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= 038528
(91 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IPK|A Chain A, Crystal Structures Of Recombinant And Native Soybean Beta-
Conglycinin Beta Homotrimers
pdb|1IPK|B Chain B, Crystal Structures Of Recombinant And Native Soybean Beta-
Conglycinin Beta Homotrimers
pdb|1IPK|C Chain C, Crystal Structures Of Recombinant And Native Soybean Beta-
Conglycinin Beta Homotrimers
Length = 416
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 1 MSWADEDDIRTLDIRRGDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTED--DSYFEP 58
++ + DD + ++ GD R+ G+ +Y+ + + + K+ AI N D +F
Sbjct: 82 LTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFF-- 139
Query: 59 VIGAYTSISDLILGFDRKVLQSAF 82
+ + + + GF +L+++F
Sbjct: 140 -LSSTQAQQSYLQGFSHNILETSF 162
>pdb|1IPJ|A Chain A, Crystal Structures Of Recombinant And Native Soybean
Beta-Conglycinin Beta Homotrimers Complexes With
N-Acetyl-D-Glucosamine
pdb|1IPJ|B Chain B, Crystal Structures Of Recombinant And Native Soybean
Beta-Conglycinin Beta Homotrimers Complexes With
N-Acetyl-D-Glucosamine
pdb|1IPJ|C Chain C, Crystal Structures Of Recombinant And Native Soybean
Beta-Conglycinin Beta Homotrimers Complexes With
N-Acetyl-D-Glucosamine
Length = 416
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 1 MSWADEDDIRTLDIRRGDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTED--DSYFEP 58
++ + DD + ++ GD R+ G+ +Y+ + + + K+ AI N D +F
Sbjct: 82 LTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFF-- 139
Query: 59 VIGAYTSISDLILGFDRKVLQSAF 82
+ + + + GF +L+++F
Sbjct: 140 -LSSTQAQQSYLQGFSHNILETSF 162
>pdb|1UIJ|A Chain A, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
pdb|1UIJ|B Chain B, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
pdb|1UIJ|C Chain C, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
pdb|1UIJ|D Chain D, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
pdb|1UIJ|E Chain E, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
pdb|1UIJ|F Chain F, Crystal Structure Of Soybean Beta-Conglycinin Beta
Homotrimer (I122mK124W)
Length = 416
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 1 MSWADEDDIRTLDIRRGDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTED--DSYFEP 58
++ + DD + ++ GD R+ G+ +Y+ + + + K+ AI N D +F
Sbjct: 82 LTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKMIWLAIPVNKPGRYDDFF-- 139
Query: 59 VIGAYTSISDLILGFDRKVLQSAF 82
+ + + + GF +L+++F
Sbjct: 140 -LSSTQAQQSYLQGFSHNILETSF 162
>pdb|1UIK|A Chain A, Crystal Structure Of Soybean Beta-Conglycinin Alpha Prime
Homotrimer
pdb|1UIK|B Chain B, Crystal Structure Of Soybean Beta-Conglycinin Alpha Prime
Homotrimer
pdb|1UIK|C Chain C, Crystal Structure Of Soybean Beta-Conglycinin Alpha Prime
Homotrimer
Length = 418
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/84 (19%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 1 MSWADEDDIRTLDIRRGDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTED--DSYFEP 58
++ + DD + +++ GD R+ G+ +Y+ + E ++ AI N +S+F
Sbjct: 79 LTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFF-- 136
Query: 59 VIGAYTSISDLILGFDRKVLQSAF 82
+ + + + GF + +L++++
Sbjct: 137 -LSSTQAQQSYLQGFSKNILEASY 159
>pdb|3MCA|A Chain A, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 592
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 2 SWADEDDIRTLDIRRGDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTEDDSYFEPVIG 61
+WA D TL + +V +L+PG + SN E ++R + T D + G
Sbjct: 459 TWAVAGDTVTLQLADIEVNQLRPGDIL---SNYENPVRRVRSFVAEIQTFD------IHG 509
Query: 62 AYTSISDLILGFDRKVLQSAFK 83
S S L+L R V + K
Sbjct: 510 PILSGSTLVLHLGRTVTSVSLK 531
>pdb|1NKW|P Chain P, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
pdb|1NWX|P Chain P, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Abt-773
pdb|1NWY|P Chain P, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Azithromycin
pdb|1PNU|P Chain P, Crystal Structure Of A Streptomycin Dependent Ribosome
From Escherichia Coli, 50s Subunit Of 70s Ribosome.
This File, 1pnu, Contains Only Molecules Of The 50s
Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna,
And A-Site Trna Are In The Pdb File 1pns.
pdb|1PNY|P Chain P, Crystal Structure Of The Wild Type Ribosome From E.
Coli, 50s Subunit Of 70s Ribosome. This File, 1pny,
Contains Only Molecules Of The 50s Ribosomal Subunit.
The 30s Subunit Is In The Pdb File 1pnx.
pdb|1SM1|P Chain P, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Quinupristin And Dalfopristin
pdb|1VOR|S Chain S, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOU|S Chain S, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOW|S Chain S, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOY|S Chain S, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VP0|S Chain S, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1XBP|P Chain P, Inhibition Of Peptide Bond Formation By Pleuromutilins:
The Structure Of The 50s Ribosomal Subunit From
Deinococcus Radiodurans In Complex With Tiamulin
pdb|1YL3|2 Chain 2, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|V Chain V, 50s Ribosomal Subunit From A Crystal Structure Of
Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome. This File Contains The 50s Subunit From A
Crystal Structure Of Release Factor Rf1, Trnas And Mrna
Bound To The Ribosome And Is Described In Remark 400
pdb|2B9N|V Chain V, 50s Ribosomal Subunit From A Crystal Structure Of
Release Factor Rf2, Trnas And Mrna Bound To The
Ribosome. This File Contains The 50s Subunit From A
Crystal Structure Of Release Factor Rf1, Trnas And Mrna
Bound To The Ribosome And Is Described In Remark 400.
pdb|2B9P|V Chain V, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex
With Trnas And Mrna With A Stop Codon In The A-Site And
Is Described In Remark 400.
pdb|2ZJP|O Chain O, Thiopeptide Antibiotic Nosiheptide Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|2ZJQ|O Chain O, Interaction Of L7 With L11 Induced By Microccocin
Binding To The Deinococcus Radiodurans 50s Subunit
pdb|2ZJR|O Chain O, Refined Native Structure Of The Large Ribosomal Subunit
(50s) From Deinococcus Radiodurans
pdb|3CF5|O Chain O, Thiopeptide Antibiotic Thiostrepton Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|3DLL|O Chain O, The Oxazolidinone Antibiotics Perturb The Ribosomal
Peptidyl-Transferase Center And Effect Trna Positioning
pdb|3PIO|O Chain O, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
pdb|3PIP|O Chain O, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
Length = 100
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 17 GDVYRLQPGSVFYIESNLEQEREKLRIYAIFSNTEDDSYFEPVIGAYTSISDLI-LGFDR 75
G YR+ G V +ES + +K+ + A+F E + E G YT ++++ G +
Sbjct: 9 GKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDA-GKYTVQAEVVEHGRGK 67
Query: 76 KVLQSAFKRAV 86
K+ +K V
Sbjct: 68 KIYIRKYKSGV 78
>pdb|3U28|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From
Saccharomyces Cerevisiae
pdb|3UAI|A Chain A, Structure Of The Shq1-Cbf5-Nop10-Gar1 Complex From
Saccharomyces Cerevisiae
Length = 400
Score = 25.8 bits (55), Expect = 6.2, Method: Composition-based stats.
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 46 IFSNTEDDSYFEPVIGAYTSISDLILGFDRKVLQSAFKRAV 86
++ NT D+SY +I + L++G+ R V++ + AV
Sbjct: 242 VYDNTRDESYLRSII---QPLETLLVGYKRIVVKDSAVNAV 279
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
0.322 0.141 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,604,116
Number of Sequences: 62578
Number of extensions: 88593
Number of successful extensions: 169
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 168
Number of HSP's gapped (non-prelim): 8
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
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)