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= 023010
(288 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 53/104 (50%), Gaps = 1/104 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
+ +R+++E SPSR+ G+D +E R +Q++G RL + Q TI TA+V HRF++
Sbjct: 10 YFTREQLEN-SPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYM 68
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYHKQ 253
+S R K EE P+ L V++ + H Q
Sbjct: 69 IQSFTRFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 112
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/102 (31%), Positives = 51/102 (50%), Gaps = 1/102 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
F +R+++E +PSR+ G++A +E R IQ +G RL + Q TI TA+V HRF++
Sbjct: 6 FFTREQLEN-TPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYM 64
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYH 251
S ++ K EE R L V++ + H
Sbjct: 65 HHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLH 106
>pdb|3TNH|B Chain B, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|3TNI|B Chain B, Structure Of Cdk9CYCLIN T F241L
Length = 259
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 1/104 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
+ +R+++E SPSR+ G+D +E R +Q++G RL + Q TI TA+V HRF++
Sbjct: 13 YFTREQLEN-SPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYM 71
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYHKQ 253
+S K EE P+ L V++ + H Q
Sbjct: 72 IQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 1/104 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
+ +R+++E SPSR+ G+D +E R +Q++G RL + Q TI TA+V HRF++
Sbjct: 13 YFTREQLEN-SPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYM 71
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYHKQ 253
+S K EE P+ L V++ + H Q
Sbjct: 72 IQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 1/104 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
+ +R+++E SPSR+ G+D +E R +Q++G RL + Q TI TA+V HRF++
Sbjct: 13 YFTREQLEN-SPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYM 71
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYHKQ 253
+S K EE P+ L V++ + H Q
Sbjct: 72 IQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
>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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 51/104 (49%), Gaps = 1/104 (0%)
Query: 150 FMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209
+ +R+++E SPSR+ G+D +E R +Q++G RL + Q TI TA+V HRF++
Sbjct: 14 YFTREQLEN-SPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYM 72
Query: 210 RRSHACHDRXXXXXXXXXXXXKSEETPRPLNDVLRASSELYHKQ 253
+S K E P+ L V++ + H Q
Sbjct: 73 IQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQ 116
>pdb|2I53|A Chain A, Crystal Structure Of Cyclin K
Length = 258
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 42/90 (46%)
Query: 160 SPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRX 219
+PS+ +G+D E R FI ++G RL L T+ T ++ HRF++ S R
Sbjct: 25 TPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRY 84
Query: 220 XXXXXXXXXXXKSEETPRPLNDVLRASSEL 249
K EETP+ D+++ + L
Sbjct: 85 VTGACCLFLAGKVEETPKKCKDIIKTARSL 114
>pdb|3B1N|A Chain A, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Adp-Mizoribine
pdb|3B1N|B Chain B, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Adp-Mizoribine
pdb|3B1O|A Chain A, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Ligand-Free Form
pdb|3B1O|B Chain B, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Ligand-Free Form
pdb|3B1P|A Chain A, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Adp-Inosine
pdb|3B1Q|A Chain A, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
pdb|3B1Q|B Chain B, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
pdb|3B1Q|C Chain C, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
pdb|3B1Q|D Chain D, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
pdb|3B1Q|E Chain E, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
pdb|3B1Q|F Chain F, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Inosine
Length = 326
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 49 YNNFHSYSGKFREHYQYDNPSYITASYVQPNNAPSFKRRKFSASA 93
Y+N ++ G+FREH D I S++ P RR+F A
Sbjct: 11 YDNIMTFEGRFREHILPDQVHLINLSFLVPT-----MRREFGGCA 50
>pdb|3B1R|A Chain A, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
pdb|3B1R|B Chain B, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
pdb|3B1R|C Chain C, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
pdb|3B1R|D Chain D, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
pdb|3B1R|E Chain E, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
pdb|3B1R|F Chain F, Structure Of Burkholderia Thailandensis Nucleoside
Kinase (Bthnk) In Complex With Amp-Mg-Amp
Length = 320
Score = 32.0 bits (71), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 49 YNNFHSYSGKFREHYQYDNPSYITASYVQPNNAPSFKRRKFSASA 93
Y+N ++ G+FREH D I S++ P RR+F A
Sbjct: 19 YDNIMTFEGRFREHILPDQVHLINLSFLVPT-----MRREFGGCA 58
>pdb|3NO0|A Chain A, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|B Chain B, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|C Chain C, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
Length = 276
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 96 DSARNYLQVPNEYETAVSSSN-KTLVPPVSISNIEVSTSMSCKRDRSKLEDDE 147
D+ + + + E E +++ N K ++ +I +ST S R R KLEDDE
Sbjct: 214 DTLVDLIPIKEEVELLITTKNGKAFYDKINQKDIPLSTKKSIPRTRWKLEDDE 266
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
0.318 0.129 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,038,455
Number of Sequences: 62578
Number of extensions: 238552
Number of successful extensions: 544
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 535
Number of HSP's gapped (non-prelim): 11
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)