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|15644673|ref|NP_206843.1| trbI protein [Helicobacter
pylori 26695]
(233 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|1DWA|M Chain M, Study On Radiation Damage On A Cryocool... 32 0.048
pdb|1E4M|M Chain M, Myrosinase From Sinapis Alba >gi|130967... 32 0.048
pdb|1MYR| Myrosinase From Sinapis Alba 32 0.063
pdb|1D7O|A Chain A, Crystal Structure Of Brassica Napus Eno... 27 2.0
pdb|1CWU|A Chain A, Brassica Napus Enoyl Acp Reductase A138... 27 2.0
pdb|1ENO| Brassica Napus Enoyl Acp ReductaseNAD BINARY CO... 27 2.0
pdb|1K32|A Chain A, Crystal Structure Of The Tricorn Protea... 26 3.5
pdb|1BFP| Blue Variant Of Green Fluorescent Protein 26 3.5
pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli >g... 26 4.5
pdb|1EMC|C Chain C, Green Fluorescent Protein From Aequorea... 26 4.5
pdb|1L3W|A Chain A, C-Cadherin Ectodomain 25 5.9
pdb|1LBC|A Chain A, Crystal Structure Of Glur2 Ligand Bindi... 25 7.7
pdb|1FTK|A Chain A, Crystal Structure Of The Glur2 Ligand B... 25 7.7
pdb|1GFL|A Chain A, Structure Of Green Fluorescent Protein ... 25 7.7
pdb|1M5D|A Chain A, X-Ray Structure Of The Glur2 Ligand Bin... 25 7.7
pdb|1LBB|A Chain A, Crystal Structure Of The Glur2 Ligand B... 25 7.7
pdb|1YFP|A Chain A, Structure Of Yellow-Emission Variant Of... 25 7.7
pdb|1M5B|A Chain A, X-Ray Structure Of The Glur2 Ligand Bin... 25 7.7
pdb|1EMB| Green Fluorescent Protein (Gfp) From Aequorea V... 25 7.7
pdb|1LB8|A Chain A, Crystal Structure Of The Non-Desensitiz... 25 7.7
pdb|1HUY|A Chain A, Crystal Structure Of Citrine, An Improv... 25 7.7
pdb|2EMD| Green Fluorescent Protein From Aequorea Victori... 25 7.7
>pdb|1DWA|M Chain M, Study On Radiation Damage On A Cryocooled Crystal. Part 1:
Structure Prior To Irradiation
pdb|1DWF|M Chain M, Study On Radiation Damage On A Cryocooled Crystal. Part 2:
Structure After Irradiation With 9.110e15 Photons
pdb|1DWG|M Chain M, Study On Radiation Damage On A Cryocooled Crystal: Part 3:
Structure After Irradiation With 18.210e15 Photons
pdb|1DWH|M Chain M, Study On Radiation Damage On A Cryocooled Crystal. Part 4:
Structure After Irradiation With 27.210e15 Photons
pdb|1DWI|M Chain M, Study On Radiation Damage On A Cryocooled Crystal. Part 5:
Structure After Irradiation With 54.010e15 Photons
pdb|1DWJ|M Chain M, Study On Radiation Damage On A Cryocooled Crystal. Refined
Part 6: Structure After A Radiation Dose Of 5410e15
Photon
Length = 499
Score = 32.3 bits (72), Expect = 0.048
Identities = 19/41 (46%), Positives = 23/41 (55%), Gaps = 3/41 (7%)
Query: 88 YRLDIVWSRIITPHGINIMLTNAKGADIKGYNGLVGELIER 128
YR I WSRII P G N KG D Y+GL+ LI++
Sbjct: 92 YRFSIAWSRII-PRGKRSRGVNEKGIDY--YHGLISGLIKK 129
>pdb|1E4M|M Chain M, Myrosinase From Sinapis Alba
pdb|1E6S|M Chain M, Myrosinase From Sinapis Alba With Bound
Gluco-Hydroximolactam And Sulfate
pdb|1E6Q|M Chain M, Myrosinase From Sinapis Alba With The Bound Transition
State Analogue Gluco-Tetrazole
pdb|1E73|M Chain M, 2-F-Glucosylated Myrosinase From Sinapis Alba With Bound
L-Ascorbate
pdb|1E71|M Chain M, Myrosinase From Sinapis Alba With Bound Ascorbate
pdb|1E72|M Chain M, Myrosinase From Sinapis Alba With Bound
Gluco-Hydroximolactam And Sulfate Or Ascorbate
pdb|1E6X|M Chain M, Myrosinase From Sinapis Alba With A Bound Transition State
Analogue,D-Glucono-1,5-Lactone
pdb|1E70|M Chain M, 2-F-Glucosylated Myrosinase From Sinapis Alba
Length = 501
Score = 32.3 bits (72), Expect = 0.048
Identities = 19/41 (46%), Positives = 23/41 (55%), Gaps = 3/41 (7%)
Query: 88 YRLDIVWSRIITPHGINIMLTNAKGADIKGYNGLVGELIER 128
YR I WSRII P G N KG D Y+GL+ LI++
Sbjct: 94 YRFSIAWSRII-PRGKRSRGVNEKGIDY--YHGLISGLIKK 131
>pdb|1MYR| Myrosinase From Sinapis Alba
Length = 501
Score = 32.0 bits (71), Expect = 0.063
Identities = 19/41 (46%), Positives = 23/41 (55%), Gaps = 3/41 (7%)
Query: 88 YRLDIVWSRIITPHGINIMLTNAKGADIKGYNGLVGELIER 128
YR I WSRII P G N KG D Y+GL+ LI++
Sbjct: 94 YRFSIAWSRII-PRGKRSRGVNQKGIDY--YHGLIDGLIKK 131
>pdb|1D7O|A Chain A, Crystal Structure Of Brassica Napus Enoyl Acyl Carrier
Protein Reductase Complexed With Nad And Triclosan
Length = 297
Score = 26.9 bits (58), Expect = 2.0
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 21 NENKLLRTITADKM--IPAFLITPISSQIAGKVI 52
N + +T+TAD++ AFL++P++S I G I
Sbjct: 246 NNAPIQKTLTADEVGNAAAFLVSPLASAITGATI 279
>pdb|1CWU|A Chain A, Brassica Napus Enoyl Acp Reductase A138g Mutant Complexed
With Nad+ And Thienodiazaborine
pdb|1CWU|B Chain B, Brassica Napus Enoyl Acp Reductase A138g Mutant Complexed
With Nad+ And Thienodiazaborine
Length = 296
Score = 26.9 bits (58), Expect = 2.0
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 21 NENKLLRTITADKM--IPAFLITPISSQIAGKVI 52
N + +T+TAD++ AFL++P++S I G I
Sbjct: 245 NNAPIQKTLTADEVGNAAAFLVSPLASAITGATI 278
>pdb|1ENO| Brassica Napus Enoyl Acp ReductaseNAD BINARY COMPLEX AT Ph 8.0 And
Room Temperature
pdb|1ENP| Brassica Napus Enoyl Acp ReductaseNADH BINARY COMPLEX AT Ph 8.0
And Room Temperature
Length = 312
Score = 26.9 bits (58), Expect = 2.0
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 21 NENKLLRTITADKM--IPAFLITPISSQIAGKVI 52
N + +T+TAD++ AFL++P++S I G I
Sbjct: 256 NNAPIQKTLTADEVGNAAAFLVSPLASAITGATI 289
>pdb|1K32|A Chain A, Crystal Structure Of The Tricorn Protease
pdb|1K32|B Chain B, Crystal Structure Of The Tricorn Protease
pdb|1K32|C Chain C, Crystal Structure Of The Tricorn Protease
pdb|1K32|D Chain D, Crystal Structure Of The Tricorn Protease
pdb|1K32|E Chain E, Crystal Structure Of The Tricorn Protease
pdb|1K32|F Chain F, Crystal Structure Of The Tricorn Protease
Length = 1045
Score = 26.2 bits (56), Expect = 3.5
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 118 YNGLVGELIERNFQRYGVPLLLSTLTNGLLIGIT 151
Y G G++ +F++ G+ L+ T T G ++GIT
Sbjct: 936 YAGSDGDIFSFSFKKLGLGKLIGTRTWGGVVGIT 969
>pdb|1BFP| Blue Variant Of Green Fluorescent Protein
Length = 236
Score = 26.2 bits (56), Expect = 3.5
Identities = 11/38 (28%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E NF + V ++ NG+ +
Sbjct: 124 KGIDFKEDGNILGHKLEYNFNSHNVYIMADKQKNGIKV 161
>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
Length = 1015
Score = 25.8 bits (55), Expect = 4.5
Identities = 16/54 (29%), Positives = 27/54 (49%), Gaps = 4/54 (7%)
Query: 48 AGKVIAQVESDIFAHMGKAVLIPKGSKVIGYYSNNNKM--GEYRL--DIVWSRI 97
A + I +E D + + L PKG+ ++ Y ++ N++ EYR W RI
Sbjct: 71 AREAIYHIEGDPDHPVSRGALCPKGAGLLDYVNSENRLRYPEYRAPGSDKWQRI 124
>pdb|1EMC|C Chain C, Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EMC|A Chain A, Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EMC|B Chain B, Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EMC|D Chain D, Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EME| Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EMK| Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EML| Green Fluorescent Protein From Aequorea Victoria, Mutant
Length = 237
Score = 25.8 bits (55), Expect = 4.5
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLIGITSALN 155
KG D K ++G +E N+ + V ++ NG+ + + N
Sbjct: 125 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKTRHN 169
>pdb|1L3W|A Chain A, C-Cadherin Ectodomain
Length = 546
Score = 25.4 bits (54), Expect = 5.9
Identities = 14/38 (36%), Positives = 20/38 (51%)
Query: 106 MLTNAKGADIKGYNGLVGELIERNFQRYGVPLLLSTLT 143
+LT AKG D + V ++ N + + VPL ST T
Sbjct: 287 ILTTAKGLDFELRKQYVLQITVENAEPFSVPLPTSTAT 324
>pdb|1LBC|A Chain A, Crystal Structure Of Glur2 Ligand Binding Core
(S1s2j-N775s) In Complex With Cyclothiazide (Ctz) As
Well As Glutamate At 1.8 A Resolution
pdb|1LBC|B Chain B, Crystal Structure Of Glur2 Ligand Binding Core
(S1s2j-N775s) In Complex With Cyclothiazide (Ctz) As
Well As Glutamate At 1.8 A Resolution
pdb|1LBC|C Chain C, Crystal Structure Of Glur2 Ligand Binding Core
(S1s2j-N775s) In Complex With Cyclothiazide (Ctz) As
Well As Glutamate At 1.8 A Resolution
Length = 263
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 63 ARDADTKIWNGMVGELV 79
>pdb|1FTK|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2i)
In Complex With Kainate At 1.6 A Resolution
pdb|1GR2|A Chain A, Structure Of A Glutamate Receptor Ligand Binding Core
(Glur2) Complexed With Kainate
Length = 279
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 75 ARDADTKIWNGMVGELV 91
>pdb|1GFL|A Chain A, Structure Of Green Fluorescent Protein
pdb|1GFL|B Chain B, Structure Of Green Fluorescent Protein
Length = 238
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E N+ + V ++ NG+ +
Sbjct: 126 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV 163
>pdb|1M5D|A Chain A, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j-
Y702f) In Complex With Br-Hibo At 1.73 A Resolution
pdb|1M5F|A Chain A, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j-
Y702f) In Complex With Acpa At 1.95 A Resolution
pdb|1M5F|B Chain B, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j-
Y702f) In Complex With Acpa At 1.95 A Resolution
pdb|1M5F|C Chain C, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j-
Y702f) In Complex With Acpa At 1.95 A Resolution
Length = 263
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 63 ARDADTKIWNGMVGELV 79
>pdb|1LBB|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Domain
Mutant (S1s2j-N754d) In Complex With Kainate At 2.1 A
Resolution
Length = 263
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 63 ARDADTKIWNGMVGELV 79
>pdb|1YFP|A Chain A, Structure Of Yellow-Emission Variant Of Gfp
pdb|1YFP|B Chain B, Structure Of Yellow-Emission Variant Of Gfp
Length = 225
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E N+ + V ++ NG+ +
Sbjct: 122 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV 159
>pdb|1M5B|A Chain A, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With 2-Me-Tet-Ampa At 1.85 A Resolution.
pdb|1M5B|B Chain B, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With 2-Me-Tet-Ampa At 1.85 A Resolution.
pdb|1M5B|C Chain C, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With 2-Me-Tet-Ampa At 1.85 A Resolution.
pdb|1M5C|A Chain A, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Br-Hibo At 1.65 A Resolution
pdb|1M5E|A Chain A, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Acpa At 1.46 A Resolution
pdb|1M5E|B Chain B, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Acpa At 1.46 A Resolution
pdb|1M5E|C Chain C, X-Ray Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Acpa At 1.46 A Resolution
pdb|1FTJ|B Chain B, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Glutamate At 1.9 Resolution
pdb|1FTM|B Chain B, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Ampa At 1.7 Resolution
pdb|1FTJ|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Glutamate At 1.9 Resolution
pdb|1FTM|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Ampa At 1.7 Resolution
pdb|1FTO|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In The Apo State At 2.0 A Resolution
pdb|1FTJ|C Chain C, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Glutamate At 1.9 Resolution
pdb|1FTO|B Chain B, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In The Apo State At 2.0 A Resolution
pdb|1FTL|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With The Antagonist Dnqx At 1.8 A Resolution
pdb|1FTL|B Chain B, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With The Antagonist Dnqx At 1.8 A Resolution
pdb|1FTM|C Chain C, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Ampa At 1.7 Resolution
pdb|1FW0|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
In Complex With Kainate At 2.0 A Resolution
Length = 263
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 63 ARDADTKIWNGMVGELV 79
>pdb|1EMB| Green Fluorescent Protein (Gfp) From Aequorea Victoria, Gln 80
Replaced With Arg
pdb|1HCJ|A Chain A, Photoproduct Of The Wild-Type Aequorea Victoria Green
Fluorescent Protein
pdb|1HCJ|B Chain B, Photoproduct Of The Wild-Type Aequorea Victoria Green
Fluorescent Protein
pdb|1HCJ|C Chain C, Photoproduct Of The Wild-Type Aequorea Victoria Green
Fluorescent Protein
pdb|1HCJ|D Chain D, Photoproduct Of The Wild-Type Aequorea Victoria Green
Fluorescent Protein
pdb|1EMG|A Chain A, Green Fluorescent Protein (65-67 Replaced By Cro, S65t
Substitution, Q80r)
pdb|1C4F|A Chain A, Green Fluorescent Protein S65t At Ph 4.6
Length = 236
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E N+ + V ++ NG+ +
Sbjct: 124 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV 161
>pdb|1LB8|A Chain A, Crystal Structure Of The Non-Desensitizing Glur2 Ligand
Binding Core Mutant (S1s2j-L483y) In Complex With Ampa
At 2.3 Resolution
pdb|1LB8|B Chain B, Crystal Structure Of The Non-Desensitizing Glur2 Ligand
Binding Core Mutant (S1s2j-L483y) In Complex With Ampa
At 2.3 Resolution
pdb|1LB9|A Chain A, Crystal Structure Of The Non-Desensitizing Glur2 Ligand
Binding Core Mutant (S1s2j-L483y) In Complex With
Antagonist Dnqx At 2.3 A Resolution
pdb|1LB9|B Chain B, Crystal Structure Of The Non-Desensitizing Glur2 Ligand
Binding Core Mutant (S1s2j-L483y) In Complex With
Antagonist Dnqx At 2.3 A Resolution
Length = 263
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/17 (58%), Positives = 14/17 (81%)
Query: 110 AKGADIKGYNGLVGELI 126
A+ AD K +NG+VGEL+
Sbjct: 63 ARDADTKIWNGMVGELV 79
>pdb|1HUY|A Chain A, Crystal Structure Of Citrine, An Improved Yellow Variant
Of Green Fluorescent Protein
Length = 239
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E N+ + V ++ NG+ +
Sbjct: 127 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV 164
>pdb|2EMD| Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|2EMN| Green Fluorescent Protein From Aequorea Victoria, Mutant
pdb|1EMM| Green Fluorescent Protein From Aequorea Victoria, Mutant
Length = 237
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (49%)
Query: 111 KGADIKGYNGLVGELIERNFQRYGVPLLLSTLTNGLLI 148
KG D K ++G +E N+ + V ++ NG+ +
Sbjct: 125 KGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV 162
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
0.320 0.140 0.395
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,345,631
Number of Sequences: 13198
Number of extensions: 58062
Number of successful extensions: 138
Number of sequences better than 10.0: 22
Number of HSP's better than 10.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 123
Number of HSP's gapped (non-prelim): 22
length of query: 233
length of database: 2,899,336
effective HSP length: 85
effective length of query: 148
effective length of database: 1,777,506
effective search space: 263070888
effective search space used: 263070888
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)