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= 029444
(193 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RQS|A Chain A, Nmr Structure Of C-Terminal Domain Of Ribosomal Protein L7
From E.Coli
pdb|1CTF|A Chain A, Structure Of The C-Terminal Domain Of The Ribosomal
Protein L7L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS
Length = 74
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 122 EKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIE 181
EKT FDV ++K V+ LG+KEAK+LVE AP LK+G++K++A + +
Sbjct: 4 EKTEFDVILKAAGANKVA-VIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKK 62
Query: 182 KIKAAG 187
++ AG
Sbjct: 63 ALEEAG 68
>pdb|1RQU|A Chain A, Nmr Structure Of L7 Dimer From E.Coli
pdb|1RQU|B Chain B, Nmr Structure Of L7 Dimer From E.Coli
pdb|1RQV|A Chain A, Spatial Model Of L7 Dimer From E.Coli With One Hinge
Region In Helical State
pdb|1RQV|B Chain B, Spatial Model Of L7 Dimer From E.Coli With One Hinge
Region In Helical State
Length = 120
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 121 KEKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNII 180
+EKT FDV ++K V+ LG+KEAK+LVE AP LK+G++K++A +
Sbjct: 49 EEKTEFDVILKAAGANKVA-VIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALK 107
Query: 181 EKIKAAG 187
+ ++ AG
Sbjct: 108 KALEEAG 114
>pdb|2XTG|L Chain L, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|L Chain L, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|3SGF|J Chain J, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|K Chain K, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|L Chain L, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|M Chain M, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOS|J Chain J, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|K Chain K, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|L Chain L, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|M Chain M, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 121
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 121 KEKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNII 180
+EKT FDV ++K V+ LG+KEAK+LVE AP LK+G++K++A +
Sbjct: 50 EEKTEFDVILKAAGANKVA-VIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALK 108
Query: 181 EKIKAAG 187
+ ++ AG
Sbjct: 109 KALEEAG 115
>pdb|2GYA|3 Chain 3, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYA|5 Chain 5, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYC|3 Chain 3, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
pdb|2GYC|5 Chain 5, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
Length = 119
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 121 KEKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNII 180
+EKT FDV ++K V+ LG+KEAK+LVE AP LK+G++K++A +
Sbjct: 48 EEKTEFDVILKAAGANKVA-VIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALK 106
Query: 181 EKIKAAG 187
+ ++ AG
Sbjct: 107 KALEEAG 113
>pdb|2FTC|E Chain E, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
pdb|2FTC|F Chain F, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
Length = 137
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 43/144 (29%), Positives = 67/144 (46%), Gaps = 20/144 (13%)
Query: 62 KVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAK----- 116
K+ QL + IASLT E ++ L K K+Q + L P GG G+A
Sbjct: 2 KIQQLVQDIASLTLLEISDLNELLKKTL---KIQDVG-----LMPMGGMVPGAAPAPTAP 53
Query: 117 ------VEEKKEKTTFDVXXXXXXXXXXXXIVKEVKTFFD-LGMKEAKELVEKAPVVLKQ 169
V ++KE+T F V ++KE+K + + + +AK+LVE P +K
Sbjct: 54 EAAEEDVPKQKERTHFTVRLTEAKPVDKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKA 113
Query: 170 GLTKEEASNIIEKIKAAGGVAIME 193
+ K EA I ++A GG ++E
Sbjct: 114 NVAKAEAEKIKAALEAVGGTVVLE 137
>pdb|2ZJQ|5 Chain 5, Interaction Of L7 With L11 Induced By Microccocin Binding
To The Deinococcus Radiodurans 50s Subunit
Length = 122
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 2/67 (2%)
Query: 121 KEKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNII 180
+EKT FDV ++KE++ LG+KEAK++ EK VLK+G+ K+EA +
Sbjct: 52 EEKTEFDVVLIDAGASKIN-VIKEIRGITGLGLKEAKDMSEKGG-VLKEGVAKDEAEKMK 109
Query: 181 EKIKAAG 187
+++AAG
Sbjct: 110 AQLEAAG 116
>pdb|2J01|L Chain L, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J01|M Chain M, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J03|L Chain L, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|2J03|M Chain M, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|3I8I|I Chain I, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I8I|J Chain J, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s)
Length = 125
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 122 EKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEK-APVVLKQGLTKEEASNII 180
EKT FDV ++KE++ LG+KEAK+L EK PV K+G++K+EA I
Sbjct: 56 EKTEFDVILKEAGAKKLE-VIKELRAITGLGLKEAKDLAEKGGPV--KEGVSKQEAEEIK 112
Query: 181 EKIKAAGGV 189
+K++A G V
Sbjct: 113 KKLEAVGAV 121
>pdb|2BCW|B Chain B, Coordinates Of The N-Terminal Domain Of Ribosomal Protein
L11,C-Terminal Domain Of Ribosomal Protein L7L12 AND A
Portion Of The G' Domain Of Elongation Factor G, As
Fitted Into Cryo-Em Map Of An Escherichia Coli 70sEf-
GGdpFusidic Acid Complex
Length = 68
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 34/47 (72%)
Query: 141 IVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAG 187
++K V+ LG+KEAK+LVE AP LK+G++K++A + + ++ AG
Sbjct: 16 VIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAG 62
>pdb|1DD3|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD3|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD4|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritim
pdb|1DD4|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritim
pdb|1GIY|I Chain I, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1GIY|J Chain J, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1YL3|I Chain I, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|1YL3|J Chain J, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4
Length = 128
Score = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 120 KKEKTTFDVXXXXXXXXXXXXIVKEVKTFFDLGMKEAKELVEKA---PVVLKQGLT 172
++EKT FDV ++K V+ LG+KEAK+LVEKA V+K G++
Sbjct: 53 QEEKTEFDVVLKSFGQNKIQ-VIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVS 107
>pdb|1GEE|A Chain A, Crystal Structure Of Glucose Dehydrogenase Mutant Q252l
Complexed With Nad+
pdb|1GEE|B Chain B, Crystal Structure Of Glucose Dehydrogenase Mutant Q252l
Complexed With Nad+
pdb|1GEE|E Chain E, Crystal Structure Of Glucose Dehydrogenase Mutant Q252l
Complexed With Nad+
pdb|1GEE|F Chain F, Crystal Structure Of Glucose Dehydrogenase Mutant Q252l
Complexed With Nad+
Length = 261
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 161 EKAPVVLKQGLTKEEASNIIEKIKAAGGVAI 191
EKA VV+ ++EA++++E+IK GG AI
Sbjct: 30 EKAKVVVNYRSKEDEANSVLEEIKKVGGEAI 60
>pdb|1GCO|A Chain A, Crystal Structure Of Glucose Dehydrogenase Complexed With
Nad+
pdb|1GCO|B Chain B, Crystal Structure Of Glucose Dehydrogenase Complexed With
Nad+
pdb|1GCO|E Chain E, Crystal Structure Of Glucose Dehydrogenase Complexed With
Nad+
pdb|1GCO|F Chain F, Crystal Structure Of Glucose Dehydrogenase Complexed With
Nad+
Length = 261
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 161 EKAPVVLKQGLTKEEASNIIEKIKAAGGVAI 191
EKA VV+ ++EA++++E+IK GG AI
Sbjct: 30 EKAKVVVNYRSKEDEANSVLEEIKKVGGEAI 60
>pdb|1RWB|A Chain A, Cooperative Effect Of Two Surface Amino Acid Mutations
(Q252l And E170k) Of Glucose Dehydrogenase From Bacillus
Megaterium Iwg3 For The Stabilization Of Oligomeric
State
pdb|1RWB|B Chain B, Cooperative Effect Of Two Surface Amino Acid Mutations
(Q252l And E170k) Of Glucose Dehydrogenase From Bacillus
Megaterium Iwg3 For The Stabilization Of Oligomeric
State
pdb|1RWB|E Chain E, Cooperative Effect Of Two Surface Amino Acid Mutations
(Q252l And E170k) Of Glucose Dehydrogenase From Bacillus
Megaterium Iwg3 For The Stabilization Of Oligomeric
State
pdb|1RWB|F Chain F, Cooperative Effect Of Two Surface Amino Acid Mutations
(Q252l And E170k) Of Glucose Dehydrogenase From Bacillus
Megaterium Iwg3 For The Stabilization Of Oligomeric
State
Length = 261
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 161 EKAPVVLKQGLTKEEASNIIEKIKAAGGVAI 191
EKA VV+ ++EA++++E+IK GG AI
Sbjct: 30 EKAKVVVNYRSKEDEANSVLEEIKKVGGEAI 60
>pdb|1G6K|A Chain A, Crystal Structure Of Glucose Dehydrogenase Mutant E96a
Complexed With Nad+
pdb|1G6K|B Chain B, Crystal Structure Of Glucose Dehydrogenase Mutant E96a
Complexed With Nad+
pdb|1G6K|E Chain E, Crystal Structure Of Glucose Dehydrogenase Mutant E96a
Complexed With Nad+
pdb|1G6K|F Chain F, Crystal Structure Of Glucose Dehydrogenase Mutant E96a
Complexed With Nad+
Length = 261
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 161 EKAPVVLKQGLTKEEASNIIEKIKAAGGVAI 191
EKA VV+ ++EA++++E+IK GG AI
Sbjct: 30 EKAKVVVNYRSKEDEANSVLEEIKKVGGEAI 60
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
0.316 0.136 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,394,341
Number of Sequences: 62578
Number of extensions: 203394
Number of successful extensions: 564
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 541
Number of HSP's gapped (non-prelim): 19
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
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: 49 (23.5 bits)