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= 030825
(171 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2K2E|A Chain A, Solution Nmr Structure Of Bordetella Pertussis Protein
Bp2786, A Mth938-Like Domain. Northeast Structural
Genomics Consortium Target Ber31
Length = 158
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/62 (46%), Positives = 41/62 (66%)
Query: 109 PEILILGCGRYIEPVNPELRQFIRSTGMKLEAIDSRNAASTYNILNEEGRIVAAALLPYG 168
PE+L++G GR + PE + + + G+ +EA+D++ AA TYNIL EGR V ALLP G
Sbjct: 89 PEVLLVGTGRRQHLLGPEQVRPLLAMGVGVEAMDTQAAARTYNILMAEGRRVVVALLPDG 148
Query: 169 VS 170
S
Sbjct: 149 DS 150
>pdb|3CPK|A Chain A, Crystal Structure Of The Q7w7n7_borpa Protein From
Bordetella Parapertussis. Northeast Structural Genomics
Consortium Target Ber31
Length = 150
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/62 (46%), Positives = 40/62 (64%)
Query: 109 PEILILGCGRYIEPVNPELRQFIRSTGMKLEAIDSRNAASTYNILNEEGRIVAAALLPYG 168
PE+L++G GR + PE + + + G+ +EA D++ AA TYNIL EGR V ALLP G
Sbjct: 89 PEVLLVGTGRRQHLLGPEQVRPLLAXGVGVEAXDTQAAARTYNILXAEGRRVVVALLPDG 148
Query: 169 VS 170
S
Sbjct: 149 DS 150
>pdb|2FVT|A Chain A, Nmr Structure Of The Rpa2829 Protein From Rhodopseudomonas
Palustris: Northeast Structural Genomics Target Rpr43
Length = 135
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 60 YTDTGFTVNGVQYEGSLLCIGNLLLSWTPKKFSEITPNCLS-IFQLVRPIPEILILGCGR 118
Y GF G+ ++GSLL + + + W K +I L +F I + LI+G G
Sbjct: 19 YGKGGFYFAGMSHQGSLLFLPDAVWGWDVTKPEQIDRYSLQRVFDNANAI-DTLIVGTGA 77
Query: 119 YIEPVNPELRQFIRSTGMKLEAIDSRNAASTYNILNEEGRIVAAALL 165
+ +LR+ +R + L+ + + A TYNI+ E R VAAAL+
Sbjct: 78 DVWIAPRQLREALRGVNVVLDTMQTGPAIRTYNIMIGERRRVAAALI 124
>pdb|2GM2|A Chain A, Nmr Structure Of Xanthomonas Campestris Xcc1710: Northeast
Structural Genomics Consortium Target Xcr35
Length = 132
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 109 PEILILGCGRYIEPVNPELRQFIRSTGMKLEAIDSRNAASTYNILNEEGRIVAAALLPYG 168
P +++LG G + + ++ + G+ LEA+ + AA TYN+L EGR VA A++ G
Sbjct: 65 PAVILLGTGERQQFPSTDVLAACLTRGIGLEAMTNAAAARTYNVLASEGRRVALAMIVGG 124
Query: 169 VS 170
+
Sbjct: 125 LE 126
>pdb|2FI9|A Chain A, The Crystal Structure Of An Outer Membrane Protein From
The Bartonella Henselae
Length = 128
Score = 33.1 bits (74), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 27/124 (21%), Positives = 48/124 (38%), Gaps = 31/124 (25%)
Query: 57 FQGYTDTGFTVNGVQYEGSLLCIGNLLLSWTPKKFSEITPNCLSIFQLVRPIP------- 109
Y + GF + + GS++CI P+ + + P+P
Sbjct: 18 IDAYGNGGFRFADMSHRGSIICI----------------PSGIYGIDMTGPVPTQEDISR 61
Query: 110 --------EILILGCGRYIEPVNPELRQFIRSTGMKLEAIDSRNAASTYNILNEEGRIVA 161
E+L++G G + + ELR + + + + + A T+N+L E R VA
Sbjct: 62 VLEESDQIEVLLIGTGVELLRLPEELRVLLWEKRISSDTMSTGAAVRTFNVLLAEDRAVA 121
Query: 162 AALL 165
A L
Sbjct: 122 ALLF 125
>pdb|1J8F|C Chain C, Human Sirt2 Histone Deacetylase
pdb|1J8F|B Chain B, Human Sirt2 Histone Deacetylase
Length = 323
Score = 29.6 bits (65), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 78 CIGNLLLSWTPKK-FSEITPNCLSIFQLVRPIPEILILG 115
C LSW +K FSE+TP C LV+ P+I+ G
Sbjct: 167 CRHEYPLSWMKEKIFSEVTPKCEDCQSLVK--PDIVFFG 203
>pdb|1J8F|A Chain A, Human Sirt2 Histone Deacetylase
Length = 323
Score = 29.6 bits (65), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 78 CIGNLLLSWTPKK-FSEITPNCLSIFQLVRPIPEILILG 115
C LSW +K FSE+TP C LV+ P+I+ G
Sbjct: 167 CRHEYPLSWMKEKIFSEVTPKCEDCQSLVK--PDIVFFG 203
>pdb|1RDS|A Chain A, Crystal Structure Of Ribonuclease Ms (As Ribonuclease T1
Homologue) Complexed With A Guanylyl-3',5'-Cytidine
Analogue
pdb|1RMS|A Chain A, Crystal Structures Of Ribonuclease Ms Complexed With 3'-
Guanylic Acid A GpC Analogue,
2'-Deoxy-2'-Fluoroguanylyl- 3',5'-Cytidine
Length = 105
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 36 RAFSLYDQINLIDNVPEDQLRFQGYTDTGFTVNGVQYE 73
+ +SLY+ + ID+ P + ++G+ F V+G YE
Sbjct: 23 KGYSLYESGDTIDDYPHEYHDYEGFD---FPVSGTYYE 57
>pdb|1OI1|A Chain A, Crystal Structure Of The Mbt Domains Of Human Scml2
pdb|2VYT|A Chain A, The Mbt Repeats Of Human Scml2 Bind To Peptides Containing
Mono Methylated Lysine.
pdb|2VYT|B Chain B, The Mbt Repeats Of Human Scml2 Bind To Peptides Containing
Mono Methylated Lysine
Length = 221
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 121 EPVNPELRQFIRSTGMKLEAIDSRN 145
EP P L F GMKLEAID +N
Sbjct: 141 EPPKPPLNNF--KVGMKLEAIDKKN 163
>pdb|2GY9|R Chain R, Structure Of The 30s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYB|R Chain R, Structure Of The 30s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
Length = 69
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 128 RQFIRSTGMKLEAIDSRNAASTYNILNEEGRIV 160
R+F R T ++ ID ++ A+ N + E G+IV
Sbjct: 2 RKFCRFTAEGVQEIDYKDIATLKNYITESGKIV 34
>pdb|4EDU|A Chain A, The Mbt Repeats Of Human Scml2 In A Complex With Histone
H2a Peptide
Length = 215
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 121 EPVNPELRQFIRSTGMKLEAIDSRN 145
EP P L F GMKLEAID +N
Sbjct: 135 EPPKPPLNNF--KVGMKLEAIDKKN 157
>pdb|1VS5|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS7|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|3I1M|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|R Chain R, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KC4|R Chain R, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be Found
In Pdb Entry 3kcr
pdb|3OR9|R Chain R, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The First
70s Ribosome.
pdb|3ORA|R Chain R, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3IZV|V Chain V, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Small Subunit Of A Ribosome Programmed With A
Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
Ef-Tu
pdb|3IZW|V Chain V, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding.This Entry Contains The
Small Subunit Of A Ribosome Programmed With A Cognate
Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
pdb|3SFS|R Chain R, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|R Chain R, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAQ|R Chain R, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|R Chain R, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 75
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 128 RQFIRSTGMKLEAIDSRNAASTYNILNEEGRIV 160
R+F R T ++ ID ++ A+ N + E G+IV
Sbjct: 8 RKFCRFTAEGVQEIDYKDIATLKNYITESGKIV 40
>pdb|2BIV|A Chain A, Crystal Structure Of The Wild-Type Mbt Domains Of Human
Scml2
pdb|2BIV|B Chain B, Crystal Structure Of The Wild-Type Mbt Domains Of Human
Scml2
pdb|2BIV|C Chain C, Crystal Structure Of The Wild-Type Mbt Domains Of Human
Scml2
Length = 243
Score = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 121 EPVNPELRQFIRSTGMKLEAIDSRN 145
EP P L F GMKLEAID +N
Sbjct: 163 EPPKPPLNNF--KVGMKLEAIDKKN 185
>pdb|1P6G|R Chain R, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P87|R Chain R, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AVY|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AW7|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|2I2P|R Chain R, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2U|R Chain R, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QOU|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The First 70s Ribosome,
With Spectinomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|2QOW|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOY|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
First 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QP0|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QAL|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAN|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QB9|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBB|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBD|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
First 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBF|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBH|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The First 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBJ|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The Second 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4K|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4M|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2VHO|R Chain R, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|R Chain R, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3DF3|R Chain R, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3J00|R Chain R, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|4ADV|R Chain R, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
pdb|3J0U|U Chain U, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|U Chain U, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|U Chain U, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|U Chain U, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|U Chain U, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
Length = 74
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 128 RQFIRSTGMKLEAIDSRNAASTYNILNEEGRIV 160
R+F R T ++ ID ++ A+ N + E G+IV
Sbjct: 7 RKFCRFTAEGVQEIDYKDIATLKNYITESGKIV 39
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
0.320 0.138 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,029,761
Number of Sequences: 62578
Number of extensions: 204118
Number of successful extensions: 464
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 452
Number of HSP's gapped (non-prelim): 21
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)