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= psy12162
(242 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 159 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 218
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 219 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 248
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 158 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 217
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 218 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 247
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 154 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 213
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 214 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 243
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 158 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 217
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 218 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 247
>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 = 0.28, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 159 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 218
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 219 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 248
>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 = 0.28, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 156 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 215
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 216 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 245
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 86 LINAPMGQLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSACKLPSNK 145
L+N L+S A C DDE+ D ED D++ + D F +VL + +K
Sbjct: 154 LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDK 213
Query: 146 ----ELDHGRLLGYLTYVLDKFVEQDYSLV 171
+ G+L + VL Y +V
Sbjct: 214 VRVFQATRGKLSSKCSVVLGPKWPSHYLMV 243
>pdb|3G1N|A Chain A, Catalytic Domain Of The Human E3 Ubiquitin-Protein Ligase
Huwe1
pdb|3G1N|B Chain B, Catalytic Domain Of The Human E3 Ubiquitin-Protein Ligase
Huwe1
Length = 388
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 175 YGLTSKNKPSLSWLWSAYRAFDRKYKKNLKALYLVHPTGFIRVVLQIFKAV 225
Y N + W W A R+FD+ +A +L TG +V LQ F A+
Sbjct: 282 YHKYQSNSIQIQWFWRALRSFDQAD----RAKFLQFVTGTSKVPLQGFAAL 328
>pdb|3H1D|A Chain A, Structure Of The Huwe1 Hect Domain
Length = 405
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 175 YGLTSKNKPSLSWLWSAYRAFDRKYKKNLKALYLVHPTGFIRVVLQIFKAV 225
Y N + W W A R+FD + +A +L TG +V LQ F A+
Sbjct: 299 YHKYQSNSIQIQWFWRALRSFD----QADRAKFLQFVTGTSKVPLQGFAAL 345
>pdb|4A0C|A Chain A, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|B Chain B, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 1253
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 16/133 (12%)
Query: 93 QLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSA--CKLPSN------ 144
Q++++ T + L D+E D++S G+ V+G+ L+A CK +
Sbjct: 106 QVETIVDTLCTNMLSDKEQLRDISSIGLKTVIGELPPASSGSALAANVCKKITGRLTSAI 165
Query: 145 -KELDHGRLLGYLTYVLDKFVEQDYSLVYFHYGLTSKNKPSLSWLWSAYRAFDRKYKKNL 203
K+ D L L + D Q LV FH + + P L+ A R K+ +
Sbjct: 166 AKQEDVSVQLEALDIMADMLSRQGGLLVNFHPSILTCLLPQLTSPRLAVR------KRTI 219
Query: 204 KAL-YLVHPTGFI 215
AL +LV G I
Sbjct: 220 IALGHLVMSCGNI 232
>pdb|1U6G|C Chain C, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
Length = 1230
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 16/133 (12%)
Query: 93 QLDSLAATCTDDELKDEEDFADVASYGIVDVVGDDMFGRKLIVLSA--CKLPSN------ 144
Q++++ T + L D+E D++S G+ V+G+ L+A CK +
Sbjct: 83 QVETIVDTLCTNMLSDKEQLRDISSIGLKTVIGELPPASSGSALAANVCKKITGRLTSAI 142
Query: 145 -KELDHGRLLGYLTYVLDKFVEQDYSLVYFHYGLTSKNKPSLSWLWSAYRAFDRKYKKNL 203
K+ D L L + D Q LV FH + + P L+ A R K+ +
Sbjct: 143 AKQEDVSVQLEALDIMADMLSRQGGLLVNFHPSILTCLLPQLTSPRLAVR------KRTI 196
Query: 204 KAL-YLVHPTGFI 215
AL +LV G I
Sbjct: 197 IALGHLVMSCGNI 209
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
0.317 0.138 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,204,945
Number of Sequences: 62578
Number of extensions: 370517
Number of successful extensions: 749
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 741
Number of HSP's gapped (non-prelim): 14
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)