKVKIE---NRKLEWKA 47
+G A P+++K I + +AH KP G +E R LEW A
Sbjct: 186 HLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGA 231
>pdb|1DXE|A Chain A, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
Coli
pdb|1DXE|B Chain B, 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia
Coli
Length = 256
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 5 QVGAAPSPNLKKVTSKIGSLQNAHYKPGGGKVKIE---NRKLEWKA 47
+G A P+++K I + +AH KP G +E R LEW A
Sbjct: 186 HLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGA 231
>pdb|1GWL|A Chain A, Carbohydrate Binding Module Family29 Complexed With
Mannohexaose
pdb|1GWM|A Chain A, Carbohydrate Binding Module Family29 Complexed With
Glucohexaose
Length = 153
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 22 GSLQNAHYKPGGGKVKIENRKLEWKAEPRIAAKNDEYVPGGGDKKIEV--VKLNWNAKPK 79
GSL+ G K+ +EN + + K E + +DEYV D ++ ++++ P
Sbjct: 61 GSLRFDMKNEGKVKILVENSEADEKFEVETISPSDEYVTYILDVDFDLPFDRIDFQDAPG 120
Query: 80 VGS---LDNATHKPGGGDKKIESVKLD 103
G + N H G D ++ + L+
Sbjct: 121 NGDRIWIKNLVHSTGSADDFVDPINLE 147
>pdb|1GWK|A Chain A, Carbohydrate Binding Module Family29
pdb|1GWK|B Chain B, Carbohydrate Binding Module Family29
Length = 153
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 22 GSLQNAHYKPGGGKVKIENRKLEWKAEPRIAAKNDEYVPGGGDKKIEV--VKLNWNAKPK 79
GSL+ G K+ +EN + + K E + +DEYV D ++ ++++ P
Sbjct: 61 GSLRFDXKNEGKVKILVENSEADEKFEVETISPSDEYVTYILDVDFDLPFDRIDFQDAPG 120
Query: 80 VGS---LDNATHKPGGGDKKIESVKLD 103
G + N H G D ++ + L+
Sbjct: 121 NGDRIWIKNLVHSTGSADDFVDPINLE 147
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
0.307 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,805,563
Number of Sequences: 62578
Number of extensions: 216606
Number of successful extensions: 215
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 212
Number of HSP's gapped (non-prelim): 19
length of query: 131
length of database: 14,973,337
effective HSP length: 88
effective length of query: 43
effective length of database: 9,466,473
effective search space: 407058339
effective search space used: 407058339
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 46 (22.3 bits)