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= psy15539
(333 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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 72/266 (27%), Positives = 124/266 (46%), Gaps = 52/266 (19%)
Query: 106 ESDLSFIGSSMALGAVFGSPVVGNLVDTVGRKNTMLLLAV-----------PTLVGWGLI 154
S L F +S +G + G + G + GR++++ + AV P L G+ I
Sbjct: 54 NSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPEL-GFTSI 112
Query: 155 IWSQSVIMFCAG--------RLLTGFGGGSFAVVVPMYTAEIAETEIRGTLGTYFQLQCT 206
+V ++ AG R++ G G G +++ PMY AE+A IRG L ++ Q
Sbjct: 113 NPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAII 172
Query: 207 AGILFVYAV---------GSWASVYGLSIICA--LLP-IFFVGLMLLMPESPQFHLKKNR 254
G L VY V SW + G + A +P + F+ L+ +PESP++ + + +
Sbjct: 173 FGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGK 232
Query: 255 VKQAKESLQWFRGSEYDIDSEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGLGVMF 314
+QA+ L+ G+ + + ++++SL+ R R L+ G+GV+
Sbjct: 233 QEQAEGILRKIMGNTLATQA-VQEIKHSLDHGRKT------------GGRLLMFGVGVIV 279
Query: 315 I-------QQFGGINAVVFYTVKIFK 333
I QQF GIN V++Y ++FK
Sbjct: 280 IGVMLSIFQQFVGINVVLYYAPEVFK 305
>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
Length = 170
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 274 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 326
S TD + E E + +PL++ F+ K G + + G F++ FGGI ++
Sbjct: 80 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 139
Query: 327 YTV 329
Y V
Sbjct: 140 YRV 142
>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
Length = 451
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 274 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 326
S TD + E E + +PL++ F+ K G + + G F++ FGGI ++
Sbjct: 369 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 428
Query: 327 YTV 329
Y V
Sbjct: 429 YRV 431
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 274 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 326
S TD + E E + +PL++ F+ K G + + G F++ FGGI ++
Sbjct: 346 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 405
Query: 327 YTV 329
Y V
Sbjct: 406 YRV 408
>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
Erf1-Mechanism Of Stop Codon Recognition And
Peptidyl-Trna Hydrolysis
Length = 437
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 274 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 326
S TD + E E + +PL++ F+ K G + + G F++ FGGI ++
Sbjct: 355 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 414
Query: 327 YTV 329
Y V
Sbjct: 415 YRV 417
>pdb|3VLH|A Chain A, Crystal Structure Analysis Of The Arg409leu Variants Of
Katg From Haloarcula Marismortui
pdb|3VLH|B Chain B, Crystal Structure Analysis Of The Arg409leu Variants Of
Katg From Haloarcula Marismortui
pdb|3VLI|A Chain A, Crystal Structure Analysis Of The Cyanide Arg409leu
Variant Katg From Haloarcula Marismortui
pdb|3VLI|B Chain B, Crystal Structure Analysis Of The Cyanide Arg409leu
Variant Katg From Haloarcula Marismortui
pdb|3VLJ|A Chain A, Crystal Structure Analysis Of The Cyanide Arg409leu
Variant Complexes With O-Dianisidine In Katg From
Haloarcula Marismortui
pdb|3VLJ|B Chain B, Crystal Structure Analysis Of The Cyanide Arg409leu
Variant Complexes With O-Dianisidine In Katg From
Haloarcula Marismortui
Length = 737
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 RLIISPFSSSAPQFDDVKPLVSPVDKMAAETKMGISQQTLVSNQQKAKRITQYMAALTAT 75
R+ P + AP FD +KP V V + +++ LV N A + + LTA
Sbjct: 561 RVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDN---ADLLNLTASELTAL 617
Query: 76 IGG 78
IGG
Sbjct: 618 IGG 620
>pdb|3VLM|A Chain A, Crystal Structure Analysis Of The Met244ala Variant Of
Katg From Haloarcula Marismortui
pdb|3VLM|B Chain B, Crystal Structure Analysis Of The Met244ala Variant Of
Katg From Haloarcula Marismortui
Length = 737
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 RLIISPFSSSAPQFDDVKPLVSPVDKMAAETKMGISQQTLVSNQQKAKRITQYMAALTAT 75
R+ P + AP FD +KP V V + +++ LV N A + + LTA
Sbjct: 561 RVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDN---ADLLNLTASELTAL 617
Query: 76 IGG 78
IGG
Sbjct: 618 IGG 620
>pdb|3VLK|A Chain A, Crystal Structure Analysis Of The Ser305ala Variant Of
Katg From Haloarcula Marismortui
pdb|3VLK|B Chain B, Crystal Structure Analysis Of The Ser305ala Variant Of
Katg From Haloarcula Marismortui
pdb|3VLL|A Chain A, Crystal Structure Analysis Of The Ser305ala Variant Of
Katg From Haloarcula Marismortui Complexes With
Inhibitor Sha
pdb|3VLL|B Chain B, Crystal Structure Analysis Of The Ser305ala Variant Of
Katg From Haloarcula Marismortui Complexes With
Inhibitor Sha
Length = 737
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 RLIISPFSSSAPQFDDVKPLVSPVDKMAAETKMGISQQTLVSNQQKAKRITQYMAALTAT 75
R+ P + AP FD +KP V V + +++ LV N A + + LTA
Sbjct: 561 RVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDN---ADLLNLTASELTAL 617
Query: 76 IGG 78
IGG
Sbjct: 618 IGG 620
>pdb|3UW8|A Chain A, Crystal Structure Analysis Of The Ser305thr Variants Of
Katg From Haloarcula Marismortui
pdb|3UW8|B Chain B, Crystal Structure Analysis Of The Ser305thr Variants Of
Katg From Haloarcula Marismortui
Length = 737
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 RLIISPFSSSAPQFDDVKPLVSPVDKMAAETKMGISQQTLVSNQQKAKRITQYMAALTAT 75
R+ P + AP FD +KP V V + +++ LV N A + + LTA
Sbjct: 561 RVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDN---ADLLNLTASELTAL 617
Query: 76 IGG 78
IGG
Sbjct: 618 IGG 620
>pdb|1ITK|A Chain A, Crystal Structure Of Catalase-peroxidase From Haloarcula
Marismortui
pdb|1ITK|B Chain B, Crystal Structure Of Catalase-peroxidase From Haloarcula
Marismortui
Length = 731
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 RLIISPFSSSAPQFDDVKPLVSPVDKMAAETKMGISQQTLVSNQQKAKRITQYMAALTAT 75
R+ P + AP FD +KP V V + +++ LV N A + + LTA
Sbjct: 561 RVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDN---ADLLNLTASELTAL 617
Query: 76 IGG 78
IGG
Sbjct: 618 IGG 620
>pdb|3HHZ|K Chain K, Complex Of The Vesicular Stomatitis Virus Nucleocapsid And
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHZ|L Chain L, Complex Of The Vesicular Stomatitis Virus Nucleocapsid And
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHZ|M Chain M, Complex Of The Vesicular Stomatitis Virus Nucleocapsid And
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHZ|N Chain N, Complex Of The Vesicular Stomatitis Virus Nucleocapsid And
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHZ|O Chain O, Complex Of The Vesicular Stomatitis Virus Nucleocapsid And
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3PTO|A Chain A, Crystal Structure Of An Empty Vesicular Stomatitis Virus
Nucleocapsid Protein Complex
pdb|3PTO|B Chain B, Crystal Structure Of An Empty Vesicular Stomatitis Virus
Nucleocapsid Protein Complex
pdb|3PTO|C Chain C, Crystal Structure Of An Empty Vesicular Stomatitis Virus
Nucleocapsid Protein Complex
pdb|3PTO|D Chain D, Crystal Structure Of An Empty Vesicular Stomatitis Virus
Nucleocapsid Protein Complex
pdb|3PTO|E Chain E, Crystal Structure Of An Empty Vesicular Stomatitis Virus
Nucleocapsid Protein Complex
pdb|3PTX|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polya Complex
pdb|3PTX|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polya Complex
pdb|3PTX|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polya Complex
pdb|3PTX|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polya Complex
pdb|3PTX|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polya Complex
pdb|3PU0|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyc Complex
pdb|3PU0|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyc Complex
pdb|3PU0|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyc Complex
pdb|3PU0|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyc Complex
pdb|3PU0|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyc Complex
pdb|3PU1|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyg Complex
pdb|3PU1|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyg Complex
pdb|3PU1|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyg Complex
pdb|3PU1|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyg Complex
pdb|3PU1|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyg Complex
pdb|3PU4|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyu Complex
pdb|3PU4|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyu Complex
pdb|3PU4|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyu Complex
pdb|3PU4|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyu Complex
pdb|3PU4|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-Polyu Complex
Length = 421
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 206 TAGILFVYAVGSWASVYGLSIICALLPIFFVGLMLLMPESPQFHLKKNRVKQAKESLQWF 265
TAG+L+ YAVGS A L F VG P+ L N Q ++ ++W
Sbjct: 328 TAGLLYAYAVGSSAD---------LAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWL 378
>pdb|3PMK|A Chain A, Crystal Structure Of The Vesicular Stomatitis Virus Rna
Free NucleoproteinPHOSPHOPROTEIN COMPLEX
pdb|3PMK|B Chain B, Crystal Structure Of The Vesicular Stomatitis Virus Rna
Free NucleoproteinPHOSPHOPROTEIN COMPLEX
pdb|3PMK|C Chain C, Crystal Structure Of The Vesicular Stomatitis Virus Rna
Free NucleoproteinPHOSPHOPROTEIN COMPLEX
pdb|3PMK|D Chain D, Crystal Structure Of The Vesicular Stomatitis Virus Rna
Free NucleoproteinPHOSPHOPROTEIN COMPLEX
pdb|3PMK|E Chain E, Crystal Structure Of The Vesicular Stomatitis Virus Rna
Free NucleoproteinPHOSPHOPROTEIN COMPLEX
Length = 404
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 206 TAGILFVYAVGSWASVYGLSIICALLPIFFVGLMLLMPESPQFHLKKNRVKQAKESLQWF 265
TAG+L+ YAVGS A L F VG P+ L N Q ++ ++W
Sbjct: 311 TAGLLYAYAVGSSAD---------LAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWL 361
>pdb|2GIC|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-rna Complex
pdb|2GIC|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-rna Complex
pdb|2GIC|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-rna Complex
pdb|2GIC|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-rna Complex
pdb|2GIC|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid-rna Complex
pdb|2WYY|A Chain A, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|C Chain C, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|D Chain D, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|H Chain H, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|F Chain F, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|I Chain I, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|J Chain J, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|K Chain K, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|L Chain L, Cryoem Model Of The Vesicular Stomatitis Virus
pdb|2WYY|M Chain M, Cryoem Model Of The Vesicular Stomatitis Virus
Length = 422
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 206 TAGILFVYAVGSWASVYGLSIICALLPIFFVGLMLLMPESPQFHLKKNRVKQAKESLQWF 265
TAG+L+ YAVGS A L F VG P+ L N Q ++ ++W
Sbjct: 329 TAGLLYAYAVGSSAD---------LAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWL 379
>pdb|2QVJ|A Chain A, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid Protein Ser290trp Mutant
pdb|2QVJ|B Chain B, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid Protein Ser290trp Mutant
pdb|2QVJ|C Chain C, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid Protein Ser290trp Mutant
pdb|2QVJ|D Chain D, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid Protein Ser290trp Mutant
pdb|2QVJ|E Chain E, Crystal Structure Of A Vesicular Stomatitis Virus
Nucleocapsid Protein Ser290trp Mutant
pdb|3HHW|K Chain K, Complex Of A Vesicular Stomatitis Virus Empty Capsid With
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHW|L Chain L, Complex Of A Vesicular Stomatitis Virus Empty Capsid With
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHW|M Chain M, Complex Of A Vesicular Stomatitis Virus Empty Capsid With
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHW|N Chain N, Complex Of A Vesicular Stomatitis Virus Empty Capsid With
The Nucleocapsid-Binding Domain Of The Phosphoprotein
pdb|3HHW|O Chain O, Complex Of A Vesicular Stomatitis Virus Empty Capsid With
The Nucleocapsid-Binding Domain Of The Phosphoprotein
Length = 421
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 206 TAGILFVYAVGSWASVYGLSIICALLPIFFVGLMLLMPESPQFHLKKNRVKQAKESLQWF 265
TAG+L+ YAVGS A L F VG P+ L N Q ++ ++W
Sbjct: 328 TAGLLYAYAVGSSAD---------LAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWL 378
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
0.323 0.138 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,095,223
Number of Sequences: 62578
Number of extensions: 350297
Number of successful extensions: 667
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 660
Number of HSP's gapped (non-prelim): 28
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)