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= 042762
(96 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 = 155 bits (391), Expect = 6e-39, Method: Compositional matrix adjust.
Identities = 74/96 (77%), Positives = 83/96 (86%)
Query: 1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
TILGYKRSKSNQY NTSL+QIEGVNTKE+V WY K +AY+YKAKTK + + RCIWGKV
Sbjct: 16 TILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAKTKSNDSTIRCIWGKV 75
Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
R HGNSGVVRA+F+SNLPP SMG KVRVFMYPS+I
Sbjct: 76 TRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 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 = 109 bits (272), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 50/94 (53%), Positives = 66/94 (70%)
Query: 3 LGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVAR 62
L Y+RSK PN SLI+IEGV T + +Y K +AY+Y+A + + R +WGKV R
Sbjct: 14 LSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTR 73
Query: 63 SHGNSGVVRAEFKSNLPPKSMGDKVRVFMYPSNI 96
+HGNSGVVRA F++NLP K+ G VR+F+YPSNI
Sbjct: 74 THGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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 = 97.1 bits (240), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 42/91 (46%), Positives = 66/91 (72%), Gaps = 1/91 (1%)
Query: 4 GYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKVARS 63
G++RSK Q N +L++++ VNTKE V +Y K + YIYK + KK+ ++YR IWG++ ++
Sbjct: 22 GFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQ-KKNGSNYRTIWGRIGKA 80
Query: 64 HGNSGVVRAEFKSNLPPKSMGDKVRVFMYPS 94
HGN+GV A F NLPP+++G +RV +YP+
Sbjct: 81 HGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111
>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 149
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 44/109 (40%), Positives = 63/109 (57%), Gaps = 15/109 (13%)
Query: 1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIY------------KAKTKK 48
T+ GY R Q NT+L++IE VNT E WY K + Y+Y KA ++
Sbjct: 43 TLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWSKAPARR 102
Query: 49 SWTHYRCIWGKVARSHGNSGVVRAEFK-SNLPPKSMGDKVRVFMYPSNI 96
S T R IWG++ R HG SG VR +F S++P ++G ++RV++YPS I
Sbjct: 103 SNT--RAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 8/91 (8%)
Query: 1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
+L Y+RSK NQ+ N +I+ VN++E+ + ++K+ + K + GK+
Sbjct: 6 VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGK------ILKGKI 57
Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVFM 91
R HG G VRA F+ LP +++GD V + +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIVL 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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 8/90 (8%)
Query: 1 TILGYKRSKSNQYPNTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGKV 60
+L Y+RSK NQ+ N +I+ VN++E+ + ++K+ + K + GK+
Sbjct: 6 VVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGK------ILKGKI 57
Query: 61 ARSHGNSGVVRAEFKSNLPPKSMGDKVRVF 90
R HG G VRA F+ LP +++GD V +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIV 87
>pdb|1CIC|B Chain B, Idiotope-Anti-Idiotope Fab-Fab Complex; D1.3-E225
Length = 217
Score = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 8/29 (27%), Positives = 20/29 (68%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYK 43
+T+ +Q+ G+ +++ V+YC + LA+ +
Sbjct: 77 STAYMQLSGLTSEDSAVYYCARGLAFYFD 105
>pdb|2H9G|B Chain B, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
pdb|2H9G|H Chain H, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
Length = 228
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGK 59
NT+ +Q+ + ++ V+YC + LA + + W Y WG+
Sbjct: 77 NTAYLQMNSLRAEDTAVYYCARRLALV------RMWMDY---WGQ 112
>pdb|4EVN|A Chain A, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|C Chain C, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|E Chain E, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|G Chain G, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|I Chain I, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|K Chain K, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|M Chain M, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
pdb|4EVN|O Chain O, Crystal Structure Of Fab Cr6261 (Somatic Heavy Chain With
Germline- Reverted Light Chain)
Length = 242
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 6/31 (19%), Positives = 19/31 (61%)
Query: 10 SNQYPNTSLIQIEGVNTKEKVVWYCCKHLAY 40
++ + T +++ + +++ ++YC KH+ Y
Sbjct: 72 ADDFAGTVYMELSSLRSEDTAMYYCAKHMGY 102
>pdb|3GBM|H Chain H, Crystal Structure Of Fab Cr6261 In Complex With A H5n1
Influenza Virus Hemagglutinin.
pdb|3GBM|I Chain I, Crystal Structure Of Fab Cr6261 In Complex With A H5n1
Influenza Virus Hemagglutinin.
pdb|3GBN|H Chain H, Crystal Structure Of Fab Cr6261 In Complex With The 1918
H1n1 Influenza Virus Hemagglutinin
Length = 226
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 6/31 (19%), Positives = 19/31 (61%)
Query: 10 SNQYPNTSLIQIEGVNTKEKVVWYCCKHLAY 40
++ + T +++ + +++ ++YC KH+ Y
Sbjct: 72 ADDFAGTVYMELSSLRSEDTAMYYCAKHMGY 102
>pdb|4FQV|H Chain H, Crystal Structure Of Broadly Neutralizing Antibody Cr9114
Bound To H7 Influenza Hemagglutinin
pdb|4FQV|I Chain I, Crystal Structure Of Broadly Neutralizing Antibody Cr9114
Bound To H7 Influenza Hemagglutinin
pdb|4FQV|J Chain J, Crystal Structure Of Broadly Neutralizing Antibody Cr9114
Bound To H7 Influenza Hemagglutinin
pdb|4FQY|H Chain H, Crystal Structure Of Broadly Neutralizing Antibody Cr9114
Bound To H3 Influenza Hemagglutinin
Length = 224
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 7/30 (23%), Positives = 19/30 (63%)
Query: 13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIY 42
+ NT+ +++ + +++ V++C +H Y Y
Sbjct: 75 FSNTAYMELNSLTSEDTAVYFCARHGNYYY 104
>pdb|4FQH|H Chain H, Crystal Structure Of Fab Cr9114
pdb|4FQH|A Chain A, Crystal Structure Of Fab Cr9114
pdb|4FQI|H Chain H, Crystal Structure Of Fab Cr9114 In Complex With A H5n1
Influenza Virus Hemagglutinin
Length = 230
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 7/30 (23%), Positives = 19/30 (63%)
Query: 13 YPNTSLIQIEGVNTKEKVVWYCCKHLAYIY 42
+ NT+ +++ + +++ V++C +H Y Y
Sbjct: 75 FSNTAYMELNSLTSEDTAVYFCARHGNYYY 104
>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 = 5.5, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIY 42
NT+ +Q+ + +++ V+YC + Y Y
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARREVYSY 104
>pdb|1ZTX|H Chain H, West Nile Virus Envelope Protein Diii In Complex With
Neutralizing E16 Antibody Fab
Length = 219
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 7/26 (26%), Positives = 17/26 (65%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAY 40
NT+ +Q+ + +++ V+YC + +Y
Sbjct: 77 NTAFMQLSSLTSEDSAVYYCARSASY 102
>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: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIY 42
NT+ +Q+ + +++ V+YC + 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 = 7.2, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIY 42
NT+ +Q+ + +++ V+YC + Y Y
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARRELYSY 104
>pdb|1HZH|H Chain H, Crystal Structure Of The Intact Human Igg B12 With Broad
And Potent Activity Against Primary Hiv-1 Isolates: A
Template For Hiv Vaccine Design
pdb|1HZH|K Chain K, Crystal Structure Of The Intact Human Igg B12 With Broad
And Potent Activity Against Primary Hiv-1 Isolates: A
Template For Hiv Vaccine Design
Length = 457
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 10/45 (22%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGK 59
NT+ +++ + + + V+YC + Y + + ++ Y +WGK
Sbjct: 77 NTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNY--YMDVWGK 119
>pdb|1N0X|H Chain H, Crystal Structure Of A Broadly Neutralizing Anti-Hiv-1
Antibody In Complex With A Peptide Mimotope
pdb|1N0X|K Chain K, Crystal Structure Of A Broadly Neutralizing Anti-Hiv-1
Antibody In Complex With A Peptide Mimotope
pdb|3RU8|H Chain H, Structure Of An Hiv Epitope Scaffold In Complex With
Neutralizing Antibody B12 Fab
Length = 230
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 10/45 (22%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGK 59
NT+ +++ + + + V+YC + Y + + + +Y +WGK
Sbjct: 77 NTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDN--YYMDVWGK 119
>pdb|2NY7|H Chain H, Hiv-1 Gp120 Envelope Glycoprotein Complexed With The
Broadly Neutralizing Cd4-Binding-Site Antibody B12
Length = 230
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 10/45 (22%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 15 NTSLIQIEGVNTKEKVVWYCCKHLAYIYKAKTKKSWTHYRCIWGK 59
NT+ +++ + + + V+YC + Y + + + +Y +WGK
Sbjct: 77 NTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDN--YYMDVWGK 119
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 0.132 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,921,607
Number of Sequences: 62578
Number of extensions: 99596
Number of successful extensions: 472
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 443
Number of HSP's gapped (non-prelim): 35
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
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)