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= psy11028
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W63|A Chain A, Ap1 Clathrin Adaptor Core
pdb|1W63|C Chain C, Ap1 Clathrin Adaptor Core
pdb|1W63|E Chain E, Ap1 Clathrin Adaptor Core
pdb|1W63|G Chain G, Ap1 Clathrin Adaptor Core
pdb|1W63|I Chain I, Ap1 Clathrin Adaptor Core
pdb|1W63|K Chain K, Ap1 Clathrin Adaptor Core
Length = 618
Score = 38.1 bits (87), Expect = 0.001, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 8 LTSTKPYLRKKAVLMMYKVFLKFPDALRPAFPRLKEKLEDPDSGVQSAAVNVVCELARKN 67
L ++ YLRKKA L V K P+ + P K L + + GV +V ++ E+ ++
Sbjct: 151 LKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERS 210
Query: 68 PK---NYLSLAPVFFKLM 82
P ++ L P +++
Sbjct: 211 PDMLAHFRKLVPQLVRIL 228
>pdb|1EG5|A Chain A, Nifs-like Protein
pdb|1EG5|B Chain B, Nifs-like Protein
Length = 384
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 42 KEKLEDPDS----GVQSAAVNVVCELARKNPKNYLSLAP--VFFKLMTTSSNNWMLIKII 95
+EK +P+S G+++ N+ E AR+ L ++P +FF T S NW+L +
Sbjct: 26 REKYGNPNSAHGXGIEA---NLHXEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVA 82
Query: 96 KLF 98
+ F
Sbjct: 83 ETF 85
>pdb|1ECX|A Chain A, Nifs-Like Protein
pdb|1ECX|B Chain B, Nifs-Like Protein
Length = 384
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 42 KEKLEDPDS----GVQSAAVNVVCELARKNPKNYLSLAP--VFFKLMTTSSNNWMLIKII 95
+EK +P+S G+++ N+ E AR+ L ++P +FF T S NW+L +
Sbjct: 26 REKYGNPNSAHGMGIEA---NLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVA 82
Query: 96 KLF 98
+ F
Sbjct: 83 ETF 85
>pdb|1H4L|A Chain A, Structure And Regulation Of The Cdk5-P25(Nck5a) Complex
pdb|1H4L|B Chain B, Structure And Regulation Of The Cdk5-P25(Nck5a) Complex
Length = 292
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 44 KLEDPDSGVQSAAVNVVCELARKNPKNYLSLAPV 77
+L+D D GV S+A+ +C L KN + L V
Sbjct: 36 RLDDDDEGVPSSALREICLLKELKHKNIVRLHDV 69
>pdb|1UNG|A Chain A, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNG|B Chain B, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNH|A Chain A, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNH|B Chain B, Structural Mechanism For The Inhibition Of Cdk5-P25 By
Roscovitine, Aloisine And Indirubin.
pdb|1UNL|A Chain A, Structural Mechanism For The Inhibition Of Cd5-P25 From
The Roscovitine, Aloisine And Indirubin.
pdb|1UNL|B Chain B, Structural Mechanism For The Inhibition Of Cd5-P25 From
The Roscovitine, Aloisine And Indirubin.
pdb|3O0G|A Chain A, Crystal Structure Of Cdk5:p25 In Complex With An Atp
Analogue
pdb|3O0G|B Chain B, Crystal Structure Of Cdk5:p25 In Complex With An Atp
Analogue
Length = 292
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 44 KLEDPDSGVQSAAVNVVCELARKNPKNYLSLAPV 77
+L+D D GV S+A+ +C L KN + L V
Sbjct: 36 RLDDDDEGVPSSALREICLLKELKHKNIVRLHDV 69
>pdb|3VUE|A Chain A, Crystal Structure Of Rice Granule Bound Starch Synthase I
Catalytic Domain
pdb|3VUF|A Chain A, Crystal Structure Of Rice Granule Bound Starch Synthase I
Catalytic Domain In Complex With Adp
Length = 536
Score = 26.6 bits (57), Expect = 4.4, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 25 KVFLKFPDALRPAFPRLKEKLEDPDSGV----QSAAVNVVCELARKNPK 69
+VF+ P L + + EK+ PD+GV +++C+ A + P+
Sbjct: 89 RVFIDHPSFLEKVWGKTGEKIYGPDTGVDYKDNQMRFSLLCQAALEAPR 137
>pdb|2QPT|A Chain A, Crystal Structure Of An Ehd Atpase Involved In Membrane
Remodelling
Length = 550
Score = 26.2 bits (56), Expect = 5.8, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 43 EKLEDPDSGVQSAAVNVVCELARKNPKNYLSLAPVFFKLMTTSSNNWML 91
E +ED + G + A VV + K + + +LAP KL + + WM+
Sbjct: 436 EAIEDGEEGSEDDAEWVVTKDKSKYDEIFYNLAPADGKLSGSKAKTWMV 484
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
0.324 0.139 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,858,332
Number of Sequences: 62578
Number of extensions: 136647
Number of successful extensions: 423
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 418
Number of HSP's gapped (non-prelim): 8
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)