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= psy4866
(537 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 89/368 (24%), Positives = 172/368 (46%), Gaps = 44/368 (11%)
Query: 162 VMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLGILYTYVLG------SE 215
+ R + G + ++SPMY+ E++ IRG + + Q + G L Y + +
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190
Query: 216 LSYMN-----YLTYSLIIP-IIFTVTFMFMPESPYFYAIKNQEGKAIESL-KWLRNKTAD 268
S++N Y+ S IP ++F + +PESP + + ++ +A L K + N A
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLAT 250
Query: 269 QVQSELQIIKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIF 328
Q E+ +++ + +T R M + V L++F+ F G+ ++ YA +F
Sbjct: 251 QAVQEI----KHSLDHGRKTGGRLLM--FGVGVIVIGVMLSIFQQFVGINVVLYYAPEVF 304
Query: 329 ASSETFLPSDYISILFAIIL----LVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIAGL 384
+T S I++L II+ L + +D+ GR+ L ++ + G ++ F G
Sbjct: 305 ---KTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGT 361
Query: 385 YYYVTIELQYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVSCAVINI 444
+Y + P V LS+ F + +GP+ LLSE F + ++ + A I +
Sbjct: 362 AFYT------QAPGI--VALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALA-IAV 412
Query: 445 LCTTLG--LISYKLFFLMDKHIGMYSNFLFG------GVSSLVCTVYLYYFLLETKGKTF 496
L +S+ F +MDK+ + ++F G G ++ ++++ F+ ETKGKT
Sbjct: 413 AAQWLANYFVSWT-FPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTL 471
Query: 497 NEIQYMFK 504
E++ +++
Sbjct: 472 EELEALWE 479
>pdb|2Y5Y|A Chain A, Crystal Structure Of Lacy In Complex With An Affinity
Inactivator
pdb|2Y5Y|B Chain B, Crystal Structure Of Lacy In Complex With An Affinity
Inactivator
Length = 423
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 38/71 (53%)
Query: 124 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 183
A +++NRIG K +LL+ G I + I + ++ S L + +++TL F + + V S Y+
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYIT 338
Query: 184 EISETSIRGTI 194
E TI
Sbjct: 339 SQFEVRFSATI 349
>pdb|2V8N|A Chain A, Wild-Type Structure Of Lactose Permease
pdb|2V8N|B Chain B, Wild-Type Structure Of Lactose Permease
Length = 417
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%)
Query: 124 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 183
A +++NRIG K +LL+ G I + I + ++ S L + +++TL F + + V Y+
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338
Query: 184 EISETSIRGTI 194
E TI
Sbjct: 339 SQFEVRFSATI 349
>pdb|1PV6|A Chain A, Crystal Structure Of Lactose Permease
pdb|1PV6|B Chain B, Crystal Structure Of Lactose Permease
pdb|1PV7|A Chain A, Crystal Structure Of Lactose Permease With Tdg
pdb|1PV7|B Chain B, Crystal Structure Of Lactose Permease With Tdg
pdb|2CFP|A Chain A, Sugar Free Lactose Permease At Acidic Ph
pdb|2CFQ|A Chain A, Sugar Free Lactose Permease At Neutral Ph
Length = 417
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%)
Query: 124 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 183
A +++NRIG K +LL+ G I + I + ++ S L + +++TL F + + V Y+
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338
Query: 184 EISETSIRGTI 194
E TI
Sbjct: 339 SQFEVRFSATI 349
>pdb|1XDO|A Chain A, Crystal Structure Of Escherichia Coli Polyphosphate Kinase
pdb|1XDO|B Chain B, Crystal Structure Of Escherichia Coli Polyphosphate Kinase
pdb|1XDP|A Chain A, Crystal Structure Of The E.Coli Polyphosphate Kinase In
Complex With Amppnp
pdb|1XDP|B Chain B, Crystal Structure Of The E.Coli Polyphosphate Kinase In
Complex With Amppnp
Length = 687
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 435 KAVSCAVINILCTTLGL-ISYKLFFLMDKHIG---MYSNFLFGGVSSLVCTVYLYYFLLE 490
K ++ A ++++ + GL I KLF + K G Y++ G + +Y Y LL
Sbjct: 415 KRLTEAGVHVIFSAPGLKIHAKLFLISRKENGEVVRYAHIGTGNFNEKTARLYTDYSLLT 474
Query: 491 TKGKTFNEIQYMFKYGKNEY 510
+ NE++ +F + +N Y
Sbjct: 475 ADARITNEVRRVFNFIENPY 494
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
0.325 0.138 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,721,843
Number of Sequences: 62578
Number of extensions: 588022
Number of successful extensions: 1323
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1316
Number of HSP's gapped (non-prelim): 8
length of query: 537
length of database: 14,973,337
effective HSP length: 103
effective length of query: 434
effective length of database: 8,527,803
effective search space: 3701066502
effective search space used: 3701066502
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)