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= 034006
(106 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|RR Chain r, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 105
Score = 199 bits (505), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 99/104 (95%), Positives = 102/104 (98%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKTKKTYCK+KECRKHTLHKVTQYKKGKDSL+AQGKRRYDRKQSGYGGQTKPVFHKK
Sbjct: 2 VNVPKTKKTYCKNKECRKHTLHKVTQYKKGKDSLSAQGKRRYDRKQSGYGGQTKPVFHKK 61
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKKGKGTSLF 106
AKTTKKIVL+LQCQ CKH SQHPIKRCKHFEIGGDKKGKGTSLF
Sbjct: 62 AKTTKKIVLKLQCQSCKHYSQHPIKRCKHFEIGGDKKGKGTSLF 105
>pdb|2ZKR|4 Chain 4, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 106
Score = 141 bits (356), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 76/105 (72%), Positives = 85/105 (80%), Gaps = 4/105 (3%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKT++T+CK +C KH HKVTQYKKGKDSL AQGKRRYDRKQSGYGGQTKP+F KK
Sbjct: 2 VNVPKTRRTFCK--KCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKK 59
Query: 63 AKTTKKIVLRLQC--QGCKHVSQHPIKRCKHFEIGGDKKGKGTSL 105
AKTTKKIVLRL+C C+ IKRCKHFE+GGDKK KG +
Sbjct: 60 AKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVI 104
>pdb|3IZS|RR Chain r, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|FF Chain f, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|FF Chain f, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|OO Chain o, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|OO Chain o, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|OO Chain o, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 106
Score = 140 bits (353), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 80/103 (77%), Positives = 89/103 (86%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKT+KTYCK K CRKHT HKVTQYK GK SL AQGKRRYDRKQSG+GGQTKPVFHKK
Sbjct: 2 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 61
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKKGKGTSL 105
AKTTKK+VLRL+C CK +Q +KRCKHFE+GG+KK KG +L
Sbjct: 62 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQAL 104
>pdb|1S1I|Z Chain Z, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 105
Score = 140 bits (352), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 80/103 (77%), Positives = 89/103 (86%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKT+KTYCK K CRKHT HKVTQYK GK SL AQGKRRYDRKQSG+GGQTKPVFHKK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKKGKGTSL 105
AKTTKK+VLRL+C CK +Q +KRCKHFE+GG+KK KG +L
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQAL 103
>pdb|3J0L|F Chain F, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0O|F Chain F, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9a Cryo-Em Map: Classic Pre State 2
Length = 95
Score = 132 bits (333), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 75/95 (78%), Positives = 83/95 (87%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKT+KTYCK K CRKHT HKVTQYK GK SL AQGKRRYDRKQSG+GGQTKPVFHKK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGD 97
AKTTKK+VLRL+C CK +Q +KRCKHFE+GG+
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGE 95
>pdb|3JYW|Z Chain Z, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 92
Score = 127 bits (319), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 73/92 (79%), Positives = 80/92 (86%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VNVPKT+KTYCK K CRKHT HKVTQYK GK SL AQGKRRYDRKQSG+GGQTKPVFHKK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEI 94
AKTTKK+VLRL+C CK +Q +KRCKHFE+
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFEL 92
>pdb|3ZF7|TT Chain t, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 106
Score = 125 bits (313), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 63/97 (64%), Positives = 72/97 (74%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
VN PK KK +C + C H KV QYK GK L A+GKRRYDRKQSGYGGQTKP+FHKK
Sbjct: 2 VNYPKKKKMHCPDERCNAHKSFKVVQYKAGKARLYARGKRRYDRKQSGYGGQTKPIFHKK 61
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKK 99
AKTTKKIVL+LQC CK + Q+ +KR KHFE+ KK
Sbjct: 62 AKTTKKIVLKLQCSNCKSIIQNVLKRTKHFELNDKKK 98
>pdb|4A18|C Chain C, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|C Chain C, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|C Chain C, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|C Chain C, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 109
Score = 95.9 bits (237), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 58/88 (65%), Positives = 67/88 (76%), Gaps = 2/88 (2%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
V VPKT+KTYCK +C HT HKV+QYKK K+S AQG+RRYD KQSG+GGQTKP+F KK
Sbjct: 2 VQVPKTRKTYCK--KCNSHTNHKVSQYKKSKESTHAQGRRRYDMKQSGFGGQTKPIFRKK 59
Query: 63 AKTTKKIVLRLQCQGCKHVSQHPIKRCK 90
AKTTKK+ L+ C CK PIKRCK
Sbjct: 60 AKTTKKVALKFDCTTCKTKRVIPIKRCK 87
>pdb|3J21|JJ Chain j, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 94
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKK 62
+ PK +TYC C+KHT+HKV + KK S + G+RR+ R GYGG +P +
Sbjct: 1 MKYPKQIRTYCPF--CKKHTIHKVERVKKRPRSELSAGQRRFRRILKGYGGFPRPKPEGR 58
Query: 63 AKTTKKIVLRLQCQGC 78
K KK+ LR +C C
Sbjct: 59 EKPVKKLDLRFRCTEC 74
>pdb|1IFH|H Chain H, A Detailed Analysis Of The Free And Bound Conformation Of
An Antibody: X-Ray Structures Of Anti-Peptide Fab
17(Slash)9 And Three Different Fab-Peptide Complexes
pdb|1HIL|B Chain B, Structural Evidence For Induced Fit As A Mechanism For
Antigen-Antibody Recognition
pdb|1HIL|D Chain D, Structural Evidence For Induced Fit As A Mechanism For
Antigen-Antibody Recognition
pdb|1HIM|L Chain L, Structural Evidence For Induced Fit As A Mechanism For
Antibody-Antigen Recognition
pdb|1HIM|M Chain M, Structural Evidence For Induced Fit As A Mechanism For
Antibody-Antigen Recognition
pdb|1HIN|H Chain H, Structural Evidence For Induced Fit As A Mechanism For
Antibody-Antigen Recognition
Length = 220
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 12 YCKSKECRKHTLHKVTQYKKGKDSLAAQGKRR--YDRKQSGYGGQTKPVFHKKAKTTKKI 69
+ S++ K+TL+ K +DS RR YD Y GQ V AKTT
Sbjct: 68 FTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVSAAKTTAPS 127
Query: 70 VLRL 73
V L
Sbjct: 128 VYPL 131
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
0.317 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,330,406
Number of Sequences: 62578
Number of extensions: 115546
Number of successful extensions: 218
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 204
Number of HSP's gapped (non-prelim): 13
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)