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= psy9485
(190 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GUX|A Chain A, Rb Pocket Bound To E7 Lxcxe Motif
pdb|1O9K|A Chain A, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|C Chain C, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|E Chain E, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|G Chain G, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
Length = 218
Score = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 54/161 (33%), Positives = 89/161 (55%), Gaps = 14/161 (8%)
Query: 26 TPVKTATQSISRLNL-LCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS- 83
TPV+T +I +L + L PS L F C NP+ I + ++G F + ++
Sbjct: 2 TPVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAK 61
Query: 84 ASGDTARDFAEKRLSVAVCLYYKLLESILADEQKKPA-YDFNVLLSLQIFHETLFACCIE 142
A G + +R + V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E
Sbjct: 62 AVGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALE 121
Query: 143 IVIFCYNSN-----------SFPWILSVLGIEPYHFYKVIE 172
+V+ Y+ + SFPWIL+VL ++ + FYKVIE
Sbjct: 122 VVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIE 162
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 88.2 bits (217), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 52/160 (32%), Positives = 89/160 (55%), Gaps = 14/160 (8%)
Query: 27 PVKTATQSISRLNLLCGRDPN-PSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-A 84
PV+T +I +L ++ + PS L F C NP+ I + ++G F + ++ A
Sbjct: 302 PVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKA 361
Query: 85 SGDTARDFAEKRLSVAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEI 143
G + +R + V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+
Sbjct: 362 VGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEV 421
Query: 144 VIFCYNSN-----------SFPWILSVLGIEPYHFYKVIE 172
V+ Y+ + SFPWIL+VL ++ + FYKVIE
Sbjct: 422 VMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIE 461
>pdb|1AD6|A Chain A, Domain A Of Human Retinoblastoma Tumor Suppressor
Length = 185
Score = 84.0 bits (206), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 80/146 (54%), Gaps = 13/146 (8%)
Query: 40 LLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKRLS 98
+L PS L F C NP+ I + ++G F + ++ A G + +R
Sbjct: 11 ILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYK 70
Query: 99 VAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEIVIFCYNSN------ 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 71 LGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLD 130
Query: 152 -----SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 131 SGTDLSFPWILNVLNLKAFDFYKVIE 156
>pdb|4ELL|A Chain A, Structure Of The Inactive Retinoblastoma Protein Pocket
Domain
pdb|4ELL|B Chain B, Structure Of The Inactive Retinoblastoma Protein Pocket
Domain
Length = 411
Score = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 80/146 (54%), Gaps = 13/146 (8%)
Query: 40 LLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKRLS 98
+L PS L F C NP+ I + ++G F + ++ A G + +R
Sbjct: 12 ILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQRYK 71
Query: 99 VAVCLYYKLLESILADEQKKPA-YDFNVLLSLQIFHETLFACCIEIVIFCYNSN------ 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 72 LGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLD 131
Query: 152 -----SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 132 SGTDLSFPWILNVLNLKAFDFYKVIE 157
>pdb|2R7G|A Chain A, Structure Of The Retinoblastoma Protein Pocket Domain In
Complex With Adenovirus E1a Cr1 Domain
pdb|2R7G|C Chain C, Structure Of The Retinoblastoma Protein Pocket Domain In
Complex With Adenovirus E1a Cr1 Domain
Length = 347
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 48/148 (32%), Positives = 81/148 (54%), Gaps = 13/148 (8%)
Query: 38 LNLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKR 96
+ +L PS L F C NP+ I + ++G F + ++ A G + +R
Sbjct: 7 MMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQR 66
Query: 97 LSVAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEIVIFCYNSN---- 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 67 YKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQN 126
Query: 152 -------SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 127 LDSGTDLSFPWILNVLNLKAFDFYKVIE 154
>pdb|3POM|A Chain A, Crystal Structure Of The Unliganded Retinoblastoma Protein
Pocket Domain
pdb|3POM|B Chain B, Crystal Structure Of The Unliganded Retinoblastoma Protein
Pocket Domain
Length = 352
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 48/148 (32%), Positives = 81/148 (54%), Gaps = 13/148 (8%)
Query: 38 LNLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKR 96
+ +L PS L F C NP+ I + ++G F + ++ A G + +R
Sbjct: 10 MMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQGCVEIGSQR 69
Query: 97 LSVAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEIVIFCYNSN---- 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 70 YKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQN 129
Query: 152 -------SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 130 LDSGTDLSFPWILNVLNLKAFDFYKVIE 157
>pdb|1N4M|A Chain A, Structure Of Rb Tumor Suppressor Bound To The
Transactivation Domain Of E2f-2
pdb|1N4M|B Chain B, Structure Of Rb Tumor Suppressor Bound To The
Transactivation Domain Of E2f-2
Length = 345
Score = 81.3 bits (199), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 48/148 (32%), Positives = 80/148 (54%), Gaps = 13/148 (8%)
Query: 38 LNLLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKR 96
+ +L PS L F C NP+ I + ++G F + ++ A G +R
Sbjct: 7 MMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGAGCVAIGSQR 66
Query: 97 LSVAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEIVIFCYNSN---- 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 67 YKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQN 126
Query: 152 -------SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 127 LDSGTDLSFPWILNVLNLKAFDFYKVIE 154
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen
Length = 333
Score = 80.9 bits (198), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 79/146 (54%), Gaps = 13/146 (8%)
Query: 40 LLCGRDPNPSPALTRIFEACNKNPQPLIDSVLTNLGDKFTQHYS-ASGDTARDFAEKRLS 98
+L PS L F C NP+ I + ++G F + ++ A G +R
Sbjct: 10 ILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGAGCVAIGSQRYK 69
Query: 99 VAVCLYYKLLESILADEQKKPAY-DFNVLLSLQIFHETLFACCIEIVIFCYNSN------ 151
+ V LYY+++ES+L E+++ + +F+ LL+ IFH +L AC +E+V+ Y+ +
Sbjct: 70 LGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNLD 129
Query: 152 -----SFPWILSVLGIEPYHFYKVIE 172
SFPWIL+VL ++ + FYKVIE
Sbjct: 130 SGTDLSFPWILNVLNLKAFDFYKVIE 155
>pdb|2KFS|A Chain A, Nmr Structure Of Rv2175c
Length = 148
Score = 30.0 bits (66), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 145 IFCYNSN----SFPWILSVLGIEPYHFYKVIEWLLTPNPEVLGSNSGNE 189
+F NS S P +L++L Y +++ WL TP+P + + G+
Sbjct: 71 VFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSR 119
>pdb|2PGG|A Chain A, Crystal Structure Of A Birnavirus (Ibdv) Rna-Dependent Rna
Polymerase Vp1
Length = 774
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 18 RDLEYGNVTPVKTATQSISRLNLLCGRDPNPSP-ALTRIFEAC 59
RD YG+ T + AT+ ++ + GR+PN P L FE+
Sbjct: 130 RDKAYGSGTYMGQATRLVAMKEVATGRNPNKDPLKLGYTFESI 172
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 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,813,305
Number of Sequences: 62578
Number of extensions: 216603
Number of successful extensions: 476
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 12
length of query: 190
length of database: 14,973,337
effective HSP length: 93
effective length of query: 97
effective length of database: 9,153,583
effective search space: 887897551
effective search space used: 887897551
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)