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= 011786
(477 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 121 bits (303), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 105/374 (28%), Positives = 164/374 (43%), Gaps = 70/374 (18%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 66 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 125
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES
Sbjct: 126 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESF 185
Query: 222 VWEKGSSLYNSLIASRPDLQEEIKRLKLLAEPMPSLHEISMNNHLASGVLAYQHNLHKHK 281
W S L++ LI D + L E L+ NNH A+ + K K
Sbjct: 186 AWLSDSPLFD-LIKQSKDREGPTDHL----ESACPLNLPLQNNHTAADMYLEPVRAPKKK 240
Query: 282 PSTGNNGMKRLCDENGSKLTKHNSYATAMKVDSPVVDSHQVKLQPVTPSSQTAFMSPVQS 341
ST T+ NS A A +T S Q+
Sbjct: 241 GST----------------TRVNSTANA----------------------ETQATSAFQT 262
Query: 342 KTPKDGGIKMDAAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVEKT 399
+ P +++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L +
Sbjct: 263 QKPLKS-----TSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQNEY 316
Query: 400 YLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKHKG 459
L +RH+D I++C G+ K+ + LKF+ I Y P + F V
Sbjct: 317 ELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI-------- 368
Query: 460 KNRENYKSIDAFYN 473
E Y SI FYN
Sbjct: 369 -KEEEYDSIIVFYN 381
>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 = 89.7 bits (221), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 66/221 (29%), Positives = 105/221 (47%), Gaps = 30/221 (13%)
Query: 31 TPVRTAQNTASNWLKTVIAPLPSKPSAELEKFLSLGSV----SIANEVESGANIVLEAIF 86
TPVRT NT L ++ +PS L + + +V SI V+ I E
Sbjct: 2 TPVRTVMNTIQQ-LMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFA 60
Query: 87 PSIKLGERLFNWSLLNVNLMDSLWSGQERTE-ALKLYYKVLESICASEAGKSSSRDLSGL 145
++ G + G +R + ++LYY+V+ES+ SE + S ++ S L
Sbjct: 61 KAVGQG---------------CVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKL 105
Query: 146 LTNEKFHRCMLACSAELVSMARTR---------VSILFPLILERAGITAFDMCKVTESFI 196
L + FH +LAC+ E+V +R + FP IL + AFD KV ESFI
Sbjct: 106 LNDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFI 165
Query: 197 RHEDSLPRELMRHLNSLEETMLESMVWEKGSSLYNSLIASR 237
+ E +L RE+++HL E ++ES+ W S L++ + S+
Sbjct: 166 KAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSK 206
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 87.8 bits (216), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 65/220 (29%), Positives = 104/220 (47%), Gaps = 30/220 (13%)
Query: 32 PVRTAQNTASNWLKTVIAPLPSKPSAELEKFLSLGSV----SIANEVESGANIVLEAIFP 87
PVRT NT L ++ +PS L + + +V SI V+ I E
Sbjct: 302 PVRTVMNTIQQ-LMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAK 360
Query: 88 SIKLGERLFNWSLLNVNLMDSLWSGQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLL 146
++ G + G +R + ++LYY+V+ES+ SE + S ++ S LL
Sbjct: 361 AVGQG---------------CVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLL 405
Query: 147 TNEKFHRCMLACSAELVSMARTR---------VSILFPLILERAGITAFDMCKVTESFIR 197
+ FH +LAC+ E+V +R + FP IL + AFD KV ESFI+
Sbjct: 406 NDNIFHMSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIK 465
Query: 198 HEDSLPRELMRHLNSLEETMLESMVWEKGSSLYNSLIASR 237
E +L RE+++HL E ++ES+ W S L++ + S+
Sbjct: 466 AEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSK 505
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 38/145 (26%), Positives = 69/145 (47%), Gaps = 13/145 (8%)
Query: 331 SQTAFMSPVQSKTPKDGGIKMDAAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTY 388
S + ++ ++G +K +++ + K+ +L +R+N++ ERL LS+ ++ +
Sbjct: 493 SDSPLFDLIKQSKDREGPLK-STSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIW 550
Query: 389 LLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGF 448
LF+ L + L +RH+D I++C G+ K+ + LKF+ I Y P + F
Sbjct: 551 TLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKR 610
Query: 449 VFAGWLSKHKGKNRENYKSIDAFYN 473
V E Y SI FYN
Sbjct: 611 VLI---------KEEEYDSIIVFYN 626
>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 = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 54/162 (33%), Positives = 87/162 (53%), Gaps = 11/162 (6%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 63 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 122
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES+
Sbjct: 123 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 182
Query: 222 VWEKGSSLYNSLIASRPDLQEEIKRLKLLAEPMPSLHEISMN 263
W S L++ LI D + + L L + + L + +N
Sbjct: 183 AWLSDSPLFD-LIKQSKDREGKSTSLSLFYKKVYRLAYLRLN 223
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 60/123 (48%), Gaps = 12/123 (9%)
Query: 353 AAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVEKTYLFFNRHIDLI 410
+++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L + L +RH+D I
Sbjct: 205 TSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQI 263
Query: 411 ILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKHKGKNRENYKSIDA 470
++C G+ K+ + LKF+ I Y P + F V E Y SI
Sbjct: 264 MMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI---------KEEEYDSIIV 314
Query: 471 FYN 473
FYN
Sbjct: 315 FYN 317
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/136 (35%), Positives = 77/136 (56%), Gaps = 10/136 (7%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 66 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 125
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES+
Sbjct: 126 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 185
Query: 222 VWEKGSSLYNSLIASR 237
W S L++ + S+
Sbjct: 186 AWLSDSPLFDLIKQSK 201
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 60/123 (48%), Gaps = 12/123 (9%)
Query: 353 AAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVEKTYLFFNRHIDLI 410
+++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L + L +RH+D I
Sbjct: 210 TSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQI 268
Query: 411 ILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKHKGKNRENYKSIDA 470
++C G+ K+ + LKF+ I Y P + F V E Y SI
Sbjct: 269 MMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI---------KEEEYDSIIV 319
Query: 471 FYN 473
FYN
Sbjct: 320 FYN 322
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/136 (35%), Positives = 77/136 (56%), Gaps = 10/136 (7%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 63 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 122
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES+
Sbjct: 123 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 182
Query: 222 VWEKGSSLYNSLIASR 237
W S L++ + S+
Sbjct: 183 AWLSDSPLFDLIKQSK 198
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 16/136 (11%)
Query: 340 QSKTPKDGGIKMDAAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVE 397
QSKT ++G +++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L
Sbjct: 196 QSKT-REGK---STSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQN 250
Query: 398 KTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKH 457
+ L +RH+D I++C G+ K+ + LKF+ I Y P + F V
Sbjct: 251 EYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI------ 304
Query: 458 KGKNRENYKSIDAFYN 473
E Y SI FYN
Sbjct: 305 ---KEEEYDSIIVFYN 317
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen
Length = 333
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 48/136 (35%), Positives = 77/136 (56%), Gaps = 10/136 (7%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 64 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 123
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES+
Sbjct: 124 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 183
Query: 222 VWEKGSSLYNSLIASR 237
W S L++ + S+
Sbjct: 184 AWLSDSPLFDLIKQSK 199
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 39/136 (28%), Positives = 64/136 (47%), Gaps = 16/136 (11%)
Query: 340 QSKTPKDGGIKMDAAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVE 397
QSK G +++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L
Sbjct: 197 QSKLVPRGS----TSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQN 251
Query: 398 KTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKH 457
+ L +RH+D I++C G+ K+ + LKF+ I Y P + F V
Sbjct: 252 EYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI------ 305
Query: 458 KGKNRENYKSIDAFYN 473
E Y SI FYN
Sbjct: 306 ---KEEEYDSIIVFYN 318
>pdb|1AD6|A Chain A, Domain A Of Human Retinoblastoma Tumor Suppressor
Length = 185
Score = 78.6 bits (192), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 44/120 (36%), Positives = 69/120 (57%), Gaps = 10/120 (8%)
Query: 112 GQERTE-ALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTR- 169
G +R + ++LYY+V+ES+ SE + S ++ S LL + FH +LAC+ E+V +R
Sbjct: 65 GSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRS 124
Query: 170 --------VSILFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESM 221
+ FP IL + AFD KV ESFI+ E +L RE+++HL E ++ES+
Sbjct: 125 TSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESL 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 = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 60/123 (48%), Gaps = 12/123 (9%)
Query: 353 AAVTFLFNKMTKLGAVRINSMAERLKLSQ--QIREKTYLLFRQILVEKTYLFFNRHIDLI 410
+++ + K+ +L +R+N++ ERL LS+ ++ + LF+ L + L +RH+D I
Sbjct: 10 TSLSLFYKKVYRLAYLRLNTLCERL-LSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQI 68
Query: 411 ILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWLSKHKGKNRENYKSIDA 470
++C G+ K+ + LKF+ I Y P + F V E Y SI
Sbjct: 69 MMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLI---------KEEEYDSIIV 119
Query: 471 FYN 473
FYN
Sbjct: 120 FYN 122
>pdb|2F07|A Chain A, Crystal Structure Of Yvdt From Bacillus Subtilis
pdb|2F07|B Chain B, Crystal Structure Of Yvdt From Bacillus Subtilis
Length = 197
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%), Gaps = 2/42 (4%)
Query: 394 ILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNY 435
IL+++T+L RH D+I+L C+ G+A I+ K+E I Y
Sbjct: 89 ILIDETFLITERHKDIIVL-CYSGLA-IDHSMEKWETIYQPY 128
>pdb|1A7Q|H Chain H, Fv Fragment Of Mouse Monoclonal Antibody D1.3 (BalbC,
IGG1, K) High Affinity Expressed Variant Containing
Ser26l->gly, Ile29l->thr, Glu81l->asp, Thr97l->ser,
Pro240h->leu, Asp258h->ala, Lys281h->glu, Asn283h->asp
And Leu312h->val
Length = 116
Score = 28.5 bits (62), Expect = 8.2, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 221 MVWEKGSSLYNSLIASRPDLQEEIKRLKLLAEPMPSLH 258
M+W G++ YNS + SR + ++ + ++ E M SLH
Sbjct: 50 MIWGDGNTAYNSALKSRLSISKDNSKSQVFLE-MDSLH 86
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
0.317 0.130 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,174,524
Number of Sequences: 62578
Number of extensions: 512014
Number of successful extensions: 1166
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1134
Number of HSP's gapped (non-prelim): 21
length of query: 477
length of database: 14,973,337
effective HSP length: 102
effective length of query: 375
effective length of database: 8,590,381
effective search space: 3221392875
effective search space used: 3221392875
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: 53 (25.0 bits)