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= psy13206
(478 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 = 88.2 bits (217), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 89/383 (23%), Positives = 165/383 (43%), Gaps = 42/383 (10%)
Query: 89 YVLYVVRFMQGLAMGIVFTVAPMYIGEISGAKCRGALSTFFIGMLNTGILLEYTV----- 143
+V+Y R + G+ +G+ ++PMYI E++ A RG L +F + G LL Y V
Sbjct: 129 FVIY--RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIA 186
Query: 144 ----GPYVDYDTLAYV--SLVIP-VVFLMTFIWMPESPYFLIMKGRDVDARKSLFWLRGG 196
+++ D Y+ S IP ++FLM +PESP +L+ +G+ A L + G
Sbjct: 187 RSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246
Query: 197 RESSKDKINLELSNIKQDVEREMKLSDDFMDIISTPANRRSLLIVQIVAVADVISGMSAV 256
+++ + IK ++ K + ++I ++++ G++ V
Sbjct: 247 TLATQ-----AVQEIKHSLDHGRKTGGRLLMF-----GVGVIVIGVMLSIFQQFVGINVV 296
Query: 257 LPYASSTFARTEGSLITPDECTLLLGILVFLSTFPTAFLVDRTGRRPLLLVSCFGSGISQ 316
L YA F S T+++G++ T VD+ GR+PL ++ G I
Sbjct: 297 LYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM 356
Query: 317 LIAGTYYLLSENYTVDLSKFNWIPLISITCFAVIYSIGLGPLVPTLQGEFFPSNTRGLAG 376
GT + V L+S+ + +++ GP+ L E FP+ RG A
Sbjct: 357 FSLGTAFYTQAPGIV--------ALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKAL 408
Query: 377 GVTTITLTVISFLV------MKMYQVICDHYGVYLNFYIYSLGCIICGVLVYFIIPESKG 430
+ + ++ V M + H+ +++IY ++ + ++ +PE+KG
Sbjct: 409 AIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKG 468
Query: 431 KTFAQIQEELNKHIAHKSKLKEQ 453
KT EEL ++K +Q
Sbjct: 469 KTL----EELEALWEPETKKTQQ 487
>pdb|2J5I|A Chain A, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
Length = 276
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G S L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFSPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2VSS|F Chain F, Wild-Type Hydroxycinnamoyl-Coa Hydratase Lyase In Complex
With Acetyl-Coa And Vanillin
Length = 276
Score = 31.6 bits (70), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G S L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFSPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2J5I|I Chain I, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
Length = 276
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G S L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFSPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2J5I|B Chain B, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|C Chain C, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|D Chain D, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|E Chain E, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|F Chain F, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|G Chain G, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|H Chain H, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|J Chain J, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|K Chain K, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2J5I|L Chain L, Crystal Structure Of Hydroxycinnamoyl-Coa Hydratase-Lyase
pdb|2VSS|A Chain A, Wild-Type Hydroxycinnamoyl-Coa Hydratase Lyase In Complex
With Acetyl-Coa And Vanillin
pdb|2VSS|B Chain B, Wild-Type Hydroxycinnamoyl-Coa Hydratase Lyase In Complex
With Acetyl-Coa And Vanillin
pdb|2VSS|C Chain C, Wild-Type Hydroxycinnamoyl-Coa Hydratase Lyase In Complex
With Acetyl-Coa And Vanillin
pdb|2VSS|D Chain D, Wild-Type Hydroxycinnamoyl-Coa Hydratase Lyase In Complex
With Acetyl-Coa And Vanillin
Length = 276
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G S L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFSPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|1VS1|A Chain A, Crystal Structure Of 3-Deoxy-D-Arabino-Heptulosonate-7-
Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix
In Complex With Mn2+ And Pep
pdb|1VS1|B Chain B, Crystal Structure Of 3-Deoxy-D-Arabino-Heptulosonate-7-
Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix
In Complex With Mn2+ And Pep
pdb|1VS1|C Chain C, Crystal Structure Of 3-Deoxy-D-Arabino-Heptulosonate-7-
Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix
In Complex With Mn2+ And Pep
pdb|1VS1|D Chain D, Crystal Structure Of 3-Deoxy-D-Arabino-Heptulosonate-7-
Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix
In Complex With Mn2+ And Pep
Length = 276
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 287 LSTFPTAFLVDRTGRRPLLLVSCFGSGISQLIAGTYYLLSE-NYTVDL 333
+ FP V R+G+ P+LL FG+ + +L+A Y+L E N+ V L
Sbjct: 132 MQNFPLLREVGRSGK-PVLLKRGFGNTVEELLAAAEYILLEGNWQVVL 178
>pdb|2VSU|F Chain F, A Ternary Complex Of Hydroxycinnamoyl-Coa Hydratase-Lyase
( Hchl) With Acetyl-Coenzyme A And Vanillin Gives
Insights Into Substrate Specificity And Mechanism
Length = 276
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G + L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFAPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2VSU|A Chain A, A Ternary Complex Of Hydroxycinnamoyl-Coa Hydratase-Lyase
( Hchl) With Acetyl-Coenzyme A And Vanillin Gives
Insights Into Substrate Specificity And Mechanism.
pdb|2VSU|B Chain B, A Ternary Complex Of Hydroxycinnamoyl-Coa Hydratase-Lyase
( Hchl) With Acetyl-Coenzyme A And Vanillin Gives
Insights Into Substrate Specificity And Mechanism.
pdb|2VSU|D Chain D, A Ternary Complex Of Hydroxycinnamoyl-Coa Hydratase-Lyase
( Hchl) With Acetyl-Coenzyme A And Vanillin Gives
Insights Into Substrate Specificity And Mechanism
Length = 276
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G + L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFAPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2VSU|C Chain C, A Ternary Complex Of Hydroxycinnamoyl-Coa Hydratase-Lyase
( Hchl) With Acetyl-Coenzyme A And Vanillin Gives
Insights Into Substrate Specificity And Mechanism
Length = 275
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 309 CFGSGISQLIAGTYYLLSENYTVDLSKFNW-IPLISITCFAVIYSIG 354
CFG G + L+A + ++ T LS+ NW IP ++ A+ ++G
Sbjct: 117 CFGGGFAPLVACDLAICADEATFGLSEINWGIPPGNLVSKAMADTVG 163
>pdb|2MJP|A Chain A, Structure-Based Identification Of The Biochemical Function
Of A Hypothetical Protein From Methanococcus
Jannaschii:mj0226
pdb|2MJP|B Chain B, Structure-Based Identification Of The Biochemical Function
Of A Hypothetical Protein From Methanococcus
Jannaschii:mj0226
pdb|1B78|A Chain A, Structure-Based Identification Of The Biochemical Function
Of A Hypothetical Protein From Methanococcus
Jannaschii:mj0226
pdb|1B78|B Chain B, Structure-Based Identification Of The Biochemical Function
Of A Hypothetical Protein From Methanococcus
Jannaschii:mj0226
Length = 193
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 425 IPESKGKTFAQIQEELNKHIAHKSKLKEQRKQNKINR 461
IPE + +TFA++ E I+H+ K E+ K+ ++R
Sbjct: 156 IPEEEERTFAEMTTEEKSQISHRKKAFEEFKKFLLDR 192
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 0.141 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,302,119
Number of Sequences: 62578
Number of extensions: 535050
Number of successful extensions: 1443
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1428
Number of HSP's gapped (non-prelim): 16
length of query: 478
length of database: 14,973,337
effective HSP length: 103
effective length of query: 375
effective length of database: 8,527,803
effective search space: 3197926125
effective search space used: 3197926125
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: 53 (25.0 bits)