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= 047073
(316 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 37 VSMEDLPLPILVDVFSRLPIKTILQIKCVCKTWHSLCSD 75
VS + LP +L+ +FS L + +L++ VCK W+ L SD
Sbjct: 7 VSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASD 45
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 37 VSMEDLPLPILVDVFSRLPIKTILQIKCVCKTWHSLCSD 75
VS + LP +L+ +FS L + +L++ VCK W+ L SD
Sbjct: 7 VSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASD 45
>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 = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 37 VSMEDLPLPILVDVFSRLPIKTILQIKCVCKTWHSLCSD 75
VS + LP +L+ +FS L + +L++ VCK W+ L SD
Sbjct: 7 VSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASD 45
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 149 GDHLVLPQLKRKNVATRIRGFGYNHCTNQYKVIQILSYKDQAAISSSKPQVEVHTIGTNT 208
G +VLP R+ +A + G N +++ ++ D + KP++ G +
Sbjct: 187 GQDIVLPDETRRAIAELVNGDA-RRALNTLEMMADMAEVDDSGKRVLKPELLTEIAGERS 245
Query: 209 WR--NIGDLPY----VLNQPYYGAFLNSALHWYAH 237
R N GD Y L++ G+ ++AL+WYA
Sbjct: 246 ARFDNKGDRFYDLISALHKSVRGSAPDAALYWYAR 280
>pdb|1LDK|E Chain E, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 41
Score = 32.3 bits (72), Expect = 0.33, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 40 EDLPLPILVDVFSRLPIKTILQIKCVCKTWHSLCSD 75
+ LP +L+ +FS L + +L++ VCK W+ L SD
Sbjct: 2 DSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASD 37
>pdb|3J25|A Chain A, Structural Basis For Tetm-Mediated Tetracycline Resistance
Length = 638
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 99 RIYTNSLVPLFTLNQGDKERL---SLLSSCNGLICLHEFSYKQDIISV------CNPILG 149
R+Y+ L ++ +KE++ + +S NG +C + +Y +I+ + N +LG
Sbjct: 268 RLYSGVLHLRDSVRVSEKEKIKVTEMYTSINGELCKIDRAYSGEIVILQNEFLKLNSVLG 327
Query: 150 DHLVLPQLKR 159
D +LPQ K+
Sbjct: 328 DTKLLPQRKK 337
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
0.324 0.139 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,798,248
Number of Sequences: 62578
Number of extensions: 401141
Number of successful extensions: 973
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 969
Number of HSP's gapped (non-prelim): 7
length of query: 316
length of database: 14,973,337
effective HSP length: 99
effective length of query: 217
effective length of database: 8,778,115
effective search space: 1904850955
effective search space used: 1904850955
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)