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= psy16987
(110 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JW0|C Chain C, E2~ubiquitin-Hect
pdb|3JW0|D Chain D, E2~ubiquitin-Hect
Length = 385
Score = 28.9 bits (63), Expect = 0.81, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 41 LGGTSVGQMFTNDFWGTPLSDPASHKSYRPLTTLTFRT 78
L G++ Q+FT + WG+P P +H S+ L + T
Sbjct: 326 LYGSNGPQLFTIEQWGSPEKLPRAHTSFNRLDLPPYET 363
>pdb|3JVZ|C Chain C, E2~ubiquitin-Hect
pdb|3JVZ|D Chain D, E2~ubiquitin-Hect
Length = 385
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 41 LGGTSVGQMFTNDFWGTPLSDPASHKSYRPLTTLTFRT 78
L G++ Q+FT + WG+P P +H ++ L + T
Sbjct: 326 LYGSNGPQLFTIEQWGSPEKLPRAHTAFNRLDLPPYET 363
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 46 VGQMFTNDFWGTPLSDPASHKSYRPLTTLTFR 77
V F N+ G P P+ H+S RPL TL R
Sbjct: 273 VATYFDNEIPGLP---PSKHRSGRPLRTLAQR 301
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 46 VGQMFTNDFWGTPLSDPASHKSYRPLTTLTFR 77
V F N+ G P P+ H+S RPL TL R
Sbjct: 273 VATYFDNEIPGLP---PSKHRSGRPLRTLAQR 301
>pdb|2ONI|A Chain A, Catalytic Domain Of The Human Nedd4-Like E3 Ligase
Length = 392
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 41 LGGTSVGQMFTNDFWGTPLSDPASHKSYRPLTTLTFRT 78
L G++ Q+FT + WG+P P +H + L + T
Sbjct: 341 LYGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYET 378
>pdb|2OR8|A Chain A, Tim-1
pdb|2OR8|B Chain B, Tim-1
Length = 116
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 56 GTPLSDPASHKSYRPLTTLTFRTVLGISSCVSSRLR-TILWEN 97
G P++ P ++ +YR +TT T G C SS + T++W N
Sbjct: 12 GHPVTLPCTYSTYRGITT----TCWGRGQCPSSACQNTLIWTN 50
>pdb|4H87|A Chain A, Crystal Structure Of A Fha Domain Of Kanadaptin
(Slc4a1ap) From Homo Sapiens At 1.55 A Resolution
pdb|4H87|B Chain B, Crystal Structure Of A Fha Domain Of Kanadaptin
(Slc4a1ap) From Homo Sapiens At 1.55 A Resolution
Length = 130
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 50 FTNDFWGTPLSDPASHKSYRPLTTLTFRTVLGISSCVSSRL 90
+ WG P + P S ++ + T L R++ G S C+ RL
Sbjct: 8 YQEPPWGGPATAPYSLETLKGGTILGTRSLKGTSYCLFGRL 48
>pdb|3O0H|A Chain A, Crystal Structure Of Glutathione Reductase From Bartonella
Henselae
pdb|3O0H|B Chain B, Crystal Structure Of Glutathione Reductase From Bartonella
Henselae
Length = 484
Score = 25.4 bits (54), Expect = 7.7, Method: Composition-based stats.
Identities = 26/117 (22%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 1 MTGRGVYSSVVLIAVG--VYFNSL--GGDLVHD-----DIVALARNQDVLGGTSVGQMFT 51
+TG + + +LIA G + NS G DL D+ L ++ ++GG +G F
Sbjct: 148 VTGERISAEKILIATGAKIVSNSAIKGSDLCLTSNEIFDLEKLPKSIVIVGGGYIGVEFA 207
Query: 52 NDFWGTPLSDPASHKSYRPLTTLTFRTVLGISSCVSSRLRTILWENFLSDTEHAKRC 108
N F G + H+ L + ++ + ++ +I++E +S + + C
Sbjct: 208 NIFHGLGVKTTLLHRGDLILRNFDYDLRQLLNDAMVAKGISIIYEATVSQVQSTENC 264
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
0.322 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,413,947
Number of Sequences: 62578
Number of extensions: 124931
Number of successful extensions: 245
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 10
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
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: 45 (21.9 bits)