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= 009409
(535 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
From E.Coli
Length = 451
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 43/184 (23%), Positives = 75/184 (40%), Gaps = 16/184 (8%)
Query: 260 PPIIENLG------WESVFYI--FGLLGIAWFSGFKILQEGETSNGATLAPRSNYINMKK 311
PP++ LG W + Y+ F + +A F+ F ++++ S G L P Y N
Sbjct: 171 PPLLFLLGMAWFNDWHAALYMPAFCAILVALFA-FAMMRDTPQSCG--LPPIEEYKNDYP 227
Query: 312 SLSASLEEMGESLKDVPWKAIFRSKAVWAMIYAHFCGSWGHYTCLSWLPTYFSEELSLNL 371
E + K + + + +K +W + A+ Y L W PTY E L
Sbjct: 228 DDYNEKAEQELTAKQIFMQYVLPNKLLWYIAIANVFVYLLRYGILDWSPTYLKEVKHFAL 287
Query: 372 TEAAWVSILPPLASVLVTSIAAQFADNLI-----ATGVETTMVRKICQTIAFLSPAVCMT 426
+++W L A + T + +D + ATGV + I + +++PA T
Sbjct: 288 DKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAGNPT 347
Query: 427 LSSI 430
+ I
Sbjct: 348 VDMI 351
>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
Fucp (N162a)
Length = 438
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 132 NLSVAIIP-MSHRFGWNSSVAGLVQSSFFWGYALSQLPGGWLAKIFGGRKVLQTGVLIWS 190
NL+ ++P F + AGL+QS+F++GY + +P G L K + + TG+ +++
Sbjct: 43 NLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYA 102
Query: 191 LATALL 196
L AL
Sbjct: 103 LGAALF 108
>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
Transporter, Fucp, In The Outward Conformation
Length = 438
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 132 NLSVAIIP-MSHRFGWNSSVAGLVQSSFFWGYALSQLPGGWLAKIFGGRKVLQTGVLIWS 190
NL+ ++P F + AGL+QS+F++GY + +P G L K + + TG+ +++
Sbjct: 43 NLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYA 102
Query: 191 LATALL 196
L AL
Sbjct: 103 LGAALF 108
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 56/123 (45%), Gaps = 17/123 (13%)
Query: 148 SSVAGLVQSSFFWGYALSQLPGGWLAKIFGGRKVLQTGVLIWSLA-----------TALL 196
+S+ G +S G + GG+ + FG R L+ +++ ++ T++
Sbjct: 54 NSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSIN 113
Query: 197 P------LLAGFMPGLVLSRVLVGIGEGVSPSAATDLIARSIPLEERSRAVSFVFGGLSF 250
P LAG++P V+ R++ GIG G++ + IA P R + VSF + F
Sbjct: 114 PDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIF 173
Query: 251 GSV 253
G +
Sbjct: 174 GQL 176
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 34/134 (25%), Positives = 55/134 (41%), Gaps = 4/134 (2%)
Query: 149 SVAGLVQSSFFWGYALSQLPGGWLA-KIFGGRKVLQTGVLIWSLATALLPLLAGFMPGLV 207
+VA V SF G L GGW+A + FG + LI+ + A L + + G
Sbjct: 54 AVAKDVFHSFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYCVGHAFLAIFEHSVQGFY 113
Query: 208 LSRVLVGIGEGVSPSAATDLIARSIPLEERS---RAVSFVFGGLSFGSVAGLLLAPPIIE 264
L+ +G G + + +S +A + ++FGS L P +++
Sbjct: 114 TGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKAFDMFYFTINFGSFFASLSMPLLLK 173
Query: 265 NLGWESVFYIFGLL 278
N G F I G+L
Sbjct: 174 NFGAAVAFGIPGVL 187
>pdb|3CSR|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CSZ|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT0|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT1|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
pdb|3CT5|A Chain A, Crystal And Cryoem Structural Studies Of A Cell Wall
Degrading Enzyme In The Bacteriophage Phi29 Tail
Length = 159
Score = 28.9 bits (63), Expect = 6.8, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 289 LQEGETSNGATL---APRSNYINMKKSLSASLEEMGESLKDVPWK 330
L EG TS G L P SNYIN S + M LK + W+
Sbjct: 56 LDEGNTSLGFGLVQWTPASNYINWANSQGLPYKNMDSELKRIIWE 100
>pdb|2D13|A Chain A, Crystal Structure Of Ph1257 From Pyrococcus Horikoshii Ot3
pdb|2D13|B Chain B, Crystal Structure Of Ph1257 From Pyrococcus Horikoshii Ot3
pdb|2D13|C Chain C, Crystal Structure Of Ph1257 From Pyrococcus Horikoshii Ot3
pdb|2D13|D Chain D, Crystal Structure Of Ph1257 From Pyrococcus Horikoshii Ot3
Length = 227
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 60 KEETDKFDEVLTGLRVDEPGSVSGFDSESGQVRGTEEVGR----ASYWPPWKNIPQRYKL 115
++E + VL GL+VD G V+G + Q E V R Y P W+ P +Y L
Sbjct: 76 EKEVEDLKNVLEGLKVD--GIVAGALASRYQKERIENVARELGLKVYTPAWEKDPYQYML 133
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 0.136 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,070,924
Number of Sequences: 62578
Number of extensions: 598407
Number of successful extensions: 1491
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1485
Number of HSP's gapped (non-prelim): 17
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
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: 54 (25.4 bits)