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= 040870
(215 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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 11/136 (8%)
Query: 53 VRLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLW 106
V F + Y+ G++ +A G+S DV A R ++ V+PK GA+LW DL
Sbjct: 194 VSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLM 253
Query: 107 AIPAASRLETKQIGGRVRGPFPLIHQWIEFCLQTARALP-----FNTRVKLPEELLKGKP 161
AIPA ++ P + + + A A+P + V EE+ +
Sbjct: 254 AIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLMDKSVSDSEEVYPPQA 313
Query: 162 SLDTKLIAGVPPAEIL 177
LD ++ V PA++L
Sbjct: 314 VLDKLYVSAVLPAKVL 329
>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 = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 11/136 (8%)
Query: 53 VRLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLW 106
V F + Y+ G++ +A G+S DV A R ++ V+PK GA+LW DL
Sbjct: 194 VSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLX 253
Query: 107 AIPAASRLETKQIGGRVRGPFPLIHQWIEFCLQTARALP-----FNTRVKLPEELLKGKP 161
AIPA ++ P + + + A A+P + V EE+ +
Sbjct: 254 AIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLXDKSVSDSEEVYPPQA 313
Query: 162 SLDTKLIAGVPPAEIL 177
LD ++ V PA++L
Sbjct: 314 VLDKLYVSAVLPAKVL 329
>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 = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 18/111 (16%)
Query: 21 ISMVNSPREVIGT-----------QAAAGRIAVQQNLAL-LGNQVRLFDRTHYLKVFGIG 68
+S +++P EV T A +L L L +R F + Y+ G
Sbjct: 151 VSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANG 210
Query: 69 DVWIAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLWAIPAASR 113
D+ +A+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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 51/220 (23%), Positives = 89/220 (40%), Gaps = 48/220 (21%)
Query: 3 ENGFKDWKDLWLPELAGRISMVNSPREVIGT-----------------QAAAGRIAVQQ- 44
+ F W L+ PEL +I +++ REV G QAA ++
Sbjct: 128 DKNFDTWNALFDPELKNQILLIDGAREVXGLGLNSLGYSLNDTNKAHLQAARDKLETXTP 187
Query: 45 NL-ALLGNQVRLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKRMSNVAVVVPKSGASLWA 103
N+ A++G++++L + + +AV +S + + ++ V+PK G++LW
Sbjct: 188 NVKAIVGDEIKLLXADN--------EAGVAVTFSGEAAEXLSENEDLEYVIPKDGSNLWF 239
Query: 104 DLWAIPAASRLETKQIGGRVRGPFPLIHQWIEFCLQ------TARALPFNTRVKLPEELL 157
D IP + K + G H++I F L+ A + + T ELL
Sbjct: 240 DNXVIPKTA----KNVDG--------AHKFINFXLKPENAAINAEYVGYATPNAKAVELL 287
Query: 158 KGKPSLDTKLIAGVPPAEILARCEFLEPLSEATLSDYEWL 197
+ S D + P + L E + L + LS Y L
Sbjct: 288 PKEISSDERF---YPDXDELNNLEVYDNLGKRXLSYYNEL 324
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 47/116 (40%), Gaps = 11/116 (9%)
Query: 9 WKDLWLPELAGRISMVNSPREVI----------GTQAAAGRIAVQQN-LALLGNQVRLFD 57
W DLW PE G + + + REV G I N L L V F+
Sbjct: 126 WADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFN 185
Query: 58 RTHYLKVFGIGDVWIAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 113
+ + G+V + + W+ A + + + VV PK G W D AIPA ++
Sbjct: 186 SDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 241
>pdb|1POT|A Chain A, Spermidine/putrescine-binding Protein Complexed With
Spermidine (monomer Form)
Length = 325
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 47/116 (40%), Gaps = 11/116 (9%)
Query: 9 WKDLWLPELAGRISMVNSPREVI----------GTQAAAGRIAVQQN-LALLGNQVRLFD 57
W DLW PE G + + + REV G I N L L V F+
Sbjct: 128 WADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFN 187
Query: 58 RTHYLKVFGIGDVWIAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASR 113
+ + G+V + + W+ A + + + VV PK G W D AIPA ++
Sbjct: 188 SDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 243
>pdb|4EDP|A Chain A, 1.85 Angstrom Resolution Crystal Structure Of An Abc
Transporter From Clostridium Perfringens Atcc 13124
pdb|4EDP|B Chain B, 1.85 Angstrom Resolution Crystal Structure Of An Abc
Transporter From Clostridium Perfringens Atcc 13124
Length = 351
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 72/174 (41%), Gaps = 35/174 (20%)
Query: 9 WKDLWLPELAGRISM-----VNSPREV--------IGTQAAAGRIAVQQNLALLGNQVRL 55
W+DLW PEL +I++ N P V + + G A ++ AL N V+
Sbjct: 156 WEDLWKPELKNKIAIPDITTTNGPAMVEIAAEKAGVDVKTDNGEAAFKELEALKPNVVKT 215
Query: 56 FDRTHYL-KVFGIGDVWIAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASRL 114
+ ++ L +F G++ AV K V V+P+SG L + I S+
Sbjct: 216 YSKSSDLANMFSNGEIVAAVASDFAFGTISKAKPEVINVIPESGTYLNFNTININKNSKN 275
Query: 115 ETKQIGGRVRGPFPLIHQWIEFCL------QTARAL---PFNTRVKLPEELLKG 159
+ L +++I + L +TA+AL P N VKL EE K
Sbjct: 276 K------------DLAYEFINYALSKEVQEKTAKALNESPVNKEVKLSEEETKN 317
>pdb|2V84|A Chain A, Crystal Structure Of The Tp0655 (Tppotd) Lipoprotein Of
Treponema Pallidum
Length = 343
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 68/176 (38%), Gaps = 29/176 (16%)
Query: 7 KDWKDLWLPELAGRISMVNSPREVIGTQAAAGRIAV----QQNLALLG---------NQV 53
+ W +LA R+SM++ REV+G A+ V +Q LA N V
Sbjct: 146 RTWSIFSRKDLAYRMSMMDDMREVMGAALASLGYNVNTKNEQELAQAAILVTDHWKPNLV 205
Query: 54 RLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKR--MSNVAVVVPKSGAS-LWADLWAIPA 110
+ FD Y K F GD +A G++ ++ +P+ AS ++ D + IP
Sbjct: 206 K-FDSDGYAKSFASGDFVVAHGFAEAFFAETPEAMHEHIDFFIPQDVASPVYVDSFCIPK 264
Query: 111 ASRLETKQIGGRVRGPFPLIHQWIEFCLQTARALPFNTRVKLPEELLKGKPSLDTK 166
G R R L H +I F L+ A F P + + + K
Sbjct: 265 ---------GARNRD---LAHAFINFFLEPAHYAEFLDTFGFPSTIHREAAAYQKK 308
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 53 VRLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLW 106
V F + Y+ G++ +A+G+S D+ A R V +PK GA + D+
Sbjct: 198 VTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMV 257
Query: 107 AIP 109
AIP
Sbjct: 258 AIP 260
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 53 VRLFDRTHYLKVFGIGDVWIAVGWSSDVLPAVKRMS------NVAVVVPKSGASLWADLW 106
V F + Y+ G++ +A+G+S D+ A R V +PK GA + D+
Sbjct: 198 VTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMV 257
Query: 107 AIP 109
AIP
Sbjct: 258 AIP 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 = 35.0 bits (79), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 48/206 (23%), Positives = 79/206 (38%), Gaps = 40/206 (19%)
Query: 9 WKDLWLPELAGRISMVNSPREVIGTQAAA-GRIAVQQNLALLGNQV-RLFDRT------- 59
W DLW E I + + REV+G + G ++ L V +L+ T
Sbjct: 131 WDDLWKLEYKNSIMLFDGAREVLGLGLNSLGYSLNSKDPQQLEETVDKLYKLTPNIKAIV 190
Query: 60 -HYLKVFGI-GDVWIAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAIPAASRLETK 117
+K + I +V I V +S + +++ N+ VVP ++LW D IP +
Sbjct: 191 ADEMKGYMIQNNVAIGVTFSGEASQMLEKNENLRYVVPTEASNLWFDNMVIPKTVK---- 246
Query: 118 QIGGRVRGPFPLIHQWI--EFCLQTARALPFNT-----RVKLPEELLKGKPSLDTKLIAG 170
+ I+ + E LQ A + ++T + LPEE + K A
Sbjct: 247 ----NQDSAYAFINFMLKPENALQNAEYVGYSTPNLPAKELLPEETKEDK--------AF 294
Query: 171 VPPAEILARCEFLEPLSEATLSDYEW 196
P E + E E D++W
Sbjct: 295 YPDVETMKHLEVYEKF------DHKW 314
>pdb|4HCH|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCH|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCL|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
pdb|4HCL|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
Length = 402
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 184 EPLSEATLSDYEWLVANLQKP 204
EP+ E +LS Y+WL NL P
Sbjct: 253 EPMDEQSLSSYKWLSDNLDIP 273
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
0.321 0.137 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,596,066
Number of Sequences: 62578
Number of extensions: 255412
Number of successful extensions: 530
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 515
Number of HSP's gapped (non-prelim): 13
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)