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= 040874
(165 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 = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 77 WAAPYRWGAMMIAYKKSKFRKHDLAPIEDWKDLWRPELAGRISMVNSPREVIGSVLKYMG 136
++ PY WG + I Y K F + + W L+ PEL +I +++ REV G L +G
Sbjct: 108 YSXPYFWGTLGIIYNKEXFPDKNF---DTWNALFDPELKNQILLIDGAREVXGLGLNSLG 164
Query: 137 ASYNSNN 143
S N N
Sbjct: 165 YSLNDTN 171
>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 = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 74 GKIWAAPYRWGAMMIAYKKSKFRKHDLAPIEDWKDLWRPELAGRISMVNSPREVIGSVLK 133
G ++ PY WG + I Y ++ D AP E W DLW+ E I + + REV+G L
Sbjct: 103 GNKFSIPYFWGTLGIVYNETMV---DEAP-EHWDDLWKLEYKNSIMLFDGAREVLGLGLN 158
Query: 134 YMGASYNS 141
+G S NS
Sbjct: 159 SLGYSLNS 166
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 7/77 (9%)
Query: 74 GKIWAAPYRWGAMMIAYKKSKFRKH--DLAPIEDWKDLWRPELAGR-----ISMVNSPRE 126
G A PY WG + I Y K + D AP++ W +++PE + +S ++SP E
Sbjct: 104 GNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTE 163
Query: 127 VIGSVLKYMGASYNSNN 143
++ + L Y+G +++N
Sbjct: 164 ILPAALHYLGYKPDTDN 180
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 7/77 (9%)
Query: 74 GKIWAAPYRWGAMMIAYKKSKFRKH--DLAPIEDWKDLWRPELAGR-----ISMVNSPRE 126
G A PY WG + I Y K + D AP++ W +++PE + +S ++SP E
Sbjct: 104 GNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTE 163
Query: 127 VIGSVLKYMGASYNSNN 143
++ + L Y+G +++N
Sbjct: 164 ILPAALHYLGYKPDTDN 180
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 77 WAAPYRWGAMMIAYKKSKFRK--HDLAPIEDWKDLWRPELAGR-----ISMVNSPREVIG 129
+A PY W I Y K + + AP++ W + +PE + +S +++P EV
Sbjct: 103 FAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFA 162
Query: 130 SVLKYMGASYNSNNID 145
+VL Y+G NS D
Sbjct: 163 TVLNYLGKDPNSTKAD 178
>pdb|1POT|A Chain A, Spermidine/putrescine-binding Protein Complexed With
Spermidine (monomer Form)
Length = 325
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 77 WAAPYRWGAMMIAYKKSKFRKHDLAPIEDWKDLWRPELAGRISMVNSPREVIGSVLKYMG 136
++ PY WGA I D + W DLW+PE G + + + REV L+ +G
Sbjct: 102 YSIPYIWGATAIGVNGDAV---DPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLG 158
Query: 137 ASYNSNN 143
S N+ +
Sbjct: 159 YSGNTTD 165
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 77 WAAPYRWGAMMIAYKKSKFRKHDLAPIEDWKDLWRPELAGRISMVNSPREVIGSVLKYMG 136
++ PY WGA I D + W DLW+PE G + + + REV L+ +G
Sbjct: 100 YSIPYIWGATAIGVNGDAV---DPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLG 156
Query: 137 ASYNSNN 143
S N+ +
Sbjct: 157 YSGNTTD 163
>pdb|3TTL|A Chain A, Crystal Structure Of Apo-Spue
pdb|3TTL|B Chain B, Crystal Structure Of Apo-Spue
Length = 340
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 74 GKIWAAPYRWGAMMIAYKKSKFRK-HDLAPIEDWKDLWRPELAGR-----ISMVNSPREV 127
G +A PY WG I Y +K ++ PI+ W L+ PE + ++ ++S E+
Sbjct: 101 GNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENMKKLAKCGVAFMDSGDEM 160
Query: 128 IGSVLKYMGASYNSNN 143
+ + L Y+G N+++
Sbjct: 161 LPAALNYLGLDPNTHD 176
>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 = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 74 GKIWAAPYRWGAMMIAYKKSKFRK-HDLAPIEDWKDLWRPELAGR-----ISMVNSPREV 127
G +A PY WG I Y +K ++ PI+ W L+ PE + ++ +S E
Sbjct: 101 GNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENXKKLAKCGVAFXDSGDEX 160
Query: 128 IGSVLKYMGASYNSNN 143
+ + L Y+G N+++
Sbjct: 161 LPAALNYLGLDPNTHD 176
>pdb|2FNC|A Chain A, Thermotoga Maritima Maltotriose Binding Protein Bound With
Maltotriose
Length = 381
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 26/63 (41%)
Query: 30 AADLVSVGDPWLSFAIEKRLIEPIAGGEDQDWFKCLSHKWKRTRGKIWAAPYRWGAMMIA 89
AD++ W+ LIEPI D F + K GK++ PY A+ +
Sbjct: 53 GADIIVGAHDWVGELAVNGLIEPIPNFSDLKNFYDTALKAFSYGGKLYGVPYAMEAVALI 112
Query: 90 YKK 92
Y K
Sbjct: 113 YNK 115
>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 = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 103 IEDWKDLWRPELAGRISM 120
I W+DLW+PEL +I++
Sbjct: 153 INSWEDLWKPELKNKIAI 170
>pdb|3UT2|A Chain A, Crystal Structure Of Fungal Magkatg2
pdb|3UT2|B Chain B, Crystal Structure Of Fungal Magkatg2
Length = 764
Score = 28.1 bits (61), Expect = 2.2, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 17 PFNKVKAKSASYMAADLVSVGDPWLSFAIEKRLI---EPIAGGEDQDWFKCL 65
PF+K K + A+ + +DL + DP I +R + E +A + WFK L
Sbjct: 387 PFDKTKFRKATMLTSDLALINDPEY-LKISQRWLEHPEELADAFAKAWFKLL 437
>pdb|2Z8D|A Chain A, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Biose
pdb|2Z8D|B Chain B, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Biose
pdb|2Z8E|A Chain A, The Galacto-n-biose-/lacto-n-biose I-binding Protein
(gl-bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Galacto- N-biose
pdb|2Z8E|B Chain B, The Galacto-n-biose-/lacto-n-biose I-binding Protein
(gl-bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Galacto- N-biose
pdb|2Z8F|A Chain A, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Tetraose
pdb|2Z8F|B Chain B, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Tetraose
Length = 412
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 30/126 (23%), Positives = 48/126 (38%), Gaps = 7/126 (5%)
Query: 20 KVKAKSASYMAADLVSVGDPWLSFAIEKRLIEPIAGGEDQ--DWFKCLSHKWKRTRGKIW 77
K++ S A DL VG L K L++ + +Q + F + + GK +
Sbjct: 64 KLETDVKSGEAPDLAQVGYAELPEVFTKGLLQDVTQYAEQYKNDFASGPYSLVQVGGKAY 123
Query: 78 AAPYRWGAMMIAYKKSKFRKHDLAPIEDWKDLW-----RPELAGRISMVNSPREVIGSVL 132
P G ++ Y K++F K + I D + AG+ M P E +
Sbjct: 124 GLPQDTGPLVYFYNKAEFEKLGITEIPQTADEFIAAAKTAAAAGKYIMSYQPDEAGNMIS 183
Query: 133 KYMGAS 138
GAS
Sbjct: 184 GLAGAS 189
>pdb|2GHA|A Chain A, Thermotoga Maritima Maltotriose Binding Protein Bound With
Maltotriose
pdb|2GHA|B Chain B, Thermotoga Maritima Maltotriose Binding Protein Bound With
Maltotriose
pdb|2GHB|A Chain A, Thermotoga Maritima Maltotriose Binding Protein, Ligand
Free Form
pdb|2GHB|B Chain B, Thermotoga Maritima Maltotriose Binding Protein, Ligand
Free Form
pdb|2GHB|C Chain C, Thermotoga Maritima Maltotriose Binding Protein, Ligand
Free Form
Length = 382
Score = 26.6 bits (57), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 4/79 (5%)
Query: 18 FNKVKAK----SASYMAADLVSVGDPWLSFAIEKRLIEPIAGGEDQDWFKCLSHKWKRTR 73
F +K+K + AD++ W+ LIEPI D F +
Sbjct: 39 FQDIKSKFLTAAPEGQGADIIVGAHDWVGELAVNGLIEPIPNFSDLKNFYETALNAFSYG 98
Query: 74 GKIWAAPYRWGAMMIAYKK 92
GK++ PY A+ + Y K
Sbjct: 99 GKLYGIPYAMEAIALIYNK 117
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 0.134 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,813,699
Number of Sequences: 62578
Number of extensions: 185730
Number of successful extensions: 393
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 16
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
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: 47 (22.7 bits)