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|15646060|ref|NP_208242.1| hypothetical protein
[Helicobacter pylori 26695]
(264 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|1LD4|A Chain A, Placement Of The Structural Proteins In... 29 0.49
pdb|1J5Y|A Chain A, Crystal Structure Of Transcriptional Re... 28 0.83
pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomeras... 27 2.4
pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 27 3.2
pdb|1A36|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 27 3.2
pdb|1KAG|A Chain A, Crystal Structure Of The Escherichia Co... 27 3.2
pdb|1M7X|A Chain A, The X-Ray Crystallographic Structure Of... 26 4.1
pdb|1KXF| Sindbis Virus Capsid, (Wild-Type) Residues 1-26... 26 4.1
pdb|1K30|A Chain A, Crystal Structure Analysis Of Squash (C... 26 5.4
pdb|1MMS|A Chain A, Crystal Structure Of The Ribosomal Prot... 25 7.0
pdb|1C8B|A Chain A, Crystal Structure Of A Novel Germinatio... 25 7.0
pdb|1GP2|G Chain G, G Protein Heterotrimer Gi_alpha_1 Beta_... 25 7.0
pdb|1EG0|K Chain K, Fitting Of Components With Known Struct... 25 7.0
pdb|1MJ1|L Chain L, Fitting The Ternary Complex Of Ef-TuTRN... 25 7.0
pdb|487D|L Chain L, Seven Ribosomal Proteins Fitted To A Cr... 25 7.0
pdb|1JQM|A Chain A, Fitting Of L11 Protein And Elongation F... 25 7.0
pdb|1GDE|A Chain A, Crystal Structure Of Pyrococcus Protein... 25 9.2
pdb|1DJU|A Chain A, Crystal Structure Of Aromatic Aminotran... 25 9.2
>pdb|1LD4|A Chain A, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|B Chain B, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|C Chain C, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|D Chain D, Placement Of The Structural Proteins In Sindbis Virus
Length = 264
Score = 29.3 bits (64), Expect = 0.49
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 78 QSAEEKKQKLETETPQEEIITPKPSKKNPKEESHSGDKLHEIKQELKDLFSHLPYKINKV 137
Q + KK K + E +++ PKP K+ D+L ++K E D+ H KV
Sbjct: 78 QPPKPKKPKTQ-EKKKKQPAKPKPGKRQRMALKLEADRLFDVKNEDGDVIGHALAMEGKV 136
Query: 138 EVSLYEPGVL 147
L+ G +
Sbjct: 137 MKPLHVKGTI 146
>pdb|1J5Y|A Chain A, Crystal Structure Of Transcriptional Regulator (Tm1602)
From Thermotoga Maritima At 2.3 A Resolution
Length = 187
Score = 28.5 bits (62), Expect = 0.83
Identities = 15/38 (39%), Positives = 21/38 (54%)
Query: 29 NLQYEVIQTPSKGFLSIGKKEAIILAGVKESVKEIKEE 66
+L Y ++ TP L+ GK L VK + +EIKEE
Sbjct: 62 SLGYNIVATPRGYVLAGGKSGVSRLVAVKHAPEEIKEE 99
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 26.9 bits (58), Expect = 2.4
Identities = 25/97 (25%), Positives = 47/97 (47%), Gaps = 12/97 (12%)
Query: 7 IKAKTLEEALIQASIALNCPIINLQYEVIQTPSKGFLSI-----GKKEAIILAGVKESVK 61
I AK L ++A+ C N Q +T K +++ KKE LA + +K
Sbjct: 410 IPAKILSYNRANRAVAILC---NHQIAPPKTFEKSMMNLQTKIDAKKEQ--LADARRDLK 464
Query: 62 EIKEES--VKETNTKEIHQSAEEKKQKLETETPQEEI 96
K ++ +K+ TK++ +S ++ Q+LE + + E+
Sbjct: 465 SAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEV 501
>pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex Containing An 8-Oxog
Lesion
Length = 564
Score = 26.6 bits (57), Expect = 3.2
Identities = 25/97 (25%), Positives = 47/97 (47%), Gaps = 12/97 (12%)
Query: 7 IKAKTLEEALIQASIALNCPIINLQYEVIQTPSKGFLSI-----GKKEAIILAGVKESVK 61
I AK L ++A+ C N Q +T K +++ KKE LA + +K
Sbjct: 411 IPAKILSYNRANRAVAILC---NHQRAPPKTFEKSMMNLQTKIDAKKEQ--LADARRDLK 465
Query: 62 EIKEES--VKETNTKEIHQSAEEKKQKLETETPQEEI 96
K ++ +K+ TK++ +S ++ Q+LE + + E+
Sbjct: 466 SAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEV 502
>pdb|1A36|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex
Length = 592
Score = 26.6 bits (57), Expect = 3.2
Identities = 25/97 (25%), Positives = 47/97 (47%), Gaps = 12/97 (12%)
Query: 7 IKAKTLEEALIQASIALNCPIINLQYEVIQTPSKGFLSI-----GKKEAIILAGVKESVK 61
I AK L ++A+ C N Q +T K +++ KKE LA + +K
Sbjct: 439 IPAKILSYNRANRAVAILC---NHQRAPPKTFEKSMMNLQTKIDAKKEQ--LADARRDLK 493
Query: 62 EIKEES--VKETNTKEIHQSAEEKKQKLETETPQEEI 96
K ++ +K+ TK++ +S ++ Q+LE + + E+
Sbjct: 494 SAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEV 530
>pdb|1KAG|A Chain A, Crystal Structure Of The Escherichia Coli Shikimate Kinase
I (Arok)
pdb|1KAG|B Chain B, Crystal Structure Of The Escherichia Coli Shikimate Kinase
I (Arok)
Length = 173
Score = 26.6 bits (57), Expect = 3.2
Identities = 19/74 (25%), Positives = 37/74 (49%), Gaps = 11/74 (14%)
Query: 47 KKEAIILAGVKESVKEIKEES----------VKETNTKEIHQSAEEKKQKL-ETETPQEE 95
+K+ I+LA SVK + + ++ T K++ ++ +KK+ L ETP E
Sbjct: 72 EKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLHVETPPRE 131
Query: 96 IITPKPSKKNPKEE 109
++ +++NP E
Sbjct: 132 VLEALANERNPLYE 145
>pdb|1M7X|A Chain A, The X-Ray Crystallographic Structure Of Branching Enzyme
pdb|1M7X|B Chain B, The X-Ray Crystallographic Structure Of Branching Enzyme
pdb|1M7X|C Chain C, The X-Ray Crystallographic Structure Of Branching Enzyme
pdb|1M7X|D Chain D, The X-Ray Crystallographic Structure Of Branching Enzyme
Length = 617
Score = 26.2 bits (56), Expect = 4.1
Identities = 22/87 (25%), Positives = 35/87 (39%), Gaps = 2/87 (2%)
Query: 130 LPYKINKVEVSLYEPGVLLIDID--GEDSALLIGEKGYRYKALSYLLFNWIHPTYGYSIR 187
L Y + EVS + G L I+ G D+ + Y+ S WI +G
Sbjct: 262 LIYNYGRREVSNFLVGNALYWIERFGIDALRVDAVASMIYRDYSRKEGEWIPNEFGGREN 321
Query: 188 LEISTFLQNQEKVMDTQLQSVIMTVHE 214
LE FL+N +++ Q+ + E
Sbjct: 322 LEAIEFLRNTNRILGEQVSGAVTMAEE 348
>pdb|1KXF| Sindbis Virus Capsid, (Wild-Type) Residues 1-264, Tetragonal
Crystal Form (Form Ii)
Length = 264
Score = 26.2 bits (56), Expect = 4.1
Identities = 18/67 (26%), Positives = 28/67 (40%), Gaps = 8/67 (11%)
Query: 81 EEKKQKLETETPQEEIITPKPSKKNPKEESHSGDKLHEIKQELKDLFSHLPYKINKVEVS 140
+EKK+K +T KP K+ D+L ++K E D+ H KV
Sbjct: 88 QEKKKKQPAKT--------KPGKRQRMALKLEADRLFDVKNEDGDVIGHALAMEGKVMKP 139
Query: 141 LYEPGVL 147
L+ G +
Sbjct: 140 LHVKGTI 146
>pdb|1K30|A Chain A, Crystal Structure Analysis Of Squash (Cucurbita Moschata)
Glycerol-3-Phosphate (1)-Acyltransferase
Length = 368
Score = 25.8 bits (55), Expect = 5.4
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 26 PIINLQYEVIQTPSKGFLSIGKKEAIILAGVKESV-KEIKEESVKETNTKEIHQSAEEKK 84
P+ L ++++ PS+ + IG+K I G SV EI E + T H++ EE +
Sbjct: 273 PLALLCHDIMPPPSQVEIEIGEKRVIAFNGAGLSVAPEISFEEIAAT-----HKNPEEVR 327
Query: 85 Q 85
+
Sbjct: 328 E 328
>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 = 25.4 bits (54), Expect = 7.0
Identities = 25/95 (26%), Positives = 43/95 (44%), Gaps = 14/95 (14%)
Query: 3 NFIEIKAKTLEEALIQASIALNCPIINLQYE------VIQTPSKGFLSIGKKEAIILAGV 56
N +E + E +A + L P++ YE +I+TP FL K+A AG+
Sbjct: 33 NIMEFCKRFNAETADKAGMIL--PVVITVYEDKSFTFIIKTPPASFLL---KKA---AGI 84
Query: 57 KESVKEIKEESVKETNTKEIHQSAEEKKQKLETET 91
++ E K + V + K+I + A+ K L +
Sbjct: 85 EKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 119
>pdb|1C8B|A Chain A, Crystal Structure Of A Novel Germination Protease From
Spores Of Bacillus Megaterium: Structural Rearrangements
And Zymogen Activation
pdb|1C8B|B Chain B, Crystal Structure Of A Novel Germination Protease From
Spores Of Bacillus Megaterium: Structural Rearrangements
And Zymogen Activation
Length = 371
Score = 25.4 bits (54), Expect = 7.0
Identities = 13/52 (25%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 30 LQYEVIQTPSKGFLSIGKKEAIILA----GVKESVKEIKEESVKETNTKEIH 77
++ +++ +G +IGKK+ + G++E E +EE+++E KE++
Sbjct: 50 VKISMVEITEEGAEAIGKKKGRYVTLESVGIREQDTEKQEEAMEEVFAKELN 101
>pdb|1GP2|G Chain G, G Protein Heterotrimer Gi_alpha_1 Beta_1 Gamma_2 With Gdp
Bound
pdb|1GG2|G Chain G, G Protein Heterotrimer Mutant Gi_alpha_1(G203a) Beta_1
Gamma_2 With Gdp Bound
Length = 71
Score = 25.4 bits (54), Expect = 7.0
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 53 LAGVKESVKEIKEESVKETNTKEIHQSAEEKKQKLETETPQEEIITPKPSKKNPKEE 109
+A ++ V+++K E+ + ++ ++A + E ++ ++TP P+ +NP E
Sbjct: 9 IAQARKLVEQLKMEA--NIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE 63
>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 = 25.4 bits (54), Expect = 7.0
Identities = 25/95 (26%), Positives = 43/95 (44%), Gaps = 14/95 (14%)
Query: 3 NFIEIKAKTLEEALIQASIALNCPIINLQYE------VIQTPSKGFLSIGKKEAIILAGV 56
N +E + E +A + L P++ YE +I+TP FL K+A AG+
Sbjct: 34 NIMEFCKRFNAETADKAGMIL--PVVITVYEDKSFTFIIKTPPASFLL---KKA---AGI 85
Query: 57 KESVKEIKEESVKETNTKEIHQSAEEKKQKLETET 91
++ E K + V + K+I + A+ K L +
Sbjct: 86 EKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 120
>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 = 25.4 bits (54), Expect = 7.0
Identities = 25/95 (26%), Positives = 43/95 (44%), Gaps = 14/95 (14%)
Query: 3 NFIEIKAKTLEEALIQASIALNCPIINLQYE------VIQTPSKGFLSIGKKEAIILAGV 56
N +E + E +A + L P++ YE +I+TP FL K+A AG+
Sbjct: 34 NIMEFCKRFNAETADKAGMIL--PVVITVYEDKSFTFIIKTPPASFLL---KKA---AGI 85
Query: 57 KESVKEIKEESVKETNTKEIHQSAEEKKQKLETET 91
++ E K + V + K+I + A+ K L +
Sbjct: 86 EKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 120
>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 = 25.4 bits (54), Expect = 7.0
Identities = 25/95 (26%), Positives = 43/95 (44%), Gaps = 14/95 (14%)
Query: 3 NFIEIKAKTLEEALIQASIALNCPIINLQYE------VIQTPSKGFLSIGKKEAIILAGV 56
N +E + E +A + L P++ YE +I+TP FL K+A AG+
Sbjct: 27 NIMEFCKRFNAETADKAGMIL--PVVITVYEDKSFTFIIKTPPASFLL---KKA---AGI 78
Query: 57 KESVKEIKEESVKETNTKEIHQSAEEKKQKLETET 91
++ E K + V + K+I + A+ K L +
Sbjct: 79 EKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 113
>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 = 25.4 bits (54), Expect = 7.0
Identities = 25/95 (26%), Positives = 43/95 (44%), Gaps = 14/95 (14%)
Query: 3 NFIEIKAKTLEEALIQASIALNCPIINLQYE------VIQTPSKGFLSIGKKEAIILAGV 56
N +E + E +A + L P++ YE +I+TP FL K+A AG+
Sbjct: 33 NIMEFCKRFNAETADKAGMIL--PVVITVYEDKSFTFIIKTPPASFLL---KKA---AGI 84
Query: 57 KESVKEIKEESVKETNTKEIHQSAEEKKQKLETET 91
++ E K + V + K+I + A+ K L +
Sbjct: 85 EKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 119
>pdb|1GDE|A Chain A, Crystal Structure Of Pyrococcus Protein A-1 E-Form
pdb|1GDE|B Chain B, Crystal Structure Of Pyrococcus Protein A-1 E-Form
pdb|1GD9|A Chain A, Crystall Structure Of Pyrococcus Protein-A1
pdb|1GD9|B Chain B, Crystall Structure Of Pyrococcus Protein-A1
Length = 389
Score = 25.0 bits (53), Expect = 9.2
Identities = 26/93 (27%), Positives = 38/93 (39%), Gaps = 4/93 (4%)
Query: 2 QNFIEIKAKTLEEALIQASIA--LNCPIINLQYEVIQTPSKGFLSIGKKEAIILAGVKES 59
QN IE KT L+ A+ A + E + P+ F+S A+ILAG K
Sbjct: 79 QNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAP--AVILAGGKPV 136
Query: 60 VKEIKEESVKETNTKEIHQSAEEKKQKLETETP 92
EE N E+ + +K + L +P
Sbjct: 137 EVPTYEEDEFRLNVDELKKYVTDKTRALIINSP 169
>pdb|1DJU|A Chain A, Crystal Structure Of Aromatic Aminotransferase From
Pyrococcus Horikoshii Ot3
pdb|1DJU|B Chain B, Crystal Structure Of Aromatic Aminotransferase From
Pyrococcus Horikoshii Ot3
Length = 388
Score = 25.0 bits (53), Expect = 9.2
Identities = 26/93 (27%), Positives = 38/93 (39%), Gaps = 4/93 (4%)
Query: 2 QNFIEIKAKTLEEALIQASIA--LNCPIINLQYEVIQTPSKGFLSIGKKEAIILAGVKES 59
QN IE KT L+ A+ A + E + P+ F+S A+ILAG K
Sbjct: 78 QNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAP--AVILAGGKPV 135
Query: 60 VKEIKEESVKETNTKEIHQSAEEKKQKLETETP 92
EE N E+ + +K + L +P
Sbjct: 136 EVPTYEEDEFRLNVDELKKYVTDKTRALIINSP 168
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
0.312 0.133 0.358
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,490,279
Number of Sequences: 13198
Number of extensions: 61472
Number of successful extensions: 126
Number of sequences better than 10.0: 18
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 122
Number of HSP's gapped (non-prelim): 19
length of query: 264
length of database: 2,899,336
effective HSP length: 86
effective length of query: 178
effective length of database: 1,764,308
effective search space: 314046824
effective search space used: 314046824
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)