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|15645929|ref|NP_208108.1| ribosomal protein L2 (rpl2)
[Helicobacter pylori 26695]
(276 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|1LNR|A Chain A, Crystal Structure Of The Large Ribosoma... 304 8e-84
pdb|1GIY|D Chain D, Crystal Structure Of The Ribosome At 5.... 189 3e-49
pdb|1RL2|B Chain B, Ribosomal Protein L2 Rna-Binding Domain... 167 9e-43
pdb|487D|I Chain I, Seven Ribosomal Proteins Fitted To A Cr... 163 2e-41
pdb|1K8A|C Chain C, Co-Crystal Structure Of Carbomycin A Bo... 127 1e-30
pdb|1GGV|A Chain A, Crystal Structure Of The C123s Mutant O... 30 0.39
pdb|1DIN| Dienelactone Hydrolase At 2.8 Angstroms 27 2.0
pdb|1KDU| Plasminogen Activator (Urokinase-Type, Kringle ... 27 3.3
pdb|1URK| Plasminogen Activator (Urokinase-Type) (Amino T... 27 3.3
pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dn... 26 4.4
pdb|242L| The Response Of T4 Lysozyme To Large-To-Small S... 25 7.4
pdb|114L| Lysozyme (E.C.3.2.1.17) Mutant With Ser 44 Repl... 25 9.7
pdb|1K8A|M Chain M, Co-Crystal Structure Of Carbomycin A Bo... 25 9.7
>pdb|1LNR|A Chain A, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 274
Score = 304 bits (778), Expect = 8e-84
Identities = 155/275 (56%), Positives = 195/275 (70%), Gaps = 3/275 (1%)
Query: 2 AIKTYKPYTPSRRFMSVLDSKDITAKSSVKGLLTKLKATAGRNNNGRITSRHKERGAKKL 61
A+K Y+PYTPSRR M+ D +T K K L L T GRNN GRITSR G K+L
Sbjct: 1 AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL 60
Query: 62 YRIIDFKR-NKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVIAAE 120
YRIIDFKR +K + KVAAIEYDP R+ARIAL+ Y DG+KRYIL P GL VG +V A
Sbjct: 61 YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP 120
Query: 121 GGLDIKVGFAMKLKNIPIGTVVHNIEMHPGAGGQLARSAGMSAQIMGRENKYTIIRMPSS 180
+ K+G A+ L+ +P+G VVH +E+ PG G QLARSAG S Q+ G+E+ Y I+R+PS
Sbjct: 121 EA-EPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSG 179
Query: 181 EMRYILSECMASVGVVGNEDFINVSIGKAGRNRHRGIRPQTRGSAMNPVDHPHGGGEGKT 240
E+R + SEC A++G VGN + N+ +GKAGR+R G +P RGSAMNPVDHPHGGGEG+T
Sbjct: 180 ELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRT 239
Query: 241 GTSGHPVSPWGTPAKGYKT-RKKKASDKLIISRKK 274
G PV+PWG P KG KT RK+K SD+ I++R+K
Sbjct: 240 GAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK 274
>pdb|1GIY|D Chain D, 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 = 178
Score = 189 bits (480), Expect = 3e-49
Identities = 98/178 (55%), Positives = 124/178 (69%), Gaps = 6/178 (3%)
Query: 62 YRIIDFKRNKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVIAAEG 121
YRIIDFKR+K I G+VA IEYDP R+A IAL+ Y DG+KRYI+ P LKVG +++
Sbjct: 2 YRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPD 61
Query: 122 GLDIKVGFAMKLKNIPIGTVVHNIEMHPGAGGQLARSAGMSAQIMGRENKYTIIRMPSSE 181
DIK+G A+ L+NIP+GT+VHNIE+ PG GGQL R+AG SAQ++G+E KY I+R+ S E
Sbjct: 62 A-DIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGE 120
Query: 182 MRYILSECMASVGVVGNEDFINVSIGKAGRNRH----RGIR-PQTRGSAMNPVDHPHG 234
+R IL +C A+VG VGN + KAG H RG + P RG AMN VDHP G
Sbjct: 121 VRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFG 178
>pdb|1RL2|B Chain B, Ribosomal Protein L2 Rna-Binding Domain From Bacillus
Stearothermophilus
pdb|1RL2|A Chain A, Ribosomal Protein L2 Rna-Binding Domain From Bacillus
Stearothermophilus
pdb|1C04|A Chain A, Identification Of Known Protein And Rna Structures In A 5
A Map Of The Large Ribosomal Subunit From Haloarcula
Marismortui
Length = 137
Score = 167 bits (424), Expect = 9e-43
Identities = 81/137 (59%), Positives = 104/137 (75%), Gaps = 1/137 (0%)
Query: 62 YRIIDFKRNKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVIAAEG 121
YRIIDFKR+K I G+VA IEYDP R+A IAL+ Y DG+KRYI+ P LKVG + +
Sbjct: 2 YRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGXEIXSGPD 61
Query: 122 GLDIKVGFAMKLKNIPIGTVVHNIEMHPGAGGQLARSAGMSAQIMGRENKYTIIRMPSSE 181
DIK+G A+ L+NIP+GT+VHNIE+ PG GGQL R+AG SAQ++G+E KY I+R+ S E
Sbjct: 62 A-DIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGE 120
Query: 182 MRYILSECMASVGVVGN 198
+R IL +C A+VG VGN
Sbjct: 121 VRXILGKCRATVGEVGN 137
>pdb|487D|I Chain I, Seven Ribosomal Proteins Fitted To A Cryo-Electron
Microscopic Map Of The Large 50s Subunit At 7.5
Angstroms Resolution
Length = 135
Score = 163 bits (412), Expect = 2e-41
Identities = 79/135 (58%), Positives = 102/135 (75%), Gaps = 1/135 (0%)
Query: 62 YRIIDFKRNKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVIAAEG 121
YRIIDFKR+K I G+VA IEYDP R+A IAL+ Y DG+KRYI+ P LKVG + +
Sbjct: 2 YRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGXEIXSGPD 61
Query: 122 GLDIKVGFAMKLKNIPIGTVVHNIEMHPGAGGQLARSAGMSAQIMGRENKYTIIRMPSSE 181
DIK+G A+ L+NIP+GT+VHNIE+ PG GGQL R+AG SAQ++G+E KY I+R+ S E
Sbjct: 62 A-DIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGE 120
Query: 182 MRYILSECMASVGVV 196
+R IL +C A+VG V
Sbjct: 121 VRXILGKCRATVGEV 135
>pdb|1K8A|C Chain C, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|C Chain C, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|C Chain C, Co-Crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|C Chain C, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|C Chain C, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1JJ2|A Chain A, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|A Chain A, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1FFK|A Chain A, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 239
Score = 127 bits (319), Expect = 1e-30
Identities = 70/170 (41%), Positives = 102/170 (59%), Gaps = 10/170 (5%)
Query: 74 IEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVIAAEGGLDIKV--GFAM 131
I G V IE+DP R+A +A V + DGD+R IL P G+ VGD + + G+D ++ G +
Sbjct: 38 IAGTVVDIEHDPARSAPVAAVEFEDGDRRLILAPEGVGVGDEL---QVGVDAEIAPGNTL 94
Query: 132 KLKNIPIGTVVHNIEMHPGAGGQLARSAGMSAQIMGRENKYTIIRMPSSEMRYILSECMA 191
L IP G V N+E PG GG+ AR++G++AQ++ + ++++PS EM+ + +C A
Sbjct: 95 PLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRA 154
Query: 192 SVGVVGNEDFINVSIGKAGRNRH----RGIR-PQTRGSAMNPVDHPHGGG 236
++GVVG + KAG H RG + P RG AMN VDHP GGG
Sbjct: 155 TIGVVGGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGG 204
>pdb|1GGV|A Chain A, Crystal Structure Of The C123s Mutant Of Dienelactone
Hydrolase (Dlh) Bound With The Pms Moiety Of The
Protease Inhibitor, Phenylmethylsulfonyl Fluoride (Pmsf)
Length = 232
Score = 29.6 bits (65), Expect = 0.39
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 11/72 (15%)
Query: 58 AKKLYRIIDFKRNKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVI 117
A KL++ D + ++E + + PY N ++ LV Y G L +
Sbjct: 84 AYKLWQAFDMEAGVGDLEAAIRYARHQPYSNGKVGLVGYXLGGALAFL-----------V 132
Query: 118 AAEGGLDIKVGF 129
AA+G +D VG+
Sbjct: 133 AAKGYVDRAVGY 144
>pdb|1DIN| Dienelactone Hydrolase At 2.8 Angstroms
Length = 234
Score = 27.3 bits (59), Expect = 2.0
Identities = 13/45 (28%), Positives = 24/45 (52%), Gaps = 1/45 (2%)
Query: 52 RHKERGAKKLYRIIDFKRNKYNIEGKVAAIEYDPYRNARIALVVY 96
R +E+ A KL++ D + ++E + + PY N ++ LV Y
Sbjct: 79 RQREQ-AYKLWQAFDMEAGVGDLEAAIRYARHQPYSNGKVGLVGY 122
>pdb|1KDU| Plasminogen Activator (Urokinase-Type, Kringle Domain) (U-Pa K)
(Nmr, Minimized Average Structure)
Length = 85
Score = 26.6 bits (57), Expect = 3.3
Identities = 13/40 (32%), Positives = 17/40 (42%)
Query: 236 GEGKTGTSGHPVSPWGTPAKGYKTRKKKASDKLIISRKKH 275
G+ T T G P PW + +T SD L + KH
Sbjct: 12 GKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKH 51
>pdb|1URK| Plasminogen Activator (Urokinase-Type) (Amino Terminal Fragment)
(Nmr, 15 Structures)
Length = 130
Score = 26.6 bits (57), Expect = 3.3
Identities = 13/40 (32%), Positives = 17/40 (42%)
Query: 236 GEGKTGTSGHPVSPWGTPAKGYKTRKKKASDKLIISRKKH 275
G+ T T G P PW + +T SD L + KH
Sbjct: 55 GKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKH 94
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 26.2 bits (56), Expect = 4.4
Identities = 21/100 (21%), Positives = 41/100 (41%), Gaps = 1/100 (1%)
Query: 59 KKLYRIIDF-KRNKYNIEGKVAAIEYDPYRNARIALVVYPDGDKRYILQPSGLKVGDSVI 117
+K++++ D K +GK+ ++E ++N I V DG L+ + +
Sbjct: 154 RKIFKLNDLLPGEKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDYLQTYL 213
Query: 118 AAEGGLDIKVGFAMKLKNIPIGTVVHNIEMHPGAGGQLAR 157
G ++ V +K +HN E+ P G + R
Sbjct: 214 KQLTGKEVFVTGTVKSNAYTGQYEIHNAEVTPKEGEYVRR 253
>pdb|242L| The Response Of T4 Lysozyme To Large-To-Small Substitutions
Within The Core And Its Relation To The Hydrophobic
Effect
Length = 164
Score = 25.4 bits (54), Expect = 7.4
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 24 ITAKSSVKGLLTKLKATAGRNNNGRITSRHKER 56
+T S+ ++L AGRN NG IT E+
Sbjct: 33 LTKSPSLNAAKSELDKAAGRNTNGVITKDEAEK 65
>pdb|114L| Lysozyme (E.C.3.2.1.17) Mutant With Ser 44 Replaced By Thr, Cys
54 Replaced By Thr, Cys 97 Replaced By Ala (S44t,C54t,
C97a)
Length = 164
Score = 25.0 bits (53), Expect = 9.7
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 24 ITAKSSVKGLLTKLKATAGRNNNGRITSRHKER 56
+T S+ T+L GRN NG IT E+
Sbjct: 33 LTKSPSLNAAKTELDKAIGRNTNGVITKDEAEK 65
>pdb|1K8A|M Chain M, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|M Chain M, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|M Chain M, Co-Crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|M Chain M, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|M Chain M, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1JJ2|K Chain K, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|K Chain K, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1FFK|J Chain J, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|O Chain O, 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 = 164
Score = 25.0 bits (53), Expect = 9.7
Identities = 13/35 (37%), Positives = 14/35 (39%)
Query: 211 RNRHRGIRPQTRGSAMNPVDHPHGGGEGKTGTSGH 245
+ R RG R GS N H GG G G H
Sbjct: 4 KKRQRGSRTHGGGSHKNRRGAGHRGGRGDAGRDKH 38
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
0.316 0.135 0.388
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,703,391
Number of Sequences: 13198
Number of extensions: 72716
Number of successful extensions: 371
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 349
Number of HSP's gapped (non-prelim): 14
length of query: 276
length of database: 2,899,336
effective HSP length: 87
effective length of query: 189
effective length of database: 1,751,110
effective search space: 330959790
effective search space used: 330959790
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)