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= psy9484
(407 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GH6|B Chain B, Retinoblastoma Pocket Complexed With Sv40 Large T Antigen
Length = 333
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 56/109 (51%), Gaps = 13/109 (11%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 102 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 149
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDS 298
K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+ S
Sbjct: 150 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQS 198
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 56/109 (51%), Gaps = 13/109 (11%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 101 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 148
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDS 298
K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+ S
Sbjct: 149 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQS 197
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 56/109 (51%), Gaps = 13/109 (11%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 104 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 151
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDS 298
K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+ S
Sbjct: 152 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQS 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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 56/109 (51%), Gaps = 13/109 (11%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 101 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 148
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDS 298
K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+ S
Sbjct: 149 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQS 197
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 56/109 (51%), Gaps = 13/109 (11%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 109 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 156
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDS 298
K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+ S
Sbjct: 157 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQS 205
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 43/62 (69%), Gaps = 2/62 (3%)
Query: 239 PCIISIL-CKHHDGCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIE 296
P I+++L K D K+ ++AE +L+R+++KHL E ++++SLAW+S+SPL+ I+
Sbjct: 443 PWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIK 502
Query: 297 DS 298
S
Sbjct: 503 QS 504
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 39/173 (22%), Positives = 73/173 (42%), Gaps = 32/173 (18%)
Query: 80 LTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKYLPMFKEM 139
T L K+ ++S+++F N ++ K+ ++ ++RL + + V +F+K
Sbjct: 68 FTELQKNIEISVHKFFNLLKEIDTSTKVDNA----MSRLLKKYDVLFALFSKL------- 116
Query: 140 FKPPDLDELLMHVRHNKKKMIHCTSTKVFEFTWILFVLTKAEYLDVSNDLVNSFHLLIAT 199
EL+ + + S V + +WI F+L K E L + +DLV SF L++
Sbjct: 117 ---ERTCELIYLTQPSSSISTEINSALVLKVSWITFLLAKGEVLQMEDDLVISFQLMLCV 173
Query: 200 CDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHF--APLDDPPCIISILCKHHD 250
D + P L + A +++ II +LCK H+
Sbjct: 174 LDYF----------------IKLSPPMLLKEPYKTAVIENDTRIIEVLCKEHE 210
>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 = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 42/62 (67%), Gaps = 2/62 (3%)
Query: 239 PCIISIL-CKHHDGCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIE 296
P I+++L K D K+ ++AE +L+R+++KHL E ++++S AW+S+SPL+ I+
Sbjct: 139 PWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESFAWLSDSPLFDLIK 198
Query: 297 DS 298
S
Sbjct: 199 QS 200
>pdb|2QDJ|A Chain A, Crystal Structure Of The Retinoblastoma Protein N-Domain
Provides Insight Into Tumor Suppression, Ligand
Interaction And Holoprotein Architecture
Length = 304
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 53/250 (21%), Positives = 98/250 (39%), Gaps = 42/250 (16%)
Query: 16 LCMALNIDSTTAKEAWNAYKEMSHHYTLEGSQLH-----WLGCSLYVSCRKATVPTVNSN 70
LC L I + AW ++++S + G + W G ++++
Sbjct: 9 LCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQKKKELW-GICIFIAAVD--------- 58
Query: 71 RTIEGNLVCLTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFT 130
++ T L K+ ++S+++F N ++ K+ ++ +RL + + V +F+
Sbjct: 59 --LDEXSFTFTELQKNIEISVHKFFNLLKEIDTSTKVDNA----XSRLLKKYDVLFALFS 112
Query: 131 KYLPMFKEMFKPPDLDELLMHVRHNKKKMIHCTSTKVFEFTWILFVLTKAEYLDVSNDLV 190
K EL+ + + S V + +WI F+L K E L +DLV
Sbjct: 113 KL----------ERTCELIYLTQPSSSISTEINSALVLKVSWITFLLAKGEVLQXEDDLV 162
Query: 191 NSFHLLIATCD----LIYANVIQSKLRDIVNPDFEGMP------SNFLDSHFAPLDDPPC 240
SF L + D L +++ + V P G P N L++
Sbjct: 163 ISFQLXLCVLDYFIKLSPPXLLKEPYKTAVIP-INGSPRTPRRGQNRSARIAKQLENDTR 221
Query: 241 IISILCKHHD 250
II +LCK H+
Sbjct: 222 IIEVLCKEHE 231
>pdb|2D54|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225a
Mutant From Thermus Thermophilus
Length = 502
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 78 VCLTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKYLP 134
V L + + K +LN+++N+ + W +K P+ R+ + R+ ++ ++ T +P
Sbjct: 402 VALEEAMAYVK-ALNRYINEKKPWELFKKEPEEARAVLYRVVEGLRIASILLTPAMP 457
>pdb|1A8H|A Chain A, Methionyl-Trna Synthetase From Thermus Thermophilus
Length = 500
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 78 VCLTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKYLP 134
V L + + K +LN+++N+ + W +K P+ R+ + R+ ++ ++ T +P
Sbjct: 402 VALEEAMAYVK-ALNRYINEKKPWELFKKEPEEARAVLYRVVEGLRIASILLTPAMP 457
>pdb|1WOY|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225f
Mutant From Thermus Thermophilus
pdb|2D5B|A Chain A, Crystal Structure Of Thermus Thermophilus Methionyl Trna
Synthetase Y225f Mutant Obtained In The Presence Of
Peg6000
Length = 500
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 78 VCLTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKYLP 134
V L + + K +LN+++N+ + W +K P+ R+ + R+ ++ ++ T +P
Sbjct: 402 VALEEAMAYVK-ALNRYINEKKPWELFKKEPEEARAVLYRVVEGLRIASILLTPAMP 457
>pdb|1AD6|A Chain A, Domain A Of Human Retinoblastoma Tumor Suppressor
Length = 185
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 191 NSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHD 250
N FH+ + C L ++V + S LDS L P + + K D
Sbjct: 103 NIFHMSLLACAL-----------EVVMATYSRSTSQNLDSG-TDLSFPWILNVLNLKAFD 150
Query: 251 GCKLC-VIVRAEASLSRDIVKHLNLTEEQVLDSLA 284
K+ ++AE +L+R+++KHL E ++++SLA
Sbjct: 151 FYKVIESFIKAEGNLTREMIKHLERCEHRIMESLA 185
>pdb|1BU8|A Chain A, Rat Pancreatic Lipase Related Protein 2
Length = 452
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 19/102 (18%)
Query: 265 SRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDSGQEIPGCEQKLRGNIEDLSAILEPEN 324
S I+ +L Q + L + N G+E+PGC++ + I D++ I E
Sbjct: 208 SAPIIPYLGFGMSQKVGHLDFFPNG---------GKEMPGCQKNILSTIVDINGIWEGTQ 258
Query: 325 FDYNFKVVNKM--YEEYILSVGDFDERIFLP-----KFQSFD 359
NF N + Y+ Y S+ + D + P KFQ D
Sbjct: 259 ---NFVACNHLRSYKYYASSILNPDGFLGYPCSSYEKFQQND 297
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 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,300,109
Number of Sequences: 62578
Number of extensions: 495199
Number of successful extensions: 1037
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1020
Number of HSP's gapped (non-prelim): 17
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
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: 53 (25.0 bits)