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= 046343
(633 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 48/152 (31%), Positives = 83/152 (54%), Gaps = 18/152 (11%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 68 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 127
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+ W
Sbjct: 128 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 187
Query: 192 EKGSSMYN----SLTVARPALSAEINLGFTDI 219
S +++ S V R + S ++L + +
Sbjct: 188 LSDSPLFDLIKQSKLVPRGSKSTSLSLFYKKV 219
Score = 68.6 bits (166), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 4/121 (3%)
Query: 372 TGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQII 431
T +++ + K+ +LA +R+N + ERL E + + TL L + H+DQI+
Sbjct: 210 TSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIM 269
Query: 432 LCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIFAPTV 487
+C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +F +
Sbjct: 270 MCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRL 329
Query: 488 K 488
K
Sbjct: 330 K 330
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 43/128 (33%), Positives = 73/128 (57%), Gaps = 14/128 (10%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 372 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 431
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+ W
Sbjct: 432 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 491
Query: 192 EKGSSMYN 199
S +++
Sbjct: 492 LSDSPLFD 499
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 4/125 (3%)
Query: 368 PCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHI 427
P T +++ + K+ +LA +R+N + ERL E + + TL L + H+
Sbjct: 510 PLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHL 569
Query: 428 DQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIF 483
DQI++C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +F
Sbjct: 570 DQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVF 629
Query: 484 APTVK 488
+K
Sbjct: 630 MQRLK 634
>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 = 77.0 bits (188), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 56/199 (28%), Positives = 93/199 (46%), Gaps = 45/199 (22%)
Query: 46 TPVSTAMTTAKWLRTIICPLPSKPSADL----------------QGANLMDNIWAE---- 85
TPV T M T + L I+ +PS +L + + I+ E
Sbjct: 2 TPVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAK 61
Query: 86 -----------QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAE 129
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E
Sbjct: 62 AVGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALE 121
Query: 130 LVLATHKTVT---------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNS 180
+V+AT+ T + F +L + + AF+ KVI+SFI+ E +L RE+ +HL
Sbjct: 122 VVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLER 181
Query: 181 LEERLLESMVWEKGSSMYN 199
E R++ES+ W S +++
Sbjct: 182 CEHRIMESLAWLSDSPLFD 200
>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 = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 43/128 (33%), Positives = 73/128 (57%), Gaps = 14/128 (10%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 65 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 124
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+ W
Sbjct: 125 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 184
Query: 192 EKGSSMYN 199
S +++
Sbjct: 185 LSDSPLFD 192
Score = 68.6 bits (166), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 4/121 (3%)
Query: 372 TGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQII 431
T +++ + K+ +LA +R+N + ERL E + + TL L + H+DQI+
Sbjct: 205 TSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIM 264
Query: 432 LCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIFAPTV 487
+C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +F +
Sbjct: 265 MCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRL 324
Query: 488 K 488
K
Sbjct: 325 K 325
>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 = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 43/128 (33%), Positives = 73/128 (57%), Gaps = 14/128 (10%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 65 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 124
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+ W
Sbjct: 125 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 184
Query: 192 EKGSSMYN 199
S +++
Sbjct: 185 LSDSPLFD 192
Score = 68.9 bits (167), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 4/121 (3%)
Query: 372 TGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQII 431
T +++ + K+ +LA +R+N + ERL E + + TL L + H+DQI+
Sbjct: 205 TSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIM 264
Query: 432 LCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIFAPTV 487
+C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +F +
Sbjct: 265 MCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRL 324
Query: 488 K 488
K
Sbjct: 325 K 325
>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 = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 43/128 (33%), Positives = 72/128 (56%), Gaps = 14/128 (10%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 68 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 127
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES W
Sbjct: 128 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESFAW 187
Query: 192 EKGSSMYN 199
S +++
Sbjct: 188 LSDSPLFD 195
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 37/126 (29%), Positives = 64/126 (50%), Gaps = 4/126 (3%)
Query: 367 EPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCH 426
+P T +++ + K+ +LA +R+N + ERL E + + TL L + H
Sbjct: 264 KPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRH 323
Query: 427 IDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKI 482
+DQI++C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +
Sbjct: 324 LDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSV 383
Query: 483 FAPTVK 488
F +K
Sbjct: 384 FMQRLK 389
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen
Length = 333
Score = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 46/150 (30%), Positives = 83/150 (55%), Gaps = 16/150 (10%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 66 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 125
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVW 191
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+ W
Sbjct: 126 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAW 185
Query: 192 EKGSSMYNSLTVAR--PALSAEINLGFTDI 219
S +++ + ++ P S ++L + +
Sbjct: 186 LSDSPLFDLIKQSKLVPRGSTSLSLFYKKV 215
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 4/125 (3%)
Query: 368 PCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHI 427
P T +++ + K+ +LA +R+N + ERL E + + TL L + H+
Sbjct: 202 PRGSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHL 261
Query: 428 DQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKIF 483
DQI++C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +F
Sbjct: 262 DQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVF 321
Query: 484 APTVK 488
+K
Sbjct: 322 MQRLK 326
>pdb|1AD6|A Chain A, Domain A Of Human Retinoblastoma Tumor Suppressor
Length = 185
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 41/118 (34%), Positives = 68/118 (57%), Gaps = 14/118 (11%)
Query: 86 QRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVT- 139
QR ++L Y+V+E+M +E + L +N + L FH +LAC+ E+V+AT+ T
Sbjct: 67 QRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTS 126
Query: 140 --------MLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESM 189
+ F +L + + AF+ KVI+SFI+ E +L RE+ +HL E R++ES+
Sbjct: 127 QNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 184
>pdb|1GUX|B Chain B, Rb Pocket Bound To E7 Lxcxe Motif
pdb|1O9K|B Chain B, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|D Chain D, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|F Chain F, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
pdb|1O9K|H Chain H, Crystal Structure Of The Retinoblastoma Tumour Suppressor
Protein Bound To E2f Peptide
Length = 152
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 37/126 (29%), Positives = 64/126 (50%), Gaps = 4/126 (3%)
Query: 367 EPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCH 426
+P T +++ + K+ +LA +R+N + ERL E + + TL L + H
Sbjct: 5 KPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRH 64
Query: 427 IDQIILCCFYGVAKISQLNLTFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNKI 482
+DQI++C YG+ K+ ++L FK I+ Y P + F+ V ++ II FYN +
Sbjct: 65 LDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSV 124
Query: 483 FAPTVK 488
F +K
Sbjct: 125 FMQRLK 130
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 0.133 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,109,273
Number of Sequences: 62578
Number of extensions: 591268
Number of successful extensions: 1392
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1360
Number of HSP's gapped (non-prelim): 16
length of query: 633
length of database: 14,973,337
effective HSP length: 105
effective length of query: 528
effective length of database: 8,402,647
effective search space: 4436597616
effective search space used: 4436597616
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)