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= 026785
(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 = 253 bits (647), Expect = 5e-68, Method: Compositional matrix adjust.
Identities = 132/215 (61%), Positives = 150/215 (69%), Gaps = 5/215 (2%)
Query: 19 GIGKFSRSKMYHKRGLWAIKAKNGGVFPRHDXXXXXXXXXXXXXXFYPADDVKKPLVNKR 78
GI + SRS YH+RGLWAIKAK+GG P+ + FYPADDVK V+ R
Sbjct: 10 GIKRASRSHTYHRRGLWAIKAKHGGALPKAEKPAAIAEPK-----FYPADDVKPRTVSTR 64
Query: 79 KPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSY 138
KP PTKLR++ITPGTVLI+LAGR+ GKRVVFLKQL SGLLL++GPFKINGVP+RRVNQ+Y
Sbjct: 65 KPHPTKLRSTITPGTVLILLAGRYMGKRVVFLKQLQSGLLLITGPFKINGVPIRRVNQAY 124
Query: 139 VIGTSTKVDISGVNVDKFDDKYFAKEVXXXXXXXXXXXXXXXXXXXXXXXXXXXDDQKSV 198
VI TSTKVDIS VNV KFDDKYFA+E DDQK +
Sbjct: 125 VIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDKEATKNLPDFKKDDQKVI 184
Query: 199 DAPLIKAIEAVPDLKAYLGARFSLRAGMKPHELVF 233
DA LIKAI+AVPDLK YLGARFSLR 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 = 165 bits (417), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 84/174 (48%), Positives = 109/174 (62%), Gaps = 4/174 (2%)
Query: 64 FYPADDVKKPLVNK--RKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVS 121
+Y ADD P + +K TKLR I PGTVLI+LAGRF+GKRVVFLKQL SGLLLV+
Sbjct: 18 WYKADDEATPFHRRQLKKATATKLRNDIAPGTVLILLAGRFRGKRVVFLKQLKSGLLLVT 77
Query: 122 GPFKINGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFAKEVXXXXXXX--XXXXXXX 179
GP+K+NGVPL+RVNQ+Y + TSTKVD++GVN KF+D YF +E
Sbjct: 78 GPYKVNGVPLKRVNQAYTLSTSTKVDLTGVNTAKFEDDYFGREKARKNHKNLFKAELTEE 137
Query: 180 XXXXXXXXXXXXXDDQKSVDAPLIKAIEAVPDLKAYLGARFSLRAGMKPHELVF 233
DQ++VD PL+ A++ 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 = 157 bits (398), Expect = 4e-39, Method: Compositional matrix adjust.
Identities = 86/170 (50%), Positives = 105/170 (61%), Gaps = 2/170 (1%)
Query: 64 FYPADDVKKPLVNKRKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGP 123
+YP++DV ++ +P KLRAS+ PGTVLI+LAGRF+GKRVV+LK L LL+SGP
Sbjct: 9 WYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLISGP 68
Query: 124 FKINGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFAKEVXXXXXXXXXXXXXXXXXX 183
FK+NGVPLRRVN YVI TSTKV + GVNV+KF+ +YFAK
Sbjct: 69 FKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAK--EKLTKKEKKEANLFPEQQ 126
Query: 184 XXXXXXXXXDDQKSVDAPLIKAIEAVPDLKAYLGARFSLRAGMKPHELVF 233
+DQK VD LI I+ P LK YL A FSL+ G KPH L F
Sbjct: 127 NKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF 176
>pdb|3ZF7|VV Chain v, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 192
Score = 97.1 bits (240), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 59/175 (33%), Positives = 91/175 (52%), Gaps = 18/175 (10%)
Query: 75 VNKRKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLP-SGLLLVSGPFKINGVPLRR 133
V+++ P+ + +R S PGT+ IILAGRF+G+R V LKQLP +G L++SGP K +GVP+RR
Sbjct: 16 VSRKSPEYSTVRKSCKPGTIAIILAGRFRGRRAVILKQLPKNGPLVISGPMKYSGVPIRR 75
Query: 134 VNQSYVIGTSTKVDISGVNVDKFDDKYF---------AKEVXXXXXXXXXXXXXXXXXXX 184
++ Y+I TST+VD++GV+ + F E
Sbjct: 76 IDSRYIIATSTRVDLTGVDTSAITPEIFKREKKEKRVKSEGEFMGDKDKKKAESKAKKTS 135
Query: 185 XXXXXXXXDD-----QKSVDAPLIKAIEAVP---DLKAYLGARFSLRAGMKPHEL 231
D Q ++D LI+AI+ P ++ YL + F+++ G PH L
Sbjct: 136 KAAPKGTVSDERAQLQNAIDTALIQAIKKDPLGKEMAGYLHSVFTIKPGDAPHRL 190
>pdb|2JOY|A Chain A, Nmr Structure Of 50s Ribosomal Protein L14e From
Sulfolobus Solfataricus: Northeast Structural Genomics
Consortium Target Ssr105
Length = 96
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVD 147
+I G + + + GR G + V + + +LV+GP I GV RRVN ++ T K+D
Sbjct: 3 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 62
Query: 148 IS 149
I
Sbjct: 63 IQ 64
>pdb|2KDS|A Chain A, Structure Of Ribosomal Protein L14e From Sulfolobus
Solfataricus
Length = 95
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVD 147
+I G + + + GR G + V + + +LV+GP I GV RRVN ++ T K+D
Sbjct: 2 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 61
Query: 148 IS 149
I
Sbjct: 62 IQ 63
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVD 147
+I G + +++AGR G++VV + + +LV+G +N V RR+N ++ K+D
Sbjct: 3 AIDVGRIAVVIAGRRAGQKVVVVDIIDKNFVLVTGA-GLNKVKRRRMNIKHIEPLPQKID 61
Query: 148 I 148
I
Sbjct: 62 I 62
>pdb|3ZF7|AA Chain a, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 133
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 25/86 (29%)
Query: 89 ITPGTVLIILAGRFKGKRVVFL-------KQLPSGLLLVSG----PFKI----------- 126
+ PG V+I+ +GR+ GK+ V + K+ P G L++G P K+
Sbjct: 4 LKPGKVVIMTSGRYAGKKAVIVQNTDTRNKERPYGHSLLAGIKKYPRKVVRGMSKRSITR 63
Query: 127 ---NGVPLRRVNQSYVIGTSTKVDIS 149
GV LR VN + + T +D+S
Sbjct: 64 RSQVGVFLRVVNHKHFLPTRYNMDLS 89
>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 = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 89 ITPGTVLIILAGRFKGKRVVFLKQL-------PSGLLLVSG 122
+ PG +I+L GRF G++ V ++ P G LV+G
Sbjct: 5 LKPGKAVILLQGRFAGRKAVIVRVFEEGTRDRPYGHCLVAG 45
>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 = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 92 GTVLIILAGRFKGKRVVFLKQLPSG 116
G V+I+L 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 0.140 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,784,755
Number of Sequences: 62578
Number of extensions: 191914
Number of successful extensions: 341
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 322
Number of HSP's gapped (non-prelim): 17
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)