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= 036621
(376 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZS|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 297
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 88 DLSLQDLSTQEPVLGSFKGLYCGIVFIEGLNNRITLWNIATRE 130
D+ LQ +T V G+ KG G +++ NR W+ T E
Sbjct: 147 DIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEE 189
>pdb|3U5E|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|D Chain D, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 297
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 88 DLSLQDLSTQEPVLGSFKGLYCGIVFIEGLNNRITLWNIATRE 130
D+ LQ +T V G+ KG G +++ NR W+ T E
Sbjct: 147 DIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEE 189
>pdb|3JYW|E Chain E, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 237
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 88 DLSLQDLSTQEPVLGSFKGLYCGIVFIEGLNNRITLWNIATRE 130
D+ LQ +T V G+ KG G +++ NR W+ T E
Sbjct: 137 DIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEE 179
>pdb|1S1I|E Chain E, 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 = 222
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 88 DLSLQDLSTQEPVLGSFKGLYCGIVFIEGLNNRITLWNIATRE 130
D+ LQ +T V G+ KG G +++ NR W+ T E
Sbjct: 137 DIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEE 179
>pdb|1FQV|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|E Chain E, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|G Chain G, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|I Chain I, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|K Chain K, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|M Chain M, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|O Chain O, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|2ASS|B Chain B, Crystal Structure Of The Skp1-Skp2-Cks1 Complex
pdb|2AST|B Chain B, Crystal Structure Of Skp1-Skp2-Cks1 In Complex With A
P27 Peptide
Length = 336
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 7 DDSPEDITIEILSRLPVKSLIRLRCVCKSWYALIKDP------NFISMHLKNDVNTRLI 59
D P+++ + I S L + L+++ VCK WY L D + +L DV RL+
Sbjct: 10 DSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLL 68
>pdb|1FS2|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FS2|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
Length = 272
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 7 DDSPEDITIEILSRLPVKSLIRLRCVCKSWYALIKDPNF 45
D P+++ + I S L + L+++ VCK WY L D +
Sbjct: 10 DSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 48
>pdb|1FS1|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FS1|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
Length = 53
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 7 DDSPEDITIEILSRLPVKSLIRLRCVCKSWYALIKDPNF 45
D P+++ + I S L + L+++ VCK WY L D +
Sbjct: 10 DSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 48
>pdb|1LDK|E Chain E, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 41
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 7 DDSPEDITIEILSRLPVKSLIRLRCVCKSWYALIKDPNF 45
D P+++ + I S L + L+++ VCK WY L D +
Sbjct: 2 DSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 40
>pdb|2KKQ|A Chain A, Solution Nmr Structure Of The Ig-Like C2-Type 2 Domain Of
Human Myotilin. Northeast Structural Genomics Target
Hr3158
Length = 116
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 304 PLLFWKKGAFFVESNSSQLLLYEPGTGE----LRDF-ELECCWFSVYIYTES 350
P LFWK+ V+ N+ ++ LY+ TG ++D + + W++V E+
Sbjct: 45 PKLFWKRNNEMVQFNTDRISLYQDNTGRVTLLIKDVNKKDAGWYTVSAVNEA 96
>pdb|3C5M|A Chain A, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
pdb|3C5M|B Chain B, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
pdb|3C5M|C Chain C, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
Length = 396
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 289 WIKQLTVGPFIGI------FQPLLFWKKGAFFVESNSS-QLLLYEPGTGELRDFELECCW 341
W+ +GI +QPL W+K A F +N + +L+ + TGEL + W
Sbjct: 130 WVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAW 189
Query: 342 FSVYIY 347
IY
Sbjct: 190 LGHPIY 195
>pdb|2NX2|A Chain A, Crystal Structure Of Protein Ypsa From Bacillus Subtilis,
Pfam Duf1273
Length = 181
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 13/61 (21%)
Query: 283 VMRKKNWIKQLTVGPFIGIFQPLLFWKKGAFFVESNSSQLLLYEP----------GTGEL 332
V+ + ++ LT P+ PL F +K FF++ + LLLY+P GT E
Sbjct: 99 VLAQADYEASLTHRPYES---PLQFKQKNQFFIDKSDGLLLLYDPEKEGSPKYMLGTAEK 155
Query: 333 R 333
R
Sbjct: 156 R 156
>pdb|4EWV|A Chain A, Crystal Structure Of Gh3.12 In Complex With Ampcpp
pdb|4EWV|B Chain B, Crystal Structure Of Gh3.12 In Complex With Ampcpp
pdb|4EPM|A Chain A, Crystal Structure Of Arabidopsis Gh3.12 (Pbs3) In Complex
With Amp
pdb|4EQL|A Chain A, Crystal Structure Of Gh3.12 In Complex With Amp And
Salicylate
pdb|4EQL|B Chain B, Crystal Structure Of Gh3.12 In Complex With Amp And
Salicylate
Length = 581
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 86 LEDLSLQDLSTQEPVLGSFKGLY----CGIVFIEGLNNRITLWNIATRESITL 134
LED+ L T EPV+ +F GLY IV + G N + RE++ L
Sbjct: 378 LEDVKLG--CTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVL 428
>pdb|4EQ4|A Chain A, Crystal Structure Of Seleno-Methionine Derivatized Gh3.12
pdb|4EQ4|B Chain B, Crystal Structure Of Seleno-Methionine Derivatized Gh3.12
Length = 581
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 86 LEDLSLQDLSTQEPVLGSFKGLY----CGIVFIEGLNNRITLWNIATRESITL 134
LED+ L T EPV+ +F GLY IV + G N + RE++ L
Sbjct: 378 LEDVKLG--CTYEPVVTNFAGLYRXRVGDIVLVTGFYNNAPQFKFVRRENVVL 428
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
0.323 0.141 0.444
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,848,333
Number of Sequences: 62578
Number of extensions: 505161
Number of successful extensions: 835
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 823
Number of HSP's gapped (non-prelim): 16
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)