BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 040509
(226 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TTL|A Chain A, Crystal Structure Of Apo-Spue
pdb|3TTL|B Chain B, Crystal Structure Of Apo-Spue
Length = 340
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 36 DVWVAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIPAASR 80
++ VA G+S DV A R ++ V+PK GA+LW DL AIPA ++
Sbjct: 210 NICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLMAIPADAK 260
>pdb|3TTN|A Chain A, Crystal Structures Of Polyamine Receptors Spud And Spue
From Pseudomonas Aeruginosa
pdb|3TTN|B Chain B, Crystal Structures Of Polyamine Receptors Spud And Spue
From Pseudomonas Aeruginosa
Length = 340
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 36 DVWVAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIPAASR 80
++ VA G+S DV A R ++ V+PK GA+LW DL AIPA ++
Sbjct: 210 NICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLXAIPADAK 260
>pdb|1A99|A Chain A, Putrescine Receptor (Potf) From E. Coli
pdb|1A99|B Chain B, Putrescine Receptor (Potf) From E. Coli
pdb|1A99|C Chain C, Putrescine Receptor (Potf) From E. Coli
pdb|1A99|D Chain D, Putrescine Receptor (Potf) From E. Coli
Length = 344
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 36 DVWVAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIPAASR 80
D+ VA+GW+ DV A R NV+ +PK GA + D++A+PA ++
Sbjct: 211 DICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAK 261
>pdb|4GL0|A Chain A, Putative SpermidinePUTRESCINE ABC TRANSPORTER FROM
LISTERIA Monocytogenes
Length = 333
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 39 VAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 80
VAV +S + + ++ V+PK G++LW D IP ++
Sbjct: 208 VAVTFSGEAAEXLSENEDLEYVIPKDGSNLWFDNXVIPKTAK 249
>pdb|3TTK|A Chain A, Crystal Structure Of Apo-Spud
pdb|3TTK|B Chain B, Crystal Structure Of Apo-Spud
pdb|3TTK|C Chain C, Crystal Structure Of Apo-Spud
Length = 345
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 36 DVWVAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIP 76
++ VA+G+S D+ A R V +PK GA + D+ AIP
Sbjct: 214 NICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIP 260
>pdb|3TTM|A Chain A, Crystal Structure Of Spud In Complex With Putrescine
pdb|3TTM|B Chain B, Crystal Structure Of Spud In Complex With Putrescine
Length = 346
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 36 DVWVAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIP 76
++ VA+G+S D+ A R V +PK GA + D+ AIP
Sbjct: 214 NICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIP 260
>pdb|4EQB|A Chain A, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE ABC
Transporter Substrate-Binding Protein From Streptococcus
Pneumoniae Strain Canada Mdr_19a In Complex With Calcium
And Hepes.
pdb|4EQB|B Chain B, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE ABC
Transporter Substrate-Binding Protein From Streptococcus
Pneumoniae Strain Canada Mdr_19a In Complex With Calcium
And Hepes
Length = 330
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 35 RDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 80
+V + V +S + +++ N+ VVP ++LW D IP +
Sbjct: 201 NNVAIGVTFSGEASQMLEKNENLRYVVPTEASNLWFDNMVIPKTVK 246
>pdb|1M9N|A Chain A, Crystal Structure Of The Homodimeric Bifunctional
Transformylase And Cyclohydrolase Enzyme Avian Atic In
Complex With Aicar And Xmp At 1.93 Angstroms.
pdb|1M9N|B Chain B, Crystal Structure Of The Homodimeric Bifunctional
Transformylase And Cyclohydrolase Enzyme Avian Atic In
Complex With Aicar And Xmp At 1.93 Angstroms.
pdb|1OZ0|A Chain A, Crystal Structure Of The Homodimeric Bifunctional
Transformylase And Cyclohydrolase Enzyme Avian Atic In
Complex With A Multisubstrate Adduct Inhibitor
Beta-dadf.
pdb|1OZ0|B Chain B, Crystal Structure Of The Homodimeric Bifunctional
Transformylase And Cyclohydrolase Enzyme Avian Atic In
Complex With A Multisubstrate Adduct Inhibitor Beta-dadf
Length = 613
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 104 LPFKQEVIPGTSPSALETTLVKLPEELLKGKPSL 137
LP + + P SP+ L TT KLP ++ G P
Sbjct: 225 LPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGF 258
>pdb|1THZ|A Chain A, Crystal Structure Of Avian Aicar Transformylase In Complex
With A Novel Inhibitor Identified By Virtual Ligand
Screening
pdb|1THZ|B Chain B, Crystal Structure Of Avian Aicar Transformylase In Complex
With A Novel Inhibitor Identified By Virtual Ligand
Screening
pdb|2B1G|A Chain A, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2B1G|B Chain B, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2B1G|C Chain C, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2B1G|D Chain D, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2B1I|A Chain A, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2B1I|B Chain B, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2IU0|A Chain A, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2IU0|B Chain B, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2IU3|A Chain A, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
pdb|2IU3|B Chain B, Crystal Structures Of Transition State Analogue Inhibitors
Of Inosine Monophosphate Cyclohydrolase
Length = 593
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 104 LPFKQEVIPGTSPSALETTLVKLPEELLKGKPSL 137
LP + + P SP+ L TT KLP ++ G P
Sbjct: 205 LPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGF 238
>pdb|1POY|1 Chain 1, SpermidinePUTRESCINE-Binding Protein Complexed With
Spermidine (Dimer Form)
pdb|1POY|2 Chain 2, SpermidinePUTRESCINE-Binding Protein Complexed With
Spermidine (Dimer Form)
pdb|1POY|3 Chain 3, SpermidinePUTRESCINE-Binding Protein Complexed With
Spermidine (Dimer Form)
pdb|1POY|4 Chain 4, SpermidinePUTRESCINE-Binding Protein Complexed With
Spermidine (Dimer Form)
Length = 323
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 43 WSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 80
W+ A + + + VV PK G W D AIPA ++
Sbjct: 204 WNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 241
>pdb|1POT|A Chain A, Spermidine/putrescine-binding Protein Complexed With
Spermidine (monomer Form)
Length = 325
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 43 WSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 80
W+ A + + + VV PK G W D AIPA ++
Sbjct: 206 WNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 243
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,489,268
Number of Sequences: 62578
Number of extensions: 253458
Number of successful extensions: 638
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 628
Number of HSP's gapped (non-prelim): 15
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
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: 50 (23.9 bits)