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= psy7170
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UNG|D Chain D, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNG|E Chain E, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNH|D Chain D, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNH|E Chain E, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNL|D Chain D, Structural Mechanism For The Inhibition Of Cd5-P25 From
The Roscovitine, Aloisine And Indirubin.
pdb|1UNL|E Chain E, Structural Mechanism For The Inhibition Of Cd5-P25 From
The Roscovitine, Aloisine And Indirubin
Length = 208
Score = 149 bits (376), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 67/100 (67%), Positives = 85/100 (85%), Gaps = 1/100 (1%)
Query: 23 DVAFINPANVVFVYMLVRELVDGDKIDSESQLQAVVLTCLYLSYSYMGNEISYPLKPFLV 82
D FI PANVVF+YML R+++ + + S+ +LQAV+LTCLYLSYSYMGNEISYPLKPFLV
Sbjct: 93 DQGFITPANVVFLYMLCRDVISSE-VGSDHELQAVLLTCLYLSYSYMGNEISYPLKPFLV 151
Query: 83 EDCKEKFWDRCLHIVNNMSSSMLRINAEPGFFTEIFTELK 122
E CKE FWDRCL ++N MSS ML+INA+P +FT++F++LK
Sbjct: 152 ESCKEAFWDRCLSVINLMSSKMLQINADPHYFTQVFSDLK 191
>pdb|3O0G|D Chain D, Crystal Structure Of Cdk5:p25 In Complex With An Atp
Analogue
pdb|3O0G|E Chain E, Crystal Structure Of Cdk5:p25 In Complex With An Atp
Analogue
Length = 149
Score = 148 bits (374), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 67/100 (67%), Positives = 85/100 (85%), Gaps = 1/100 (1%)
Query: 23 DVAFINPANVVFVYMLVRELVDGDKIDSESQLQAVVLTCLYLSYSYMGNEISYPLKPFLV 82
D FI PANVVF+YML R+++ + + S+ +LQAV+LTCLYLSYSYMGNEISYPLKPFLV
Sbjct: 48 DQGFITPANVVFLYMLCRDVISSE-VGSDHELQAVLLTCLYLSYSYMGNEISYPLKPFLV 106
Query: 83 EDCKEKFWDRCLHIVNNMSSSMLRINAEPGFFTEIFTELK 122
E CKE FWDRCL ++N MSS ML+INA+P +FT++F++LK
Sbjct: 107 ESCKEAFWDRCLSVINLMSSKMLQINADPHYFTQVFSDLK 146
>pdb|1H4L|D Chain D, Structure And Regulation Of The Cdk5-P25(Nck5a) Complex
pdb|1H4L|E Chain E, Structure And Regulation Of The Cdk5-P25(Nck5a) Complex
Length = 147
Score = 148 bits (374), Expect = 9e-37, Method: Compositional matrix adjust.
Identities = 67/100 (67%), Positives = 85/100 (85%), Gaps = 1/100 (1%)
Query: 23 DVAFINPANVVFVYMLVRELVDGDKIDSESQLQAVVLTCLYLSYSYMGNEISYPLKPFLV 82
D FI PANVVF+YML R+++ + + S+ +LQAV+LTCLYLSYSYMGNEISYPLKPFLV
Sbjct: 46 DQGFITPANVVFLYMLCRDVISSE-VGSDHELQAVLLTCLYLSYSYMGNEISYPLKPFLV 104
Query: 83 EDCKEKFWDRCLHIVNNMSSSMLRINAEPGFFTEIFTELK 122
E CKE FWDRCL ++N MSS ML+INA+P +FT++F++LK
Sbjct: 105 ESCKEAFWDRCLSVINLMSSKMLQINADPHYFTQVFSDLK 144
>pdb|3K6J|A Chain A, Crystal Structure Of The Dehydrogenase Part Of
Multifuctional Enzyme 1 From C.Elegans
Length = 460
Score = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 16/91 (17%)
Query: 15 LYGPHATVDVAFINPANVVFVYMLVRELVDGDKIDSESQLQAVVLTCLYLSYSYMGNEIS 74
L P V + F NPANV+ + E++ G S++ ++ ++ E
Sbjct: 178 LRDPSNLVGIHFFNPANVIRLV----EIIYGSHTSSQA-----------IATAFQACESI 222
Query: 75 YPLKPFLVEDCKEKFWDRCLHIVNNMSSSML 105
L P LV +CK ++R LH+ + S ++
Sbjct: 223 KKL-PVLVGNCKSFVFNRLLHVYFDQSQKLM 252
>pdb|2GCU|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|B Chain B, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|C Chain C, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|D Chain D, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
Length = 245
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 26/41 (63%)
Query: 65 SYSYMGNEISYPLKPFLVEDCKEKFWDRCLHIVNNMSSSML 105
+++Y+ ++S+P KP L+ D +K DR L +++ + ++
Sbjct: 15 TFTYLLADVSHPDKPALLIDPVDKTVDRDLKLIDELGLKLI 55
>pdb|2D1F|A Chain A, Structure Of Mycobacterium Tuberculosis Threonine Synthase
pdb|2D1F|B Chain B, Structure Of Mycobacterium Tuberculosis Threonine Synthase
Length = 360
Score = 26.6 bits (57), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 5 LEEKDEEYMYLYGPHATVDVAFINPANVVFVYMLVRELVDG 45
L DEE + Y A V+ F+ PA+ + L++ + DG
Sbjct: 273 LAASDEEILAAYHLVARVEGVFVEPASAASIAGLLKAIDDG 313
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPANVVFVYMLVRELVDGD 46
MD + + + E Y+ PH T+ V F +P N ++ ++ D
Sbjct: 350 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPD 395
>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 = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPANVVFVYMLVRELVDGD 46
MD + + + E Y+ PH T+ V F +P N ++ ++ D
Sbjct: 351 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPD 396
>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 = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPAN 31
MD + + + E Y+ PH T+ V F +P N
Sbjct: 348 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRN 378
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPAN 31
MD + + + E Y+ PH T+ V F +P N
Sbjct: 346 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRN 376
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPAN 31
MD + + + E Y+ PH T+ V F +P N
Sbjct: 346 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRN 376
>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 = 26.2 bits (56), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPANVVFVYMLVRELVDGD 46
MD + + + E Y+ PH T+ V F +P N ++ ++ D
Sbjct: 351 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPD 396
>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 = 26.2 bits (56), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 1 MDMELEEKDEEYMYLYGPHATVDVAFINPAN 31
MD + + + E Y+ PH T+ V F +P N
Sbjct: 350 MDDQWMQDEMEIGYIQAPHKTLPVVFDSPRN 380
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 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,992,069
Number of Sequences: 62578
Number of extensions: 142646
Number of successful extensions: 299
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 283
Number of HSP's gapped (non-prelim): 13
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)