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= psy1631
(77 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZXI|C Chain C, Reconstituted Co Dehydrogenase From Oligotropha
Carboxidovorans
pdb|1ZXI|F Chain F, Reconstituted Co Dehydrogenase From Oligotropha
Carboxidovorans
Length = 288
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 35 PGSFAYHMSRSIHLVVDLLSEI-KDAKTL 62
PGSF YH +SI V LL+++ +DA+ L
Sbjct: 3 PGSFDYHRPKSIADAVALLTKLGEDARPL 31
>pdb|1N5W|C Chain C, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Oxidized Form
pdb|1N5W|F Chain F, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Oxidized Form
pdb|1N60|C Chain C, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Cyanide- Inactivated Form
pdb|1N60|F Chain F, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Cyanide- Inactivated Form
pdb|1N61|C Chain C, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Dithionite Reduced State
pdb|1N61|F Chain F, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Dithionite Reduced State
pdb|1N62|C Chain C, Crystal Structure Of The Mo,cu-co Dehydrogenase (codh),
N- Butylisocyanide-bound State
pdb|1N62|F Chain F, Crystal Structure Of The Mo,cu-co Dehydrogenase (codh),
N- Butylisocyanide-bound State
pdb|1N63|C Chain C, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Carbon Monoxide Reduced State
pdb|1N63|F Chain F, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Carbon Monoxide Reduced State
Length = 288
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 35 PGSFAYHMSRSIHLVVDLLSEI-KDAKTL 62
PGSF YH +SI V LL+++ +DA+ L
Sbjct: 3 PGSFDYHRPKSIADAVALLTKLGEDARPL 31
>pdb|1S1H|B Chain B, 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,
1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
In File 1s1i
Length = 185
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 7 TYHPQSCLTSVVHFGLGLWRTPIADLDRPGSFAYHMSRSIH-----LVVDLLSE---IKD 58
T+ ++ L H G TPIA PGSF +++RS +V D S+ IK+
Sbjct: 67 TFGQRAVLKFAAHTGA----TPIAGRFTPGSFTNYITRSFKEPRLVIVTDPRSDAQAIKE 122
Query: 59 AKTLMDIAVALKD 71
A + +AL D
Sbjct: 123 ASYVNIPVIALTD 135
>pdb|3JYV|B Chain B, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 193
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 7 TYHPQSCLTSVVHFGLGLWRTPIADLDRPGSFAYHMSRSIH-----LVVDLLSE---IKD 58
T+ ++ L H G TPIA PGSF +++RS +V D S+ IK+
Sbjct: 72 TFGQRAVLKFAAHTGA----TPIAGRFTPGSFTNYITRSFKEPRLVIVTDPRSDAQAIKE 127
Query: 59 AKTLMDIAVALKD 71
A + +AL D
Sbjct: 128 ASYVNIPVIALTD 140
>pdb|3IZB|A Chain A, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|A Chain A, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|A Chain A, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|A Chain A, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|A Chain A, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 252
Score = 25.4 bits (54), Expect = 8.7, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 16 SVVHFGLGLWRTPIADLDRPGSFAYHMSRSIH-----LVVDLLSE---IKDAKTLMDIAV 67
+V+ F TPIA PGSF +++RS +V D S+ IK+A + +
Sbjct: 85 AVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLVIVTDPRSDAQAIKEASYVNIPVI 144
Query: 68 ALKD 71
AL D
Sbjct: 145 ALTD 148
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 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,247,243
Number of Sequences: 62578
Number of extensions: 68879
Number of successful extensions: 144
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 144
Number of HSP's gapped (non-prelim): 5
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
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)