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= 029973
(184 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 = 217 bits (552), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 109/165 (66%), Positives = 127/165 (76%), Gaps = 5/165 (3%)
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 VIGTSTKVDISGVNVDKFDDKYFAKEVERKKKKGENEFFESEKEV 183
VI TSTKVDIS VNV KFDDKYFA+E + + KK E E FES+KE
Sbjct: 125 VIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDKEA 169
>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 = 142 bits (357), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 72/122 (59%), Positives = 89/122 (72%), Gaps = 4/122 (3%)
Query: 64 FYPADDVKKPLVNK--RKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVS 121
+Y ADD P + +K TKLR I PGTVLI+LAGRF+GKRVVFLKQL SGLLLV+
Sbjct: 18 WYKADDEATPFHRRQLKKATATKLRNDIAPGTVLILLAGRFRGKRVVFLKQLKSGLLLVT 77
Query: 122 GPFKINGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFAKEVERKKKKG--ENEFFES 179
GP+K+NGVPL+RVNQ+Y + TSTKVD++GVN KF+D YF +E RK K + E E
Sbjct: 78 GPYKVNGVPLKRVNQAYTLSTSTKVDLTGVNTAKFEDDYFGREKARKNHKNLFKAELTEE 137
Query: 180 EK 181
+K
Sbjct: 138 QK 139
>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 = 132 bits (333), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 62/99 (62%), Positives = 78/99 (78%)
Query: 64 FYPADDVKKPLVNKRKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGP 123
+YP++DV ++ +P KLRAS+ PGTVLI+LAGRF+GKRVV+LK L LL+SGP
Sbjct: 9 WYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLISGP 68
Query: 124 FKINGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFA 162
FK+NGVPLRRVN YVI TSTKV + GVNV+KF+ +YFA
Sbjct: 69 FKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFA 107
>pdb|3ZF7|VV Chain v, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 192
Score = 98.2 bits (243), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 49/104 (47%), Positives = 74/104 (71%), Gaps = 1/104 (0%)
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 VNQSYVIGTSTKVDISGVNVDKFDDKYFAKEVERKKKKGENEFF 177
++ Y+I TST+VD++GV+ + F +E + K+ K E EF
Sbjct: 76 IDSRYIIATSTRVDLTGVDTSAITPEIFKREKKEKRVKSEGEFM 119
>pdb|2KDS|A Chain A, Structure Of Ribosomal Protein L14e From Sulfolobus
Solfataricus
Length = 95
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 45/95 (47%), Gaps = 10/95 (10%)
Query: 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVD 147
+I G + + + GR G + V + + +LV+GP I GV RRVN ++ T K+D
Sbjct: 2 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 61
Query: 148 ISGVNVDKFDDKYFAKEVERKKKKGENEFFESEKE 182
I + A + E KKK E+ E KE
Sbjct: 62 I----------QKGASDEEVKKKLEESNLTEYMKE 86
>pdb|2JOY|A Chain A, Nmr Structure Of 50s Ribosomal Protein L14e From
Sulfolobus Solfataricus: Northeast Structural Genomics
Consortium Target Ssr105
Length = 96
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 45/95 (47%), Gaps = 10/95 (10%)
Query: 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVD 147
+I G + + + GR G + V + + +LV+GP I GV RRVN ++ T K+D
Sbjct: 3 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 62
Query: 148 ISGVNVDKFDDKYFAKEVERKKKKGENEFFESEKE 182
I + A + E KKK E+ E KE
Sbjct: 63 I----------QKGASDEEVKKKLEESNLTEYMKE 87
>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 = 32.3 bits (72), Expect = 0.16, 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 = 29.6 bits (65), Expect = 0.92, 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|3IZS|AA Chain a, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|Z Chain Z, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 136
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 57/128 (44%), Gaps = 37/128 (28%)
Query: 89 ITPGTVLIILAGRFKGKRVVFL-------KQLPSGLLLVSG----PFKI---NGVP---- 130
+ G V +++ GR+ GK+VV + K P G LV+G P K+ +G
Sbjct: 5 LKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAK 64
Query: 131 -------LRRVNQSYVIGTSTKVDI----SGVNVDKFDD--------KYFAKEVERKKKK 171
++ VN ++++ T +D+ S V+ + F+ K K E + +
Sbjct: 65 RTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQA 124
Query: 172 GENEFFES 179
G+N++F S
Sbjct: 125 GKNQWFFS 132
>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 = 3.0, 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 = 4.8, 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
>pdb|1R8W|A Chain A, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R8W|B Chain B, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|A Chain A, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|B Chain B, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9E|A Chain A, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
pdb|1R9E|B Chain B, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
Length = 787
Score = 26.9 bits (58), Expect = 6.6, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 126 INGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFAKEVERKKKKGENEFFESEK 181
+ +P+ +Q ++G+ TK S +F +K+ E++R K+ + F SE+
Sbjct: 59 LENIPITIRDQELIVGSLTKEPRSSQVFPEFSNKWLQDELDRLNKRTGDAFQISEE 114
>pdb|3OF5|A Chain A, Crystal Structure Of A Dethiobiotin Synthetase From
Francisella Tularensis Subsp. Tularensis Schu S4
pdb|3OF5|B Chain B, Crystal Structure Of A Dethiobiotin Synthetase From
Francisella Tularensis Subsp. Tularensis Schu S4
Length = 228
Score = 26.2 bits (56), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 125 KINGVPLRRVNQSYVIGTSTKVDISGVNVDKF-DDKY 160
+IN + + ++I TKVDIS N+ +F +DKY
Sbjct: 71 EINLISFNQAVAPHIIAAKTKVDISIENLKQFIEDKY 107
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
0.318 0.139 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,297,301
Number of Sequences: 62578
Number of extensions: 197699
Number of successful extensions: 423
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 407
Number of HSP's gapped (non-prelim): 19
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
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: 48 (23.1 bits)