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= 038406
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IVX|A Chain A, Crystal Structure Of Human Cyclin T2 At 1.8 A Resolution
(Casp Target)
pdb|2IVX|B Chain B, Crystal Structure Of Human Cyclin T2 At 1.8 A Resolution
(Casp Target)
Length = 257
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYY 66
E +PS++ G+ K+ + + +QE+G +L + Q+ + A++ H+FYMH H
Sbjct: 13 ENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH--HSFTK 70
Query: 67 KQKELILTAERLLPATI 83
K +I + L A +
Sbjct: 71 FNKNIISSTALFLAAKV 87
>pdb|3BLH|B Chain B, Crystal Structure Of Human Cdk9CYCLINT1
pdb|3BLQ|B Chain B, Crystal Structure Of Human Cdk9CYCLINT1 IN COMPLEX WITH
ATP
pdb|3BLR|B Chain B, Crystal Structure Of Human Cdk9CYCLINT1 IN COMPLEX WITH
Flavopiridol
pdb|3MY1|B Chain B, Structure Of Cdk9CYCLINT1 IN COMPLEX WITH DRB
pdb|3LQ5|B Chain B, Structure Of Cdk9CYCLINT IN COMPLEX WITH S-Cr8
pdb|3TN8|B Chain B, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|4EC8|B Chain B, Structure Of Full Length Cdk9 In Complex With Cyclint
And Drb
pdb|4EC9|B Chain B, Crystal Structure Of Full-Length Cdk9 In Complex With
Cyclin T
pdb|4BCF|B Chain B, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
pdb|4BCH|B Chain B, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
pdb|4BCI|B Chain B, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
pdb|4BCJ|B Chain B, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
Length = 260
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
E SPS++ G+ K+ + + LQ++G +L + Q+ + A++ H+FYM Q
Sbjct: 21 ENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ 74
>pdb|3TNH|B Chain B, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|3TNI|B Chain B, Structure Of Cdk9CYCLIN T F241L
Length = 259
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
E SPS++ G+ K+ + + LQ++G +L + Q+ + A++ H+FYM Q
Sbjct: 20 ENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ 73
>pdb|2PK2|A Chain A, Cyclin Box Structure Of The P-Tefb Subunit Cyclin T1
Derived From A Fusion Complex With Eiav Tat
pdb|2PK2|B Chain B, Cyclin Box Structure Of The P-Tefb Subunit Cyclin T1
Derived From A Fusion Complex With Eiav Tat
pdb|2PK2|C Chain C, Cyclin Box Structure Of The P-Tefb Subunit Cyclin T1
Derived From A Fusion Complex With Eiav Tat
pdb|2PK2|D Chain D, Cyclin Box Structure Of The P-Tefb Subunit Cyclin T1
Derived From A Fusion Complex With Eiav Tat
Length = 358
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
E SPS++ G+ K+ + + LQ++G +L + Q+ + A++ H+FYM Q
Sbjct: 20 ENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ 73
>pdb|3MI9|B Chain B, Crystal Structure Of Hiv-1 Tat Complexed With Human
P-Tefb
pdb|3MIA|B Chain B, Crystal Structure Of Hiv-1 Tat Complexed With Atp-Bound
Human P-Tefb
Length = 266
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
E SPS++ G+ K+ + + LQ++G +L + Q+ + A++ H+FYM Q
Sbjct: 20 ENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ 73
>pdb|2W2H|A Chain A, Structural Basis Of Transcription Activation By The
Cyclin T1-Tat-Tar Rna Complex From Eiav
pdb|2W2H|B Chain B, Structural Basis Of Transcription Activation By The
Cyclin T1-Tat-Tar Rna Complex From Eiav
Length = 264
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
E SPS++ G+ K+ + + LQ++G +L + Q+ + A++ H+FYM Q
Sbjct: 17 ENSPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ 70
>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC
Length = 285
Score = 33.1 bits (74), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 2 VLHRREFSPSKKDGISFKKDSELWKL---YCSFLQELGTKLKLPQVIVACAMMLCHQFY 57
+L +++ ++ + F + E WKL + + +Q LG LKL Q ++A A + +FY
Sbjct: 17 ILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFY 75
>pdb|2I53|A Chain A, Crystal Structure Of Cyclin K
Length = 258
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 28/129 (21%), Positives = 51/129 (39%), Gaps = 43/129 (33%)
Query: 9 SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ-------- 60
+PS+ +G+ ++ + F+ ++GT+L L +A ++ H+FYM
Sbjct: 25 TPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRY 84
Query: 61 ------------------------------LHDVYYKQ-----KELILTAERLLPATIAF 85
L+DV + Q KE ++ ER+L TI F
Sbjct: 85 VTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKF 144
Query: 86 DFDIQLPYE 94
D ++ PY+
Sbjct: 145 DLQVEHPYQ 153
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 27.7 bits (60), Expect = 1.7, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 11 SKKDGISFKKDSELWKLYC-SFLQELGTKLKLPQVIVACAMMLCHQFYMHQL--HDVYYK 67
+ K+G +FK D E ++L+C SF E T Q I A +C M +L DV +
Sbjct: 579 AAKEGFAFKHDREQYQLFCDSFPFE--TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFG 636
Query: 68 QKELILTAERL 78
+ E+ + A L
Sbjct: 637 KTEVAMRAAFL 647
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
0.328 0.139 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,310,947
Number of Sequences: 62578
Number of extensions: 114878
Number of successful extensions: 243
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 235
Number of HSP's gapped (non-prelim): 10
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)