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|15645927|ref|NP_208106.1| ribosomal protein L22
(rpl22) [Helicobacter pylori 26695]
(122 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|1GIY|S Chain S, Crystal Structure Of The Ribosome At 5.... 74 5e-15
pdb|1LNR|Q Chain Q, Crystal Structure Of The Large Ribosoma... 74 6e-15
pdb|1BXE|A Chain A, Ribosomal Protein L22 From Thermus Ther... 73 8e-15
pdb|1I4J|A Chain A, Crystal Structure Of L22 Ribosomal Prot... 66 1e-12
pdb|1LNR|A Chain A, Crystal Structure Of The Large Ribosoma... 28 0.22
pdb|1K8A|S Chain S, Co-Crystal Structure Of Carbomycin A Bo... 27 0.85
pdb|1OEN| Phosphoenolpyruvate Carboxykinase 25 2.5
pdb|1GP0|A Chain A, Human Igf2r Domain 11 >gi|20149853|pdb|... 23 7.2
pdb|1E7K|A Chain A, Crystal Structure Of The Spliceosomal 1... 23 9.4
>pdb|1GIY|S Chain S, 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 = 113
Score = 73.9 bits (180), Expect = 5e-15
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 4/107 (3%)
Query: 2 SKALLRFVRLSPTKARLIARQIQGMNAELAIASLEFTPNKAARVLSKVVASAVANG---- 57
+KA+ R+VR+SP K RL+ I+G + E A L +T + A ++KV+ SA AN
Sbjct: 3 AKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNH 62
Query: 58 SLDAKSALIVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFVEVAE 104
+ + + VD GP L+R +PRA+GRA I+K TSH+ V + E
Sbjct: 63 DMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGE 109
>pdb|1LNR|Q Chain Q, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
pdb|1JZX|L Chain L, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1K01|L Chain L, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1J5A|L Chain L, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1JZY|L Chain L, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1JZZ|L Chain L, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
Length = 134
Score = 73.6 bits (179), Expect = 6e-15
Identities = 42/105 (40%), Positives = 61/105 (58%), Gaps = 4/105 (3%)
Query: 4 ALLRFVRLSPTKARLIARQIQGMNAELAIASLEFTPNKA----ARVLSKVVASAVANGSL 59
A+ ++VR+SP K RL+ I+G + + A L F P A A+VL+ A+A+ N +
Sbjct: 26 AVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEM 85
Query: 60 DAKSALIVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFVEVAE 104
+ VDAGP L+R IPRA+G A I+K TSH+ + VAE
Sbjct: 86 LEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAE 130
>pdb|1BXE|A Chain A, Ribosomal Protein L22 From Thermus Thermophilus
Length = 113
Score = 73.2 bits (178), Expect = 8e-15
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 4/107 (3%)
Query: 2 SKALLRFVRLSPTKARLIARQIQGMNAELAIASLEFTPNKAARVLSKVVASAVANGSLDA 61
+KA+ R+VR+SP K RL+ I+G + E A L +T + A ++KV+ SA AN +
Sbjct: 3 AKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNH 62
Query: 62 KSA----LIVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFVEVAE 104
+ + VD GP L+R +PRA+GRA I+K TSH+ V + E
Sbjct: 63 DXLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGE 109
>pdb|1I4J|A Chain A, Crystal Structure Of L22 Ribosomal Protein Mutant
pdb|1I4J|B Chain B, Crystal Structure Of L22 Ribosomal Protein Mutant
Length = 110
Score = 66.2 bits (160), Expect = 1e-12
Identities = 42/108 (38%), Positives = 65/108 (59%), Gaps = 9/108 (8%)
Query: 2 SKALLRFVRLSPTKARLIARQIQGMNAELAIASLEFTPNKAARVLSKVVASAVANGSLDA 61
+KA+ R+VR+SP K RL+ I+G + E A L +T + A ++KV+ SA AN +++
Sbjct: 3 AKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAAN-AVNN 61
Query: 62 KSAL-----IVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFVEVAE 104
AL + + VD GP + +PRA+GRA I+K TSH+ V + E
Sbjct: 62 HDALEDRLYVKAAYVDEGPAV---LPRARGRADIIKKRTSHITVILGE 106
>pdb|1LNR|A Chain A, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 274
Score = 28.5 bits (62), Expect = 0.22
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 21 RQIQGMNAELAIASLEFTPNKAARVLSKVVASAVANGSLDAKSALIVSCRVDAGP 75
R G+NA+ +A++E+ PN++AR+ A L A L V V+AGP
Sbjct: 69 RDKSGVNAK--VAAIEYDPNRSARIALLHYADGEKRYIL-APEGLTVGATVNAGP 120
>pdb|1K8A|S Chain S, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|S Chain S, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|S Chain S, Co-Crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|S Chain S, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|S Chain S, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1JJ2|Q Chain Q, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|Q Chain Q, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1FFK|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 154
Score = 26.6 bits (57), Expect = 0.85
Identities = 30/126 (23%), Positives = 48/126 (37%), Gaps = 33/126 (26%)
Query: 2 SKALLRFVRLSPTKARLIARQIQGMNAELAIASLEFT----------------------- 38
+KA+LR ++S ++ IAR+I+G A A+ LE
Sbjct: 14 AKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQHNSGVGHKSKVD 73
Query: 39 -------PNKAARVLSKVVASAVANG---SLDAKSALIVSCRVDAGPVLRRSIPRAKGRA 88
P KA++ ++ +AV N D ++ I + PRA GRA
Sbjct: 74 GWDAGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVGEQQGRKPRAMGRA 133
Query: 89 TAIRKP 94
+A P
Sbjct: 134 SAWNSP 139
>pdb|1OEN| Phosphoenolpyruvate Carboxykinase
Length = 540
Score = 25.0 bits (53), Expect = 2.5
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 8 FVRLSPTK-ARLIARQIQGMNAELAIASLEF--TPNKAARVLSKVVASAVANGSLD 60
F+ L PT+ A ++ +++Q A+ + + + T + + ++ + A+ NGSLD
Sbjct: 413 FLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISAADTRAIIDAILNGSLD 468
>pdb|1GP0|A Chain A, Human Igf2r Domain 11
pdb|1GP3|A Chain A, Human Igf2r Domain 11
pdb|1E6F|B Chain B, Human Mir-Receptor, Repeat 11
pdb|1E6F|A Chain A, Human Mir-Receptor, Repeat 11
Length = 143
Score = 23.5 bits (49), Expect = 7.2
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 40 NKAARVLSKVVASAVANGS-------LDAKSALIVSCRVDAGPVLR 78
NK R + +V+ +GS L KS + CR +AGP R
Sbjct: 71 NKRLRYVDQVLQLVYKDGSPCPSKSGLSYKSVISFVCRPEAGPTNR 116
>pdb|1E7K|A Chain A, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
pdb|1E7K|B Chain B, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
Length = 128
Score = 23.1 bits (48), Expect = 9.4
Identities = 16/66 (24%), Positives = 28/66 (42%)
Query: 44 RVLSKVVASAVANGSLDAKSALIVSCRVDAGPVLRRSIPRAKGRATAIRKPTSHVFVEVA 103
R +S+ + A L+ L + C P + +A GRA + +P V +
Sbjct: 48 RGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIK 107
Query: 104 EGKEMK 109
EG ++K
Sbjct: 108 EGSQLK 113
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
0.315 0.126 0.330
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 518,009
Number of Sequences: 13198
Number of extensions: 15137
Number of successful extensions: 35
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 25
Number of HSP's gapped (non-prelim): 9
length of query: 122
length of database: 2,899,336
effective HSP length: 77
effective length of query: 45
effective length of database: 1,883,090
effective search space: 84739050
effective search space used: 84739050
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: 48 (23.1 bits)