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= psy873
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|XX Chain x, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 125
Score = 82.8 bits (203), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 38/49 (77%), Positives = 45/49 (91%)
Query: 91 IRSVPFRIRVRLSRRRNDDEDSPHKLYTLVTWVPVPTFKELQTENVDAS 139
IR+VP+RIRVRLSR+RN+DEDSP+KLYTLVT+VPV TFK LQT NVD +
Sbjct: 77 IRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN 125
>pdb|4A17|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 111
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 80 FWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHKLYTLVTWVPVPTFKELQTENVDA 138
F W IR++P R+RVRL +R+N++E + + YTLV + V ++ L TE A
Sbjct: 57 FIWSNG-----IRNIPRRVRVRLCKRKNEEEGAQSQFYTLVQHLQVDSYHGLLTEKTKA 110
>pdb|2WW9|M Chain M, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|M Chain M, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|M Chain M, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3IZS|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|DD Chain d, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 113
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 12/90 (13%)
Query: 54 TKESSKYISSMHLS---VLCTVDLSCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDE 110
KE K+ + +H+ V +L+ IW ++ V +R+R+R+SR+RN++E
Sbjct: 33 VKEIKKF-AKLHMGTDDVRLAPELNQAIW--------KRGVKGVEYRLRLRISRKRNEEE 83
Query: 111 DSPHKLYTLVTWVPVPTFKELQTENVDASA 140
D+ + L++ V V V + K LQT V+ A
Sbjct: 84 DAKNPLFSYVEPVLVASAKGLQTVVVEEDA 113
>pdb|1S1I|W Chain W, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 112
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 52/99 (52%), Gaps = 12/99 (12%)
Query: 45 AYPSQISMMTKESSKYISSMHLS---VLCTVDLSCPIWFWWGTSLINMDIRSVPFRIRVR 101
++ + KE K+ + +H+ V +L+ IW ++ V +R+R+R
Sbjct: 23 SFKKRAPRAVKEIKKF-AKLHMGTDDVRLAPELNQAIW--------KRGVKGVEYRLRLR 73
Query: 102 LSRRRNDDEDSPHKLYTLVTWVPVPTFKELQTENVDASA 140
+SR+RN++ED+ + L++ V V V + K LQT V+ A
Sbjct: 74 ISRKRNEEEDAKNPLFSYVEPVLVASAKGLQTVVVEEDA 112
>pdb|3ZF7|HH Chain h, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 188
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 7/67 (10%)
Query: 72 VDLSCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK-LYTLVTWVPVPTFKE 130
+D S + W + ++ VP R+RVR+ R+ E K YT+++ +PVP+FK
Sbjct: 127 IDASLNTFIW------HKGVKGVPGRVRVRVERKSETMEGGKRKHFYTVISHIPVPSFKN 180
Query: 131 LQTENVD 137
L T+ ++
Sbjct: 181 LTTKVIE 187
>pdb|3JYW|W Chain W, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 79
Score = 33.1 bits (74), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 11/57 (19%)
Query: 59 KYISSMHLS---VLCTVDLSCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDS 112
K + +H+ V +L+ IW ++ V +R+R+R+SR+RN++ED+
Sbjct: 29 KKFAKLHMGTDDVRLAPELNQAIW--------KRGVKGVEYRLRLRISRKRNEEEDA 77
>pdb|3V0J|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Deletion Of 401-405
pdb|3V0J|B Chain B, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Deletion Of 401-405
Length = 334
Score = 29.6 bits (65), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 282 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 311
>pdb|3AWF|A Chain A, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (236-576)
pdb|3AWF|B Chain B, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (236-576)
pdb|3AWF|C Chain C, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (236-576)
Length = 346
Score = 29.3 bits (64), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 294 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 323
>pdb|3V0D|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s)
pdb|3V0D|B Chain B, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s)
pdb|3V0F|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Ii
pdb|3V0F|B Chain B, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Ii
pdb|3V0G|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Iii
pdb|3V0G|B Chain B, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Iii
pdb|3V0G|C Chain C, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Iii
pdb|3V0G|D Chain D, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Form Iii
pdb|3V0H|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Complexed With D-Myo-
Inositol-1,4,5-Triphosphate
pdb|3V0H|B Chain B, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
241-576(C363s), Complexed With D-Myo-
Inositol-1,4,5-Triphosphate
Length = 339
Score = 29.3 bits (64), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 287 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 316
>pdb|3AWG|A Chain A, Crystal Structure Of Pten-Like Domain Of Ci-Vsp G356a
Mutant (248-576)
pdb|3AWG|B Chain B, Crystal Structure Of Pten-Like Domain Of Ci-Vsp G356a
Mutant (248-576)
pdb|3AWG|C Chain C, Crystal Structure Of Pten-Like Domain Of Ci-Vsp G356a
Mutant (248-576)
Length = 334
Score = 29.3 bits (64), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 282 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 311
>pdb|3V0E|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
256-576(C363s)
Length = 324
Score = 29.3 bits (64), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 272 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 301
>pdb|3AWE|A Chain A, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (248-576)
pdb|3AWE|B Chain B, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (248-576)
pdb|3AWE|C Chain C, Crystal Structure Of Pten-Like Domain Of Ci-Vsp (248-576)
Length = 334
Score = 29.3 bits (64), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 282 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 311
>pdb|3V0I|A Chain A, Crystal Structure Of Ciona Intestinalis Voltage
Sensor-Containing Phosphatase (Ci-Vsp), Residues
256-576, E411f
Length = 324
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 75 SCPIWFWWGTSLINMDIRSVPFRIRVRLSRRRNDDEDSPHK 115
+CP +FW+ TSL+ D V L R ++ D+PHK
Sbjct: 272 NCPFYFWFNTSLVEGD--------HVTLKR---EEIDNPHK 301
>pdb|4DX8|H Chain H, Icap1 In Complex With Krit1 N-terminus
pdb|4DX8|I Chain I, Icap1 In Complex With Krit1 N-terminus
pdb|4DX8|J Chain J, Icap1 In Complex With Krit1 N-terminus
pdb|4DX8|K Chain K, Icap1 In Complex With Krit1 N-terminus
Length = 203
Score = 29.3 bits (64), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 3 EDLLLENSQKLQAVLPSVKDKSKPSAATSYTIGGVKVEFPVKAYPSQISMMTKESSKYI- 61
E L NS+ Q +L V + +KP + + I G +V +K +P M +E+S +I
Sbjct: 60 ETKLQGNSEITQGILDYVVETTKPISPANQGIRGKRVVL-MKKFPLDGEKMGREASLFIV 118
Query: 62 -SSMHLSVLCTVDLSCPIWF 80
S + + T CPI++
Sbjct: 119 PSVVKDNTKYTYTPGCPIFY 138
>pdb|2KL8|A Chain A, Solution Nmr Structure Of De Novo Designed
Ferredoxin-like Fold Protein, Northeast Structural
Genomics Consortium Target Or15
Length = 85
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 14 QAVLPSVKDKSKPSAATSYTIGGVKVEFPVKAYPSQISM-MTKESSKYISSMHLSVLCTV 72
+A+ ++ K + +YT+ G +E + P Q+ + KE+ + +++V T+
Sbjct: 17 KALKEMIRQARKFAGTVTYTLDGNDLEIRITGVPEQVRKELAKEAERLAKEFNITVTYTI 76
Query: 73 DLS 75
L
Sbjct: 77 RLE 79
>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2H5E|B Chain B, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2O0F|A Chain A, Docking Of The Modified Rf3 X-Ray Structure Into Cryo-Em
Map Of E.Coli 70s Ribosome Bound With Rf3
pdb|3ZVO|Y Chain Y, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3SFS|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
Length = 529
Score = 28.5 bits (62), Expect = 1.2, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 114 HKLYTLVTWVPVPTFKELQTENVDASAD 141
H L LV W P P ++ T V+AS D
Sbjct: 267 HMLDGLVEWAPAPMPRQTDTRTVEASED 294
>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 534
Score = 28.5 bits (62), Expect = 1.3, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 114 HKLYTLVTWVPVPTFKELQTENVDASAD 141
H L LV W P P ++ T V+AS D
Sbjct: 267 HMLDGLVEWAPAPMPRQTDTRTVEASED 294
>pdb|3IZR|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 123
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 107 NDDEDSPHKLYTLVTWVPVP 126
ND+ED+ +LY+LVT +P
Sbjct: 88 NDEEDAKEELYSLVTVAEIP 107
>pdb|2GO5|6 Chain 6, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
pdb|2J37|6 Chain 6, Model Of Mammalian Srp Bound To 80s Rncs
Length = 123
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 107 NDDEDSPHKLYTLVTWVPVP 126
ND+ED+ +LY+LVT VP
Sbjct: 88 NDEEDAKEELYSLVTVAEVP 107
>pdb|2DAY|A Chain A, Solution Structure Of The Rwd Domain Of Human Ring Finger
Protein 25
Length = 128
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 86 LINMDIRSVPFRIRVRLSRRRNDDEDSPHKLYTLVTWVP 124
+I + R+ P+ I + L +D+DS + +TLV VP
Sbjct: 30 VIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVP 68
>pdb|2DMF|A Chain A, An Extended Conformation Of The Rwd Domain Of Human Ring
Finger Protein 25
Length = 137
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 86 LINMDIRSVPFRIRVRLSRRRNDDEDSPHKLYTLVTWVPV 125
+I + R+ P+ I + L +D+DS + +TLV VP
Sbjct: 30 VIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVPA 69
>pdb|2ICS|A Chain A, Crystal Structure Of An Adenine Deaminase
Length = 379
Score = 25.8 bits (55), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 1 MDEDLLLENSQKLQAVLPSVKDKSKPSAATSYTIGG 36
+D DLL++N Q + + K K AA + TI G
Sbjct: 3 LDYDLLIKNGQTVNGXPVEIAIKEKKIAAVAATISG 38
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 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,741,080
Number of Sequences: 62578
Number of extensions: 128025
Number of successful extensions: 446
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 425
Number of HSP's gapped (non-prelim): 30
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)