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= 039068
(166 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMC|A Chain A, Solution Structure Of The 18th Filamin Domain From Human
Filamin-B
Length = 116
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 28/58 (48%)
Query: 31 FNIHVEEGNAADILHVLEPPPLPIKPCTKSKYPSRFLHCSFVPKETKDVWDKLFKEGN 88
F + + E + + + ++ P +PC + P+ + SF+P+E + + K GN
Sbjct: 35 FLLDISETDLSSLTASIKAPSGRDEPCLLKRLPNNHIGISFIPREVGEHLVSIKKNGN 92
>pdb|1PQK|A Chain A, Repacking Of The Core Of T4 Lysozyme By Automated Design
pdb|1PQK|B Chain B, Repacking Of The Core Of T4 Lysozyme By Automated Design
pdb|1PQK|C Chain C, Repacking Of The Core Of T4 Lysozyme By Automated Design
Length = 164
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 10/86 (11%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ------SKVNNDF 129
TKD +KLF + A V AV + PV+ S+ ++ L N++ Q + N
Sbjct: 59 TKDEAEKLFNQDVDAAVRAVLRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSI 118
Query: 130 IYIKIPGVPHEAVYAFVRFLYSSWYS 155
Y++ A V F S WY+
Sbjct: 119 RYLQQKRWDEAA----VNFAKSRWYN 140
>pdb|2DEW|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With Histone H3 N-Terminal Tail Including
Arg8
pdb|2DEX|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With Histone H3 N-Terminal Peptide Including
Arg17
pdb|2DEY|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With Histone H4 N-Terminal Tail Including
Arg3
Length = 671
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 30 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 77
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 29 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 76
>pdb|4DKT|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With
N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1e)-2-
Fluoroethanimidoyl]-L-Ornithinamide
Length = 668
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 27 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 74
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 25 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 72
>pdb|1WD9|A Chain A, Calcium Bound Form Of Human Peptidylarginine Deiminase
Type4 (pad4)
pdb|1WDA|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase
Type4 (Pad4) In Complex With Benzoyl-L-Arginine Amide
Length = 670
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 29 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 76
>pdb|2DW5|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With
N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine
Amide
pdb|3B1T|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With O-Cl-Amidine
pdb|3B1U|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4
In Complex With O-F-Amidine
Length = 671
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 30 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---SPPAKKKSTGSSTWP 77
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 13 SNLSRKNLCAAGESFCGSFNIHVEEGNAADILHVLEPPPLPIKPCTKSKYP 63
L++ ++C++ C SF+I+ G DI H PP K S +P
Sbjct: 25 GTLTQLDICSSAPEDCTSFSINASPGVVVDIAH---GPPAKKKSTGSSTWP 72
>pdb|229L|A Chain A, Generating Ligand Binding Sites In T4 Lysozyme Using
Deficiency-Creating Substitutions
Length = 164
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ 122
TKD +KLF + A V + + PV+ S+ ++A L N++ Q
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVARAALINMVFQ 105
>pdb|244L|A Chain A, The Response Of T4 Lysozyme To Large-To-Small
Substitutions Within The Core And Its Relation To The
Hydrophobic Effect
Length = 164
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ 122
TKD +KLF + A V + + PV+ S+ ++ L N++ Q
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALANMVFQ 105
>pdb|1QS9|A Chain A, The Introduction Of Strain And Its Effects On The
Structure And Stability Of T4 Lysozyme
Length = 162
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ 122
TKD +KLF + A V + + PV+ S+ ++ VL N++ Q
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAVLINMVFQ 105
>pdb|1PQD|A Chain A, T4 Lysozyme Core Repacking Mutant Core10TA
Length = 164
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 10/86 (11%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ------SKVNNDF 129
TKD +KLF + A V + + P++ S+ ++ L N++ Q + N
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPIYDSLDAVRRAALVNLIFQIGETGAAGFTNSL 118
Query: 130 IYIKIPGVPHEAVYAFVRFLYSSWYS 155
Y++ A V F S WY+
Sbjct: 119 RYLQQKRWDEAA----VNFAKSRWYN 140
>pdb|1CV0|A Chain A, T4 Lysozyme Mutant F104m
Length = 164
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ 122
TKD +KLF + A V + + PV+ S+ ++ L N++ Q
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVMQ 105
>pdb|3GDF|A Chain A, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDF|B Chain B, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDF|C Chain C, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDF|D Chain D, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDG|A Chain A, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDG|B Chain B, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDG|C Chain C, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum.
pdb|3GDG|D Chain D, Crystal Structure Of The Nadp-Dependent Mannitol
Dehydrogenase From Cladosporium Herbarum
Length = 267
Score = 26.9 bits (58), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 71 FVPKETKDVW--------DKLFKEGNGADVY 93
FVPKET+ +W D L KE GA VY
Sbjct: 214 FVPKETQQLWHSMIPMGRDGLAKELKGAYVY 244
>pdb|1PQJ|A Chain A, T4 Lysozyme Core Repacking Mutant A111vCORE10TA
Length = 164
Score = 26.6 bits (57), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 10/86 (11%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ------SKVNNDF 129
TKD +KLF + A V + + P++ S+ ++ L N++ Q + N
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPIYDSLDAVRRAALVNLIFQIGETGVAGFTNSL 118
Query: 130 IYIKIPGVPHEAVYAFVRFLYSSWYS 155
Y++ A V F S WY+
Sbjct: 119 RYLQQKRWDEAA----VNFAKSRWYN 140
>pdb|224L|A Chain A, The Energetic Cost And The Structural Consequences Of
Burying A Hydroxyl Group Within The Core Of A Protein
Determined From Ala To Ser And Val To Thr Substitutions
In T4 Lysozyme
Length = 164
Score = 26.2 bits (56), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 76 TKDVWDKLFKEGNGADVYAVTEDKSCIPVHSSILSIASPVLGNILQQ 122
TKD +KLF + A V + + PV+ S+ S+ L N++ Q
Sbjct: 59 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDSVRRAALINMVFQ 105
>pdb|2K7Q|A Chain A, Filamin A Ig-Like Domains 18-19
Length = 191
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 34 HVEEGNAADI-LHVLE-----------PPPLPIKPCTKSKYPSRFLHCSFVPKETKDVWD 81
H++ G+AADI +++ E PP +PC + + + SFVPKET +
Sbjct: 12 HLKVGSAADIPINISETDLSLLTATVVPPSGREEPCLLKRLRNGHVGISFVPKETGEHLV 71
Query: 82 KLFKEGN 88
+ K G
Sbjct: 72 HVKKNGQ 78
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 0.136 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,081,560
Number of Sequences: 62578
Number of extensions: 207567
Number of successful extensions: 773
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 757
Number of HSP's gapped (non-prelim): 20
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
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: 47 (22.7 bits)