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= 024049
(273 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 15/137 (10%)
Query: 16 APIEDWKDLWRPELAGR-----ISMVNSPREVIGSVLKYMGASYNSNNIDLQVAGGKISV 70
AP++ W + +PE + +S +++P EV +VL Y+G NS D
Sbjct: 129 APVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTG----PA 184
Query: 71 XXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMS------NVAVVVPK 124
R F S+ Y+ GD+ VA+GW+ DV A R NV+ +PK
Sbjct: 185 TDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPK 244
Query: 125 SGASLWADLWAIPAASR 141
GA + D++A+PA ++
Sbjct: 245 EGAMAFFDVFAMPADAK 261
>pdb|4GL0|A Chain A, Putative SpermidinePUTRESCINE ABC TRANSPORTER FROM
LISTERIA Monocytogenes
Length = 333
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 66/243 (27%), Positives = 100/243 (41%), Gaps = 33/243 (13%)
Query: 3 IAYKKSKFRKHNLAPIEDWKDLWRPELAGRISMVNSPREVIGSVLKYMGASYN-SNNIDL 61
I Y K F N + W L+ PEL +I +++ REV G L +G S N +N L
Sbjct: 119 IIYNKEXFPDKNF---DTWNALFDPELKNQILLIDGAREVXGLGLNSLGYSLNDTNKAHL 175
Query: 62 QVAGGKISVXXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMSNVAVV 121
Q A K+ + D L A + VAV +S + + ++ V
Sbjct: 176 QAARDKLETXTPNVKAI----VGDEIKLLXA--DNEAGVAVTFSGEAAEXLSENEDLEYV 229
Query: 122 VPKSGASLWADLWAIPAASRLETKQIGGRVRGPSPLIHQWIEFCLQTARALPFKQEVIPG 181
+PK G++LW D IP + K + G H++I F L+ A E +
Sbjct: 230 IPKDGSNLWFDNXVIPKTA----KNVDG--------AHKFINFXLKPENA-AINAEYVGY 276
Query: 182 ASPSALETTLVKLPEELLKGKPSQDTNLIVGVPPAEILARCEFLEPLSEATLSDYEWLVA 241
A+P+A L LP+E+ S D P + L E + L + LS Y L
Sbjct: 277 ATPNAKAVEL--LPKEI-----SSDERF---YPDXDELNNLEVYDNLGKRXLSYYNELFL 326
Query: 242 DLQ 244
+ +
Sbjct: 327 EFK 329
>pdb|3TTL|A Chain A, Crystal Structure Of Apo-Spue
pdb|3TTL|B Chain B, Crystal Structure Of Apo-Spue
Length = 340
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 56/220 (25%), Positives = 96/220 (43%), Gaps = 37/220 (16%)
Query: 17 PIEDWKDLWRPELAGR-----ISMVNSPREVIGSVLKYMGASYNSNN-IDLQVAGGKISV 70
PI+ W L+ PE + ++ ++S E++ + L Y+G N+++ D + A ++
Sbjct: 130 PIDSWAILFEPENMKKLAKCGVAFMDSGDEMLPAALNYLGLDPNTHDPKDYKKAEEVLT- 188
Query: 71 XXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMS------NVAVVVPK 124
F S+ Y+ G++ VA G+S DV A R ++ V+PK
Sbjct: 189 -----KVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPK 243
Query: 125 SGASLWADLWAIPAASRLETKQIGGRVRGPSPLIHQWIEFCLQ---TARALPF--KQEVI 179
GA+LW DL AIPA ++ + +I++ L+ A+ + I
Sbjct: 244 EGANLWFDLMAIPADAKAADNA------------YAFIDYLLRPEVIAKVSDYVGYANAI 291
Query: 180 PGASPSALETTLVKLPEELLKGKPSQDTNLIVGVPPAEIL 219
PGA P L V EE+ + D + V PA++L
Sbjct: 292 PGARP--LMDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVL 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 = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 56/220 (25%), Positives = 94/220 (42%), Gaps = 37/220 (16%)
Query: 17 PIEDWKDLWRPELAGR-----ISMVNSPREVIGSVLKYMGASYNSNN-IDLQVAGGKISV 70
PI+ W L+ PE + ++ +S E + + L Y+G N+++ D + A ++
Sbjct: 130 PIDSWAILFEPENXKKLAKCGVAFXDSGDEXLPAALNYLGLDPNTHDPKDYKKAEEVLT- 188
Query: 71 XXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMS------NVAVVVPK 124
F S+ Y+ G++ VA G+S DV A R ++ V+PK
Sbjct: 189 -----KVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPK 243
Query: 125 SGASLWADLWAIPAASRLETKQIGGRVRGPSPLIHQWIEFCLQ---TARALPF--KQEVI 179
GA+LW DL AIPA ++ + +I++ L+ A+ + I
Sbjct: 244 EGANLWFDLXAIPADAKAADNA------------YAFIDYLLRPEVIAKVSDYVGYANAI 291
Query: 180 PGASPSALETTLVKLPEELLKGKPSQDTNLIVGVPPAEIL 219
PGA P L V EE+ + D + V PA++L
Sbjct: 292 PGARP--LXDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVL 329
>pdb|2V84|A Chain A, Crystal Structure Of The Tp0655 (Tppotd) Lipoprotein Of
Treponema Pallidum
Length = 343
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 69/157 (43%), Gaps = 19/157 (12%)
Query: 21 WKDLWRPELAGRISMVNSPREVIGSVLKYMGASYNSNNIDLQVAGGKISVXXXXXXXXXX 80
W R +LA R+SM++ REV+G+ L +G + N+ N + ++A I V
Sbjct: 148 WSIFSRKDLAYRMSMMDDMREVMGAALASLGYNVNTKN-EQELAQAAILVTDHWKPNLVK 206
Query: 81 XRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKR--MSNVAVVVPKSGAS-LWADLWAIP 137
FDS Y K+F GD VA G++ ++ +P+ AS ++ D + IP
Sbjct: 207 ---FDSDGYAKSFASGDFVVAHGFAEAFFAETPEAMHEHIDFFIPQDVASPVYVDSFCIP 263
Query: 138 AASRLETKQIGGRVRGPSPLIHQWIEFCLQTARALPF 174
G R R L H +I F L+ A F
Sbjct: 264 K---------GARNRD---LAHAFINFFLEPAHYAEF 288
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 81/188 (43%), Gaps = 23/188 (12%)
Query: 16 APIEDWKDLWRPELAGR-----ISMVNSPREVIGSVLKYMGASYNSNNIDLQVAGGKISV 70
AP++ W +++PE + +S ++SP E++ + L Y+G +++N A ++ +
Sbjct: 133 APVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPDTDNPKELKAAEELFL 192
Query: 71 XXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMS------NVAVVVPK 124
F S+ Y+ G++ VA+G+S D+ A R V +PK
Sbjct: 193 KIRPYVT-----YFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPK 247
Query: 125 SGASLWADLWAIPAASRLETKQIG--GRVRGPSPL--IHQWIEFCLQTARALPFKQEVI- 179
GA + D+ AIP + + + P + I ++F A A P E I
Sbjct: 248 EGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAAATPLVSEAIR 307
Query: 180 --PGASPS 185
PG PS
Sbjct: 308 NDPGIYPS 315
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 81/188 (43%), Gaps = 23/188 (12%)
Query: 16 APIEDWKDLWRPELAGR-----ISMVNSPREVIGSVLKYMGASYNSNNIDLQVAGGKISV 70
AP++ W +++PE + +S ++SP E++ + L Y+G +++N A ++ +
Sbjct: 133 APVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPDTDNPKELKAAEELFL 192
Query: 71 XXXXXXXXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMS------NVAVVVPK 124
F S+ Y+ G++ VA+G+S D+ A R V +PK
Sbjct: 193 KIRPYVT-----YFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPK 247
Query: 125 SGASLWADLWAIPAASRLETKQIG--GRVRGPSPL--IHQWIEFCLQTARALPFKQEVI- 179
GA + D+ AIP + + + P + I ++F A A P E I
Sbjct: 248 EGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAAATPLVSEAIR 307
Query: 180 --PGASPS 185
PG PS
Sbjct: 308 NDPGIYPS 315
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/125 (25%), Positives = 58/125 (46%), Gaps = 7/125 (5%)
Query: 18 IEDWKDLWRPELAGRISMVNSPREVIGSVLKYMGASYNSNN-IDLQVAGGKISVXXXXXX 76
+ W DLW+PE G + + + REV L+ +G S N+ + +++ A ++
Sbjct: 123 VTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVA 182
Query: 77 XXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAI 136
F+S + + G+V + + W+ A + + + VV PK G W D AI
Sbjct: 183 A------FNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAI 236
Query: 137 PAASR 141
PA ++
Sbjct: 237 PANAK 241
>pdb|1POT|A Chain A, Spermidine/putrescine-binding Protein Complexed With
Spermidine (monomer Form)
Length = 325
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 32/125 (25%), Positives = 58/125 (46%), Gaps = 7/125 (5%)
Query: 18 IEDWKDLWRPELAGRISMVNSPREVIGSVLKYMGASYNSNN-IDLQVAGGKISVXXXXXX 76
+ W DLW+PE G + + + REV L+ +G S N+ + +++ A ++
Sbjct: 125 VTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVA 184
Query: 77 XXXXXRLFDSTHYLKAFGIGDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAI 136
F+S + + G+V + + W+ A + + + VV PK G W D AI
Sbjct: 185 A------FNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAI 238
Query: 137 PAASR 141
PA ++
Sbjct: 239 PANAK 243
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 45/186 (24%), Positives = 75/186 (40%), Gaps = 24/186 (12%)
Query: 19 EDWKDLWRPELAGRISMVNSPREVIGSVLKYMGASYNSNN-IDLQVAGGKISVXXXXXXX 77
E W DLW+ E I + + REV+G L +G S NS + L+ K+
Sbjct: 129 EHWDDLWKLEYKNSIMLFDGAREVLGLGLNSLGYSLNSKDPQQLEETVDKLYKLTPNIKA 188
Query: 78 XXXXRLFDSTHYLKAFGI-GDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASLWADLWAI 136
+ K + I +V + V +S + +++ N+ VVP ++LW D I
Sbjct: 189 IVADEM-------KGYMIQNNVAIGVTFSGEASQMLEKNENLRYVVPTEASNLWFDNMVI 241
Query: 137 PAASRLETKQIGGRVRGPSPLIHQWIEFCLQTARALPFKQEVIPGASPSALETTLVKLPE 196
P + + + +I F L+ AL E + ++P+ L LPE
Sbjct: 242 PKTVKNQDS------------AYAFINFMLKPENALQ-NAEYVGYSTPNLPAKEL--LPE 286
Query: 197 ELLKGK 202
E + K
Sbjct: 287 ETKEDK 292
>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 = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 39/176 (22%), Positives = 66/176 (37%), Gaps = 35/176 (19%)
Query: 18 IEDWKDLWRPELAGRISM-----VNSPREVIGSVLKYMGASYNSNNIDLQVAGGKISVXX 72
I W+DLW+PEL +I++ N P V + K +D++ G+ +
Sbjct: 153 INSWEDLWKPELKNKIAIPDITTTNGPAMVEIAAEKA--------GVDVKTDNGEAAFKE 204
Query: 73 XXXXXXXXXRLFD-STHYLKAFGIGDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASLWA 131
+ + S+ F G++ AV K V V+P+SG L
Sbjct: 205 LEALKPNVVKTYSKSSDLANMFSNGEIVAAVASDFAFGTISKAKPEVINVIPESGTYLNF 264
Query: 132 DLWAIPAASRLETKQIGGRVRGPSPLIHQWIEFCL------QTARAL---PFKQEV 178
+ I S+ L +++I + L +TA+AL P +EV
Sbjct: 265 NTININKNSK------------NKDLAYEFINYALSKEVQEKTAKALNESPVNKEV 308
>pdb|2XPI|A Chain A, Crystal Structure Of ApcC HETERO-Tetramer Cut9-Hcn1
pdb|2XPI|D Chain D, Crystal Structure Of ApcC HETERO-Tetramer Cut9-Hcn1
Length = 597
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 3/108 (2%)
Query: 95 IGDVWVAVGWSSDVLPAVKRMSNVAVVVPKSGASL--WADLWAIPAASRLETKQIGGRVR 152
+ ++ V SD+ A+ N ++V K+ ++ WA WA + + K +
Sbjct: 478 LNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAID 537
Query: 153 GPSP-LIHQWIEFCLQTARALPFKQEVIPGASPSALETTLVKLPEELL 199
+ L+ + + TA AL + + IPG + + L +L P E++
Sbjct: 538 ALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAISPNEIM 585
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
0.318 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,810,612
Number of Sequences: 62578
Number of extensions: 297077
Number of successful extensions: 647
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: 628
Number of HSP's gapped (non-prelim): 14
length of query: 273
length of database: 14,973,337
effective HSP length: 97
effective length of query: 176
effective length of database: 8,903,271
effective search space: 1566975696
effective search space used: 1566975696
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)