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= 026764
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|G Chain G, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 219
Score = 252 bits (643), Expect = 1e-67, Method: Compositional matrix adjust.
Identities = 129/215 (60%), Positives = 151/215 (70%), Gaps = 5/215 (2%)
Query: 19 GVGKFSRSKMYHKRGLWAIKAKNGGVFPKHDXXXXXXXXXXXXXXFYPADDVKKPLVNKR 78
G+ + SRS YH+RGLWAIKAK+GG PK + FYPADDVK V+ R
Sbjct: 10 GIKRASRSHTYHRRGLWAIKAKHGGALPKAEKPAAIAEPK-----FYPADDVKPRTVSTR 64
Query: 79 KHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSY 138
K PTKLR++ITPGTV ILLAGR+MGKRVVFLKQL SGLLL+TGPFK+NGVP+RRVNQ+Y
Sbjct: 65 KPHPTKLRSTITPGTVLILLAGRYMGKRVVFLKQLQSGLLLITGPFKINGVPIRRVNQAY 124
Query: 139 VIATSTKVDISGVDLGKFDDQYFXXXXXXXXXXXXXXXXXXXXXXXXVLPDDKKDDQKTV 198
VIATSTKVDIS V++ KFDD+YF LPD KKDDQK +
Sbjct: 125 VIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDKEATKNLPDFKKDDQKVI 184
Query: 199 DAQLIKSIEAVLDLKTYLSARFSLKSGMKPHELVF 233
DA+LIK+I+AV DLK YL ARFSL+ G KPHE+ F
Sbjct: 185 DAELIKAIDAVPDLKNYLGARFSLRDGDKPHEMTF 219
>pdb|4A18|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 191
Score = 157 bits (398), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 83/174 (47%), Positives = 109/174 (62%), Gaps = 4/174 (2%)
Query: 64 FYPADDVKKPLVNK--RKHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVT 121
+Y ADD P + +K TKLR I PGTV ILLAGRF GKRVVFLKQL SGLLLVT
Sbjct: 18 WYKADDEATPFHRRQLKKATATKLRNDIAPGTVLILLAGRFRGKRVVFLKQLKSGLLLVT 77
Query: 122 GPFKVNGVPLRRVNQSYVIATSTKVDISGVDLGKFDDQYFXXXXXXXXXXX--XXXXXXX 179
GP+KVNGVPL+RVNQ+Y ++TSTKVD++GV+ KF+D YF
Sbjct: 78 GPYKVNGVPLKRVNQAYTLSTSTKVDLTGVNTAKFEDDYFGREKARKNHKNLFKAELTEE 137
Query: 180 XXXXXXVLPDDKKDDQKTVDAQLIKSIEAVLDLKTYLSARFSLKSGMKPHELVF 233
+ +K DQ+ VD L+ +++ V LK YL+++F+L + +PHE+ F
Sbjct: 138 QKKKETERKNARKQDQQAVDTPLLAAVKKVEFLKNYLASKFTLNNNDRPHEMKF 191
>pdb|3IZS|G 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|F Chain F, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|F Chain F, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|E Chain E, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 176
Score = 154 bits (389), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 84/170 (49%), Positives = 105/170 (61%), Gaps = 2/170 (1%)
Query: 64 FYPADDVKKPLVNKRKHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGP 123
+YP++DV ++ +P KLRAS+ PGTV ILLAGRF GKRVV+LK L LL++GP
Sbjct: 9 WYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLISGP 68
Query: 124 FKVNGVPLRRVNQSYVIATSTKVDISGVDLGKFDDQYFXXXXXXXXXXXXXXXXXXXXXX 183
FKVNGVPLRRVN YVIATSTKV + GV++ KF+ +YF
Sbjct: 69 FKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANLFPEQQNK 128
Query: 184 XXVLPDDKKDDQKTVDAQLIKSIEAVLDLKTYLSARFSLKSGMKPHELVF 233
+ ++ +DQK VD LI I+ LK YLSA FSLK+G KPH L F
Sbjct: 129 E--IKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF 176
>pdb|3ZF7|VV Chain v, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 192
Score = 92.4 bits (228), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 55/175 (31%), Positives = 89/175 (50%), Gaps = 18/175 (10%)
Query: 75 VNKRKHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLT-SGLLLVTGPFKVNGVPLRR 133
V+++ + + +R S PGT+ I+LAGRF G+R V LKQL +G L+++GP K +GVP+RR
Sbjct: 16 VSRKSPEYSTVRKSCKPGTIAIILAGRFRGRRAVILKQLPKNGPLVISGPMKYSGVPIRR 75
Query: 134 VNQSYVIATSTKVDISGVDLGKFDDQYFXXXXXXXXXXXX--------------XXXXXX 179
++ Y+IATST+VD++GVD + F
Sbjct: 76 IDSRYIIATSTRVDLTGVDTSAITPEIFKREKKEKRVKSEGEFMGDKDKKKAESKAKKTS 135
Query: 180 XXXXXXVLPDDKKDDQKTVDAQLIKSIEA---VLDLKTYLSARFSLKSGMKPHEL 231
+ D++ Q +D LI++I+ ++ YL + F++K G PH L
Sbjct: 136 KAAPKGTVSDERAQLQNAIDTALIQAIKKDPLGKEMAGYLHSVFTIKPGDAPHRL 190
>pdb|2KDS|A Chain A, Structure Of Ribosomal Protein L14e From Sulfolobus
Solfataricus
Length = 95
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 88 SITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVD 147
+I G + + + GR G + V + + +LVTGP + GV RRVN ++ T K+D
Sbjct: 2 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 61
Query: 148 IS 149
I
Sbjct: 62 IQ 63
>pdb|2JOY|A Chain A, Nmr Structure Of 50s Ribosomal Protein L14e From
Sulfolobus Solfataricus: Northeast Structural Genomics
Consortium Target Ssr105
Length = 96
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 88 SITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVD 147
+I G + + + GR G + V + + +LVTGP + GV RRVN ++ T K+D
Sbjct: 3 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 62
Query: 148 IS 149
I
Sbjct: 63 IQ 64
>pdb|3J21|5 Chain 5, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|K Chain K, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 83
Score = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 88 SITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVD 147
+I G + +++AGR G++VV + + +LVTG +N V RR+N ++ K+D
Sbjct: 3 AIDVGRIAVVIAGRRAGQKVVVVDIIDKNFVLVTGA-GLNKVKRRRMNIKHIEPLPQKID 61
Query: 148 I 148
I
Sbjct: 62 I 62
>pdb|3IZR|AA Chain a, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 136
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 89 ITPGTVFILLAGRFMGKRVVFLKQLTSG 116
+ PG ILL GRF G++ V ++ G
Sbjct: 5 LKPGKAVILLQGRFAGRKAVIVRVFEEG 32
>pdb|4A18|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 144
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 92 GTVFILLAGRFMGKRVVFLKQLTSG 116
G V ILL GRF GK+ V +K G
Sbjct: 8 GRVVILLQGRFAGKKAVIVKSSEDG 32
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 0.138 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,617,134
Number of Sequences: 62578
Number of extensions: 182080
Number of successful extensions: 280
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 12
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
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: 50 (23.9 bits)