BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= gi|15645816|ref|NP_207993.1| ribosomal protein L11
(rpl11) [Helicobacter pylori 26695]
(141 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1MJ1|L Chain L, Fitting The Ternary Complex Of Ef-TuTRN... 191 4e-50
pdb|1MMS|A Chain A, Crystal Structure Of The Ribosomal Prot... 189 1e-49
pdb|1EG0|K Chain K, Fitting Of Components With Known Struct... 188 2e-49
pdb|1JQM|A Chain A, Fitting Of L11 Protein And Elongation F... 186 7e-49
pdb|487D|L Chain L, Seven Ribosomal Proteins Fitted To A Cr... 179 8e-47
pdb|1LNR|G Chain G, Crystal Structure Of The Large Ribosoma... 168 2e-43
pdb|1HC8|A Chain A, Crystal Structure Of A Conserved Riboso... 86 1e-18
pdb|1ACI| L11 Ribosomal Protein Rna Binding Domain, Nmr, ... 86 2e-18
pdb|1QA6|A Chain A, Crystal Structure Of A Conserved Riboso... 75 2e-15
pdb|1AT0| 17-Kda Fragment Of Hedgehog C-Terminal Autoproc... 27 0.68
pdb|1DMH|A Chain A, Structure Of Catechol 1,2-Dioxygenase F... 27 0.89
pdb|1ETX|B Chain B, The Crystal Structure Of E. Coli Fis Mu... 25 2.6
pdb|1GE9|A Chain A, Solution Structure Of The Ribosome Recy... 25 3.4
pdb|1C7J|A Chain A, Pnb Esterase 56c8 25 4.4
pdb|1YFM| Recombinant Yeast Fumarase 24 5.8
pdb|1C7I|A Chain A, Thermophylic Pnb Esterase 23 9.8
>pdb|1MJ1|L Chain L, Fitting The Ternary Complex Of Ef-TuTRNAGTP AND BOSOMAL
Proteins Into A 13 A Cryo-Em Map Of The Coli 70s
Ribosome
pdb|1GIY|L Chain L, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
Length = 141
Score = 191 bits (484), Expect = 4e-50
Identities = 90/141 (63%), Positives = 112/141 (78%)
Query: 1 MAKKVVGEIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITV 60
MAKKV +IKLQ+PAGKA P+PPVGPALGQ GVNIMEFCK FN T D +PV+ITV
Sbjct: 1 MAKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITV 60
Query: 61 YQDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTST 120
Y+DKSFTFI K PP + L+KKA+G+EKGS P + + K+T KQ+EEIA+ KM DLN ++
Sbjct: 61 YEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 120
Query: 121 MEAAKKIVMGSARSMGVEVVD 141
+EAA KI+ G+A+SMG+EVVD
Sbjct: 121 LEAAMKIIEGTAKSMGIEVVD 141
>pdb|1MMS|A Chain A, Crystal Structure Of The Ribosomal Protein L11-Rna Complex
pdb|1MMS|B Chain B, Crystal Structure Of The Ribosomal Protein L11-Rna Complex
Length = 140
Score = 189 bits (479), Expect = 1e-49
Identities = 89/140 (63%), Positives = 111/140 (78%)
Query: 2 AKKVVGEIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITVY 61
AKKV +IKLQ+PAGKA P+PPVGPALGQ GVNIMEFCK FN T D +PV+ITVY
Sbjct: 1 AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVY 60
Query: 62 QDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTM 121
+DKSFTFI K PP + L+KKA+G+EKGS P + + K+T KQ+EEIA+ KM DLN +++
Sbjct: 61 EDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSL 120
Query: 122 EAAKKIVMGSARSMGVEVVD 141
EAA KI+ G+A+SMG+EVVD
Sbjct: 121 EAAMKIIEGTAKSMGIEVVD 140
>pdb|1EG0|K Chain K, Fitting Of Components With Known Structure Into An 11.5 A
Cryo-Em Map Of The E.Coli 70s Ribosome
Length = 140
Score = 188 bits (478), Expect = 2e-49
Identities = 89/140 (63%), Positives = 111/140 (78%)
Query: 1 MAKKVVGEIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITV 60
MAKKV +IKLQ+PAGKA P+PPVGPALGQ GVNIMEFCK FN T D +PV+ITV
Sbjct: 1 MAKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITV 60
Query: 61 YQDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTST 120
Y+DKSFTFI K PP + L+KKA+G+EKGS P + + K+T KQ+EEIA+ KM DLN ++
Sbjct: 61 YEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 120
Query: 121 MEAAKKIVMGSARSMGVEVV 140
+EAA KI+ G+A+SMG+EVV
Sbjct: 121 LEAAMKIIEGTAKSMGIEVV 140
>pdb|1JQM|A Chain A, Fitting Of L11 Protein And Elongation Factor G (Ef-G) In
The Cryo-Em Map Of E. Coli 70s Ribosome Bound With Ef-G,
Gdp And Fusidic Acid
pdb|1JQS|A Chain A, Fitting Of L11 Protein And Elongation Factor G (Domain G'
And V) In The Cryo-Em Map Of E. Coli 70s Ribosome Bound
With Ef-G And Gmppcp, A Nonhydrolysable Gtp Analog
pdb|1JQT|A Chain A, Fitting Of L11 Protein In The Low Resolution Cryo-Em Map
Of E.Coli 70s Ribosome
Length = 139
Score = 186 bits (473), Expect = 7e-49
Identities = 88/139 (63%), Positives = 110/139 (78%)
Query: 2 AKKVVGEIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITVY 61
AKKV +IKLQ+PAGKA P+PPVGPALGQ GVNIMEFCK FN T D +PV+ITVY
Sbjct: 1 AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVY 60
Query: 62 QDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTM 121
+DKSFTFI K PP + L+KKA+G+EKGS P + + K+T KQ+EEIA+ KM DLN +++
Sbjct: 61 EDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSL 120
Query: 122 EAAKKIVMGSARSMGVEVV 140
EAA KI+ G+A+SMG+EVV
Sbjct: 121 EAAMKIIEGTAKSMGIEVV 139
>pdb|487D|L Chain L, Seven Ribosomal Proteins Fitted To A Cryo-Electron
Microscopic Map Of The Large 50s Subunit At 7.5
Angstroms Resolution
Length = 133
Score = 179 bits (455), Expect = 8e-47
Identities = 84/133 (63%), Positives = 106/133 (79%)
Query: 8 EIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITVYQDKSFT 67
+IKLQ+PAGKA P+PPVGPALGQ GVNIMEFCK FN T D +PV+ITVY+DKSFT
Sbjct: 1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFT 60
Query: 68 FITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAKKI 127
FI K PP + L+KKA+G+EKGS P + + K+T KQ+EEIA+ KM DLN +++EAA KI
Sbjct: 61 FIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKI 120
Query: 128 VMGSARSMGVEVV 140
+ G+A+SMG+EVV
Sbjct: 121 IEGTAKSMGIEVV 133
>pdb|1LNR|G Chain G, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 144
Score = 168 bits (426), Expect = 2e-43
Identities = 86/137 (62%), Positives = 102/137 (73%)
Query: 3 KKVVGEIKLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNERTKDMGSFNIPVIITVYQ 62
KKV G +KLQ+PAGKA P+PPVGPALGQ G NIMEF KAFN +T D G IPV IT+Y
Sbjct: 2 KKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYA 61
Query: 63 DKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTME 122
D+SFTFITK PP++ LI+KA+G+ KGS P K K+ KL QV EIA+ KM DLN ++E
Sbjct: 62 DRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVE 121
Query: 123 AAKKIVMGSARSMGVEV 139
AA V G+ARSMGV V
Sbjct: 122 AAANTVAGTARSMGVTV 138
>pdb|1HC8|A Chain A, Crystal Structure Of A Conserved Ribosomal Protein-Rna
Complex
pdb|1HC8|B Chain B, Crystal Structure Of A Conserved Ribosomal Protein-Rna
Complex
Length = 76
Score = 86.3 bits (212), Expect = 1e-18
Identities = 40/74 (54%), Positives = 56/74 (75%)
Query: 66 FTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAK 125
FTFITK PP L+KKA+G+E GS P +NK+A + +V EIA+LKM DLN +++EAA
Sbjct: 1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAM 60
Query: 126 KIVMGSARSMGVEV 139
+++ G+ARSMG+ V
Sbjct: 61 RMIEGTARSMGIVV 74
>pdb|1ACI| L11 Ribosomal Protein Rna Binding Domain, Nmr, 20 Structures
pdb|1FOW| Nmr Structure Of L11-C76, The C-Terminal Domain Of 50s Ribosomal
Protein L11, Minimized Average Structure
pdb|1FOX| Nmr Structure Of L11-C76, The C-Terminal Domain Of 50s Ribosomal
Protein L11, 33 Structures
pdb|1FOY| The Rna Binding Domain Of Ribosomal Protein L11: Three-Dimensional
Structure Of The Rna-Bound Form Of The Protein, Nmr,
Minimized Average Structure
pdb|2FOW| The Rna Binding Domain Of Ribosomal Protein L11: Three-Dimensional
Structure Of The Rna-Bound Form Of The Protein, Nmr, 26
Structures
Length = 76
Score = 85.5 bits (210), Expect = 2e-18
Identities = 40/75 (53%), Positives = 56/75 (74%)
Query: 67 TFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAKK 126
TFITK PP L+KKA+G+E GS P +NK+A + +V EIA+LKM DLN +++EAA +
Sbjct: 2 TFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMR 61
Query: 127 IVMGSARSMGVEVVD 141
++ G+ARSMG+ V D
Sbjct: 62 MIEGTARSMGIVVED 76
>pdb|1QA6|A Chain A, Crystal Structure Of A Conserved Ribosomal Protein-Rna
Complex
pdb|1QA6|B Chain B, Crystal Structure Of A Conserved Ribosomal Protein-Rna
Complex
pdb|1C04|C Chain C, Identification Of Known Protein And Rna Structures In A 5
A Map Of The Large Ribosomal Subunit From Haloarcula
Marismortui
Length = 67
Score = 75.5 bits (184), Expect = 2e-15
Identities = 34/67 (50%), Positives = 50/67 (73%)
Query: 71 KKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAKKIVMG 130
K PP L+KKA+G+E GS P +NK+A + +V EIA+LKM DLN +++EAA +++ G
Sbjct: 1 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEG 60
Query: 131 SARSMGV 137
+ARSMG+
Sbjct: 61 TARSMGI 67
>pdb|1AT0| 17-Kda Fragment Of Hedgehog C-Terminal Autoprocessing Domain
Length = 145
Score = 27.3 bits (59), Expect = 0.68
Identities = 13/46 (28%), Positives = 24/46 (51%)
Query: 92 PLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAKKIVMGSARSMGV 137
P K+ + ++EE Q+ + D+ T + + + +GS RS GV
Sbjct: 79 PESQKLTFVFADRIEEKNQVLVRDVETGELRPQRVVKVGSVRSKGV 124
>pdb|1DMH|A Chain A, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 With Bound 4-Methylcatechol
pdb|1DMH|B Chain B, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 With Bound 4-Methylcatechol
pdb|1DLT|A Chain A, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 With Bound Catechol
pdb|1DLT|B Chain B, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 With Bound Catechol
pdb|1DLM|A Chain A, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Calcoaceticus Native Data
pdb|1DLM|B Chain B, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Calcoaceticus Native Data
pdb|1DLQ|A Chain A, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 Inhibited By Bound Mercury
pdb|1DLQ|B Chain B, Structure Of Catechol 1,2-Dioxygenase From Acinetobacter
Sp. Adp1 Inhibited By Bound Mercury
Length = 311
Score = 26.9 bits (58), Expect = 0.89
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 75 VTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTME 122
V D ++ ASG+E+ NP ++ ++ H+ + ++ + +EDLN ++ E
Sbjct: 11 VQDFLRVASGLEQEGGNP---RVKQIIHRVLSDLYK-AIEDLNITSDE 54
>pdb|1ETX|B Chain B, The Crystal Structure Of E. Coli Fis Mutant Q74a
pdb|1ETX|A Chain A, The Crystal Structure Of E. Coli Fis Mutant Q74a
Length = 98
Score = 25.4 bits (54), Expect = 2.6
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 11/76 (14%)
Query: 57 IITVYQDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDL 116
++TV S +T+KP + D +K+A LKN A+L + V ++ +L + ++
Sbjct: 10 VLTVSTVNSQDQVTQKP-LRDSVKQA----------LKNYFAQLNGQDVNDLYELVLAEV 58
Query: 117 NTSTMEAAKKIVMGSA 132
++ + G+A
Sbjct: 59 EQPLLDMVMQYTRGNA 74
>pdb|1GE9|A Chain A, Solution Structure Of The Ribosome Recycling Factor
Length = 184
Score = 25.0 bits (53), Expect = 3.4
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 77 DLIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMEDLNTSTMEAAKKIVM 129
++I++ G+ + ++ KLT K ++EI +L MEA +K +M
Sbjct: 139 EMIEELEGISEDEKKRALERLQKLTDKYIDEINKL---------MEAKEKEIM 182
>pdb|1C7J|A Chain A, Pnb Esterase 56c8
Length = 489
Score = 24.6 bits (52), Expect = 4.4
Identities = 14/53 (26%), Positives = 23/53 (42%)
Query: 54 IPVIITVYQDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVE 106
IP++I +D+ + F T V + +E PL K A L + +E
Sbjct: 300 IPLLIGTTRDEGYLFFTSDSDVRSQETLDAALEYSLGKPLAEKAADLYPRSLE 352
>pdb|1YFM| Recombinant Yeast Fumarase
Length = 488
Score = 24.3 bits (51), Expect = 5.8
Identities = 11/38 (28%), Positives = 22/38 (56%)
Query: 78 LIKKASGVEKGSDNPLKNKIAKLTHKQVEEIAQLKMED 115
++KK++ + S L KI+K + +E+A K++D
Sbjct: 76 VLKKSAAIVNESLGGLDPKISKAIQQAADEVASGKLDD 113
>pdb|1C7I|A Chain A, Thermophylic Pnb Esterase
Length = 489
Score = 23.5 bits (49), Expect = 9.8
Identities = 14/53 (26%), Positives = 24/53 (44%)
Query: 54 IPVIITVYQDKSFTFITKKPPVTDLIKKASGVEKGSDNPLKNKIAKLTHKQVE 106
IP++I +D+ + F T V + +E PL K+A L + +E
Sbjct: 300 IPLLIGTTRDEGYFFFTPDSDVYSQETLDAALEYLLGKPLAEKVADLYPRSLE 352
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.313 0.132 0.359
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 739,604
Number of Sequences: 13198
Number of extensions: 27138
Number of successful extensions: 41
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 27
Number of HSP's gapped (non-prelim): 16
length of query: 141
length of database: 2,899,336
effective HSP length: 79
effective length of query: 62
effective length of database: 1,856,694
effective search space: 115115028
effective search space used: 115115028
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)