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= psy12795
(121 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LLW|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Complex With
2-Oxoglutarate
pdb|1LLZ|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Reduced Enzyme
pdb|1LM1|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Native Enzyme
pdb|1OFD|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFD|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFE|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
pdb|1OFE|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
Length = 1520
Score = 84.3 bits (207), Expect = 2e-17, Method: Composition-based stats.
Identities = 49/117 (41%), Positives = 64/117 (54%), Gaps = 21/117 (17%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVM 60
MG+D PLA LS LLYDYFKQ FAQ VTNPPIDP RE +VM
Sbjct: 475 MGDDTPLAVLSHKPRLLYDYFKQRFAQ------------------VTNPPIDPLRENLVM 516
Query: 61 SLMCPIGPEANILEPSAKQCHRLFLPNPLLSLYDLEVIRLNTHRGWKVMKVSLMADL 117
SL +G N+LEP A+ + L +PL++ +L+ I+ +V +VS + DL
Sbjct: 517 SLAMFLGKRGNLLEPKAESARTIKLRSPLVNEVELQAIKTGQ---LQVAEVSTLYDL 570
>pdb|2VDC|A Chain A, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|B Chain B, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|C Chain C, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|D Chain D, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|E Chain E, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|F Chain F, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications
Length = 1472
Score = 60.5 bits (145), Expect = 2e-10, Method: Composition-based stats.
Identities = 35/99 (35%), Positives = 51/99 (51%), Gaps = 18/99 (18%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVM 60
MG+D+P+A LS+ L+ +F+Q F+Q VTNPPID RE+ VM
Sbjct: 479 MGDDSPIAVLSDKYRGLHHFFRQNFSQ------------------VTNPPIDSLRERRVM 520
Query: 61 SLMCPIGPEANILEPSAKQCHRLFLPNPLLSLYDLEVIR 99
SL +G NIL+ Q L L +P+L+ + +R
Sbjct: 521 SLKTRLGNLGNILDEDETQTRLLQLESPVLTTAEFRAMR 559
>pdb|1EA0|A Chain A, Alpha Subunit Of A. Brasilense Glutamate Synthase
pdb|1EA0|B Chain B, Alpha Subunit Of A. Brasilense Glutamate Synthase
Length = 1479
Score = 60.5 bits (145), Expect = 2e-10, Method: Composition-based stats.
Identities = 35/99 (35%), Positives = 51/99 (51%), Gaps = 18/99 (18%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVM 60
MG+D+P+A LS+ L+ +F+Q F+Q VTNPPID RE+ VM
Sbjct: 479 MGDDSPIAVLSDKYRGLHHFFRQNFSQ------------------VTNPPIDSLRERRVM 520
Query: 61 SLMCPIGPEANILEPSAKQCHRLFLPNPLLSLYDLEVIR 99
SL +G NIL+ Q L L +P+L+ + +R
Sbjct: 521 SLKTRLGNLGNILDEDETQTRLLQLESPVLTTAEFRAMR 559
>pdb|3THC|A Chain A, Crystal Structure Of Human Beta-Galactosidase In Complex
With Galactose
pdb|3THC|B Chain B, Crystal Structure Of Human Beta-Galactosidase In Complex
With Galactose
pdb|3THC|C Chain C, Crystal Structure Of Human Beta-Galactosidase In Complex
With Galactose
pdb|3THC|D Chain D, Crystal Structure Of Human Beta-Galactosidase In Complex
With Galactose
pdb|3THD|A Chain A, Crystal Structure Of Human Beta-Galactosidase In Complex
With 1- Deoxygalactonojirimycin
pdb|3THD|B Chain B, Crystal Structure Of Human Beta-Galactosidase In Complex
With 1- Deoxygalactonojirimycin
pdb|3THD|C Chain C, Crystal Structure Of Human Beta-Galactosidase In Complex
With 1- Deoxygalactonojirimycin
pdb|3THD|D Chain D, Crystal Structure Of Human Beta-Galactosidase In Complex
With 1- Deoxygalactonojirimycin
Length = 654
Score = 28.5 bits (62), Expect = 0.95, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 12/73 (16%)
Query: 49 PPIDP--FREKVVMSLMCPIGPEANILEPSAKQCHRLFLPNPLLSLYDLEVIRLNTHRGW 106
PP P KV + + +G +IL PS P+ SLY L I++ H G+
Sbjct: 343 PPSTPKFAYGKVTLEKLKTVGAALDILCPSG----------PIKSLYPLTFIQVKQHYGF 392
Query: 107 KVMKVSLMADLTN 119
+ + +L D +N
Sbjct: 393 VLYRTTLPQDCSN 405
>pdb|4II2|A Chain A, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1)
In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg
pdb|4II3|A Chain A, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
pdb|4II3|C Chain C, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
Length = 1001
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 10 LSEFQPLLYDYFK--QLFAQLLPVLLSVTTMYCSLSLQVTNPPIDPFREKVVMSLMC 64
LS LLY F+ + A+ LP+ +S L Q+T ++PFR+ +V+ + C
Sbjct: 934 LSSGVSLLYANFQPPKKLAERLPLKIS------ELVEQITKKKLEPFRKHLVLEICC 984
>pdb|3OZH|A Chain A, Crystal Structure Of Beta-LactamaseD-Alanine
Carboxypeptidase From Yersinia Pestis
pdb|3RJU|A Chain A, Crystal Structure Of Beta-LactamaseD-Alanine
Carboxypeptidase From Yersinia Pestis Complexed With
Citrate
Length = 351
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 41 SLSLQVTNPPIDPFREKVVMSLMCPIGPEANILEPSAKQCHRLFL 85
+LS P R+K+ P+G + L P+A+QC RL +
Sbjct: 170 ALSRAAGKPYAHLLRDKIT----APLGXKNTTLTPTAEQCKRLXI 210
>pdb|3T5O|A Chain A, Crystal Structure Of Human Complement Component C6
pdb|4A5W|B Chain B, Crystal Structure Of C5b6
pdb|4E0S|B Chain B, Crystal Structure Of C5b-6
Length = 913
Score = 25.8 bits (55), Expect = 6.6, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 1 MGNDAPLACLSEFQPLLYDYFKQL 24
+G D ++CL+ F+ + Y YF+ L
Sbjct: 643 VGEDVEISCLTGFETVGYQYFRCL 666
>pdb|2THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus
pdb|2THI|B Chain B, Thiaminase I From Bacillus Thiaminolyticus
Length = 379
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 29 LPVLLSVTTMYCSLSLQVTNPPIDPFREKVVMSL 62
L L+ VT Y L PP+DP +KV+ L
Sbjct: 170 LEALIDVTGQYTEYDLL---PPLDPLNDKVIRGL 200
>pdb|4THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus With Covalently
Bound 4-amino-2,5-dimethylpyrimidine
Length = 362
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 29 LPVLLSVTTMYCSLSLQVTNPPIDPFREKVVMSL 62
L L+ VT Y L PP+DP +KV+ L
Sbjct: 162 LEALIDVTGQYTEYDLL---PPLDPLNDKVIRGL 192
>pdb|3THI|A Chain A, Thiaminase I From Bacillus Thiaminolyticus
Length = 371
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 29 LPVLLSVTTMYCSLSLQVTNPPIDPFREKVVMSL 62
L L+ VT Y L PP+DP +KV+ L
Sbjct: 162 LEALIDVTGQYTEYDLL---PPLDPLNDKVIRGL 192
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
0.324 0.138 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,281,034
Number of Sequences: 62578
Number of extensions: 106233
Number of successful extensions: 202
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 10
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)