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= 033755
(112 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 111
Score = 192 bits (488), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 91/111 (81%), Positives = 100/111 (90%)
Query: 2 VKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
+KGRQG+RVRLYVRGTILGYKRSKSNQY NTSL+QIEGVNTKE+V WY GKR+AY+YKAK
Sbjct: 1 MKGRQGQRVRLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAK 60
Query: 62 VKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
K N S RCIWGKV RPHGNSGVVRAKF+SNLPP SMG +VRVFMYPS+I
Sbjct: 61 TKSNDSTIRCIWGKVTRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 111
>pdb|3IZS|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|FF Chain f, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 107
Score = 128 bits (321), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 61/106 (57%), Positives = 76/106 (71%)
Query: 7 GERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNG 66
E RLYV+G L Y+RSK PN SLI+IEGV T +D +Y GKR+AY+Y+A + G
Sbjct: 2 AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61
Query: 67 SHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112
S R +WGKV R HGNSGVVRA F++NLP K+ G VR+F+YPSNI
Sbjct: 62 SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107
>pdb|4A18|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 113
Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 51/101 (50%), Positives = 76/101 (75%), Gaps = 1/101 (0%)
Query: 10 VRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHY 69
RL+V+ G++RSK Q N +L++++ VNTKEDV++Y GKR+ YIYK + KKNGS+Y
Sbjct: 12 TRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQ-KKNGSNY 70
Query: 70 RCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPS 110
R IWG++ + HGN+GV A+F NLPP+++G +RV +YP+
Sbjct: 71 RTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111
>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 149
Score = 105 bits (263), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 52/113 (46%), Positives = 71/113 (62%), Gaps = 11/113 (9%)
Query: 11 RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYK----------A 60
RLY++GT+ GY R Q NT+L++IE VNT ED WY GKR+ Y+Y +
Sbjct: 37 RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96
Query: 61 KVKKNGSHYRCIWGKVARPHGNSGVVRAKFK-SNLPPKSMGDRVRVFMYPSNI 112
K S+ R IWG++ RPHG SG VR KF S++P ++G R+RV++YPS I
Sbjct: 97 KAPARRSNTRAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 149
>pdb|1SQR|A Chain A, Solution Structure Of The 50s Ribosomal Protein L35ae From
Pyrococcus Furiosus. Northeast Structural Genomics
Consortium Target Pfr48.
pdb|2LP6|A Chain A, Refined Solution Nmr Structure Of The 50s Ribosomal
Protein L35ae From Pyrococcus Furiosus, Northeast
Structural Genomics Consortium Target (Nesg) Pfr48
Length = 95
Score = 62.4 bits (150), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 54/96 (56%), Gaps = 8/96 (8%)
Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
+ ++G +L Y+RSK NQ+ N +I+ VN++E+ S G+ + + +
Sbjct: 1 MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLW--------KSPSGKI 52
Query: 72 IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFM 107
+ GK+ R HG G VRA+F+ LP +++GD V + +
Sbjct: 53 LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIVL 88
>pdb|3J21|CC Chain c, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 87
Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 53/95 (55%), Gaps = 8/95 (8%)
Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRC 71
+ ++G +L Y+RSK NQ+ N +I+ VN++E+ S G+ + + +
Sbjct: 1 MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLW--------KSPSGKI 52
Query: 72 IWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVF 106
+ GK+ R HG G VRA+F+ LP +++GD V +
Sbjct: 53 LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIV 87
>pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution.
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
Length = 814
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 35 IQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFK 91
+ EG+N + WY G M YIY + + SHY + P+ +G K
Sbjct: 484 LNYEGMNDENTRGWYTGDGMFYIYNS----DQSHYSNHFWPTVNPYKMAGTTEKDAK 536
>pdb|2OV7|A Chain A, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OV7|B Chain B, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OV7|C Chain C, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OUM|A Chain A, The First Domain Of L1 From Thermus Thermophilus
pdb|2VPL|A Chain A, The Structure Of The Complex Between The First Domain Of
L1 Protein From Thermus Thermophilus And Mrna From
Methanococcus Jannaschii
pdb|2VPL|C Chain C, The Structure Of The Complex Between The First Domain Of
L1 Protein From Thermus Thermophilus And Mrna From
Methanococcus Jannaschii
Length = 137
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 72 IWGKVARPHG--------NSGVVRAKF-KSNLPPKSMGDRVRVFM 107
+ G V+ PHG +G + A K++ PP+ + D +R F+
Sbjct: 58 VRGTVSLPHGGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFI 102
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 66 GSHYRCIWGKVARPHGNSGVVRAKF-KSNLPPKSMGDRVRVFM 107
G R I G++ + +G + A K++ PP+ + D +R F+
Sbjct: 151 GEIIREIKGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFI 193
>pdb|1AP2|B Chain B, Single Chain Fv Of C219
pdb|1AP2|D Chain D, Single Chain Fv Of C219
Length = 123
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 11/55 (20%)
Query: 31 NTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWG---KVARPHGN 82
NT+ +Q+ + +++ +YC +R Y Y + + +WG V P G+
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARREVYSYYSPLD--------VWGAGTTVTVPSGS 123
>pdb|3M84|A Chain A, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis
pdb|3M84|B Chain B, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis
pdb|3QTY|A Chain A, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis Complexed With
Pyrophosphate
pdb|3QTY|B Chain B, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis Complexed With
Pyrophosphate
Length = 350
Score = 26.2 bits (56), Expect = 5.0, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 27 NQYPNTSLIQ-IEGVNTKEDVSWYCGK 52
N Y + L+Q I+GV TK V+ CGK
Sbjct: 56 NNYDDPVLVQSIDGVGTKTKVAVXCGK 82
>pdb|2AP2|B Chain B, Single Chain Fv Of C219 In Complex With Synthetic Epitope
Peptide
pdb|2AP2|D Chain D, Single Chain Fv Of C219 In Complex With Synthetic Epitope
Peptide
Length = 122
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 31 NTSLIQIEGVNTKEDVSWYCGKRMAYIY 58
NT+ +Q+ + +++ +YC +R Y Y
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARREVYSY 104
>pdb|1MVU|B Chain B, Single Chain Fv Of C219 Heavy Chain V101l Mutant In
Complex With Synthetic Epitope Peptide
Length = 121
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 31 NTSLIQIEGVNTKEDVSWYCGKRMAYIY 58
NT+ +Q+ + +++ +YC +R Y Y
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARRELYSY 104
>pdb|3RVT|D Chain D, Structure Of 4c1 Fab In P212121 Space Group
pdb|3RVU|D Chain D, Structure Of 4c1 Fab In C2221 Space Group
pdb|3RVV|D Chain D, Crystal Structure Of Der F 1 Complexed With Fab 4c1
pdb|3RVW|D Chain D, Crystal Structure Of Der P 1 Complexed With Fab 4c1
pdb|3RVX|D Chain D, Crystal Structure Of Der P 1 Complexed With Fab 4c1
Length = 255
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 31 NTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK 61
N +Q+ V T++ ++YCG+ Y Y +
Sbjct: 77 NQFFLQLNSVTTEDTATYYCGRTGVYRYPER 107
>pdb|3HK4|A Chain A, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|B Chain B, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|C Chain C, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|D Chain D, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
Length = 136
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 74 GKVARPHGNSGVVRAKFKSNLPPKSMGDRV 103
G V P+ N +FK ++ PK+ G+RV
Sbjct: 85 GSVEGPYVNGDQFALRFKFDVTPKATGERV 114
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
0.319 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,405,275
Number of Sequences: 62578
Number of extensions: 126261
Number of successful extensions: 406
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 385
Number of HSP's gapped (non-prelim): 20
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)