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= 045168
(405 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 32.0 bits (71), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 323 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 364
>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 = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 321 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 362
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 319 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 360
>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 = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 323 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 364
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 319 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 360
>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 = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 324 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 365
>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 = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 212 NPDFAKSVIQLRAEEEAKLTGIPVRPNFNEEMREWVRDWLELDYI 256
N DF KSV L + + KLT P N ++ +W++D +E+ YI
Sbjct: 324 NEDFLKSVTTLAMKAKCKLTICPEEENMDD---QWMQDEMEIGYI 365
>pdb|1FTS|A Chain A, Signal Recognition Particle Receptor From E. Coli
Length = 295
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 236 RPNFNEEMREWVRDWLELDYISPYEDVSNLDQSSQEMEKRTVAVFHELLSLS 287
+ + EE+++ VR +LD +P+E + +D S+ + +FHE + L+
Sbjct: 190 KSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLT 241
>pdb|2XXA|B Chain B, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
pdb|2XXA|D Chain D, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
Length = 302
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 236 RPNFNEEMREWVRDWLELDYISPYEDVSNLDQSSQEMEKRTVAVFHELLSLS 287
+ + EE+++ VR +LD +P+E + +D S+ + +FHE + L+
Sbjct: 195 KSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLT 246
>pdb|2QY9|A Chain A, Structure Of The Ng+1 Construct Of The E. Coli Srp
Receptor Ftsy
Length = 309
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 236 RPNFNEEMREWVRDWLELDYISPYEDVSNLDQSSQEMEKRTVAVFHELLSLS 287
+ + EE+++ VR +LD +P+E + +D S+ + +FHE + L+
Sbjct: 196 KSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLT 247
>pdb|2R8R|A Chain A, Crystal Structure Of The N-Terminal Region (19..243) Of
Sensor Protein Kdpd From Pseudomonas Syringae Pv. Tomato
Str. Dc3000
pdb|2R8R|B Chain B, Crystal Structure Of The N-Terminal Region (19..243) Of
Sensor Protein Kdpd From Pseudomonas Syringae Pv. Tomato
Str. Dc3000
Length = 228
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 195 LVGCPGEGQSFLELESWNPDFAKSV--------IQLRAEEEAKLTGIPVRPNFNEEMREW 246
L PG G+++ L++ + + V RAE EA L G+P +P E R
Sbjct: 11 LGAAPGVGKTYAXLQAAHAQLRQGVRVXAGVVETHGRAETEALLNGLPQQPLLRTEYRGX 70
Query: 247 VRDWLELDYI 256
+ +LD +
Sbjct: 71 TLEEXDLDAL 80
>pdb|3NFV|A Chain A, Crystal Structure Of An Alginate Lyase (Bacova_01668) From
Bacteroides Ovatus At 1.95 A Resolution
pdb|3NNB|A Chain A, Crystal Structure Of An Alginate Lyase (Bacova_01668) From
Bacteroides Ovatus At 1.60 A Resolution
Length = 382
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 22/46 (47%)
Query: 326 KGGIKTAMLREAYRHSELIDRDPLLEIKERFVELLEKGKHEWTEQL 371
KG + A + Y +E ID L E + F ++KG EW QL
Sbjct: 157 KGXGRGAGXIDIYSFTEXIDAXTLXENSKAFTPKVKKGXKEWFTQL 202
>pdb|2PT5|A Chain A, Crystal Structure Of Shikimate Kinase (Aq_2177) From
Aquifex Aeolicus Vf5
pdb|2PT5|B Chain B, Crystal Structure Of Shikimate Kinase (Aq_2177) From
Aquifex Aeolicus Vf5
pdb|2PT5|C Chain C, Crystal Structure Of Shikimate Kinase (Aq_2177) From
Aquifex Aeolicus Vf5
pdb|2PT5|D Chain D, Crystal Structure Of Shikimate Kinase (Aq_2177) From
Aquifex Aeolicus Vf5
Length = 168
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 106 FYTYYDRIKPKSDAVLFLRPSDRLRDFLEEERKIY 140
F + +R K + L RP D +++ EE RKIY
Sbjct: 103 FEVFLERCKDSKERPLLKRPLDEIKNLFEERRKIY 137
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 241 EEMREWVRDWLELDYISPYEDVSNLDQSSQEMEKRTVAVFHELLSLS 287
EE+++ VR +LD +P+E + +D S+ + +FHE + L+
Sbjct: 395 EELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLT 441
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 0.137 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,305,479
Number of Sequences: 62578
Number of extensions: 520386
Number of successful extensions: 1440
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1430
Number of HSP's gapped (non-prelim): 23
length of query: 405
length of database: 14,973,337
effective HSP length: 101
effective length of query: 304
effective length of database: 8,652,959
effective search space: 2630499536
effective search space used: 2630499536
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: 53 (25.0 bits)