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= 034642
(88 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 = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 49/69 (71%), Positives = 60/69 (86%)
Query: 3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
QI YS+KY D+ +EYRHV+LP D+AKL+PK L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 5 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64
Query: 63 HIMLFRRPL 71
HI+LFRRPL
Sbjct: 65 HILLFRRPL 73
>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 = 110 bits (276), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 49/69 (71%), Positives = 60/69 (86%)
Query: 3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
QI YS+KY D+ +EYRHV+LP D+AKL+PK L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 1 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 60
Query: 63 HIMLFRRPL 71
HI+LFRRPL
Sbjct: 61 HILLFRRPL 69
>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 = 106 bits (265), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 48/69 (69%), Positives = 58/69 (84%)
Query: 3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
QI YS+KYFD+ YEYRHV+LP +++K +PK L+SE EWR +GVQQS GWVHY IH PEP
Sbjct: 5 QIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEP 64
Query: 63 HIMLFRRPL 71
HI+LFRRPL
Sbjct: 65 HILLFRRPL 73
>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 = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 40/77 (51%), Positives = 52/77 (67%), Gaps = 9/77 (11%)
Query: 4 IQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVH 54
I YS +Y DD YEYRHV+LP + K++P + R+L+E EWR +G+ QS GW H
Sbjct: 28 IHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEH 87
Query: 55 YAIHRPEPHIMLFRRPL 71
Y H PEPHI+LF+RPL
Sbjct: 88 YECHAPEPHILLFKRPL 104
>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 = 85.1 bits (209), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 39/77 (50%), Positives = 51/77 (66%), Gaps = 9/77 (11%)
Query: 4 IQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVH 54
I YS +Y DD YEYRHV+LP + K++P + R+L+E EWR +G+ QS GW H
Sbjct: 28 IHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEH 87
Query: 55 YAIHRPEPHIMLFRRPL 71
Y H EPHI+LF+RPL
Sbjct: 88 YECHAAEPHILLFKRPL 104
>pdb|1PUC|A Chain A, P13suc1 In A Strand-Exchanged Dimer
Length = 105
Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 9/78 (11%)
Query: 1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
+ QI YS +Y DD YEYRHV+LP + K +P + R+L E EWR +G+ QS G
Sbjct: 21 IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 80
Query: 52 WVHYAIHRPEPHIMLFRR 69
W Y +H PEPHI+LF+R
Sbjct: 81 WEMYEVHVPEPHILLFKR 98
>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 = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 9/78 (11%)
Query: 1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
+ QI YS +Y DD YEYRHV+LP + K +P + R+L E EWR +G+ QS G
Sbjct: 22 IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 81
Query: 52 WVHYAIHRPEPHIMLFRR 69
W Y +H PEPHI+LF+R
Sbjct: 82 WEMYEVHVPEPHILLFKR 99
>pdb|2IT1|A Chain A, Structure Of Ph0203 Protein From Pyrococcus Horikoshii
pdb|2IT1|B Chain B, Structure Of Ph0203 Protein From Pyrococcus Horikoshii
Length = 362
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 25 DVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPL 71
+VAK+L ++LL+ W+ G QQ R + A+ + EP ++L PL
Sbjct: 116 EVAKMLHIDKLLNRYPWQLSGGQQQRVAIARALVK-EPEVLLLDEPL 161
>pdb|2NWQ|A Chain A, Short Chain Dehydrogenase From Pseudomonas Aeruginosa
pdb|2NWQ|B Chain B, Short Chain Dehydrogenase From Pseudomonas Aeruginosa
pdb|2NWQ|C Chain C, Short Chain Dehydrogenase From Pseudomonas Aeruginosa
pdb|2NWQ|D Chain D, Short Chain Dehydrogenase From Pseudomonas Aeruginosa
Length = 272
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 11 FDDTYEYRHVVLPPDVAKLL------PKNRLLSETEWRAIGVQQSRGWVHYAIHR 59
+D TY H + P D+A+ + P + ++ E + S+ W +AIHR
Sbjct: 220 YDKTYAGAHPIQPEDIAETIFWIXNQPAHLNINSLEIXPV----SQSWAGFAIHR 270
>pdb|4B0T|A Chain A, Structure Of The Pup Ligase Pafa Of The Prokaryotic
Ubiquitin-Like Modification Pathway In Complex With Adp
pdb|4B0T|B Chain B, Structure Of The Pup Ligase Pafa Of The Prokaryotic
Ubiquitin-Like Modification Pathway In Complex With Adp
Length = 493
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 20 VVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPL 71
V PD + + R+L + +GV + W+ + ++RPEP + P
Sbjct: 410 VDTAPDTTRAHLRGRILKAAD--TLGVPVTVDWMRHKVNRPEPQSVELGDPF 459
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 0.140 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,331,671
Number of Sequences: 62578
Number of extensions: 73861
Number of successful extensions: 216
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 205
Number of HSP's gapped (non-prelim): 10
length of query: 88
length of database: 14,973,337
effective HSP length: 56
effective length of query: 32
effective length of database: 11,468,969
effective search space: 367007008
effective search space used: 367007008
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)