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|15644756|ref|NP_206926.1| ribosomal protein L20
(rpl20) [Helicobacter pylori 26695]
(116 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|O Chain O, Crystal Structure Of The Large Ribosoma... 125 2e-30
pdb|1GYZ|A Chain A, Bacterial Ribosomal Protein L20 From Aq... 64 3e-12
pdb|1HW5|A Chain A, The CapCRP VARIANT T127LS128A >gi|13096... 25 1.7
pdb|1DB9|A Chain A, Protein-Dna Recognition And Dna Deforma... 25 1.7
pdb|1G6N|B Chain B, 2.1 Angstrom Structure Of Cap-Camp >gi|... 25 1.7
pdb|1DB7|A Chain A, Protein-Dna Recognition And Dna Deforma... 25 1.7
pdb|1LB2|A Chain A, Structure Of The E. Coli Alpha C-Termin... 25 1.7
pdb|1CGP|A Chain A, Catabolite Gene Activator Protein Compl... 25 1.7
pdb|1RUO|B Chain B, Cap-Dna Recognition: Interactions Invol... 25 1.7
pdb|1JZS|A Chain A, Isoleucyl-Trna Synthetase Complexed Wit... 25 2.2
pdb|1KF6|B Chain B, E. Coli Quinol-Fumarate Reductase With ... 23 6.5
pdb|1DXL|A Chain A, Dihydrolipoamide Dehydrogenase Of Glyci... 23 8.4
>pdb|1LNR|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 118
Score = 125 bits (313), Expect = 2e-30
Identities = 58/110 (52%), Positives = 82/110 (73%)
Query: 2 RVKTGVVRRRRHKKVLKLARGFYSGRRKHFRKAKEQLERSMYYAFRDRKQKKREFRSLWV 61
R KTG+VRRRRHKKVLK A+GF+ R K +R A + L + Y +RDR+ KKR+FR LW+
Sbjct: 3 RAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWI 62
Query: 62 VRINAACRMHNTSYSRFMHALKVANIELDRKVLADMAMNDMQAFTSVLES 111
RINA R+H +YS F++ LK ANI+L+RKVLAD+A + +AF +++++
Sbjct: 63 QRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDA 112
>pdb|1GYZ|A Chain A, Bacterial Ribosomal Protein L20 From Aquifex Aeolicus
Length = 60
Score = 64.3 bits (155), Expect = 3e-12
Identities = 32/56 (57%), Positives = 40/56 (71%)
Query: 61 VVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMAMNDMQAFTSVLESVKEHL 116
+ RINAA R + +YS F++ LK A IELDRK+LADMA+ D QAF V+ VKE L
Sbjct: 2 IARINAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEAL 57
>pdb|1HW5|A Chain A, The CapCRP VARIANT T127LS128A
pdb|1HW5|B Chain B, The CapCRP VARIANT T127LS128A
Length = 210
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 83 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 122
>pdb|1DB9|A Chain A, Protein-Dna Recognition And Dna Deformation Revealed In
Crystal Structures Of Cap-Dna Complexes
Length = 200
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 75 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 114
>pdb|1G6N|B Chain B, 2.1 Angstrom Structure Of Cap-Camp
pdb|1G6N|A Chain A, 2.1 Angstrom Structure Of Cap-Camp
pdb|2CGP|A Chain A, Catabolite Gene Activator ProteinDNA COMPLEX,
ADENOSINE-3', 5'-Cyclic-Monophosphate
Length = 210
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 83 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 122
>pdb|1DB7|A Chain A, Protein-Dna Recognition And Dna Deformation Revealed In
Crystal Structures Of Cap-Dna Complexes
pdb|1DB8|A Chain A, Protein-Dna Recognition And Dna Deformation Revealed In
Crystal Structures Of Cap-Dna Complexes
pdb|1DBC|A Chain A, Protein-Dna Recognition And Dna Deformation Revealed In
Crystal Structures Of Cap-Dna Complexes
pdb|1DBC|B Chain B, Protein-Dna Recognition And Dna Deformation Revealed In
Crystal Structures Of Cap-Dna Complexes
Length = 200
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 75 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 114
>pdb|1LB2|A Chain A, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
Polymerase In Complex With Cap And Dna
pdb|1RUN|A Chain A, Cap-Dna Recognition: Interactions Involving Aromatic Amino
Acids
pdb|1J59|A Chain A, Catabolite Gene Activator Protein (Cap)DNA COMPLEX +
Adenosine-3',5'-Cyclic-Monophosphate
pdb|1J59|B Chain B, Catabolite Gene Activator Protein (Cap)DNA COMPLEX +
Adenosine-3',5'-Cyclic-Monophosphate
pdb|1RUN|B Chain B, Cap-Dna Recognition: Interactions Involving Aromatic Amino
Acids
Length = 209
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 82 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 121
>pdb|1CGP|A Chain A, Catabolite Gene Activator Protein Complex With Dna
(Cap-Dna Complex)
pdb|1CGP|B Chain B, Catabolite Gene Activator Protein Complex With Dna
(Cap-Dna Complex)
Length = 205
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 82 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 121
>pdb|1RUO|B Chain B, Cap-Dna Recognition: Interactions Involving Aromatic Amino
Acids
pdb|1RUO|A Chain A, Cap-Dna Recognition: Interactions Involving Aromatic Amino
Acids
Length = 209
Score = 25.4 bits (54), Expect = 1.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 57 RSLWVVRINAACRMHNTSYSRFMHALKVANIELDRKVLADMA 98
RS WV R AC + SY +F ++V N ++ ++ A MA
Sbjct: 82 RSAWV-RAKTACEVAEISYKKFRQLIQV-NPDILMRLSAQMA 121
>pdb|1JZS|A Chain A, Isoleucyl-Trna Synthetase Complexed With Mupirocin
pdb|1ILE| Isoleucyl-Trna Synthetase
pdb|1JZQ|A Chain A, Isoleucyl-Trna Synthetase Complexed With Isoleucyl-
Adenylate Analogue
Length = 821
Score = 25.0 bits (53), Expect = 2.2
Identities = 17/64 (26%), Positives = 29/64 (44%), Gaps = 10/64 (15%)
Query: 18 KLARGFYSGRRK----HFRKAKEQLERSMYYAFRDRKQKKREFRSLWVVRINAACRMHNT 73
K RG+Y+ RR H + ++E+ + + KRE + + R N ACR
Sbjct: 71 KTMRGYYAPRRAGWDTHGLPVELEVEKKLGL------KSKREIEAYGIERFNQACRESVF 124
Query: 74 SYSR 77
+Y +
Sbjct: 125 TYEK 128
>pdb|1KF6|B Chain B, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1KF6|N Chain N, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1L0V|B Chain B, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|1L0V|N Chain N, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|1KFY|B Chain B, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
pdb|1KFY|N Chain N, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
Length = 243
Score = 23.5 bits (49), Expect = 6.5
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 67 ACRMHNTSYSRFMHALKVANIELDRKVLADMAMNDMQAFTSVLESVKEHL 116
AC+ Y+ M +AN ++R ++ DM F LE++K ++
Sbjct: 76 ACKTFLRDYTDGMKVEALANFPIERDLVVDMT-----HFIESLEAIKPYI 120
>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 = 23.1 bits (48), Expect = 8.4
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 71 HNTSYSRFMHALKVANIELD 90
H +S H +KV+N+E+D
Sbjct: 64 HEAKHSFANHGVKVSNVEID 83
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
0.328 0.134 0.384
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 524,409
Number of Sequences: 13198
Number of extensions: 15855
Number of successful extensions: 43
Number of sequences better than 10.0: 12
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 40
Number of HSP's gapped (non-prelim): 12
length of query: 116
length of database: 2,899,336
effective HSP length: 76
effective length of query: 40
effective length of database: 1,896,288
effective search space: 75851520
effective search space used: 75851520
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)