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|15645915|ref|NP_208094.1| ribosomal protein S5 (rps5)
[Helicobacter pylori 26695]
(153 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|1EG0|B Chain B, Fitting Of Components With Known Struct... 185 2e-48
pdb|1PKP| Ribosomal Protein S5 (Prokaryotic) 185 2e-48
pdb|1DV4|E Chain E, Partial Structure Of 16s Rna Of The Sma... 185 2e-48
pdb|1FJG|E Chain E, Structure Of The Thermus Thermophilus 3... 145 2e-36
pdb|1J5E|E Chain E, Structure Of The Thermus Thermophilus 3... 145 2e-36
pdb|1E9Z|B Chain B, Crystal Structure Of Helicobacter Pylor... 28 0.36
pdb|1E9Y|B Chain B, Crystal Structure Of Helicobacter Pylor... 28 0.36
pdb|1LFW|A Chain A, Crystal Structure Of Pepv 27 0.79
pdb|1FO6|A Chain A, Crystal Structure Analysis Of N-Carbamo... 27 1.0
pdb|1ERZ|A Chain A, Crystal Structure Of N-Carbamyl-D-Amino... 27 1.0
pdb|1J6R|A Chain A, Crystal Structure Of Hypothetical Prote... 26 2.3
pdb|1GTM|A Chain A, Structure Of Glutamate Dehydrogenase >g... 26 2.3
pdb|1A6D|B Chain B, Thermosome From T. Acidophilum >gi|4699... 25 3.0
pdb|2PTH| Peptidyl-Trna Hydrolase From Escherichia Coli 25 3.0
>pdb|1EG0|B Chain B, Fitting Of Components With Known Structure Into An 11.5 A
Cryo-Em Map Of The E.Coli 70s Ribosome
Length = 148
Score = 185 bits (470), Expect = 2e-48
Identities = 93/142 (65%), Positives = 114/142 (79%)
Query: 11 NREEFQEVVVNIGRVTKVVKGGRRFRFNALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDD 70
N+ E +E VV + RV KVVKGGRR RF+ALVVVG+KNG VGFG GKA+EVP+AI+KA++D
Sbjct: 7 NKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIED 66
Query: 71 AFKNLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVELAGIKDILTK 130
A KNLI V I GTTI H++ + A I+LKPASEGTGVIAGG R ++ELAGI DIL+K
Sbjct: 67 AKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSK 126
Query: 131 SLGSNNPYNVVRATFDALAKIK 152
S+GSN P N+VRATFD L ++K
Sbjct: 127 SIGSNTPINMVRATFDGLKQLK 148
>pdb|1PKP| Ribosomal Protein S5 (Prokaryotic)
Length = 150
Score = 185 bits (470), Expect = 2e-48
Identities = 93/142 (65%), Positives = 114/142 (79%)
Query: 11 NREEFQEVVVNIGRVTKVVKGGRRFRFNALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDD 70
N+ E +E VV + RV KVVKGGRR RF+ALVVVG+KNG VGFG GKA+EVP+AI+KA++D
Sbjct: 7 NKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIED 66
Query: 71 AFKNLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVELAGIKDILTK 130
A KNLI V I GTTI H++ + A I+LKPASEGTGVIAGG R ++ELAGI DIL+K
Sbjct: 67 AKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSK 126
Query: 131 SLGSNNPYNVVRATFDALAKIK 152
S+GSN P N+VRATFD L ++K
Sbjct: 127 SIGSNTPINMVRATFDGLKQLK 148
>pdb|1DV4|E Chain E, Partial Structure Of 16s Rna Of The Small Ribosomal
Subunit From Thermus Thermophilus
pdb|1QD7|D Chain D, Partial Model For 30s Ribosomal Subunit
Length = 145
Score = 185 bits (470), Expect = 2e-48
Identities = 93/142 (65%), Positives = 114/142 (79%)
Query: 11 NREEFQEVVVNIGRVTKVVKGGRRFRFNALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDD 70
N+ E +E VV + RV KVVKGGRR RF+ALVVVG+KNG VGFG GKA+EVP+AI+KA++D
Sbjct: 4 NKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIED 63
Query: 71 AFKNLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVELAGIKDILTK 130
A KNLI V I GTTI H++ + A I+LKPASEGTGVIAGG R ++ELAGI DIL+K
Sbjct: 64 AKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSK 123
Query: 131 SLGSNNPYNVVRATFDALAKIK 152
S+GSN P N+VRATFD L ++K
Sbjct: 124 SIGSNTPINMVRATFDGLKQLK 145
>pdb|1FJG|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1IBL|E Chain E, 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|E Chain E, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNZ|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|E Chain E, 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|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1FKA|E Chain E, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
pdb|1JGQ|H Chain H, 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|H Chain H, 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|H Chain H, 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|H Chain H, 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 = 162
Score = 145 bits (366), Expect = 2e-36
Identities = 73/139 (52%), Positives = 101/139 (72%)
Query: 14 EFQEVVVNIGRVTKVVKGGRRFRFNALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDDAFK 73
+F+E ++ I R ++ GGRRFRF ALVVVG++ G VG G GKA EVP A++KA A +
Sbjct: 5 DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR 64
Query: 74 NLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVELAGIKDILTKSLG 133
N++ V ++ TI H+IE ++ AS+I+LKPA+ GTGVIAG R I+ELAG+ DILTK LG
Sbjct: 65 NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG 124
Query: 134 SNNPYNVVRATFDALAKIK 152
S NP N+ AT +AL +++
Sbjct: 125 SRNPINIAYATMEALRQLR 143
>pdb|1J5E|E Chain E, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1I94|E Chain E, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|E Chain E, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|E Chain E, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|E Chain E, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 161
Score = 145 bits (366), Expect = 2e-36
Identities = 73/139 (52%), Positives = 101/139 (72%)
Query: 14 EFQEVVVNIGRVTKVVKGGRRFRFNALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDDAFK 73
+F+E ++ I R ++ GGRRFRF ALVVVG++ G VG G GKA EVP A++KA A +
Sbjct: 4 DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR 63
Query: 74 NLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVELAGIKDILTKSLG 133
N++ V ++ TI H+IE ++ AS+I+LKPA+ GTGVIAG R I+ELAG+ DILTK LG
Sbjct: 64 NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG 123
Query: 134 SNNPYNVVRATFDALAKIK 152
S NP N+ AT +AL +++
Sbjct: 124 SRNPINIAYATMEALRQLR 142
>pdb|1E9Z|B Chain B, Crystal Structure Of Helicobacter Pylori Urease
Length = 569
Score = 28.5 bits (62), Expect = 0.36
Identities = 30/98 (30%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 48 GLVGFGLGKA-KEVPDAIKKAVDDAFKNLIHVTIKGTTI--AHDIEHKYNA--SRILLKP 102
G +GF + + P AI A+D A K + V I T+ A +E A R +
Sbjct: 214 GAIGFXIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTF 273
Query: 103 ASEGTGVIAGGSTRPIVELAGIKDILTKSLGSNNPYNV 140
+EG G GG I+++AG +IL S P+ V
Sbjct: 274 HTEGAG---GGHAPDIIKVAGEHNILPASTNPTIPFTV 308
>pdb|1E9Y|B Chain B, Crystal Structure Of Helicobacter Pylori Urease In Complex
With Acetohydroxamic Acid
Length = 569
Score = 28.5 bits (62), Expect = 0.36
Identities = 30/98 (30%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 48 GLVGFGLGKA-KEVPDAIKKAVDDAFKNLIHVTIKGTTI--AHDIEHKYNA--SRILLKP 102
G +GF + + P AI A+D A K + V I T+ A +E A R +
Sbjct: 214 GAIGFXIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTF 273
Query: 103 ASEGTGVIAGGSTRPIVELAGIKDILTKSLGSNNPYNV 140
+EG G GG I+++AG +IL S P+ V
Sbjct: 274 HTEGAG---GGHAPDIIKVAGEHNILPASTNPTIPFTV 308
>pdb|1LFW|A Chain A, Crystal Structure Of Pepv
Length = 470
Score = 27.3 bits (59), Expect = 0.79
Identities = 19/60 (31%), Positives = 26/60 (42%), Gaps = 5/60 (8%)
Query: 61 PDAIKKAVDDAFKNLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTG-----VIAGGST 115
PD + K V D F ++ VT G H + + LLK + TG V+ GG T
Sbjct: 357 PDTMIKQVLDKFSGILDVTYNGFEEPHYVPGSDPMVQTLLKVYEKQTGKPGHEVVIGGGT 416
>pdb|1FO6|A Chain A, Crystal Structure Analysis Of N-Carbamoyl-D-Amino-Acid
Amidohydrolase
pdb|1FO6|B Chain B, Crystal Structure Analysis Of N-Carbamoyl-D-Amino-Acid
Amidohydrolase
pdb|1FO6|C Chain C, Crystal Structure Analysis Of N-Carbamoyl-D-Amino-Acid
Amidohydrolase
pdb|1FO6|D Chain D, Crystal Structure Analysis Of N-Carbamoyl-D-Amino-Acid
Amidohydrolase
Length = 304
Score = 26.9 bits (58), Expect = 1.0
Identities = 12/31 (38%), Positives = 18/31 (57%)
Query: 21 NIGRVTKVVKGGRRFRFNALVVVGNKNGLVG 51
N+G VV+GG + RFN ++V +VG
Sbjct: 93 NLGYAELVVEGGVKRRFNTSILVDKSGKIVG 123
>pdb|1ERZ|A Chain A, Crystal Structure Of N-Carbamyl-D-Amino Acid
Amidohydrolase With A Novel Catalytic Framework Common
To Amidohydrolases
pdb|1ERZ|B Chain B, Crystal Structure Of N-Carbamyl-D-Amino Acid
Amidohydrolase With A Novel Catalytic Framework Common
To Amidohydrolases
Length = 303
Score = 26.9 bits (58), Expect = 1.0
Identities = 12/31 (38%), Positives = 18/31 (57%)
Query: 21 NIGRVTKVVKGGRRFRFNALVVVGNKNGLVG 51
N+G VV+GG + RFN ++V +VG
Sbjct: 92 NLGYAELVVEGGVKRRFNTSILVDKSGKIVG 122
>pdb|1J6R|A Chain A, Crystal Structure Of Hypothetical Protein (Tm0269) From
Thermotoga Maritima At 2.2 A Resolution
pdb|1J6R|B Chain B, Crystal Structure Of Hypothetical Protein (Tm0269) From
Thermotoga Maritima At 2.2 A Resolution
Length = 214
Score = 25.8 bits (55), Expect = 2.3
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 53 GLGKAKEVPDAIKKAVDDAFKNLI 76
G G A+E+P+ +K V+ A++ L+
Sbjct: 35 GFGGAEEIPEEFRKTVNRAYEELL 58
>pdb|1GTM|A Chain A, Structure Of Glutamate Dehydrogenase
pdb|1GTM|B Chain B, Structure Of Glutamate Dehydrogenase
pdb|1GTM|C Chain C, Structure Of Glutamate Dehydrogenase
Length = 419
Score = 25.8 bits (55), Expect = 2.3
Identities = 22/71 (30%), Positives = 32/71 (44%), Gaps = 2/71 (2%)
Query: 39 ALVVVGNKNGLVGFGLGKAKEVPDAIKKAVDDAFKNLIHVTIKGTTIAHDIEHKYNASRI 98
A ++ K +G LG+ + + +A K L T+KG TIA I+ NA
Sbjct: 169 AFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIA--IQGYGNAGYY 226
Query: 99 LLKPASEGTGV 109
L K SE G+
Sbjct: 227 LAKIMSEDFGM 237
>pdb|1A6D|B Chain B, Thermosome From T. Acidophilum
pdb|1A6E|B Chain B, Thermosome - Mg-Adp-Alf3 Complex
Length = 543
Score = 25.4 bits (54), Expect = 3.0
Identities = 11/64 (17%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 61 PDAIKKAVDDAFKNLIHVTIKGTTIAHDIEHKYNASRILLKPASEGTGVIAGGSTRPIVE 120
P + K + D+ +++ +T G TI +++ ++ A++++++ + + G+T ++
Sbjct: 43 PRGMDKMLVDSLGDIV-ITNDGVTILKEMDVEHPAAKMMVEVSKTQDSFVGDGTTTAVII 101
Query: 121 LAGI 124
G+
Sbjct: 102 AGGL 105
>pdb|2PTH| Peptidyl-Trna Hydrolase From Escherichia Coli
Length = 193
Score = 25.4 bits (54), Expect = 3.0
Identities = 19/56 (33%), Positives = 27/56 (47%), Gaps = 7/56 (12%)
Query: 44 GNKNGLVGFGLGKAKEVPDAIKKAVDDAFKNLIHVT----IKGTTIAHDIEHKYNA 95
G+KN +VGF LGK P + +K +D+A T G T A + H + A
Sbjct: 140 GDKNKVVGFVLGKP---PVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKA 192
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
0.317 0.137 0.375
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 882,290
Number of Sequences: 13198
Number of extensions: 37037
Number of successful extensions: 68
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 59
Number of HSP's gapped (non-prelim): 14
length of query: 153
length of database: 2,899,336
effective HSP length: 80
effective length of query: 73
effective length of database: 1,843,496
effective search space: 134575208
effective search space used: 134575208
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: 50 (23.9 bits)