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= 043001
(121 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 421 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 459
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 423 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 461
>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 = 29.3 bits (64), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 423 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 461
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 29.3 bits (64), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 419 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 457
>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 = 28.9 bits (63), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 424 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 462
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 419 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 457
>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 = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFVMSK 119
+ VR + +P + C+P N R++ +A+ DF+ ++
Sbjct: 424 VTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQ 462
>pdb|2IV2|X Chain X, Reinterpretation Of Reduced Form Of Formate Dehydrogenase
H From E. Coli
pdb|1AA6|A Chain A, Reduced Form Of Formate Dehydrogenase H From E. Coli
pdb|1FDI|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
Complexed With The Inhibitor Nitrite
pdb|1FDO|A Chain A, Oxidized Form Of Formate Dehydrogenase H From E. Coli
Length = 715
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 48 WKIISETCTALDVPRTANQCRRKWDSL 74
W+IISE T + P N + WD L
Sbjct: 479 WQIISEIATRMGYPMHYNNTQEIWDEL 505
>pdb|1E3L|A Chain A, P47h Mutant Of Mouse Class Ii Alcohol Dehydrogenase
Complex With Nadh
pdb|1E3L|B Chain B, P47h Mutant Of Mouse Class Ii Alcohol Dehydrogenase
Complex With Nadh
Length = 376
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFV 116
I + FPK++ TDC P REL K + D +
Sbjct: 226 IDINGEKFPKAKALGATDCLNP---RELDKPVQDVI 258
>pdb|1E3E|A Chain A, Mouse Class Ii Alcohol Dehydrogenase Complex With Nadh
pdb|1E3E|B Chain B, Mouse Class Ii Alcohol Dehydrogenase Complex With Nadh
pdb|1E3I|A Chain A, Mouse Class Ii Alcohol Dehydrogenase Complex With Nadh And
Inhibitor
pdb|1E3I|B Chain B, Mouse Class Ii Alcohol Dehydrogenase Complex With Nadh And
Inhibitor
Length = 376
Score = 27.3 bits (59), Expect = 1.9, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 81 IIVRSRTFPKSQTQAHTDCFPPNFDRELFKAIHDFV 116
I + FPK++ TDC P REL K + D +
Sbjct: 226 IDINGEKFPKAKALGATDCLNP---RELDKPVQDVI 258
>pdb|1JMM|A Chain A, Crystal Structure Of The V-Region Of Streptococcus Mutans
Antigen III
Length = 377
Score = 25.4 bits (54), Expect = 7.5, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 2 EGGSSRTRHTRSQVGPDWSSKEA 24
EGGS T + SQ G W S +A
Sbjct: 279 EGGSRWTXYKNSQAGSGWDSSDA 301
>pdb|3IPK|A Chain A, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
pdb|3IPK|B Chain B, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
pdb|3IOX|A Chain A, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
Length = 497
Score = 25.4 bits (54), Expect = 9.1, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 2 EGGSSRTRHTRSQVGPDWSSKEA 24
EGGS T + SQ G W S +A
Sbjct: 357 EGGSRWTMYKNSQAGSGWDSSDA 379
>pdb|2EBI|A Chain A, Arabidopsis Gt-1 Dna-Binding Domain With T133d
Phosphomimetic Mutation
Length = 86
Score = 25.0 bits (53), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 48 WKIISETCTALDVPRTANQCRRKWDSLIDEYKK 80
W+ IS R+ + C KW +L+ E+KK
Sbjct: 36 WEQISSKMREKGFDRSPDMCTDKWRNLLKEFKK 68
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
0.318 0.130 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,563,235
Number of Sequences: 62578
Number of extensions: 114310
Number of successful extensions: 188
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 174
Number of HSP's gapped (non-prelim): 17
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)