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|15646085|ref|NP_208267.1| phenylacrylic acid
decarboxylase [Helicobacter pylori 26695]
(187 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|1K3E|B Chain B, Type Iii Secretion Chaperone Cest >gi|1... 30 0.22
pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of... 27 1.9
pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bo... 27 1.9
pdb|1JXE| Stoffel Fragment Of Taq Dna Polymerase I >gi|67... 27 1.9
pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of... 27 1.9
pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragm... 27 1.9
pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An ... 27 1.9
pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of... 27 1.9
pdb|1TAQ| Structure Of Taq Dna Polymerase 26 2.5
pdb|1TAU|A Chain A, Structure Of Dna Polymerase 26 2.5
pdb|1J6N|A Chain A, Crystal Structure Of Cysteine Synthase ... 25 5.5
pdb|1LBC|A Chain A, Crystal Structure Of Glur2 Ligand Bindi... 25 7.2
pdb|1M5D|A Chain A, X-Ray Structure Of The Glur2 Ligand Bin... 25 7.2
pdb|1LBB|A Chain A, Crystal Structure Of The Glur2 Ligand B... 25 7.2
pdb|1M5B|A Chain A, X-Ray Structure Of The Glur2 Ligand Bin... 25 7.2
pdb|1EIA| X-Ray Crystal Structure Of Equine Infectious An... 24 9.4
pdb|1C4Z|A Chain A, Structure Of E6ap: Insights Into Ubiqui... 24 9.4
pdb|2EIA|A Chain A, X-Ray Crystal Structure Of Equine Infec... 24 9.4
>pdb|1K3E|B Chain B, Type Iii Secretion Chaperone Cest
pdb|1K3E|A Chain A, Type Iii Secretion Chaperone Cest
Length = 156
Score = 29.6 bits (65), Expect = 0.22
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 7/50 (14%)
Query: 8 SGASGIPLALRFL------EKLPKEIEVFVVASKNAHVVALEESNINLKN 51
+GA + LALRF EKL EIEV V + +N ++V L I L+N
Sbjct: 88 AGAQSLLLALRFPLDDATPEKLENEIEVVVKSMENLYLV-LHNQGITLEN 136
>pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 298 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 357
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 358 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 401
>pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bound To Dctp
pdb|1KTQ| Dna Polymerase
Length = 543
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 301 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 360
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 361 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 404
>pdb|1JXE| Stoffel Fragment Of Taq Dna Polymerase I
pdb|3KTQ|A Chain A, Crystal Structure Of An Active Ternary Complex Of The
Large Fragment Of Dna Polymerase I From Thermus
Aquaticus
Length = 540
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 298 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 357
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 358 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 401
>pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
pdb|1QSS|A Chain A, Ddgtp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 298 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 357
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 358 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 401
>pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus
Length = 538
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 296 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 355
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 356 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 399
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1CMW|A Chain A, Crystal Structure Of Taq Dna-Polymerase Shows A New
Orientation For The Structure-Specific Nuclease Domain
Length = 832
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 590 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 649
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 650 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 693
>pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of Dna Polymerase I
From T. Aquaticus Bound To A PrimerTEMPLATE DNA
Length = 539
Score = 26.6 bits (57), Expect = 1.9
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)
Query: 23 LPKEIEVFVVASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGI 79
L + I +A + +VAL+ S I L+ + D F +DIH AS +G+
Sbjct: 297 LGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 356
Query: 80 HKMAIIP----ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
+ A+ P A+ + + +G +S+ ++ +E + +
Sbjct: 357 PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 400
>pdb|1TAQ| Structure Of Taq Dna Polymerase
Length = 832
Score = 26.2 bits (56), Expect = 2.5
Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 32 VASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGIHKMAIIP-- 86
+A + +VAL+ S I L+ + D F +DIH AS +G+ + A+ P
Sbjct: 599 IAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLM 658
Query: 87 --ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
A+ + + +G +S+ ++ +E + +
Sbjct: 659 RRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 693
>pdb|1TAU|A Chain A, Structure Of Dna Polymerase
Length = 832
Score = 26.2 bits (56), Expect = 2.5
Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 32 VASKNAHVVALEESNINLK---NAMKDLRPSGTFFNEQDIHASIASGSYGIHKMAIIP-- 86
+A + +VAL+ S I L+ + D F +DIH AS +G+ + A+ P
Sbjct: 599 IAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLM 658
Query: 87 --ASMDMVAKIAHGFGGDLISRSASVMLKEKRPLL 119
A+ + + +G +S+ ++ +E + +
Sbjct: 659 RRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI 693
>pdb|1J6N|A Chain A, Crystal Structure Of Cysteine Synthase (Tm0665) From
Thermotoga Maritima At 1.8 A Resolution
pdb|1J6N|B Chain B, Crystal Structure Of Cysteine Synthase (Tm0665) From
Thermotoga Maritima At 1.8 A Resolution
pdb|1J6N|C Chain C, Crystal Structure Of Cysteine Synthase (Tm0665) From
Thermotoga Maritima At 1.8 A Resolution
pdb|1J6N|D Chain D, Crystal Structure Of Cysteine Synthase (Tm0665) From
Thermotoga Maritima At 1.8 A Resolution
Length = 303
Score = 25.0 bits (53), Expect = 5.5
Identities = 12/35 (34%), Positives = 20/35 (56%)
Query: 3 LVLGISGASGIPLALRFLEKLPKEIEVFVVASKNA 37
L++GIS + + AL+ +KL + V VA +A
Sbjct: 262 LLVGISSGANVAAALKVAQKLGPDARVVTVAPDHA 296
>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 = 24.6 bits (52), Expect = 7.2
Identities = 12/42 (28%), Positives = 22/42 (51%)
Query: 77 YGIHKMAIIPASMDMVAKIAHGFGGDLISRSASVMLKEKRPL 118
YG +AI P ++ +V + F +S S+M+K+ P+
Sbjct: 80 YGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPI 121
>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 = 24.6 bits (52), Expect = 7.2
Identities = 12/42 (28%), Positives = 22/42 (51%)
Query: 77 YGIHKMAIIPASMDMVAKIAHGFGGDLISRSASVMLKEKRPL 118
YG +AI P ++ +V + F +S S+M+K+ P+
Sbjct: 80 YGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPI 121
>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 = 24.6 bits (52), Expect = 7.2
Identities = 12/42 (28%), Positives = 22/42 (51%)
Query: 77 YGIHKMAIIPASMDMVAKIAHGFGGDLISRSASVMLKEKRPL 118
YG +AI P ++ +V + F +S S+M+K+ P+
Sbjct: 80 YGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPI 121
>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 = 24.6 bits (52), Expect = 7.2
Identities = 12/42 (28%), Positives = 22/42 (51%)
Query: 77 YGIHKMAIIPASMDMVAKIAHGFGGDLISRSASVMLKEKRPL 118
YG +AI P ++ +V + F +S S+M+K+ P+
Sbjct: 80 YGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPI 121
>pdb|1EIA| X-Ray Crystal Structure Of Equine Infectious Anemia Virus (Eiav)
Capsid Protein P26
Length = 207
Score = 24.3 bits (51), Expect = 9.4
Identities = 12/38 (31%), Positives = 21/38 (54%), Gaps = 5/38 (13%)
Query: 24 PKEIEVFVVASKNAHVVALEESNINLKNAMKDLRPSGT 61
P+EI F+ + + ++ +N +NAM+ LRP T
Sbjct: 163 PQEISKFLTDT-----LTIQNANEECRNAMRHLRPEDT 195
>pdb|1C4Z|A Chain A, Structure Of E6ap: Insights Into Ubiquitination Pathway
pdb|1C4Z|B Chain B, Structure Of E6ap: Insights Into Ubiquitination Pathway
pdb|1C4Z|C Chain C, Structure Of E6ap: Insights Into Ubiquitination Pathway
pdb|1D5F|A Chain A, Structure Of An E6ap-Ubch7 Complex: Insights Into The
Ubiquitination Pathway
pdb|1D5F|B Chain B, Structure Of An E6ap-Ubch7 Complex: Insights Into The
Ubiquitination Pathway
pdb|1D5F|C Chain C, Structure Of An E6ap-Ubch7 Complex: Insights Into The
Ubiquitination Pathway
Length = 358
Score = 24.3 bits (51), Expect = 9.4
Identities = 10/22 (45%), Positives = 15/22 (67%)
Query: 24 PKEIEVFVVASKNAHVVALEES 45
P+EIE+ + S+N ALEE+
Sbjct: 235 PEEIELLICGSRNLDFQALEET 256
>pdb|2EIA|A Chain A, X-Ray Crystal Structure Of Equine Infectious Anemia Virus
(Eiav) Capsid Protein P26
pdb|2EIA|B Chain B, X-Ray Crystal Structure Of Equine Infectious Anemia Virus
(Eiav) Capsid Protein P26
Length = 206
Score = 24.3 bits (51), Expect = 9.4
Identities = 12/38 (31%), Positives = 21/38 (54%), Gaps = 5/38 (13%)
Query: 24 PKEIEVFVVASKNAHVVALEESNINLKNAMKDLRPSGT 61
P+EI F+ + + ++ +N +NAM+ LRP T
Sbjct: 162 PQEISKFLTDT-----LTIQNANEECRNAMRHLRPEDT 194
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 0.135 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: 964,997
Number of Sequences: 13198
Number of extensions: 34437
Number of successful extensions: 73
Number of sequences better than 10.0: 18
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 67
Number of HSP's gapped (non-prelim): 18
length of query: 187
length of database: 2,899,336
effective HSP length: 83
effective length of query: 104
effective length of database: 1,803,902
effective search space: 187605808
effective search space used: 187605808
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: 51 (24.3 bits)