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|15646055|ref|NP_208237.1| biopolymer transport
protein (exbD) [Helicobacter pylori 26695]
(133 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|1KW2|A Chain A, Crystal Structure Of Uncomplexed Vitami... 29 0.21
pdb|1LOT|A Chain A, Crystal Structure Of The Complex Of Act... 29 0.21
pdb|1JF5|A Chain A, Crystal Structure Of Thermoactinomyces ... 25 2.3
pdb|1JI2|A Chain A, Improved X-Ray Structure Of Thermoactin... 25 2.3
pdb|1JF6|A Chain A, Crystal Structure Of Thermoactinomyces ... 25 2.3
pdb|1G1Y|A Chain A, Crystal Structure Of Alpha-Amylase Ii (... 25 2.3
pdb|1JL8|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) Fr... 25 2.3
pdb|1BF6|B Chain B, Phosphotriesterase Homology Protein Fro... 25 3.9
pdb|1XJO| Structure Of Aminopeptidase 25 3.9
pdb|1QQ9|A Chain A, Streptomyces Griseus Aminopeptidase Com... 25 3.9
pdb|1QMP|A Chain A, Phosphorylated Aspartate In The Crystal... 24 5.1
pdb|1DZ3|A Chain A, Domain-Swapping In The Sporulation Resp... 24 5.1
pdb|1C3E|A Chain A, New Insights Into Inhibitor Design From... 23 8.8
pdb|2PGD| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.... 23 8.8
pdb|1B9Z|A Chain A, Bacillus Cereus Beta-Amylase Complexed ... 23 8.8
pdb|1CDD|A Chain A, Phosphoribosylglycinamide Formyltransfe... 23 8.8
pdb|1JKX|A Chain A, Unexpected Formation Of An Epoxide-Deri... 23 8.8
>pdb|1KW2|A Chain A, Crystal Structure Of Uncomplexed Vitamin D-Binding Protein
pdb|1KW2|B Chain B, Crystal Structure Of Uncomplexed Vitamin D-Binding Protein
pdb|1KXP|D Chain D, Crystal Structure Of Human Vitamin D-Binding Protein In
Complex With Skeletal Actin
Length = 458
Score = 28.9 bits (63), Expect = 0.21
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 97 GDKKSNLDNFIKVVDLLQTNNLKQLYILVEDKKN 130
G+KKS L N IK+ + T +L+ + L ED N
Sbjct: 211 GEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITN 244
>pdb|1LOT|A Chain A, Crystal Structure Of The Complex Of Actin With Vitamin D-
Binding Protein
pdb|1J7E|B Chain B, A Structural Basis For The Unique Binding Features Of The
Human Vitamin D-Binding Protein
pdb|1J7E|A Chain A, A Structural Basis For The Unique Binding Features Of The
Human Vitamin D-Binding Protein
pdb|1J78|B Chain B, Crystallographic Analysis Of The Human Vitamin D Binding
Protein
pdb|1J78|A Chain A, Crystallographic Analysis Of The Human Vitamin D Binding
Protein
Length = 458
Score = 28.9 bits (63), Expect = 0.21
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 97 GDKKSNLDNFIKVVDLLQTNNLKQLYILVEDKKN 130
G+KKS L N IK+ + T +L+ + L ED N
Sbjct: 211 GEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITN 244
>pdb|1JF5|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2 Mutant F286a
pdb|1JF5|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2 Mutant F286a
Length = 585
Score = 25.4 bits (54), Expect = 2.3
Identities = 14/47 (29%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 64 NKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVV 110
N+G F F + I L+H++++L + DK++NL F++ V
Sbjct: 480 NRGLFEFYKELI---RLRHRLASLTRGNVRSWHADKQANLYAFVRTV 523
>pdb|1JI2|A Chain A, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
R-47 Alpha-Amylase 2
pdb|1JI2|B Chain B, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
R-47 Alpha-Amylase 2
pdb|1BVZ|A Chain A, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
R- 47
pdb|1BVZ|B Chain B, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
R- 47
Length = 585
Score = 25.4 bits (54), Expect = 2.3
Identities = 14/47 (29%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 64 NKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVV 110
N+G F F + I L+H++++L + DK++NL F++ V
Sbjct: 480 NRGLFEFYKELI---RLRHRLASLTRGNVRSWHADKQANLYAFVRTV 523
>pdb|1JF6|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Mutant F286y
pdb|1JF6|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Mutant F286y
Length = 585
Score = 25.4 bits (54), Expect = 2.3
Identities = 14/47 (29%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 64 NKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVV 110
N+G F F + I L+H++++L + DK++NL F++ V
Sbjct: 480 NRGLFEFYKELI---RLRHRLASLTRGNVRSWHADKQANLYAFVRTV 523
>pdb|1G1Y|A Chain A, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
Complex
pdb|1G1Y|B Chain B, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
Complex
Length = 585
Score = 25.4 bits (54), Expect = 2.3
Identities = 14/47 (29%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 64 NKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVV 110
N+G F F + I L+H++++L + DK++NL F++ V
Sbjct: 480 NRGLFEFYKELI---RLRHRLASLTRGNVRSWHADKQANLYAFVRTV 523
>pdb|1JL8|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
Based On A Co- Crystallization With Methyl
Beta-Cyclodextrin
pdb|1JL8|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
Based On A Co- Crystallization With Methyl
Beta-Cyclodextrin
pdb|1JIB|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
On A Crystal Soaked With Maltohexaose.
pdb|1JIB|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
On A Crystal Soaked With Maltohexaose
Length = 585
Score = 25.4 bits (54), Expect = 2.3
Identities = 14/47 (29%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 64 NKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFIKVV 110
N+G F F + I L+H++++L + DK++NL F++ V
Sbjct: 480 NRGLFEFYKELI---RLRHRLASLTRGNVRSWHADKQANLYAFVRTV 523
>pdb|1BF6|B Chain B, Phosphotriesterase Homology Protein From Escherichia Coli
pdb|1BF6|A Chain A, Phosphotriesterase Homology Protein From Escherichia Coli
Length = 291
Score = 24.6 bits (52), Expect = 3.9
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 98 DKKSNLDNFIKVVDL 112
D K NLDN +K++DL
Sbjct: 187 DLKDNLDNILKMIDL 201
>pdb|1XJO| Structure Of Aminopeptidase
Length = 284
Score = 24.6 bits (52), Expect = 3.9
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 60 IAISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSN 102
I N G F +DD + + K+ + L T I +GD +S+
Sbjct: 162 IGSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDGRSD 204
>pdb|1QQ9|A Chain A, Streptomyces Griseus Aminopeptidase Complexed With
Methionine
pdb|1F2O|A Chain A, Crystal Structure Of The Streptomyces Griseus
Aminopeptidase Complexed With L-Leucine
pdb|1F2P|A Chain A, Crystal Structure Of The Streptomyces Griseus
Aminopeptidase Complexed With L-Phenylalanine
pdb|1CP7|A Chain A, Aminopeptidase From Streptomyces Griseus
Length = 284
Score = 24.6 bits (52), Expect = 3.9
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 60 IAISNKGSFYFDDKEISFENLKHKVSTLAKDTPIVLQGDKKSN 102
I N G F +DD + + K+ + L T I +GD +S+
Sbjct: 162 IGSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDGRSD 204
>pdb|1QMP|A Chain A, Phosphorylated Aspartate In The Crystal Structure Of The
Sporulation Response Regulator, Spo0a
pdb|1QMP|C Chain C, Phosphorylated Aspartate In The Crystal Structure Of The
Sporulation Response Regulator, Spo0a
pdb|1QMP|D Chain D, Phosphorylated Aspartate In The Crystal Structure Of The
Sporulation Response Regulator, Spo0a
pdb|1QMP|B Chain B, Phosphorylated Aspartate In The Crystal Structure Of The
Sporulation Response Regulator, Spo0a
Length = 130
Score = 24.3 bits (51), Expect = 5.1
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 55 KKQVTIAISNKGSFYFDDKEISFENLKHKV-STLAKDTPIV 94
++ VT G+ YF K ENL H + K TP+V
Sbjct: 88 QEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
>pdb|1DZ3|A Chain A, Domain-Swapping In The Sporulation Response Regulator
Spo0a
Length = 130
Score = 24.3 bits (51), Expect = 5.1
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 55 KKQVTIAISNKGSFYFDDKEISFENLKHKV-STLAKDTPIV 94
++ VT G+ YF K ENL H + K TP+V
Sbjct: 88 QEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
>pdb|1C3E|A Chain A, New Insights Into Inhibitor Design From The Crystal
Structure And Nmr Studies Of E. Coli Gar Transformylate
In Complex With Beta-Gar And
10-Formyl-5,8,10-Trideazafolic Acid.
pdb|1C3E|B Chain B, New Insights Into Inhibitor Design From The Crystal
Structure And Nmr Studies Of E. Coli Gar Transformylate
In Complex With Beta-Gar And
10-Formyl-5,8,10-Trideazafolic Acid
Length = 209
Score = 23.5 bits (49), Expect = 8.8
Identities = 17/67 (25%), Positives = 31/67 (45%), Gaps = 1/67 (1%)
Query: 31 QTSKLPISIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKD 90
+T+K+ ++ V + D+ + +Q IA + FD +E L H++ A D
Sbjct: 22 KTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPD 81
Query: 91 TPIVLQG 97
+VL G
Sbjct: 82 V-VVLAG 87
>pdb|2PGD| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.1.1.1.44)
pdb|1PGN| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.1.1.1.44) Complexed
With Coenzyme Analogue Nicotinamide 8-Bromo-Adenine
Dinucleotide Phosphate
pdb|1PGO| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.1.1.1.44) Complexed
With Reduced Coenzyme Nadph
pdb|1PGP| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.1.1.1.44) Complexed
With Substrate 6-Phosphogluconic Acid
pdb|1PGQ| 6-Phosphogluconate Dehydrogenase (6-Pgdh) (E.C.1.1.1.44) Complexed
With Inhibitor 2'-Adenylic Acid (Adenosine
2'-Monophosphate)
Length = 482
Score = 23.5 bits (49), Expect = 8.8
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 73 KEISFENLKHKVSTLAKDTPIVLQGDKKSNLDNFI-KVVDLLQTNNL 118
K + +L+ VS L K I+L +DNFI K+V LL ++
Sbjct: 50 KVLGAHSLEEMVSKLKKPRRIILLVKAGQAVDNFIEKLVPLLDIGDI 96
>pdb|1B9Z|A Chain A, Bacillus Cereus Beta-Amylase Complexed With Maltose
pdb|5BCA|A Chain A, Beta-Amylase From Bacillus Cereus Var. Mycoides
pdb|5BCA|B Chain B, Beta-Amylase From Bacillus Cereus Var. Mycoides
pdb|5BCA|C Chain C, Beta-Amylase From Bacillus Cereus Var. Mycoides
pdb|5BCA|D Chain D, Beta-Amylase From Bacillus Cereus Var. Mycoides
pdb|1B90|A Chain A, Bacillus Cereus Beta-Amylase Apo Form
Length = 516
Score = 23.5 bits (49), Expect = 8.8
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 53 LDKKQVTIAISNKGSFYFDDKEISF-ENLKHKVSTLAKDTPIVLQGDKKSNLDN 105
LD + +++KGS+ E S + L ++TLA + IVL G+ ++ N
Sbjct: 325 LDVTFTCLEMTDKGSY----PEYSMPKTLVQNIATLANEKGIVLNGENALSIGN 374
>pdb|1CDD|A Chain A, Phosphoribosylglycinamide Formyltransferase
(E.C.2.1.2.2) (5'-Phosphoribosylglycinamide
Transformylase)
pdb|1CDD|B Chain B, Phosphoribosylglycinamide Formyltransferase
(E.C.2.1.2.2) (5'-Phosphoribosylglycinamide
Transformylase)
Length = 212
Score = 23.5 bits (49), Expect = 8.8
Identities = 17/67 (25%), Positives = 31/67 (45%), Gaps = 1/67 (1%)
Query: 31 QTSKLPISIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKD 90
+T+K+ ++ V + D+ + +Q IA + FD +E L H++ A D
Sbjct: 22 KTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPD 81
Query: 91 TPIVLQG 97
+VL G
Sbjct: 82 V-VVLAG 87
>pdb|1JKX|A Chain A, Unexpected Formation Of An Epoxide-Derived
Multisubstrate Adduct Inhibitor On The Active Site Of
Gar Transformylase
pdb|1JKX|B Chain B, Unexpected Formation Of An Epoxide-Derived
Multisubstrate Adduct Inhibitor On The Active Site Of
Gar Transformylase
pdb|1JKX|C Chain C, Unexpected Formation Of An Epoxide-Derived
Multisubstrate Adduct Inhibitor On The Active Site Of
Gar Transformylase
pdb|1JKX|D Chain D, Unexpected Formation Of An Epoxide-Derived
Multisubstrate Adduct Inhibitor On The Active Site Of
Gar Transformylase
pdb|1C2T|A Chain A, New Insights Into Inhibitor Design From The Crystal
Structure And Nmr Studies Of E. Coli Gar Transformylase
In Complex With Beta-Gar And
10-Formyl-5,8,10-Trideazafolic Acid.
pdb|1C2T|B Chain B, New Insights Into Inhibitor Design From The Crystal
Structure And Nmr Studies Of E. Coli Gar Transformylase
In Complex With Beta-Gar And
10-Formyl-5,8,10-Trideazafolic Acid.
pdb|1CDE| Phosphoribosylglycinamide Formyltransferase (E.C.2.1.2.2)
(5'-Phosphoribosylglycinamide Transformylase) Complex
With Glycinamide Ribonucleotide And The Inhibitor
5-Deaza-5,6,7,8-Tetrahydrofolate
pdb|1GAR|A Chain A, Glycinamide Ribonucleotide Transformylase
(10-Formyltetrahydrofolate-5'-Phosphoribosylglycinamide
Formyltransferase) (E.C.2.1.2.2) Complexed With
Burroughs-Wellcome Inhibitor 1476u89
pdb|1GAR|B Chain B, Glycinamide Ribonucleotide Transformylase
(10-Formyltetrahydrofolate-5'-Phosphoribosylglycinamide
Formyltransferase) (E.C.2.1.2.2) Complexed With
Burroughs-Wellcome Inhibitor 1476u89
pdb|1GRC|A Chain A, Glycinamide Ribonucleotide Transformylase (E.C.2.1.2.2)
pdb|1GRC|B Chain B, Glycinamide Ribonucleotide Transformylase (E.C.2.1.2.2)
Length = 212
Score = 23.5 bits (49), Expect = 8.8
Identities = 17/67 (25%), Positives = 31/67 (45%), Gaps = 1/67 (1%)
Query: 31 QTSKLPISIPQVDKDSTDSKDVLDKKQVTIAISNKGSFYFDDKEISFENLKHKVSTLAKD 90
+T+K+ ++ V + D+ + +Q IA + FD +E L H++ A D
Sbjct: 22 KTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPD 81
Query: 91 TPIVLQG 97
+VL G
Sbjct: 82 V-VVLAG 87
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
0.315 0.134 0.348
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 655,569
Number of Sequences: 13198
Number of extensions: 24853
Number of successful extensions: 53
Number of sequences better than 10.0: 17
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 48
Number of HSP's gapped (non-prelim): 17
length of query: 133
length of database: 2,899,336
effective HSP length: 78
effective length of query: 55
effective length of database: 1,869,892
effective search space: 102844060
effective search space used: 102844060
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 49 (23.5 bits)