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= psy4005
(202 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DKS|A Chain A, Ckshs1: Human Cyclin Dependent Kinase Subunit, Type 1 In
Complex With Phosphate
pdb|1DKS|B Chain B, Ckshs1: Human Cyclin Dependent Kinase Subunit, Type 1 In
Complex With Phosphate
pdb|1DKT|A Chain A, Ckshs1: Human Cyclin Dependent Kinase Subunit, Type 1
Complex With Metavanadate
pdb|1DKT|B Chain B, Ckshs1: Human Cyclin Dependent Kinase Subunit, Type 1
Complex With Metavanadate
pdb|1BUH|B Chain B, Crystal Structure Of The Human Cdk2 Kinase Complex With
Cell Cycle-Regulatory Protein Ckshs1
Length = 79
Score = 100 bits (248), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 44/62 (70%), Positives = 52/62 (83%)
Query: 81 MSADDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLH 140
MS I YSDKY+D+ + YRHVMLP D+AK VPKTHLM+E+EWRNLGVQQS GW+HYM+H
Sbjct: 1 MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH 60
Query: 141 LP 142
P
Sbjct: 61 EP 62
>pdb|2ASS|C Chain C, Crystal Structure Of The Skp1-Skp2-Cks1 Complex
pdb|2AST|C Chain C, Crystal Structure Of Skp1-Skp2-Cks1 In Complex With A P27
Peptide
Length = 69
Score = 97.1 bits (240), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 42/57 (73%), Positives = 50/57 (87%)
Query: 86 IRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLP 142
I YSDKY+D+ + YRHVMLP D+AK VPKTHLM+E+EWRNLGVQQS GW+HYM+H P
Sbjct: 2 IYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEP 58
>pdb|1CKS|A Chain A, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
Assembly In Cell Cycle Control
pdb|1CKS|B Chain B, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
Assembly In Cell Cycle Control
pdb|1CKS|C Chain C, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
Assembly In Cell Cycle Control
Length = 79
Score = 95.9 bits (237), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 43/62 (69%), Positives = 51/62 (82%)
Query: 81 MSADDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLH 140
M+ I YSDKY D++Y YRHVMLP +L+KQVPKTHLM+E EWR LGVQQS GW+HYM+H
Sbjct: 1 MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIH 60
Query: 141 LP 142
P
Sbjct: 61 EP 62
>pdb|1QB3|A Chain A, Crystal Structure Of The Cell Cycle Regulatory Protein
Cks1
pdb|1QB3|B Chain B, Crystal Structure Of The Cell Cycle Regulatory Protein
Cks1
pdb|1QB3|C Chain C, Crystal Structure Of The Cell Cycle Regulatory Protein
Cks1
Length = 150
Score = 67.8 bits (164), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 33/68 (48%), Positives = 40/68 (58%), Gaps = 9/68 (13%)
Query: 84 DDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTH---------LMTETEWRNLGVQQSPGW 134
D I YS +Y DDNY YRHVMLP + K +P + ++TE EWR LG+ QS GW
Sbjct: 26 DSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGW 85
Query: 135 IHYMLHLP 142
HY H P
Sbjct: 86 EHYECHAP 93
>pdb|3QY2|A Chain A, Crystal Structure Of The P93a Monomer Mutant Of S.
Cerevisiae Cks1
pdb|3QY2|B Chain B, Crystal Structure Of The P93a Monomer Mutant Of S.
Cerevisiae Cks1
Length = 117
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 39/66 (59%), Gaps = 9/66 (13%)
Query: 84 DDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTH---------LMTETEWRNLGVQQSPGW 134
D I YS +Y DDNY YRHVMLP + K +P + ++TE EWR LG+ QS GW
Sbjct: 26 DSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGW 85
Query: 135 IHYMLH 140
HY H
Sbjct: 86 EHYECH 91
>pdb|1SCE|A Chain A, Crystal Structure Of The Cell Cycle Regulatory Protein
Suc1 Reveals A Novel Beta-Hinge Conformational Switch
pdb|1SCE|B Chain B, Crystal Structure Of The Cell Cycle Regulatory Protein
Suc1 Reveals A Novel Beta-Hinge Conformational Switch
pdb|1SCE|C Chain C, Crystal Structure Of The Cell Cycle Regulatory Protein
Suc1 Reveals A Novel Beta-Hinge Conformational Switch
pdb|1SCE|D Chain D, Crystal Structure Of The Cell Cycle Regulatory Protein
Suc1 Reveals A Novel Beta-Hinge Conformational Switch
Length = 112
Score = 63.2 bits (152), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 36/101 (35%), Positives = 53/101 (52%), Gaps = 20/101 (19%)
Query: 84 DDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTH---------LMTETEWRNLGVQQSPGW 134
D I YS +Y DD Y YRHVMLP + K +P + ++ E EWR LG+ QS GW
Sbjct: 23 DQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLGW 82
Query: 135 IHYMLHLPGNENWVKNRYETLVRLRGKRDFSVLSQQDKQGG 175
Y +H+P ++ + ++D+ + SQQ +GG
Sbjct: 83 EMYEVHVPEPH---------ILLFKREKDYQMKSQQ--RGG 112
>pdb|1PUC|A Chain A, P13suc1 In A Strand-Exchanged Dimer
Length = 105
Score = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 39/68 (57%), Gaps = 9/68 (13%)
Query: 84 DDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTH---------LMTETEWRNLGVQQSPGW 134
D I YS +Y DD Y YRHVMLP + K +P + ++ E EWR LG+ QS GW
Sbjct: 22 DQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLGW 81
Query: 135 IHYMLHLP 142
Y +H+P
Sbjct: 82 EMYEVHVP 89
>pdb|2VKD|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKD|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKD|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKH|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VKH|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VKH|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VL8|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
pdb|2VL8|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
pdb|2VL8|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
Length = 546
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 82 SADDIRYSDKYEDDNYIYRHV-MLP---PDLAKQVPKTHLMTETEWRNLGVQQSPGWIHY 137
+A DI ++D +Y V MLP PDL K + K +T T W + ++ + Y
Sbjct: 267 AASDILRISMLKEDGGVYLDVDMLPGIQPDLFKSINKPDSITNTSWEMIKLE---AIMKY 323
Query: 138 MLHLPG 143
++PG
Sbjct: 324 KEYIPG 329
>pdb|3EG9|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
MEMBRIN
pdb|3EGD|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 764
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 15/111 (13%)
Query: 37 NSVQEESAYGKFEFCRAAAAPSLIPVSSCLLAFTVSSFSGKTTTMSADDIRYSDKYEDDN 96
N+ +ES+Y + F R SLI + L A+ SFSG + D +
Sbjct: 594 NNSPDESSYYRHHFMRQDLTQSLIMIQPILYAY---SFSGPPEPV----------LLDSS 640
Query: 97 YIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGW--IHYMLHLPGNE 145
I +L D Q+ H T +WR G Q P + ++L P ++
Sbjct: 641 SILADRILLMDTFFQILIYHGETIAQWRKSGYQDMPEYENFRHLLQAPVDD 691
>pdb|3EFO|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
SYNTAXIN 5
Length = 765
Score = 27.3 bits (59), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 15/111 (13%)
Query: 37 NSVQEESAYGKFEFCRAAAAPSLIPVSSCLLAFTVSSFSGKTTTMSADDIRYSDKYEDDN 96
N+ +ES+Y + F R SLI + L A+ SFSG + D +
Sbjct: 594 NNSPDESSYYRHHFMRQDLTQSLIMIQPILYAY---SFSGPPEPV----------LLDSS 640
Query: 97 YIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGW--IHYMLHLPGNE 145
I +L D Q+ H T +WR G Q P + ++L P ++
Sbjct: 641 SILADRILLMDTFFQILIYHGETIAQWRKSGYQDMPEYENFRHLLQAPVDD 691
>pdb|2NUP|A Chain A, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|A Chain A, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 769
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 15/111 (13%)
Query: 37 NSVQEESAYGKFEFCRAAAAPSLIPVSSCLLAFTVSSFSGKTTTMSADDIRYSDKYEDDN 96
N+ +ES+Y + F R SLI + L A+ SFSG + D +
Sbjct: 598 NNSPDESSYYRHHFMRQDLTQSLIMIQPILYAY---SFSGPPEPV----------LLDSS 644
Query: 97 YIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGW--IHYMLHLPGNE 145
I +L D Q+ H T +WR G Q P + ++L P ++
Sbjct: 645 SILADRILLMDTFFQILIYHGETIAQWRKSGYQDMPEYENFRHLLQAPVDD 695
>pdb|3NIP|A Chain A, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIP|B Chain B, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIP|C Chain C, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIP|D Chain D, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIP|E Chain E, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIP|F Chain F, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase Complexed With 1,6-Diaminohexane
pdb|3NIQ|A Chain A, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase
pdb|3NIQ|B Chain B, Crystal Structure Of Pseudomonas Aeruginosa
Guanidinopropionase
Length = 326
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 99 YRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLPGNENWVKN 150
YR V L V HL+T +R LG ++ G +H+ H N+ + +
Sbjct: 109 YRQVHAAGTLPLSVGGDHLVTLPIFRALGRERPLGMVHFDAHSDTNDRYFGD 160
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
0.321 0.135 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,686,643
Number of Sequences: 62578
Number of extensions: 265975
Number of successful extensions: 470
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 439
Number of HSP's gapped (non-prelim): 32
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)