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= 020628
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AIP|C Chain C, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|D Chain D, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|G Chain G, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|H Chain H, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
Length = 196
Score = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 46/88 (52%), Positives = 62/88 (70%), Gaps = 2/88 (2%)
Query: 77 QVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLA- 135
Q+ LIK+LRE T A M DVK AL D WD E A++ LR+RG + A+KK+ R A EG++
Sbjct: 3 QMELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLRERGAMKAAKKADREAREGIIGH 62
Query: 136 -LAQNESKAAVIELNCETDFVSRNEIFQ 162
+ N+ ++ELNCETDFV+RNE+FQ
Sbjct: 63 YIHHNQRVGVLVELNCETDFVARNELFQ 90
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 237 SSPGVVSTYLHTSPQSGLGRIAGLLSLEVE-DGSSSFDPLKRVGSELAMHIVAQKPLFLT 295
+ G++ Y+H + + G+ L+ L E D + + + + +LAMHI P +++
Sbjct: 55 AREGIIGHYIHHNQRVGV-----LVELNCETDFVARNELFQNLAKDLAMHIAMMNPRYVS 109
Query: 296 KELVSADALENEREI 310
E + A+ LE ER+I
Sbjct: 110 AEEIPAEELEKERQI 124
>pdb|3AGP|A Chain A, Structure Of Viral Polymerase Form I
pdb|3AGQ|A Chain A, Structure Of Viral Polymerase Form Ii
pdb|3AVT|A Chain A, Structure Of Viral Rna Polymerase Complex 1
pdb|3AVU|A Chain A, Structure Of Viral Rna Polymerase Complex 2
pdb|3AVV|A Chain A, Structure Of Viral Rna Polymerase Complex 3
pdb|3AVW|A Chain A, Structure Of Viral Rna Polymerase Complex 4
pdb|3AVX|A Chain A, Structure Of Viral Rna Polymerase Complex 5
pdb|3AVY|A Chain A, Structure Of Viral Rna Polymerase Complex 6
pdb|3VNU|A Chain A, Complex Structure Of Viral Rna Polymerase I
pdb|3VNV|A Chain A, Complex Structure Of Viral Rna Polymerase Ii
pdb|4FWT|A Chain A, Complex Structure Of Viral Rna Polymerase Form Iii
Length = 1289
Score = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 65/232 (28%), Positives = 117/232 (50%), Gaps = 41/232 (17%)
Query: 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQ 138
+L+K+LRE+T A M D K AL + + DIE A++ +RK G + A+KK+ A +G++
Sbjct: 7 SLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGVIKTKI 66
Query: 139 NESKAAVIELNCETDFVSRNEIFQYXXXXXXXXXXXXENVSQPVSGLFPVGPEYLEGLKL 198
+ + ++E+NC+TDFV+++ FQ + + V+G +E LK
Sbjct: 67 DGNYGIILEVNCQTDFVAKDAGFQ---------AFADKVLDAAVAGKI----TDVEVLKA 113
Query: 199 NLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIA 258
+ ++ + A +GEN+ +RR ++A V+ +Y H + RI
Sbjct: 114 QFEEERVA-----------LVAKIGENINIRR---VAALEGDVLGSYQHGA------RIG 153
Query: 259 GLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREI 310
L++ + D + + +AMH+ A KP F+ E VSA+ +E E ++
Sbjct: 154 VLVAAKGAD--------EELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQV 197
>pdb|1EFU|B Chain B, Elongation Factor Complex Ef-TuEF-Ts From Escherichia Coli
pdb|1EFU|D Chain D, Elongation Factor Complex Ef-TuEF-Ts From Escherichia Coli
Length = 282
Score = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 65/232 (28%), Positives = 116/232 (50%), Gaps = 41/232 (17%)
Query: 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQ 138
+L+K+LRE+T A M D K AL + + DIE A++ +RK G + A+KK+ A +G++
Sbjct: 6 SLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGVIKTKI 65
Query: 139 NESKAAVIELNCETDFVSRNEIFQYXXXXXXXXXXXXENVSQPVSGLFPVGPEYLEGLKL 198
+ + ++E+NC+TDFV+++ FQ + V+G +E LK
Sbjct: 66 DGNYGIILEVNCQTDFVAKDAGFQAFADKV---------LDAAVAGKIT----DVEVLKA 112
Query: 199 NLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIA 258
+ ++ + A +GEN+ +RR ++A V+ +Y H + RI
Sbjct: 113 QFEEERVA-----------LVAKIGENINIRR---VAALEGDVLGSYQHGA------RIG 152
Query: 259 GLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREI 310
L++ + D + + +AMH+ A KP F+ E VSA+ +E E ++
Sbjct: 153 VLVAAKGAD--------EELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQV 196
>pdb|3MMP|A Chain A, Structure Of The Qb Replicase, An Rna-Dependent Rna
Polymerase Consisting Of Viral And Host Proteins
pdb|3MMP|C Chain C, Structure Of The Qb Replicase, An Rna-Dependent Rna
Polymerase Consisting Of Viral And Host Proteins
Length = 678
Score = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 65/232 (28%), Positives = 117/232 (50%), Gaps = 41/232 (17%)
Query: 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQ 138
+L+K+LRE+T A M D K AL + + DIE A++ +RK G + A+KK+ A +G++
Sbjct: 7 SLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGVIKTKI 66
Query: 139 NESKAAVIELNCETDFVSRNEIFQYXXXXXXXXXXXXENVSQPVSGLFPVGPEYLEGLKL 198
+ + ++E+NC+TDFV+++ FQ + + V+G +E LK
Sbjct: 67 DGNYGIILEVNCQTDFVAKDAGFQ---------AFADKVLDAAVAGKIT----DVEVLKA 113
Query: 199 NLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIA 258
+ ++ + A +GEN+ +RR ++A V+ +Y H + RI
Sbjct: 114 QFEEERVA-----------LVAKIGENINIRR---VAALEGDVLGSYQHGA------RIG 153
Query: 259 GLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREI 310
L++ + D + + +AMH+ A KP F+ E VSA+ +E E ++
Sbjct: 154 VLVAAKGAD--------EELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQV 197
>pdb|1XB2|B Chain B, Crystal Structure Of Bos Taurus Mitochondrial Elongation
Factor TuTS COMPLEX
Length = 291
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 97/236 (41%), Gaps = 41/236 (17%)
Query: 80 LIKQLREQTSAPMKDVKLALVDCDWDIEAA----LKELRKRGKVLASKKSSRTATEGLLA 135
L+ +LR +T + K AL C D++ A K+ +K G A++ R EGL+
Sbjct: 7 LLMKLRRKTGYSFINCKKALETCGGDLKQAESWLHKQAQKEGWSKAARLHGRKTKEGLIG 66
Query: 136 LAQNESKAAVIELNCETDFVSRNEIF-QYXXXXXXXXXXXXENVSQPVSGL--------- 185
L Q ++E+NCETDFVSRN F Q +N+ +S
Sbjct: 67 LLQEGDTTVLVEVNCETDFVSRNLKFQQLVQQVALGTLLHCQNLKDQLSTYSKGFLNSSE 126
Query: 186 ---FPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSASSPGVV 242
P GPE E ++++ + +GEN+ L+R + + V
Sbjct: 127 LSELPAGPER---------------EGSLKDQLALAIGKLGENMILKRAAWVKVPAGFYV 171
Query: 243 STYLHTSPQSG------LGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPL 292
+Y+H + S LG+ L+ E + ++ L +G L H+V PL
Sbjct: 172 GSYVHGAMHSPSLHNLVLGKYGALVICETSELKAN---LADLGRRLGQHVVGMAPL 224
>pdb|1TFE|A Chain A, Dimerization Domain Of Ef-Ts From T. Thermophilus
Length = 145
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 26/36 (72%), Gaps = 2/36 (5%)
Query: 129 ATEGLLA--LAQNESKAAVIELNCETDFVSRNEIFQ 162
A EG++ + N+ ++ELNCETDFV+RNE+FQ
Sbjct: 1 AREGIIGHYIHHNQRVGVLVELNCETDFVARNELFQ 36
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 237 SSPGVVSTYLHTSPQSGLGRIAGLLSLEVE-DGSSSFDPLKRVGSELAMHIVAQKPLFLT 295
+ G++ Y+H + + G+ L+ L E D + + + + +LAMHI P +++
Sbjct: 1 AREGIIGHYIHHNQRVGV-----LVELNCETDFVARNELFQNLAKDLAMHIAMMNPRYVS 55
Query: 296 KELVSADALENEREI 310
E + A+ LE ER+I
Sbjct: 56 AEEIPAEELEKERQI 70
>pdb|3PER|A Chain A, Crystal Structure Of Boxb With Phosphate Bound To The
Diiron Center
pdb|3PER|B Chain B, Crystal Structure Of Boxb With Phosphate Bound To The
Diiron Center
pdb|3PF7|A Chain A, Crystal Structure Of Boxb With Malonate Bound To The
Diiron Center
pdb|3PF7|B Chain B, Crystal Structure Of Boxb With Malonate Bound To The
Diiron Center
pdb|3PM5|A Chain A, Crystal Structure Of Boxb In Mixed Valent State With Bound
Benzoyl-Coa
pdb|3PM5|B Chain B, Crystal Structure Of Boxb In Mixed Valent State With Bound
Benzoyl-Coa
pdb|3PM5|C Chain C, Crystal Structure Of Boxb In Mixed Valent State With Bound
Benzoyl-Coa
pdb|3PM5|D Chain D, Crystal Structure Of Boxb In Mixed Valent State With Bound
Benzoyl-Coa
pdb|3Q1G|A Chain A, Crystal Structure Of Boxb Crystallized With Peg
pdb|3Q1G|B Chain B, Crystal Structure Of Boxb Crystallized With Peg
pdb|3Q1G|C Chain C, Crystal Structure Of Boxb Crystallized With Peg
pdb|3Q1G|D Chain D, Crystal Structure Of Boxb Crystallized With Peg
Length = 481
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 192 YLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQ 251
Y GLK + KIG + +QN+ EV + G+ + R LSA + + ++ T Q
Sbjct: 311 YTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLRDDWI-TDVQ 369
Query: 252 SGLGR 256
+G+ R
Sbjct: 370 AGVDR 374
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
0.315 0.130 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,041,577
Number of Sequences: 62578
Number of extensions: 288991
Number of successful extensions: 803
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 784
Number of HSP's gapped (non-prelim): 19
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
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: 51 (24.3 bits)