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= 036082
(315 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GL0|A Chain A, Putative SpermidinePUTRESCINE ABC TRANSPORTER FROM
LISTERIA Monocytogenes
Length = 333
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 54/203 (26%), Positives = 81/203 (39%), Gaps = 43/203 (21%)
Query: 20 CAAPYRWGTVVIAYKKSKFRKHNLAPIEDWKDLWRPELAGRISMVNSPREVIG------- 72
+ PY WGT+ I Y K F N + W L+ PEL +I +++ REV G
Sbjct: 108 YSXPYFWGTLGIIYNKEXFPDKNF---DTWNALFDPELKNQILLIDGAREVXGLGLNSLG 164
Query: 73 ------SIAVXXXXXXXXXXXXXXXKAFGIGD----------VWVAVGWSSDVLPAVKHM 116
+ A KA +GD VAV +S + +
Sbjct: 165 YSLNDTNKAHLQAARDKLETXTPNVKAI-VGDEIKLLXADNEAGVAVTFSGEAAEXLSEN 223
Query: 117 SNVA-VVPKSGASLWADLWAIPAASRLETKQIGGRVRGLSPLIHQWIEFCLQTARALPFK 175
++ V+PK G++LW D IP + K + G H++I F L+ A
Sbjct: 224 EDLEYVIPKDGSNLWFDNXVIPKTA----KNVDG--------AHKFINFXLKPENA-AIN 270
Query: 176 QEVIPGASPSALESTLVKLPGEL 198
E + A+P+A L LP E+
Sbjct: 271 AEYVGYATPNAKAVEL--LPKEI 291
>pdb|3TTL|A Chain A, Crystal Structure Of Apo-Spue
pdb|3TTL|B Chain B, Crystal Structure Of Apo-Spue
Length = 340
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 61/243 (25%), Positives = 92/243 (37%), Gaps = 44/243 (18%)
Query: 12 EIDPRGKICAAPYRWGTVVIAYKKSKFRK-HNLAPIEDWKDLWRPELAGR-----ISMVN 65
E+ G A PY WGT I Y +K ++ PI+ W L+ PE + ++ ++
Sbjct: 96 EVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENMKKLAKCGVAFMD 155
Query: 66 SPREVIGSIAVXXXXXXXXXXXXXXXKA----------------------FGIGDVWVAV 103
S E++ + KA G++ VA
Sbjct: 156 SGDEMLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAF 215
Query: 104 GWSSDVLPAV-------KHMSNVAVVPKSGASLWADLWAIPAASRLETKQIGGRVRGLSP 156
G+S DV A K + V+PK GA+LW DL AIPA ++ L P
Sbjct: 216 GYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLMAIPADAKAADNAYAFIDYLLRP 275
Query: 157 LIHQWIEFCLQTARALPFKQEVIPGASPSALESTLVKLPGELLKGKPSLDTNLIAGVPPA 216
+ + + A A IPGA P L V E+ + LD ++ V PA
Sbjct: 276 EVIAKVSDYVGYANA-------IPGARP--LMDKSVSDSEEVYPPQAVLDKLYVSAVLPA 326
Query: 217 EIL 219
++L
Sbjct: 327 KVL 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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 61/243 (25%), Positives = 90/243 (37%), Gaps = 44/243 (18%)
Query: 12 EIDPRGKICAAPYRWGTVVIAYKKSKFRK-HNLAPIEDWKDLWRPELAGR-----ISMVN 65
E+ G A PY WGT I Y +K ++ PI+ W L+ PE + ++ +
Sbjct: 96 EVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENXKKLAKCGVAFXD 155
Query: 66 SPREVIGSIAVXXXXXXXXXXXXXXXKA----------------------FGIGDVWVAV 103
S E + + KA G++ VA
Sbjct: 156 SGDEXLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAF 215
Query: 104 GWSSDVLPAV-------KHMSNVAVVPKSGASLWADLWAIPAASRLETKQIGGRVRGLSP 156
G+S DV A K + V+PK GA+LW DL AIPA ++ L P
Sbjct: 216 GYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLXAIPADAKAADNAYAFIDYLLRP 275
Query: 157 LIHQWIEFCLQTARALPFKQEVIPGASPSALESTLVKLPGELLKGKPSLDTNLIAGVPPA 216
+ + + A A IPGA P L V E+ + LD ++ V PA
Sbjct: 276 EVIAKVSDYVGYANA-------IPGARP--LXDKSVSDSEEVYPPQAVLDKLYVSAVLPA 326
Query: 217 EIL 219
++L
Sbjct: 327 KVL 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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 40/165 (24%), Positives = 65/165 (39%), Gaps = 38/165 (23%)
Query: 14 DPRGKICAAPYRWGTVVIAYKKSKFRK--HNLAPIEDWKDLWRPELAGR-----ISMVNS 66
DP K A PY W T I Y K + AP++ W + +PE + +S +++
Sbjct: 98 DPDNKF-AMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDA 156
Query: 67 PREVIGSIA-----------------------VXXXXXXXXXXXXXXXKAFGIGDVWVAV 103
P EV ++ + GD+ VA+
Sbjct: 157 PEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAI 216
Query: 104 GWSSDVLPA------VKHMSNVAV-VPKSGASLWADLWAIPAASR 141
GW+ DV A K+ NV+ +PK GA + D++A+PA ++
Sbjct: 217 GWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAK 261
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 59/152 (38%), Gaps = 28/152 (18%)
Query: 13 IDPRGKICAAPYRWGTVVIAYKKSKFRKHNLAPIEDWKDLWRPELAGRISMVNSPREVIG 72
DP G + PY WGT+ I Y ++ + AP E W DLW+ E I + + REV+G
Sbjct: 100 FDP-GNKFSIPYFWGTLGIVYNETMVDE---AP-EHWDDLWKLEYKNSIMLFDGAREVLG 154
Query: 73 ----SIAVXXXXXXXXXXXXXXXKAFGI------------------GDVWVAVGWSSDVL 110
S+ K + + +V + V +S +
Sbjct: 155 LGLNSLGYSLNSKDPQQLEETVDKLYKLTPNIKAIVADEMKGYMIQNNVAIGVTFSGEAS 214
Query: 111 PAVKHMSNV-AVVPKSGASLWADLWAIPAASR 141
++ N+ VVP ++LW D IP +
Sbjct: 215 QMLEKNENLRYVVPTEASNLWFDNMVIPKTVK 246
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 56/227 (24%), Positives = 87/227 (38%), Gaps = 47/227 (20%)
Query: 12 EIDPRGKICAAPYRWGTVVIAYKKSKFRKH--NLAPIEDWKDLWRPELAGR-----ISMV 64
E+ G A PY WGT+ I Y K + + AP++ W +++PE + +S +
Sbjct: 99 EVSDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFL 158
Query: 65 NSPREVIGSIAVXXXXXXXXXXXXXXXKA-----------------------FGIGDVWV 101
+SP E++ + A+ KA G++ V
Sbjct: 159 DSPTEILPA-ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICV 217
Query: 102 AVGWSSDVLPA------VKHMSNVAV-VPKSGASLWADLWAIPAASRLETKQIGGRVRGL 154
A+G+S D+ A K+ V +PK GA + D+ AIP + + +
Sbjct: 218 AIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLM 277
Query: 155 SPLIHQWIEFCLQ----TARALPFKQEVI---PGASPSALESTLVKL 194
P I I +Q A A P E I PG PS E + KL
Sbjct: 278 KPEIMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPS--EEVMKKL 322
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 56/227 (24%), Positives = 87/227 (38%), Gaps = 47/227 (20%)
Query: 12 EIDPRGKICAAPYRWGTVVIAYKKSKFRKH--NLAPIEDWKDLWRPELAGR-----ISMV 64
E+ G A PY WGT+ I Y K + + AP++ W +++PE + +S +
Sbjct: 99 EVSDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFL 158
Query: 65 NSPREVIGSIAVXXXXXXXXXXXXXXXKA-----------------------FGIGDVWV 101
+SP E++ + A+ KA G++ V
Sbjct: 159 DSPTEILPA-ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICV 217
Query: 102 AVGWSSDVLPA------VKHMSNVAV-VPKSGASLWADLWAIPAASRLETKQIGGRVRGL 154
A+G+S D+ A K+ V +PK GA + D+ AIP + + +
Sbjct: 218 AIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLM 277
Query: 155 SPLIHQWIEFCLQ----TARALPFKQEVI---PGASPSALESTLVKL 194
P I I +Q A A P E I PG PS E + KL
Sbjct: 278 KPEIMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPS--EEVMKKL 322
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 54/153 (35%), Gaps = 29/153 (18%)
Query: 13 IDPRGKICAAPYRWGTVVIAYKKSKFRKHNLAPIEDWKDLWRPELAGRISMVNSPREVIG 72
DP + PY WG I + + W DLW+PE G + + + REV
Sbjct: 94 FDPNND-YSIPYIWGATAIGVNGDAVDPKS---VTSWADLWKPEYKGSLLLTDDAREVF- 148
Query: 73 SIAVXXXXXXXXXXXXXXXKA-----------------------FGIGDVWVAVGWSSDV 109
+A+ +A + G+V + + W+
Sbjct: 149 QMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSA 208
Query: 110 LPAVKHMSNVAVV-PKSGASLWADLWAIPAASR 141
A + + + VV PK G W D AIPA ++
Sbjct: 209 FVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 241
>pdb|1POT|A Chain A, Spermidine/putrescine-binding Protein Complexed With
Spermidine (monomer Form)
Length = 325
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 54/153 (35%), Gaps = 29/153 (18%)
Query: 13 IDPRGKICAAPYRWGTVVIAYKKSKFRKHNLAPIEDWKDLWRPELAGRISMVNSPREVIG 72
DP + PY WG I + + W DLW+PE G + + + REV
Sbjct: 96 FDPNND-YSIPYIWGATAIGVNGDAVDPKS---VTSWADLWKPEYKGSLLLTDDAREVF- 150
Query: 73 SIAVXXXXXXXXXXXXXXXKA-----------------------FGIGDVWVAVGWSSDV 109
+A+ +A + G+V + + W+
Sbjct: 151 QMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSA 210
Query: 110 LPAVKHMSNVAVV-PKSGASLWADLWAIPAASR 141
A + + + VV PK G W D AIPA ++
Sbjct: 211 FVARQAGTPIDVVWPKEGGIFWMDSLAIPANAK 243
>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 = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 47/108 (43%), Gaps = 4/108 (3%)
Query: 96 IGDVWVAVGWSSDVLPAVKHMSNVAVVPK---SGASLWADLWAIPAASRLETKQIGGRVR 152
+ ++ V SD+ A+ H N ++ K S WA WA + + K +
Sbjct: 478 LNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAID 537
Query: 153 GLSP-LIHQWIEFCLQTARALPFKQEVIPGASPSALESTLVKLPGELL 199
L+ L+ + + TA AL + + IPG + + L +L P E++
Sbjct: 538 ALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAISPNEIM 585
>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 = 3.1, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 46 IEDWKDLWRPELAGRISM 63
I W+DLW+PEL +I++
Sbjct: 153 INSWEDLWKPELKNKIAI 170
>pdb|3RRW|A Chain A, Crystal Structure Of The Tl29 Protein From Arabidopsis
Thaliana
pdb|3RRW|B Chain B, Crystal Structure Of The Tl29 Protein From Arabidopsis
Thaliana
Length = 268
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 7 RNDAGEIDPRGKICAAPYRWGTVVIAYKKSKFRKHNLAP 45
R+DA E DP G++ +WG + K KF L P
Sbjct: 151 RSDATEADPEGRVP----QWGKATVQEXKDKFIAVGLGP 185
>pdb|3AWJ|A Chain A, Crystal Structure Of The Huperzia Serrata Polyketide
Synthase 1 Complexed With Coa-Sh
pdb|3AWJ|B Chain B, Crystal Structure Of The Huperzia Serrata Polyketide
Synthase 1 Complexed With Coa-Sh
pdb|3AWK|A Chain A, Crystal Structure Of The Polyketide Synthase 1 From
Huperzia Serrata
Length = 402
Score = 27.7 bits (60), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 48/104 (46%), Gaps = 5/104 (4%)
Query: 185 SALESTLVKLPGELLKGKPSLDTNLIAGVPPAEILARFEFLEPLSEATLSDMSGWEIGSG 244
S ++ L E+L+ PS+ A + P + +A E + EA +S + W G
Sbjct: 76 SGIKKRHFHLTDEILRKNPSICKFKEASLDPRQDIAVLEVPKLAKEAAISAIKQW----G 131
Query: 245 QLGQSITSLVKEASAALYITGCT-EMAEVLEVLRETKDECLFEQ 287
Q IT LV ++ + + G ++A++L + K L++Q
Sbjct: 132 QPKSKITHLVFATTSGVDMPGADFQLAKLLGLRPTVKRVMLYQQ 175
>pdb|3ZEN|D Chain D, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|E Chain E, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|F Chain F, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|A Chain A, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|B Chain B, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|C Chain C, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
Length = 3089
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 238 GWEIGSGQLGQS--ITSLVKEASAALYITGCTEMAEVL 273
GW G+G +GQ+ I S V+EA Y T EMA +L
Sbjct: 2338 GWTKGTGLMGQNDAIVSAVEEAGVTTYTT--DEMAAML 2373
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
0.319 0.135 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,317,204
Number of Sequences: 62578
Number of extensions: 306923
Number of successful extensions: 618
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 597
Number of HSP's gapped (non-prelim): 24
length of query: 315
length of database: 14,973,337
effective HSP length: 99
effective length of query: 216
effective length of database: 8,778,115
effective search space: 1896072840
effective search space used: 1896072840
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)