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= psy6045
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 126 bits (317), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 68/102 (66%), Positives = 76/102 (74%), Gaps = 2/102 (1%)
Query: 4 VNVPKQRRTFXXXXXXXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
VNVPK RRTF TQYKK K+ QG+RRYDRKQ+GYGGQTKPIFRKKAK
Sbjct: 2 VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAK 61
Query: 64 TTKKIVLRMECTE--CKYRKQLPLKRCKHFELGGDKKRKVQT 103
TTKKIVLR+EC E C+ ++ L +KRCKHFELGGDKKRK Q
Sbjct: 62 TTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQV 103
>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 = 117 bits (293), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 59/99 (59%), Positives = 73/99 (73%), Gaps = 2/99 (2%)
Query: 4 VNVPKQRRTFXXXXX--XXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
VNVPK ++T+ TQYKK K+ + QG+RRYDRKQ+GYGGQTKP+F KK
Sbjct: 2 VNVPKTKKTYCKNKECRKHTLHKVTQYKKGKDSLSAQGKRRYDRKQSGYGGQTKPVFHKK 61
Query: 62 AKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKRK 100
AKTTKKIVL+++C CK+ Q P+KRCKHFE+GGDKK K
Sbjct: 62 AKTTKKIVLKLQCQSCKHYSQHPIKRCKHFEIGGDKKGK 100
>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 = 99.4 bits (246), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 62/102 (60%), Positives = 73/102 (71%), Gaps = 2/102 (1%)
Query: 4 VNVPKQRRTFXXXXX--XXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
VNVPK R+T+ TQYK K QG+RRYDRKQ+G+GGQTKP+F KK
Sbjct: 2 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 61
Query: 62 AKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKRKVQT 103
AKTTKK+VLR+EC +CK R QL LKRCKHFELGG+KK+K Q
Sbjct: 62 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQA 103
>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 = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 62/102 (60%), Positives = 73/102 (71%), Gaps = 2/102 (1%)
Query: 4 VNVPKQRRTFXXXXX--XXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
VNVPK R+T+ TQYK K QG+RRYDRKQ+G+GGQTKP+F KK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 62 AKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKRKVQT 103
AKTTKK+VLR+EC +CK R QL LKRCKHFELGG+KK+K Q
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQA 102
>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 = 94.7 bits (234), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 58/95 (61%), Positives = 68/95 (71%), Gaps = 2/95 (2%)
Query: 4 VNVPKQRRTFXXXXX--XXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
VNVPK R+T+ TQYK K QG+RRYDRKQ+G+GGQTKP+F KK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 62 AKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGD 96
AKTTKK+VLR+EC +CK R QL LKRCKHFELGG+
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGE 95
>pdb|3ZF7|TT Chain t, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 106
Score = 92.8 bits (229), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 48/73 (65%), Positives = 55/73 (75%)
Query: 26 TQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQLPL 85
QYK K R +G+RRYDRKQ+GYGGQTKPIF KKAKTTKKIVL+++C+ CK Q L
Sbjct: 26 VQYKAGKARLYARGKRRYDRKQSGYGGQTKPIFHKKAKTTKKIVLKLQCSNCKSIIQNVL 85
Query: 86 KRCKHFELGGDKK 98
KR KHFEL KK
Sbjct: 86 KRTKHFELNDKKK 98
>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 = 89.0 bits (219), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 56/92 (60%), Positives = 65/92 (70%), Gaps = 2/92 (2%)
Query: 4 VNVPKQRRTFXXXXX--XXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
VNVPK R+T+ TQYK K QG+RRYDRKQ+G+GGQTKP+F KK
Sbjct: 1 VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKK 60
Query: 62 AKTTKKIVLRMECTECKYRKQLPLKRCKHFEL 93
AKTTKK+VLR+EC +CK R QL LKRCKHFEL
Sbjct: 61 AKTTKKVVLRLECVKCKTRAQLTLKRCKHFEL 92
>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 = 85.5 bits (210), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 50/86 (58%), Positives = 62/86 (72%)
Query: 4 VNVPKQRRTFXXXXXXXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
V VPK R+T+ +QYKKSKE QGRRRYD KQ+G+GGQTKPIFRKKAK
Sbjct: 2 VQVPKTRKTYCKKCNSHTNHKVSQYKKSKESTHAQGRRRYDMKQSGFGGQTKPIFRKKAK 61
Query: 64 TTKKIVLRMECTECKYRKQLPLKRCK 89
TTKK+ L+ +CT CK ++ +P+KRCK
Sbjct: 62 TTKKVALKFDCTTCKTKRVIPIKRCK 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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%)
Query: 4 VNVPKQRRTFXXXXXXXXXXXXTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
+ PKQ RT+ + KK + G+RR+ R GYGG +P + K
Sbjct: 1 MKYPKQIRTYCPFCKKHTIHKVERVKKRPRSELSAGQRRFRRILKGYGGFPRPKPEGREK 60
Query: 64 TTKKIVLRMECTEC 77
KK+ LR CTEC
Sbjct: 61 PVKKLDLRFRCTEC 74
>pdb|3T4P|A Chain A, Crystal Structure Of O-Acetyl Serine Sulfhydrylase From
Leishmania Donovani In Complex With Designed
Tetrapeptide
pdb|3TBH|A Chain A, Crystal Structure Of O-Acetyl Serine Sulfhydrylase In
Complex With Octapeptide Derived From Serine Acetyl
Transferase Of Leishmania Donovani
pdb|3SPX|A Chain A, Crystal Structure Of O-Acetyl Serine Sulfhydrylase From
Leishmania Donovani
Length = 334
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 52 GQTKPIFRKKAKTTK-KIVLRMEC 74
GQT ++ K TK K+VL+MEC
Sbjct: 20 GQTPALYLNKLNNTKAKVVLKMEC 43
>pdb|4AIR|A Chain A, Leishmania Major Cysteine Synthase
pdb|4AIR|B Chain B, Leishmania Major Cysteine Synthase
Length = 354
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 52 GQTKPIFRKKAKTTK-KIVLRMEC 74
GQT ++ K TK K+VL+MEC
Sbjct: 41 GQTPALYLNKLNNTKAKVVLKMEC 64
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
0.321 0.134 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,545,647
Number of Sequences: 62578
Number of extensions: 73631
Number of successful extensions: 126
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 115
Number of HSP's gapped (non-prelim): 12
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)