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|15645811|ref|NP_207988.1| ribosomal protein S12
(rps12) [Helicobacter pylori 26695]
(135 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|O Chain O, Fitting The Ternary Complex Of Ef-TuTRN... 190 4e-50
pdb|1I94|L Chain L, Crystal Structures Of The Small Ribosom... 189 7e-50
pdb|1DS6|B Chain B, Crystal Structure Of A Rac-Rhogdi Complex 26 1.8
pdb|1B25|A Chain A, Formaldehyde Ferredoxin Oxidoreductase ... 25 4.0
pdb|1DXL|A Chain A, Dihydrolipoamide Dehydrogenase Of Glyci... 24 5.2
pdb|1EAH|1 Chain 1, Pv2l Complexed With Antiviral Agent Sch... 24 6.8
>pdb|1MJ1|O Chain O, Fitting The Ternary Complex Of Ef-TuTRNAGTP AND BOSOMAL
Proteins Into A 13 A Cryo-Em Map Of The Coli 70s
Ribosome
pdb|1FJG|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1J5E|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1IBL|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1HR0|L Chain L, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1IBK|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1JGQ|O Chain O, The Path Of Messenger Rna Through The Ribosome. This File,
1jgq, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1GIX|O Chain O, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1JGO|O Chain O, The Path Of Messenger Rna Through The Ribosome. This File,
1jgo, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGP|O Chain O, The Path Of Messenger Rna Through The Ribosome. This File,
1jgp, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
Length = 135
Score = 190 bits (483), Expect = 4e-50
Identities = 96/129 (74%), Positives = 105/129 (80%)
Query: 1 MPTINQLIRKERKKVVKKTKSPALVECPQRRGVCTRVYTTTPKKPNSALRKVAKVRLTSK 60
+PTINQL+RK R+KV KK+K PAL P RRGVCT V T TPKKPNSALRKVAKVRLTS
Sbjct: 4 LPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG 63
Query: 61 FEVISYIPGEGHNLQEHSIVLVRGGRVKDLPGVKYHIVRGALDTAGVNKRTVSRSKYGTK 120
+EV +YIPGEGHNLQEHS+VL+RGGRVKDLPGV+YHIVRG D AGV R SRSKYGTK
Sbjct: 64 YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK 123
Query: 121 KAKATDKKA 129
K K K A
Sbjct: 124 KPKEAAKTA 132
>pdb|1I94|L Chain L, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|L Chain L, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|L Chain L, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|L Chain L, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 131
Score = 189 bits (481), Expect = 7e-50
Identities = 96/128 (75%), Positives = 104/128 (81%)
Query: 2 PTINQLIRKERKKVVKKTKSPALVECPQRRGVCTRVYTTTPKKPNSALRKVAKVRLTSKF 61
PTINQL+RK R+KV KK+K PAL P RRGVCT V T TPKKPNSALRKVAKVRLTS +
Sbjct: 1 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY 60
Query: 62 EVISYIPGEGHNLQEHSIVLVRGGRVKDLPGVKYHIVRGALDTAGVNKRTVSRSKYGTKK 121
EV +YIPGEGHNLQEHS+VL+RGGRVKDLPGV+YHIVRG D AGV R SRSKYGTKK
Sbjct: 61 EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK 120
Query: 122 AKATDKKA 129
K K A
Sbjct: 121 PKEAAKTA 128
>pdb|1DS6|B Chain B, Crystal Structure Of A Rac-Rhogdi Complex
Length = 180
Score = 25.8 bits (55), Expect = 1.8
Identities = 26/93 (27%), Positives = 39/93 (40%), Gaps = 19/93 (20%)
Query: 40 TTPKKPNSALRKVAKVRLTSKFEVISYIPGEGHNLQEHSIVLVRGGRVKDLPGVKYHIVR 99
T PK PN + ++ V ++ + + G+ L++ +IVL G + VK H
Sbjct: 39 TDPKAPNVVVTRLTLVCESAPGPITMDLTGDLEALKKETIVLKEGSEYR----VKIHF-- 92
Query: 100 GALDTAGVNKRTVSRSKY-------GTKKAKAT 125
VN+ VS KY G K KAT
Sbjct: 93 ------KVNRDIVSGLKYVQHTYRTGVKVDKAT 119
>pdb|1B25|A Chain A, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus
pdb|1B25|B Chain B, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus
pdb|1B25|C Chain C, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus
pdb|1B25|D Chain D, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus
pdb|1B4N|A Chain A, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus, Complexed With Glutarate
pdb|1B4N|B Chain B, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus, Complexed With Glutarate
pdb|1B4N|C Chain C, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus, Complexed With Glutarate
pdb|1B4N|D Chain D, Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus
Furiosus, Complexed With Glutarate
Length = 619
Score = 24.6 bits (52), Expect = 4.0
Identities = 18/58 (31%), Positives = 29/58 (49%), Gaps = 9/58 (15%)
Query: 71 GHNLQEHSIVLVRGGRVKDLPGVKYHIVRGALDTAGVNKRTVSRSKYGTKKAKATDKK 128
G NL ++++V+ + GR PG+ GA+ + K V R GTK+ DK+
Sbjct: 165 GENLVKYAVVISQEGRAAGRPGM------GAVMGSKKLKAVVIR---GTKEIPVADKE 213
>pdb|1DXL|A Chain A, Dihydrolipoamide Dehydrogenase Of Glycine Decarboxylase
From Pisum Sativum
pdb|1DXL|B Chain B, Dihydrolipoamide Dehydrogenase Of Glycine Decarboxylase
From Pisum Sativum
pdb|1DXL|C Chain C, Dihydrolipoamide Dehydrogenase Of Glycine Decarboxylase
From Pisum Sativum
pdb|1DXL|D Chain D, Dihydrolipoamide Dehydrogenase Of Glycine Decarboxylase
From Pisum Sativum
Length = 470
Score = 24.3 bits (51), Expect = 5.2
Identities = 17/54 (31%), Positives = 25/54 (45%), Gaps = 5/54 (9%)
Query: 64 ISYIPGEGHNLQEHSIVLVRGGRVKDLPGV-----KYHIVRGALDTAGVNKRTV 112
+ I GE ++ I++ G VK LPGV K GAL + + K+ V
Sbjct: 128 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLV 181
>pdb|1EAH|1 Chain 1, Pv2l Complexed With Antiviral Agent Sch48973
Length = 301
Score = 23.9 bits (50), Expect = 6.8
Identities = 21/64 (32%), Positives = 27/64 (41%), Gaps = 9/64 (14%)
Query: 12 RKKVVKKTKSPALVECPQRRGVCT---RVYTTTPKKPNSALRKVAK------VRLTSKFE 62
R + K+T+S + VE RG C V P K S L V K V+L K E
Sbjct: 64 RHVIQKRTRSESTVESFFARGACVAIIEVDNDAPTKRASKLFSVWKITYKDTVQLRRKLE 123
Query: 63 VISY 66
+Y
Sbjct: 124 FFTY 127
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
0.314 0.131 0.365
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 715,803
Number of Sequences: 13198
Number of extensions: 26014
Number of successful extensions: 34
Number of sequences better than 10.0: 6
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 31
Number of HSP's gapped (non-prelim): 6
length of query: 135
length of database: 2,899,336
effective HSP length: 79
effective length of query: 56
effective length of database: 1,856,694
effective search space: 103974864
effective search space used: 103974864
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)