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= 020019
(332 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GHS|A Chain A, The Three-Dimensional Structures Of Two Plant Beta-Glucan
Endohydrolases With Distinct Substrate Specificities
pdb|1GHS|B Chain B, The Three-Dimensional Structures Of Two Plant Beta-Glucan
Endohydrolases With Distinct Substrate Specificities
Length = 306
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 263 LVVAGNPSARLVESSDGWETAAVVAKFSGPVHRLATAATVKDGRVYLNHMLGFGYPKKKH 322
L AG P+ ++V S GW +A A +G A T G +NH +G G PKK+
Sbjct: 217 LEKAGAPAVKVVVSESGWPSAGGFAASAG------NARTYNQG--LINH-VGGGTPKKRE 267
Query: 323 ALVEAVFS 330
AL +F+
Sbjct: 268 ALETYIFA 275
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
pdb|4DZS|B Chain B, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
Length = 357
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 4/92 (4%)
Query: 54 DSGRRFIVSFLDGGIGQVAVPDDYPPGTVLEEVTLVKDLELTGNGSLGLVLDHPRNRLLV 113
+ RF + LD IG + G L K L++ G+ + + + ++ +
Sbjct: 20 EESSRFADAVLDQYIGSIHSLCKDQHGCRF----LQKQLDILGSKAADAIFEETKDYTVE 75
Query: 114 VAADVFGNKYSAVAAYDLSTWNRLFLTQLSGP 145
+ D FGN +++T R+ LT++S P
Sbjct: 76 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSP 107
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 58 RFIVSFLDGGIGQV-AVPDDYPPGTVLEEVTLVKDLELTGNGSLGLVLDHPRNRLLVVAA 116
RF + LD IG + ++ D L+ K L++ G+ + + + ++ + +
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQ-----KQLDILGSKAADAIFEETKDYTVELMT 56
Query: 117 DVFGNKYSAVAAYDLSTWNRLFLTQLSGP 145
D FGN +++T R+ LT++S P
Sbjct: 57 DSFGNYLIQKLLEEVTTEQRIVLTKISSP 85
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
pdb|3BX3|B Chain B, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
Length = 335
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 58 RFIVSFLDGGIGQV-AVPDDYPPGTVLEEVTLVKDLELTGNGSLGLVLDHPRNRLLVVAA 116
RF + LD IG + ++ D L+ K L++ G+ + + + ++ + +
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQ-----KQLDILGSKAADAIFEETKDYTVELMT 56
Query: 117 DVFGNKYSAVAAYDLSTWNRLFLTQLSGP 145
D FGN +++T R+ LT++S P
Sbjct: 57 DSFGNYLIQKLLEEVTTEQRIVLTKISSP 85
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 58 RFIVSFLDGGIGQV-AVPDDYPPGTVLEEVTLVKDLELTGNGSLGLVLDHPRNRLLVVAA 116
RF + LD IG + ++ D L+ K L++ G+ + + + ++ + +
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQ-----KQLDILGSKAADAIFEETKDYTVELMT 56
Query: 117 DVFGNKYSAVAAYDLSTWNRLFLTQLSGP 145
D FGN +++T R+ LT++S P
Sbjct: 57 DSFGNYLIQKLLEEVTTEQRIVLTKISSP 85
>pdb|2C1X|A Chain A, Structure And Activity Of A Flavonoid 3-O
Glucosyltransferase Reveals The Basis For Plant Natural
Product Modification
pdb|2C1Z|A Chain A, Structure And Activity Of A Flavonoid 3-O
Glucosyltransferase Reveals The Basis For Plant Natural
Product Modification
pdb|2C9Z|A Chain A, Structure And Activity Of A Flavonoid 3-0
Glucosyltransferase Reveals The Basis For Plant Natural
Product Modification
Length = 456
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 217 IHTFSGNLFKIDIVDGVGEG--------EEIKLIRVAGGPLSFGDGLELLSPTKLVVAGN 268
+HT N+ DI DGV EG E+I+L A P SF G+ + + G
Sbjct: 57 MHTMQCNIKSYDISDGVPEGYVFAGRPQEDIELFTRA-APESFRQGMVM----AVAETGR 111
Query: 269 PSARLVESSDGWETAAVVAKF 289
P + LV + W A + A+
Sbjct: 112 PVSCLVADAFIWFAADMAAEM 132
>pdb|2I5E|A Chain A, Crystal Structure Of A Protein Of Unknown Function Mm2497
From Methanosarcina Mazei Go1, Probable
Nucleotidyltransferase
pdb|2I5E|B Chain B, Crystal Structure Of A Protein Of Unknown Function Mm2497
From Methanosarcina Mazei Go1, Probable
Nucleotidyltransferase
Length = 211
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 32 NPATHVYHYHSSSFFRECAKWDDSGRRFIVSFLDGGIGQVAVPDDYPPGTVLEEVTLVKD 91
NP+ + Y+ SSF C+ DSG+ F + D + GT ++E + +
Sbjct: 133 NPSKYRVKYYGSSFLTHCSIATDSGQDF------------EIYDSFXAGTDIDEPEDLVE 180
Query: 92 LELTGNGS 99
L + G G+
Sbjct: 181 LLIHGKGA 188
>pdb|1RWI|B Chain B, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
pdb|1RWI|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
pdb|1RWL|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
Length = 270
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 140 TQLSGPSDGKSCADDVTVDAEGNAYVTDVTGSKIWKV 176
TQ P G + D V VD GN YVTD +++ K+
Sbjct: 140 TQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKL 176
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
0.320 0.138 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,951,315
Number of Sequences: 62578
Number of extensions: 501544
Number of successful extensions: 1119
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1110
Number of HSP's gapped (non-prelim): 15
length of query: 332
length of database: 14,973,337
effective HSP length: 99
effective length of query: 233
effective length of database: 8,778,115
effective search space: 2045300795
effective search space used: 2045300795
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: 52 (24.6 bits)