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= 023880
(276 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I53|A Chain A, Crystal Structure Of Cyclin K
Length = 258
Score = 96.3 bits (238), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 65/204 (31%), Positives = 104/204 (50%), Gaps = 21/204 (10%)
Query: 20 VMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 79
+ATG + FHRFY SF +F + A ++LA K+EE+P+K + +I + R
Sbjct: 61 TLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDII------KTARSL 114
Query: 80 LPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP----LE 135
L F + K E+ ER +L+ + F VEHP++F+ Y L+ +
Sbjct: 115 LNDVQFGQFG---DDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQK 171
Query: 136 LRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQIPLPENPP----WWKAF-- 187
L Q AW NDSL TTL ++++ E++A V+Y A R +F+I + P WW+ F
Sbjct: 172 LVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQ 231
Query: 188 DAEKSGIDEVCRVLAHLYSLPKAK 211
D ++++C + LYS K +
Sbjct: 232 DVPVDVLEDICHQILDLYSQGKQQ 255
>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 = 84.3 bits (207), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 53/175 (30%), Positives = 92/175 (52%), Gaps = 8/175 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY SF +F+ I+++++++LA+K+EE RK VI V H C
Sbjct: 49 QLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAH--ACLH 106
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
P+ LD + + E+ E +L+ +GF +EHPH + + +L
Sbjct: 107 PLEPL--LDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLA 164
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPL-PENPPWWKAFD 188
Q ++ +A +SL TT C+++K V+AC ++ A + ++IP+ + WW+ D
Sbjct: 165 QTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVD 219
>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 = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 55/176 (31%), Positives = 92/176 (52%), Gaps = 8/176 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY +SF RF VA ++++LA+K+EE P+K VI V H +
Sbjct: 53 QLTINTAIVYMHRFYMIQSFTRFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 112
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
E LP D S+ + + ++ E IL+ +GF ++HPH + + +L
Sbjct: 113 ESLP----DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLA 168
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPL-PENPPWWKAFDA 189
Q ++ +A +SL TT +++ VVAC ++ A + ++IP+ + WW+ DA
Sbjct: 169 QTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 224
>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 = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 55/176 (31%), Positives = 92/176 (52%), Gaps = 8/176 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY +SF RF VA ++++LA+K+EE P+K VI V H +
Sbjct: 56 QLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
E LP D S+ + + ++ E IL+ +GF ++HPH + + +L
Sbjct: 116 ESLP----DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLA 171
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPLP-ENPPWWKAFDA 189
Q ++ +A +SL TT +++ VVAC ++ A + ++IP+ + WW+ DA
Sbjct: 172 QTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 227
>pdb|3TNH|B Chain B, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|3TNI|B Chain B, Structure Of Cdk9CYCLIN T F241L
Length = 259
Score = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 54/176 (30%), Positives = 92/176 (52%), Gaps = 8/176 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY +SF +F VA ++++LA+K+EE P+K VI V H +
Sbjct: 56 QLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
E LP D S+ + + ++ E IL+ +GF ++HPH + + +L
Sbjct: 116 ESLP----DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLA 171
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPLP-ENPPWWKAFDA 189
Q ++ +A +SL TT +++ VVAC ++ A + ++IP+ + WW+ DA
Sbjct: 172 QTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 227
>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 = 81.3 bits (199), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 54/176 (30%), Positives = 92/176 (52%), Gaps = 8/176 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY +SF +F VA ++++LA+K+EE P+K VI V H +
Sbjct: 56 QLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQ 115
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
E LP D S+ + + ++ E IL+ +GF ++HPH + + +L
Sbjct: 116 ESLP----DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLA 171
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPL-PENPPWWKAFDA 189
Q ++ +A +SL TT +++ VVAC ++ A + ++IP+ + WW+ DA
Sbjct: 172 QTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 227
>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 = 80.9 bits (198), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 54/176 (30%), Positives = 91/176 (51%), Gaps = 8/176 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q + T V HRFY +SF RF VA ++++LA+K+E P+K VI V H +
Sbjct: 57 QLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQ 116
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
E LP D S+ + + ++ E IL+ +GF ++HPH + + +L
Sbjct: 117 ESLP----DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLA 172
Query: 138 QEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQIPLP-ENPPWWKAFDA 189
Q ++ +A +SL TT +++ VVAC ++ A + ++IP+ + WW+ DA
Sbjct: 173 QTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 228
>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC
Length = 285
Score = 60.5 bits (145), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 8/188 (4%)
Query: 18 QAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRR 77
Q V+AT V F RFY + S D ++A + V+LASK+EE + +I
Sbjct: 61 QQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIA-----AAT 115
Query: 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELR 137
L F K+F + E ++L+ M V HP++ + Y+ + L
Sbjct: 116 SVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLL 175
Query: 138 QEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEV 197
AW + ND+ RT LC+ + ++A ++ A + + W+ + I E+
Sbjct: 176 PLAWRIVNDTYRTDLCLLYPPFMIALACLHVACV---VQQKDARQWFAELSVDMEKILEI 232
Query: 198 CRVLAHLY 205
RV+ LY
Sbjct: 233 IRVILKLY 240
>pdb|1ZP2|A Chain A, Structure Of The Mediator Subunit Cyclin C
Length = 235
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 15/138 (10%)
Query: 18 QAVMATGQVLFHRFYCKRSFAR-FDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECR 76
Q V+AT VL R+ K++ + F ++ + A+ ++L+ K+EE P R + C
Sbjct: 46 QRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTI--------CN 97
Query: 77 REGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLEL 136
DL+S K + +S E I+ + V HP+ + +
Sbjct: 98 EAN------DLWSLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQKQ 151
Query: 137 RQEAWNLANDSLRTTLCV 154
+ AW++ NDS ++LC+
Sbjct: 152 LEFAWSIVNDSYASSLCL 169
>pdb|2O36|A Chain A, Crystal Structure Of Engineered Thimet Oligopeptidase With
Neurolysin Specificity In Neurotensin Cleavage Site
Length = 674
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 3/94 (3%)
Query: 52 LASKLEESPRKARQVIIVFHRMECRREGLPIE-HLDLFSKKFSELKMEMSR--TERHILK 108
LA KL+ + R VI+ R EC R GLP + + + ++ ++E +R ++++LK
Sbjct: 283 LAQKLKPLGEQERAVILELKRAECERRGLPFDGRIRAWDMRYYMNQVEETRYCVDQNLLK 342
Query: 109 EMGFVCHVEHPHKFISNYLATLETPLELRQEAWN 142
E V V H I L L E AW+
Sbjct: 343 EYFPVQVVTHGLLGIYQELLGLAFHHEEGASAWH 376
>pdb|1S4B|P Chain P, Crystal Structure Of Human Thimet Oligopeptidase
Length = 674
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 3/94 (3%)
Query: 52 LASKLEESPRKARQVIIVFHRMECRREGLPIE-HLDLFSKKFSELKMEMSR--TERHILK 108
LA KL+ + R VI+ R EC R GLP + + + ++ ++E +R ++++LK
Sbjct: 283 LAQKLKPLGEQERAVILELKRAECERRGLPFDGRIRAWDMRYYMNQVEETRYCVDQNLLK 342
Query: 109 EMGFVCHVEHPHKFISNYLATLETPLELRQEAWN 142
E V V H I L L E AW+
Sbjct: 343 EYFPVQVVTHGLLGIYQELLGLAFHHEEGASAWH 376
>pdb|3OL2|B Chain B, Receptor-Ligand Structure Of Human Semaphorin 4d With
Plexin B1
Length = 528
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 217 KDGTSFTFSSKTVDSQPQSTPKEVLQSSPQANNHTTFPIEALVPI 261
+DGT + V+S P + L + P ++HT P+ + VP+
Sbjct: 332 EDGTEVAYIEYDVNSDCAQLPVDTLDAYPCGSDHTPSPMASRVPL 376
>pdb|3D34|A Chain A, Structure Of The F-Spondin Domain Of Mindin
pdb|3D34|B Chain B, Structure Of The F-Spondin Domain Of Mindin
Length = 223
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 220 TSFTFSSKTVDSQPQSTPKEVLQSSPQ--ANNHTTFPIEALVPI 261
+ FTFSS + PQ T E+ SSP AN+ ++AL PI
Sbjct: 167 SGFTFSSPNFATIPQDTVTEITSSSPSHPANSFYYPRLKALPPI 210
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
0.322 0.134 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,100,442
Number of Sequences: 62578
Number of extensions: 315362
Number of successful extensions: 672
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 648
Number of HSP's gapped (non-prelim): 15
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)