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|15645931|ref|NP_208110.1| ribosomal protein L4 (rpl4)
[Helicobacter pylori 26695]
(215 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|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4 100 1e-22
pdb|1JZX|K Chain K, Structural Basis For The Interaction Of... 86 3e-18
pdb|1LNR|C Chain C, Crystal Structure Of The Large Ribosoma... 86 3e-18
pdb|8ACN| Aconitase (E.C.4.2.1.3) Complex With Nitroisoci... 31 0.096
pdb|1AMJ| Aconitase (E.C.4.2.1.3) Complexed With Sulfate ... 31 0.096
pdb|1NIS| Aconitase (E.C.4.2.1.3) Complex With Nitrocitra... 29 0.36
pdb|1JC9|A Chain A, Tachylectin 5a From Tachypleus Tridenta... 27 1.4
pdb|1DYK|A Chain A, Laminin Alpha 2 Chain Lg4-5 Domain Pair 27 1.4
pdb|1QU0|C Chain C, Crystal Structure Of The Fifth Laminin ... 27 1.4
pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyos... 27 2.4
pdb|1JRY|A Chain A, Crystal Structure Of Arg402lys Mutant F... 26 3.1
pdb|1QJH|A Chain A, Protein Aggregation And Alzheimer's Dis... 26 3.1
pdb|1M64|A Chain A, Crystal Structure Of Q363f Mutant Flavo... 26 4.0
pdb|1KSS|A Chain A, Crystal Structure Of His505ala Mutant F... 26 4.0
pdb|1QJD|A Chain A, Flavocytochrome C3 From Shewanella Frig... 26 4.0
pdb|1KSU|A Chain A, Crystal Structure Of His505tyr Mutant F... 26 4.0
pdb|1E39|A Chain A, Flavocytochrome C3 From Shewanella Frig... 26 4.0
pdb|1CQM|A Chain A, Protein Aggregation And Alzheimer's Dis... 26 4.0
pdb|1DGM|A Chain A, Crystal Structure Of Adenosine Kinase F... 25 5.3
pdb|2DPM|A Chain A, Dpnm Dna Adenine Methyltransferase From... 25 6.9
>pdb|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4
Length = 225
Score = 100 bits (250), Expect = 1e-22
Identities = 64/131 (48%), Positives = 81/131 (60%), Gaps = 7/131 (5%)
Query: 31 LYLYVKHYLSSARANTAKSKNRAEVSGGGRKPWAQKGGGRARAGSITSPVFVGGGVSHGA 90
++ YV LS+ RA TA +K R EVSGGGRKPW QK GRAR GSI SP++ GGV HG
Sbjct: 32 MWRYVDMQLSNRRAGTASTKTRGEVSGGGRKPWPQKHTGRARHGSIRSPIWRHGGVVHG- 90
Query: 91 TNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKHLTKEANQMF 150
R+++ K+NKK K+LAL AL K + NKL V++ + + E K K L KE Q
Sbjct: 91 PKPRDWSKKLNKKMKKLALRSALSVKYRENKLLVLDDLKL----ERPKTKSL-KEILQNL 145
Query: 151 QALEQRDTLFV 161
Q L + TL V
Sbjct: 146 Q-LSDKKTLIV 155
>pdb|1JZX|K Chain K, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1K01|K Chain K, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1J5A|K Chain K, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1JZY|K Chain K, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
pdb|1JZZ|K Chain K, Structural Basis For The Interaction Of Antibiotics With
The Peptidyl Transferase Center In Eubacteria
Length = 205
Score = 85.9 bits (211), Expect = 3e-18
Identities = 63/200 (31%), Positives = 103/200 (51%), Gaps = 10/200 (5%)
Query: 16 SVELPKRYESINSHNLYLYVKHYLSSARANTAKSKNRAEVSGGGRKPWAQKGGGRARAGS 75
++ELP +NS L+ V L+S R TA ++ RA+VS GRK + QKG G AR G
Sbjct: 14 TIELP--LPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGD 71
Query: 76 ITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVE 135
+ P FVGGGV+ G R+Y+ + ++ ++L L A+ + + KL V+ I
Sbjct: 72 RSVPTFVGGGVAFG-PKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDI----A 126
Query: 136 DNKRKHLTKEANQMFQALEQRDTLFVCMNMDEYTELAFSNLKKCLIVDVSELNAYLLAAF 195
D K K+ A Q L+ + + + + DE T A N+ ++ V+ +N Y +
Sbjct: 127 DAKTKNFISWAKQ--NGLDGTEKVLLVTD-DENTRRAARNVSWVSVLPVAGVNVYDILRH 183
Query: 196 SSVVMEEAAFQHVVQDKTEE 215
+V++ AA + V ++ EE
Sbjct: 184 DRLVIDAAALEIVEEEAGEE 203
>pdb|1LNR|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
Length = 204
Score = 85.9 bits (211), Expect = 3e-18
Identities = 63/200 (31%), Positives = 103/200 (51%), Gaps = 10/200 (5%)
Query: 16 SVELPKRYESINSHNLYLYVKHYLSSARANTAKSKNRAEVSGGGRKPWAQKGGGRARAGS 75
++ELP +NS L+ V L+S R TA ++ RA+VS GRK + QKG G AR G
Sbjct: 13 TIELP--LPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGD 70
Query: 76 ITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVE 135
+ P FVGGGV+ G R+Y+ + ++ ++L L A+ + + KL V+ I
Sbjct: 71 RSVPTFVGGGVAFG-PKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDI----A 125
Query: 136 DNKRKHLTKEANQMFQALEQRDTLFVCMNMDEYTELAFSNLKKCLIVDVSELNAYLLAAF 195
D K K+ A Q L+ + + + + DE T A N+ ++ V+ +N Y +
Sbjct: 126 DAKTKNFISWAKQ--NGLDGTEKVLLVTD-DENTRRAARNVSWVSVLPVAGVNVYDILRH 182
Query: 196 SSVVMEEAAFQHVVQDKTEE 215
+V++ AA + V ++ EE
Sbjct: 183 DRLVIDAAALEIVEEEAGEE 202
>pdb|8ACN| Aconitase (E.C.4.2.1.3) Complex With Nitroisocitrate
pdb|1ACO| Aconitase (Mitochondrial) (E.C.4.2.1.3) Complex With
Transaconitate
pdb|1FGH| Complex With 4-Hydroxy-Trans-Aconitate
Length = 754
Score = 31.2 bits (69), Expect = 0.096
Identities = 25/77 (32%), Positives = 38/77 (48%), Gaps = 3/77 (3%)
Query: 67 GGGRARAGSITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVE 126
G G +R S P F+GG + R + + KKQ L L +A + A NK+ V+
Sbjct: 639 GEGSSREHSALEPRFLGGRAIITKSFARIHETNL-KKQGLLPLTFA--DPADYNKIHPVD 695
Query: 127 KIAIKGVVEDNKRKHLT 143
K+ I+G+ + K LT
Sbjct: 696 KLTIQGLKDFAPGKPLT 712
>pdb|1AMJ| Aconitase (E.C.4.2.1.3) Complexed With Sulfate And Hydroxide
pdb|1AMI| Aconitase (E.C.4.2.1.3) Complexed With Alpha-Methyl-Isocitrate
Length = 754
Score = 31.2 bits (69), Expect = 0.096
Identities = 25/77 (32%), Positives = 38/77 (48%), Gaps = 3/77 (3%)
Query: 67 GGGRARAGSITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVE 126
G G +R S P F+GG + R + + KKQ L L +A + A NK+ V+
Sbjct: 639 GEGSSREHSALEPRFLGGRAIITKSFARIHETNL-KKQGLLPLTFA--DPADYNKIHPVD 695
Query: 127 KIAIKGVVEDNKRKHLT 143
K+ I+G+ + K LT
Sbjct: 696 KLTIQGLKDFAPGKPLT 712
>pdb|1NIS| Aconitase (E.C.4.2.1.3) Complex With Nitrocitrate (Major Occupancy
Form)
pdb|1NIT| Aconitase (E.C.4.2.1.3) Complex With Sulfate (Minor Occupancy
Form)
Length = 754
Score = 29.3 bits (64), Expect = 0.36
Identities = 24/77 (31%), Positives = 37/77 (47%), Gaps = 3/77 (3%)
Query: 67 GGGRARAGSITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVE 126
G G +R P F+GG + R + + KKQ L L +A + A NK+ V+
Sbjct: 639 GEGSSREHRALEPRFLGGRAIITKSFARIHETNL-KKQGLLPLTFA--DPADYNKIHPVD 695
Query: 127 KIAIKGVVEDNKRKHLT 143
K+ I+G+ + K LT
Sbjct: 696 KLTIQGLKDFAPGKPLT 712
>pdb|1JC9|A Chain A, Tachylectin 5a From Tachypleus Tridentatus (Japanese
Horseshoe Crab)
Length = 269
Score = 27.3 bits (59), Expect = 1.4
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 61 KPWAQKGGGRARAGSITSPVFVGGGVSHGATNNRNYNLKINKKQKRLALEYAL 113
KPW G G+I ++G TN RNY ++ + K K YA+
Sbjct: 107 KPWKNYKLG---FGNIEKDFWLGNDRIFALTNQRNYMIRFDLKDKENDTRYAI 156
>pdb|1DYK|A Chain A, Laminin Alpha 2 Chain Lg4-5 Domain Pair
Length = 394
Score = 27.3 bits (59), Expect = 1.4
Identities = 14/42 (33%), Positives = 19/42 (44%)
Query: 43 RANTAKSKNRAEVSGGGRKPWAQKGGGRARAGSITSPVFVGG 84
+ K KNR E+ G + AQ + + PVFVGG
Sbjct: 299 KVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGG 340
>pdb|1QU0|C Chain C, Crystal Structure Of The Fifth Laminin G-Like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|A Chain A, Crystal Structure Of The Fifth Laminin G-Like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|B Chain B, Crystal Structure Of The Fifth Laminin G-Like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|D Chain D, Crystal Structure Of The Fifth Laminin G-Like Module Of
The Mouse Laminin Alpha2 Chain
Length = 191
Score = 27.3 bits (59), Expect = 1.4
Identities = 14/42 (33%), Positives = 19/42 (44%)
Query: 43 RANTAKSKNRAEVSGGGRKPWAQKGGGRARAGSITSPVFVGG 84
+ K KNR E+ G + AQ + + PVFVGG
Sbjct: 96 KVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGG 137
>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment.
pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment
Length = 1184
Score = 26.6 bits (57), Expect = 2.4
Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 20/98 (20%)
Query: 94 RNYNLKINKK---QKRLALEYALEEKAQANKLFVVEKIAIKG----------VVEDNKRK 140
R+ L+ KK Q+ L LE LEE+ A + +EK+ G ++ED K
Sbjct: 942 RSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNK 1001
Query: 141 HLTKEANQMFQALEQRDTLFVCMNMDEYTELAFSNLKK 178
LTKE + + + T N+ E E A NL K
Sbjct: 1002 -LTKERKLLEERVSDLTT-----NLAEEEEKA-KNLTK 1032
>pdb|1JRY|A Chain A, Crystal Structure Of Arg402lys Mutant Flavocytochrome C3
From Shewanella Frigidimarina
pdb|1JRY|B Chain B, Crystal Structure Of Arg402lys Mutant Flavocytochrome C3
From Shewanella Frigidimarina
Length = 571
Score = 26.2 bits (56), Expect = 3.1
Identities = 20/63 (31%), Positives = 30/63 (46%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E ++KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTKDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1QJH|A Chain A, Protein Aggregation And Alzheimer's Disease.
Crystallographic Analysis Of The Phenomenon. Engineered
Version Of The Ribosomal Protein S6 Used As A Stable
Scaffold To Study Oligomerization
Length = 101
Score = 26.2 bits (56), Expect = 3.1
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 95 NYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVV 134
N L N Q +LALE + ++A N VEK+AI G++
Sbjct: 7 NIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLM 46
>pdb|1M64|A Chain A, Crystal Structure Of Q363f Mutant Flavocytochrome C3
pdb|1M64|B Chain B, Crystal Structure Of Q363f Mutant Flavocytochrome C3
Length = 571
Score = 25.8 bits (55), Expect = 4.0
Identities = 20/63 (31%), Positives = 29/63 (45%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E +KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1KSS|A Chain A, Crystal Structure Of His505ala Mutant Flavocytochrome C3
From Shewanella Frigidimarina
Length = 571
Score = 25.8 bits (55), Expect = 4.0
Identities = 20/63 (31%), Positives = 29/63 (45%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E +KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1QJD|A Chain A, Flavocytochrome C3 From Shewanella Frigidimarina
Length = 571
Score = 25.8 bits (55), Expect = 4.0
Identities = 20/63 (31%), Positives = 29/63 (45%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E +KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1KSU|A Chain A, Crystal Structure Of His505tyr Mutant Flavocytochrome C3
From Shewanella Frigidimarina
pdb|1KSU|B Chain B, Crystal Structure Of His505tyr Mutant Flavocytochrome C3
From Shewanella Frigidimarina
Length = 571
Score = 25.8 bits (55), Expect = 4.0
Identities = 20/63 (31%), Positives = 29/63 (45%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E +KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1E39|A Chain A, Flavocytochrome C3 From Shewanella Frigidimarina Histidine
365 Mutated To Alanine
Length = 571
Score = 25.8 bits (55), Expect = 4.0
Identities = 20/63 (31%), Positives = 29/63 (45%), Gaps = 1/63 (1%)
Query: 82 VGGGVSHGATNNRNYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGVVEDNKRKH 141
V GGV N + +N++ KR E +KA A L K A + +D+ RK
Sbjct: 370 VKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYL-IFDDSVRKS 428
Query: 142 LTK 144
L+K
Sbjct: 429 LSK 431
>pdb|1CQM|A Chain A, Protein Aggregation And Alzheimer's Disease:
Crystallographic Analysis Of The Phenomenon. Engineered
Version Of The Ribosomal Protein S6 Used As A Stable
Scaffold To Study Oligomerization.
pdb|1CQM|B Chain B, Protein Aggregation And Alzheimer's Disease:
Crystallographic Analysis Of The Phenomenon. Engineered
Version Of The Ribosomal Protein S6 Used As A Stable
Scaffold To Study Oligomerization.
pdb|1CQN|A Chain A, Protein Aggregation And Alzheimer's Disease:
Crystallographic Analysis Of The Phenomenon. Engineered
Version Of The Ribosomal Protein S6 Used As A Stable
Scaffold To Study Oligomerization.
pdb|1CQN|B Chain B, Protein Aggregation And Alzheimer's Disease:
Crystallographic Analysis Of The Phenomenon. Engineered
Version Of The Ribosomal Protein S6 Used As A Stable
Scaffold To Study Oligomerization
Length = 101
Score = 25.8 bits (55), Expect = 4.0
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 95 NYNLKINKKQKRLALEYALEEKAQANKLFVVEKIAIKGV 133
N L N Q +LALE + ++A N VEK+AI G+
Sbjct: 7 NIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGL 45
>pdb|1DGM|A Chain A, Crystal Structure Of Adenosine Kinase From Toxoplasma
Gondii
Length = 363
Score = 25.4 bits (54), Expect = 5.3
Identities = 19/55 (34%), Positives = 26/55 (46%), Gaps = 5/55 (9%)
Query: 3 KAIVLDSHLKEKGSVELPKRYESINSHNLYLYVKHYLSSARANTAKSKNRAEVSG 57
K L +HL GS LP+ + + S L Y ++A TA KN EV+G
Sbjct: 134 KERTLCTHLGACGSFRLPEDWTTFASGALIFY-----ATAYTLTATPKNAFEVAG 183
>pdb|2DPM|A Chain A, Dpnm Dna Adenine Methyltransferase From Streptoccocus
Pneumoniae Complexed With S-Adenosylmethionine
Length = 284
Score = 25.0 bits (53), Expect = 6.9
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 37 HYLSSARANTAKSKNRAEVS 56
HY+ + R N AKS +R ++S
Sbjct: 256 HYVEATRTNGAKSSSRGKIS 275
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
0.314 0.129 0.351
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,090,088
Number of Sequences: 13198
Number of extensions: 40155
Number of successful extensions: 119
Number of sequences better than 10.0: 20
Number of HSP's better than 10.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 109
Number of HSP's gapped (non-prelim): 20
length of query: 215
length of database: 2,899,336
effective HSP length: 84
effective length of query: 131
effective length of database: 1,790,704
effective search space: 234582224
effective search space used: 234582224
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)