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= psy6621
(133 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AQ7|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucyl-Adenylate Analogue In The
Aminoacylation Conformation
pdb|4AQ7|D Chain D, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucyl-Adenylate Analogue In The
Aminoacylation Conformation
pdb|4ARC|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucine In The Editing Conformation
pdb|4ARI|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And The Benzoxaborole An2679 In The Editing
Conformation
pdb|4AS1|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And The Benzoxaborole An2679 In The Editing
Conformation
pdb|3ZGZ|A Chain A, Ternary Complex Of E. Coli Leucyl-trna Synthetase,
Trna(leu) And Toxic Moiety From Agrocin 84 (tm84) In
Aminoacylation- Like Conformation
pdb|3ZGZ|D Chain D, Ternary Complex Of E. Coli Leucyl-trna Synthetase,
Trna(leu) And Toxic Moiety From Agrocin 84 (tm84) In
Aminoacylation- Like Conformation
Length = 880
Score = 102 bits (254), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 45/80 (56%), Positives = 56/80 (70%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V QP+GWDAFGLPAE AA ++ P WT NIA MK+QL+ G ++W ELATC P+Y
Sbjct: 93 VLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEY 152
Query: 100 YKWTQALFLDLYHAGLVYRK 119
Y+W Q F +LY GLVY+K
Sbjct: 153 YRWEQKFFTELYKKGLVYKK 172
>pdb|2V0C|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate In The
Synthetic Site And An Adduct Of Amp With 5-Fluoro-1,3-
Dihydro-1-Hydroxy-2,1-Benzoxaborole (An2690) In The
Editing Site
Length = 878
Score = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 40/79 (50%), Positives = 55/79 (69%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V PMGWDAFGLPAENAA + G+ P++WT NI K L+ G ++W+ E+ TC+P+Y
Sbjct: 73 VLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEY 132
Query: 100 YKWTQALFLDLYHAGLVYR 118
Y+W Q +FL ++ GL YR
Sbjct: 133 YRWNQWIFLKMWEKGLAYR 151
>pdb|1OBH|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Pre-Transfer Editing Substrate Analogue In Both
Synthetic Active Site And Editing Site
pdb|2BTE|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BTE|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BYT|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|2BYT|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|1H3N|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate
pdb|1OBC|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Post-Transfer Editing Substrate Analogue
pdb|2V0G|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site.
pdb|2V0G|D Chain D, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site
Length = 878
Score = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 40/79 (50%), Positives = 55/79 (69%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V PMGWDAFGLPAENAA + G+ P++WT NI K L+ G ++W+ E+ TC+P+Y
Sbjct: 73 VLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEY 132
Query: 100 YKWTQALFLDLYHAGLVYR 118
Y+W Q +FL ++ GL YR
Sbjct: 133 YRWNQWIFLKMWEKGLAYR 151
>pdb|3ZIU|A Chain A, Crystal Structure Of Mycoplasma Mobile Leucyl-trna
Synthetase With Leu-ams In The Active Site
pdb|3ZIU|B Chain B, Crystal Structure Of Mycoplasma Mobile Leucyl-trna
Synthetase With Leu-ams In The Active Site
Length = 637
Score = 89.4 bits (220), Expect = 5e-19, Method: Composition-based stats.
Identities = 39/83 (46%), Positives = 52/83 (62%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V P+GWDAFGLPAE A G P+ +T+ NI + QL+ G F++E E+ T DP Y
Sbjct: 77 VLHPIGWDAFGLPAEQYALSSGKHPQPFTLKNIENFRRQLKSLGFSFDYEKEVNTTDPSY 136
Query: 100 YKWTQALFLDLYHAGLVYRKEVD 122
Y+WTQ +F +Y GL +EVD
Sbjct: 137 YRWTQWIFKQIYKKGLAEIREVD 159
>pdb|1QU2|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
pdb|1QU3|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
pdb|1FFY|A Chain A, Insights Into Editing From An Ile-Trna Synthetase
Structure With Trna(Ile) And Mupirocin
Length = 917
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 21/111 (18%)
Query: 29 GINSIIKGPVRVFQPM---------GWDAFGLPAENAAHQHGIDP------------REW 67
+N I+K + ++ M GWD GLP E A + G+D +E+
Sbjct: 68 ALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEF 127
Query: 68 TVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 118
+ I K + G + ++ T P+Y +F ++ GL+Y+
Sbjct: 128 ALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMADKGLIYK 178
>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
Length = 862
Score = 34.3 bits (77), Expect = 0.020, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 24/53 (45%)
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 118
+W + T+ QL+ G +W E T D K + + F YH GL YR
Sbjct: 116 QWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYR 168
>pdb|3KCS|A Chain A, Crystal Structure Of Pamcherry1 In The Dark State
pdb|3KCT|A Chain A, Crystal Structure Of Pamcherry1 In The Photoactivated
State
Length = 234
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 13 GGVVVKTHSGA--------ECRLAGINSIIKGPVRVFQPMGWDAFG--LPAENAAHQHGI 62
GGVV T + + +L G N GPV + MGW+A + E+ A + +
Sbjct: 105 GGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEV 164
Query: 63 DPR 65
PR
Sbjct: 165 KPR 167
>pdb|4ELZ|A Chain A, Ccdbvfi:gyra14vfi
pdb|4ELZ|B Chain B, Ccdbvfi:gyra14vfi
Length = 153
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 52 PAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNW-ESELATCDPKYY---KWTQALF 107
PAE + G+ R W +GN+A+M + + +W E E + KY+ + QA+
Sbjct: 62 PAEA---KEGLISRGWDLGNVASMLERAGTDAARPDWLEPEFGIREGKYFLTEQQAQAIL 118
Query: 108 LDLYH--AGLVYRKEVDYSQNL 127
H GL + K +D + L
Sbjct: 119 ELRLHRLTGLEHEKILDEYKAL 140
>pdb|3M24|A Chain A, Crystal Structure Of Tagbfp Fluorescent Protein
pdb|3M24|B Chain B, Crystal Structure Of Tagbfp Fluorescent Protein
pdb|3M24|C Chain C, Crystal Structure Of Tagbfp Fluorescent Protein
pdb|3M24|D Chain D, Crystal Structure Of Tagbfp Fluorescent Protein
Length = 232
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 13 GGVVVKTHSGA--------ECRLAGINSIIKGPVRVFQPMGWDAF 49
GGV+ T + ++ G+N GPV + +GW+AF
Sbjct: 98 GGVLTATQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAF 142
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
0.321 0.137 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,456,367
Number of Sequences: 62578
Number of extensions: 175254
Number of successful extensions: 329
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 317
Number of HSP's gapped (non-prelim): 15
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)