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= psy4327
(187 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 = 125 bits (314), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 61/108 (56%), Positives = 74/108 (68%), Gaps = 6/108 (5%)
Query: 80 RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
RLY R G+KR + NQ+ NTSLL IE NTKE+ +Y GKR ++YKAKTK
Sbjct: 10 RLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAKTKS------ 63
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
S +R IWGKVTRPHG+SG VRAKF NLP MG+KVR+ +YPS+I
Sbjct: 64 NDSTIRCIWGKVTRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 111
>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 149
Score = 106 bits (264), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 55/113 (48%), Positives = 76/113 (67%), Gaps = 5/113 (4%)
Query: 80 RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKA-KTKELKPHS 138
RLY + G+ RG Q+ NT+L+ IE NT EDA++YVGKR ++Y K K S
Sbjct: 37 RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96
Query: 139 K---RKSRLRAIWGKVTRPHGSSGSVRAKFH-RNLPAIYMGRKVRIMLYPSNI 187
K R+S RAIWG++TRPHG+SG+VR KF+ ++PA +GR++R+ LYPS I
Sbjct: 97 KAPARRSNTRAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 149
>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 = 106 bits (264), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 54/108 (50%), Positives = 72/108 (66%), Gaps = 6/108 (5%)
Query: 80 RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
RLY + ++R +R +PN SL+ IE T +DA+FY+GKR ++Y+A +KE+
Sbjct: 6 RLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRA-SKEV----- 59
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
R S++R +WGKVTR HG+SG VRA F NLPA G VRI LYPSNI
Sbjct: 60 RGSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 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 = 96.7 bits (239), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 45/106 (42%), Positives = 66/106 (62%), Gaps = 7/106 (6%)
Query: 80 RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
RL+ +A FTGF+R + Q+ N +LL ++ NTKED FY GKR V++YK + K
Sbjct: 13 RLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKN------ 66
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPS 185
S R IWG++ + HG++G A+F NLP +G +R+MLYP+
Sbjct: 67 -GSNYRTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 53/99 (53%), Gaps = 14/99 (14%)
Query: 84 RAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSR 143
+ + ++R + NQH N ++ N++E+A +G+ + L+K+ + ++
Sbjct: 4 KGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGKI--------- 52
Query: 144 LRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIML 182
+ GK+ R HG+ G+VRA+F + LP +G V I+L
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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 52/98 (53%), Gaps = 14/98 (14%)
Query: 84 RAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSR 143
+ + ++R + NQH N ++ N++E+A +G+ + L+K+ + ++
Sbjct: 4 KGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGKI--------- 52
Query: 144 LRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIM 181
+ GK+ R HG+ G+VRA+F + LP +G V I+
Sbjct: 53 ---LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIV 87
>pdb|1KCZ|A Chain A, Crystal Structure Of Beta-Methylaspartase From Clostridium
Tetanomorphum. Mg-Complex.
pdb|1KCZ|B Chain B, Crystal Structure Of Beta-Methylaspartase From Clostridium
Tetanomorphum. Mg-Complex
Length = 413
Score = 30.4 bits (67), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 100 NTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
+ L+A E CNT ED +F+ + + + KT +L
Sbjct: 301 DAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDL 335
>pdb|3ZVH|A Chain A, Methylaspartate Ammonia Lyase From Clostridium
Tetanomorphum Mutant Q73a
pdb|3ZVH|B Chain B, Methylaspartate Ammonia Lyase From Clostridium
Tetanomorphum Mutant Q73a
Length = 438
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 100 NTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
+ L+A E CNT ED +F+ + + + KT +L
Sbjct: 301 DAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDL 335
>pdb|3ZVI|A Chain A, Methylaspartate Ammonia Lyase From Clostridium
Tetanomorphum Mutant L384a
pdb|3ZVI|B Chain B, Methylaspartate Ammonia Lyase From Clostridium
Tetanomorphum Mutant L384a
Length = 438
Score = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 100 NTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
+ L+A E CNT ED +F+ + + + KT +L
Sbjct: 301 DAELVADEWCNTVEDVKFFTDNKAGHMVQIKTPDL 335
>pdb|1KD0|A Chain A, Crystal Structure Of Beta-Methylaspartase From Clostridium
Tetanomorphum. Apo-Structure.
pdb|1KD0|B Chain B, Crystal Structure Of Beta-Methylaspartase From Clostridium
Tetanomorphum. Apo-Structure
Length = 413
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 100 NTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
+ L+A E CNT ED +F+ + + KT +L
Sbjct: 301 DAELVADEWCNTVEDVKFFTDNKAGHXVQIKTPDL 335
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
0.327 0.137 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,447,559
Number of Sequences: 62578
Number of extensions: 108877
Number of successful extensions: 372
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 355
Number of HSP's gapped (non-prelim): 10
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)