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|15644924|ref|NP_207094.1| ribosomal protein L21
(rpl21) [Helicobacter pylori 26695]
(104 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|P Chain P, Crystal Structure Of The Large Ribosoma... 55 1e-09
pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 26 0.76
pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomeras... 26 0.76
pdb|1GHT|A Chain A, Solution Structure Of The Catalytic Dom... 26 0.76
pdb|2RSL|B Chain B, Gamma Delta Resolvase (Large Fragment, ... 26 0.76
pdb|1A36|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 26 0.76
pdb|1GDT|A Chain A, Crystal Structure Of A Site-Specific Re... 26 0.76
pdb|1A26| The Catalytic Fragment Of Poly(Adp-Ribose) Poly... 23 4.9
pdb|1EFY|A Chain A, Crystal Structure Of The Catalytic Frag... 23 4.9
pdb|1LNR|O Chain O, Crystal Structure Of The Large Ribosoma... 23 4.9
pdb|1A5C|A Chain A, Fructose-1,6-Bisphosphate Aldolase From... 23 6.4
pdb|1I7E|A Chain A, C-Terminal Domain Of Mouse Brain Tubby ... 22 8.4
pdb|1C8Z|A Chain A, C-Terminal Domain Of Mouse Brain Tubby ... 22 8.4
>pdb|1LNR|P Chain P, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 100
Score = 55.1 bits (131), Expect = 1e-09
Identities = 31/100 (31%), Positives = 55/100 (55%), Gaps = 3/100 (3%)
Query: 3 YAIFKHGGKQYKVVEGDIVLLDKMDKEPKALVELVEVLAVSKEGKLSCGKPFVNGAKIEA 62
+AI + GGKQY+V EGD++ ++ + E + VE+ A+ G+ + ++A
Sbjct: 2 FAIIQTGGKQYRVSEGDVIRVESLQGEAG---DKVELKALFVGGEQTVFGEDAGKYTVQA 58
Query: 63 EVINEGRGKKVITFKKRRRKDSKTKRGFRRDFTRVRITKI 102
EV+ GRGKK+ K + + + G R++FT ++I I
Sbjct: 59 EVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGI 98
>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 = 25.8 bits (55), Expect = 0.76
Identities = 14/49 (28%), Positives = 29/49 (58%), Gaps = 1/49 (2%)
Query: 31 KALVELVEVLAVSKEGKLSCGKPFVNGAKIEAEVINEGRGKKVITFKKR 79
K+++ L + KE +L+ + + AK +A+V+ + + KKV+ KK+
Sbjct: 441 KSMMNLQTKIDAKKE-QLADARRDLKSAKADAKVMKDAKTKKVVESKKK 488
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 25.8 bits (55), Expect = 0.76
Identities = 14/49 (28%), Positives = 29/49 (58%), Gaps = 1/49 (2%)
Query: 31 KALVELVEVLAVSKEGKLSCGKPFVNGAKIEAEVINEGRGKKVITFKKR 79
K+++ L + KE +L+ + + AK +A+V+ + + KKV+ KK+
Sbjct: 440 KSMMNLQTKIDAKKE-QLADARRDLKSAKADAKVMKDAKTKKVVESKKK 487
>pdb|1GHT|A Chain A, Solution Structure Of The Catalytic Domain Of Gamma
Delta Resolvase
pdb|1HX7|A Chain A, Solution Structure Of The Catalytic Domain Of Gamma
Delta Resolvase
Length = 105
Score = 25.8 bits (55), Expect = 0.76
Identities = 8/27 (29%), Positives = 20/27 (73%)
Query: 14 KVVEGDIVLLDKMDKEPKALVELVEVL 40
KV EGD++L+ K+D+ + ++++++
Sbjct: 54 KVEEGDVILVKKLDRLGRDTADMIQLI 80
>pdb|2RSL|B Chain B, Gamma Delta Resolvase (Large Fragment, Catalytic Domain)
pdb|2RSL|C Chain C, Gamma Delta Resolvase (Large Fragment, Catalytic Domain)
pdb|2RSL|A Chain A, Gamma Delta Resolvase (Large Fragment, Catalytic Domain)
pdb|1GDR| Gamma Delta Resolvase
Length = 140
Score = 25.8 bits (55), Expect = 0.76
Identities = 8/27 (29%), Positives = 20/27 (73%)
Query: 14 KVVEGDIVLLDKMDKEPKALVELVEVL 40
KV EGD++L+ K+D+ + ++++++
Sbjct: 54 KVEEGDVILVKKLDRLGRDTADMIQLI 80
>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 = 25.8 bits (55), Expect = 0.76
Identities = 14/49 (28%), Positives = 29/49 (58%), Gaps = 1/49 (2%)
Query: 31 KALVELVEVLAVSKEGKLSCGKPFVNGAKIEAEVINEGRGKKVITFKKR 79
K+++ L + KE +L+ + + AK +A+V+ + + KKV+ KK+
Sbjct: 469 KSMMNLQTKIDAKKE-QLADARRDLKSAKADAKVMKDAKTKKVVESKKK 516
>pdb|1GDT|A Chain A, Crystal Structure Of A Site-Specific Recombinase,
Gamma-Delta Resolvase Complexed With A 34 Bp Cleavage
Site
pdb|1GDT|B Chain B, Crystal Structure Of A Site-Specific Recombinase,
Gamma-Delta Resolvase Complexed With A 34 Bp Cleavage
Site
Length = 183
Score = 25.8 bits (55), Expect = 0.76
Identities = 8/27 (29%), Positives = 20/27 (73%)
Query: 14 KVVEGDIVLLDKMDKEPKALVELVEVL 40
KV EGD++L+ K+D+ + ++++++
Sbjct: 54 KVEEGDVILVKKLDRLGRDTADMIQLI 80
>pdb|1A26| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase Complexed
With Carba-Nad
pdb|1PAX| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase Complexed
With 3,4-Dihydro-5-Methyl-Isoquinolinone
pdb|2PAX| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase Complexed
With 4-Amino-1,8-Naphthalimide
pdb|3PAX| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase Complexed
With 3-Methoxybenzamide
pdb|4PAX| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase Complexed
With 8-Hydroxy-2-Methyl-3-Hydro-Quinazolin-4-One
pdb|2PAW| The Catalytic Fragment Of Poly(Adp-Ribose) Polymerase
Length = 361
Score = 23.1 bits (48), Expect = 4.9
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 16/58 (27%)
Query: 13 YKVVEGDIVLLDKMDKEPKAL----------------VELVEVLAVSKEGKLSCGKPF 54
Y+ + DI ++DK +E K + +++VE+ + +EG+ KPF
Sbjct: 141 YEKLRTDIKVVDKDSEEAKIIKQYVKNTHAATHNAYDLKVVEIFRIEREGESQRYKPF 198
>pdb|1EFY|A Chain A, Crystal Structure Of The Catalytic Fragment Of Poly (Adp-
Ribose) Polymerase Complexed With A Benzimidazole
Inhibitor
Length = 350
Score = 23.1 bits (48), Expect = 4.9
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 16/58 (27%)
Query: 13 YKVVEGDIVLLDKMDKEPKAL----------------VELVEVLAVSKEGKLSCGKPF 54
Y+ + DI ++DK +E K + +++VE+ + +EG+ KPF
Sbjct: 133 YEKLRTDIKVVDKDSEEAKIIKQYVKNTHAATHNAYDLKVVEIFRIEREGESQRYKPF 190
>pdb|1LNR|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 118
Score = 23.1 bits (48), Expect = 4.9
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 1 MSYAIFKHGGKQYKVVEGDIVLLDKMDKEPKALVELVE 38
M+Y+ F +G K+ + VL D +EP+A LV+
Sbjct: 74 MNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVD 111
>pdb|1A5C|A Chain A, Fructose-1,6-Bisphosphate Aldolase From Plasmodium
Falciparum
pdb|1A5C|B Chain B, Fructose-1,6-Bisphosphate Aldolase From Plasmodium
Falciparum
Length = 368
Score = 22.7 bits (47), Expect = 6.4
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 20 IVLLDKMDKEPKALVELVEVLAVSKEGKLSCGKPFVNGAKIEAEVINEGRGKKVITFKKR 79
+V L E +A V L + A+ G F G ++A V+N +GKK K R
Sbjct: 274 VVFLSGGQSEEEASVNLNSINAL---GPHPWALTFSYGRALQASVLNTWQGKKENVAKAR 330
>pdb|1I7E|A Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein Bound To
Phosphatidylinositol 4,5-Bis-Phosphate
Length = 265
Score = 22.3 bits (46), Expect = 8.4
Identities = 10/17 (58%), Positives = 11/17 (63%)
Query: 70 GKKVITFKKRRRKDSKT 86
GKKV R+RK SKT
Sbjct: 52 GKKVFLLAGRKRKKSKT 68
>pdb|1C8Z|A Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein
Length = 265
Score = 22.3 bits (46), Expect = 8.4
Identities = 10/17 (58%), Positives = 11/17 (63%)
Query: 70 GKKVITFKKRRRKDSKT 86
GKKV R+RK SKT
Sbjct: 52 GKKVFLLAGRKRKKSKT 68
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
0.319 0.139 0.379
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 560,815
Number of Sequences: 13198
Number of extensions: 19722
Number of successful extensions: 44
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 33
Number of HSP's gapped (non-prelim): 13
length of query: 104
length of database: 2,899,336
effective HSP length: 80
effective length of query: 24
effective length of database: 1,843,496
effective search space: 44243904
effective search space used: 44243904
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)