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|15644714|ref|NP_206884.1| ribosomal protein L13
(rpl13) [Helicobacter pylori 26695]
(141 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|H Chain H, Crystal Structure Of The Large Ribosoma... 129 2e-31
pdb|1K8A|K Chain K, Co-Crystal Structure Of Carbomycin A Bo... 37 0.001
pdb|1KSH|B Chain B, Complex Of Arl2 And Pde Delta, Crystal ... 31 0.061
pdb|1KSG|B Chain B, Complex Of Arl2 And Pde Delta, Crystal ... 30 0.10
pdb|1KSJ|B Chain B, Complex Of Arl2 And Pde Delta, Crystal ... 27 0.68
pdb|2CD0|A Chain A, Structure Of Human Lambda-6 Light Chain... 25 2.6
pdb|1QH8|C Chain C, Nitrogenase Mofe Protein From Klebsiell... 25 4.4
pdb|1H1L|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiel... 25 4.4
pdb|1H2T|C Chain C, Structure Of The Human Nuclear Cap-Bind... 24 5.8
pdb|1H6K|C Chain C, Nuclear Cap Binding Complex >gi|1598838... 24 5.8
pdb|1CJ0|A Chain A, Crystal Structure Of Rabbit Cytosolic S... 24 5.8
pdb|1H2V|C Chain C, Structure Of The Human Nuclear Cap-Bind... 24 5.8
pdb|1ML7|A Chain A, Crystal Structure Of Nitrophorin 4 Comp... 24 7.5
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex >g... 24 7.5
pdb|1DQD|H Chain H, Crystal Structure Of Fab Hgr-2 F6, A Co... 23 9.8
pdb|1NP1|A Chain A, Crystal Structure Of The Complex Of Nit... 23 9.8
pdb|1CD0|B Chain B, Structure Of Human Lamda-6 Light Chain ... 23 9.8
>pdb|1LNR|H Chain H, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 174
Score = 129 bits (323), Expect = 2e-31
Identities = 65/123 (52%), Positives = 86/123 (69%)
Query: 12 RDWVVLDAKDKVFGRLITEIAVLLRGKHRPFYTPNVDCGDFVVVINANKVKFSGMKLEDK 71
++WVV+DA GRL T IA +RGKHRP +TPN+ GDFVVVINA +V +G KL+DK
Sbjct: 39 QNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDK 98
Query: 72 EYFTHSGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPKTKLGKAMIKKLKVYRDDKHPH 131
Y ++GY G K++T +E L K PE++ AV GMLPK + G+AM +LKVY + HPH
Sbjct: 99 VYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPH 158
Query: 132 TAQ 134
+AQ
Sbjct: 159 SAQ 161
>pdb|1K8A|K Chain K, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|K Chain K, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|K Chain K, Co-Crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|K Chain K, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|K Chain K, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1JJ2|I Chain I, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|I Chain I, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1FFK|G Chain G, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|M Chain M, 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 = 145
Score = 36.6 bits (83), Expect = 0.001
Identities = 26/111 (23%), Positives = 51/111 (45%), Gaps = 17/111 (15%)
Query: 15 VVLDAKDKVFGRLITEIAVLLRGKHRPFYTPNVDCGDFVVVINANKVKFSGMKLEDKEYF 74
V++DA+D + GR+ +++A G+ V V+NA + +G + + E +
Sbjct: 10 VIVDARDCIMGRVASQVA------------EQALDGETVAVVNAERAVITGREEQIVEKY 57
Query: 75 THSGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLP-KTKLGKAMIKKLKVY 124
G+ K P+ ++ +RGMLP K + G+ + ++VY
Sbjct: 58 EKRVDIGNDNG----YFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVY 104
>pdb|1KSH|B Chain B, Complex Of Arl2 And Pde Delta, Crystal Form 2 (Native)
Length = 152
Score = 30.8 bits (68), Expect = 0.061
Identities = 22/68 (32%), Positives = 32/68 (46%), Gaps = 9/68 (13%)
Query: 60 KVKFSGMKLEDKEYFTHSGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPKTKLGKAMIK 119
KV F G LE E+F G+ + T Q ++E APE M+P + L +I
Sbjct: 81 KVYFKGQXLE--EWFFEFGFVIPNSTNTWQSLIEAAPES-------QMMPASVLTGNVII 131
Query: 120 KLKVYRDD 127
+ K + DD
Sbjct: 132 ETKFFDDD 139
>pdb|1KSG|B Chain B, Complex Of Arl2 And Pde Delta, Crystal Form 1
Length = 152
Score = 30.0 bits (66), Expect = 0.10
Identities = 22/68 (32%), Positives = 32/68 (46%), Gaps = 9/68 (13%)
Query: 60 KVKFSGMKLEDKEYFTHSGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPKTKLGKAMIK 119
KV F G LE E+F G+ + T Q ++E APE M+P + L +I
Sbjct: 81 KVYFKGQCLE--EWFFEFGFVIPNSTNTWQSLIEAAPES-------QMMPASVLTGNVII 131
Query: 120 KLKVYRDD 127
+ K + DD
Sbjct: 132 ETKFFDDD 139
>pdb|1KSJ|B Chain B, Complex Of Arl2 And Pde Delta, Crystal Form 2 (Semet)
Length = 152
Score = 27.3 bits (59), Expect = 0.68
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 60 KVKFSGMKLEDKEYFTHSGYFGSTKSKTLQEMLEKAPE 97
KV F G LE E+F G+ + T Q ++E APE
Sbjct: 81 KVYFKGQXLE--EWFFEFGFVIPNSTNTWQSLIEAAPE 116
>pdb|2CD0|A Chain A, Structure Of Human Lambda-6 Light Chain Dimer Wil
pdb|2CD0|B Chain B, Structure Of Human Lambda-6 Light Chain Dimer Wil
Length = 111
Score = 25.4 bits (54), Expect = 2.6
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 33 VLLRGKHRPFYTPNVDCGDFVVVINANKVKFSGMKLEDK-EYFTHS 77
V+ HRP P+ G N+ + SG+K ED+ +Y+ S
Sbjct: 48 VIFEDDHRPSGVPDRFSGSVDTSSNSASLTISGLKTEDEADYYCQS 93
>pdb|1QH8|C Chain C, Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-
Crystallized (Mixed Oxidation) State
pdb|1QH8|A Chain A, Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-
Crystallized (Mixed Oxidation) State
pdb|1QH1|C Chain C, Nitrogenase Mofe Protein From Klebsiella Pneumoniae,
Phenosafranin Oxidized State
pdb|1QGU|C Chain C, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae,
Dithionite-Reduced State
pdb|1QGU|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae,
Dithionite-Reduced State
pdb|1QH1|A Chain A, Nitrogenase Mofe Protein From Klebsiella Pneumoniae,
Phenosafranin Oxidized State
Length = 478
Score = 24.6 bits (52), Expect = 4.4
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 8 NDIVRDWVVLDAKDKVFGRLITEIAVL 34
ND+VRDW++ + + + F ++A++
Sbjct: 198 NDVVRDWILNNREGQPFETTPYDVAII 224
>pdb|1H1L|A Chain A, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv
Mutant
pdb|1H1L|C Chain C, Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv
Mutant
Length = 481
Score = 24.6 bits (52), Expect = 4.4
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 8 NDIVRDWVVLDAKDKVFGRLITEIAVL 34
ND+VRDW++ + + + F ++A++
Sbjct: 198 NDVVRDWILNNREGQPFETTPYDVAII 224
>pdb|1H2T|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|A Chain A, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|B Chain B, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
Length = 723
Score = 24.3 bits (51), Expect = 5.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 82 STKSKTLQEMLEKAPEKLYHLAVRGMLPKT 111
S K K ++E+LEK YH + ++P T
Sbjct: 424 SPKPKFVREVLEKCMRLSYHQRILDIVPPT 453
>pdb|1H6K|C Chain C, Nuclear Cap Binding Complex
pdb|1H6K|B Chain B, Nuclear Cap Binding Complex
pdb|1H6K|A Chain A, Nuclear Cap Binding Complex
Length = 757
Score = 24.3 bits (51), Expect = 5.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 82 STKSKTLQEMLEKAPEKLYHLAVRGMLPKT 111
S K K ++E+LEK YH + ++P T
Sbjct: 424 SPKPKFVREVLEKCMRLSYHQRILDIVPPT 453
>pdb|1CJ0|A Chain A, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
pdb|1CJ0|B Chain B, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
Length = 470
Score = 24.3 bits (51), Expect = 5.8
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 70 DKEYFTHSGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPKTKL-----GKAMIK--KLK 122
DK SG T + T + +LEK +K+ H RG+ ++ +A +K K K
Sbjct: 378 DKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEK 437
Query: 123 VYRDDKHPHTAQTSKKDAK 141
+ D+KH + +++ +
Sbjct: 438 LAGDEKHQRAVRALRQEVE 456
>pdb|1H2V|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
Length = 771
Score = 24.3 bits (51), Expect = 5.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 82 STKSKTLQEMLEKAPEKLYHLAVRGMLPKT 111
S K K ++E+LEK YH + ++P T
Sbjct: 424 SPKPKFVREVLEKCMRLSYHQRILDIVPPT 453
>pdb|1ML7|A Chain A, Crystal Structure Of Nitrophorin 4 Complexed With 4-
Iodopyrazole
pdb|1KOI|A Chain A, Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus
Complexed With Nitric Oxide At 1.08 A Resolution
pdb|1D2U|A Chain A, 1.15 A Crystal Structure Of Nitrophorin 4 From Rhodnius
Prolixus
pdb|1IKJ|A Chain A, 1.27 A Crystal Structure Of Nitrophorin 4 From Rhodnius
Prolixus Complexed With Imidazole
pdb|1ERX|A Chain A, Crystal Structure Of Nitrophorin 4 Complexed With No
pdb|1D3S|A Chain A, 1.4 A Crystal Structure Of Nitrophorin 4 From Rhodnius
Prolixis At Ph5.6.
pdb|1IKE|A Chain A, Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus
Complexed With Histamine At 1.5 A Resolution
pdb|1NP4|A Chain A, Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus
pdb|1EQD|A Chain A, Crystal Structure Of Nitrophorin 4 Complexed With Cn
Length = 184
Score = 23.9 bits (50), Expect = 7.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 39 HRPFYTPNVDCGDFVVVINANKVKFSGMKLE 69
H + N D GD V+N NK +G K++
Sbjct: 120 HTCLHKGNKDLGDLYAVLNRNKDAAAGDKVK 150
>pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
Length = 1224
Score = 23.9 bits (50), Expect = 7.5
Identities = 14/63 (22%), Positives = 27/63 (42%)
Query: 77 SGYFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPKTKLGKAMIKKLKVYRDDKHPHTAQTS 136
SG F K +T + + E Y L ++ GK I +L + K+ + ++ +
Sbjct: 126 SGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEAT 185
Query: 137 KKD 139
+ D
Sbjct: 186 ESD 188
>pdb|1DQD|H Chain H, Crystal Structure Of Fab Hgr-2 F6, A Competitive
Antagonist Of The Glucagon Receptor
Length = 222
Score = 23.5 bits (49), Expect = 9.8
Identities = 16/52 (30%), Positives = 25/52 (47%), Gaps = 5/52 (9%)
Query: 62 KFSGMKLEDKEYFTHSG---YFGSTKSKTLQEMLEKAPEKLYHLAVRGMLPK 110
KF G KLE Y ++SG Y S KS+ + Y+L ++ + P+
Sbjct: 39 KFPGNKLEYMGYISYSGSTYYNPSLKSRL--SITRDTSRNQYYLQLKSVTPE 88
>pdb|1NP1|A Chain A, Crystal Structure Of The Complex Of Nitrophorin 1 From
Rhodnius Prolixus With Histamine
pdb|1NP1|B Chain B, Crystal Structure Of The Complex Of Nitrophorin 1 From
Rhodnius Prolixus With Histamine
pdb|2NP1|A Chain A, Crystal Structure Of Nitrophorin 1 From Rhodnius Prolixus
pdb|2NP1|B Chain B, Crystal Structure Of Nitrophorin 1 From Rhodnius Prolixus
pdb|4NP1|A Chain A, Nitrophorin 1 Complex With Nitric Oxide
pdb|4NP1|B Chain B, Nitrophorin 1 Complex With Nitric Oxide
pdb|3NP1|A Chain A, Crystal Structure Of The Complex Of Nitrophorin 1 From
Rhodnius Prolixus With Cyanide
pdb|3NP1|B Chain B, Crystal Structure Of The Complex Of Nitrophorin 1 From
Rhodnius Prolixus With Cyanide
Length = 184
Score = 23.5 bits (49), Expect = 9.8
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 39 HRPFYTPNVDCGDFVVVINANKVKFSGMKLE 69
H + N D GD V+N NK +G K++
Sbjct: 120 HTCLHKGNKDLGDLYAVLNRNKDTNAGDKVK 150
>pdb|1CD0|B Chain B, Structure Of Human Lamda-6 Light Chain Dimer Jto
pdb|1CD0|A Chain A, Structure Of Human Lamda-6 Light Chain Dimer Jto
Length = 111
Score = 23.5 bits (49), Expect = 9.8
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 31 IAVLLRGKHRPFYTPNVDCGDFVVVINANKVKFSGMKLEDK-EYFTHS 77
I V+ RP P+ G N+ + SG+K ED+ +Y+ S
Sbjct: 46 ITVIYEDNQRPSGVPDRFAGSIDRSSNSASLTISGLKTEDEADYYCQS 93
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 0.135 0.390
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 823,267
Number of Sequences: 13198
Number of extensions: 32913
Number of successful extensions: 109
Number of sequences better than 10.0: 17
Number of HSP's better than 10.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 98
Number of HSP's gapped (non-prelim): 17
length of query: 141
length of database: 2,899,336
effective HSP length: 79
effective length of query: 62
effective length of database: 1,856,694
effective search space: 115115028
effective search space used: 115115028
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: 49 (23.5 bits)