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= 040165
(358 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|HH Chain h, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 133
Score = 34.7 bits (78), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 275 GVHSSWERLTKIDNDIMVRYHGSLVTLCTATGTDGGDEIIMINKWREFISCNLNERTLEE 334
G+ +SW R ID+ + ++ G + G+D + NK+++F+ N++E LE
Sbjct: 28 GLKTSWRRPKGIDSRVRRKFKGCTLMPNIGYGSDKKTRHYLPNKFKKFVVHNVSE--LEL 85
Query: 335 IYRPNFDWCETVSYTES 351
+ N +C +++ S
Sbjct: 86 LMMHNRTYCAEIAHNVS 102
>pdb|1MG4|A Chain A, Structure Of N-Terminal Doublecortin Domain From Dclk:
Wild Type Protein
Length = 113
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 38 DPKFALYRQKKQGEID--NNNTIHQRVLVLAISPDRLQSLHC----LTRCITELNFNFP 90
DP+F L +KK ++ N + + +V AISPDR +S LTR +++ N N P
Sbjct: 4 DPEFTLSSEKKAKKVRFYRNGDRYFKGIVYAISPDRFRSFEALLADLTRTLSD-NVNLP 61
>pdb|2ZKR|YY Chain y, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 135
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 276 VHSSWERLTKIDNDIMVRYHGSLVTLCTATGTDGGDEIIMINKWREFISCNLNERTLEEI 335
+ +W + IDN + R+ G ++ G++ + ++ + +R+F+ N+ E LE +
Sbjct: 31 IKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKE--LEVL 88
Query: 336 YRPNFDWCETVSYTES 351
N +C +++ S
Sbjct: 89 LMCNKSYCAEIAHNVS 104
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 282 RLTKIDNDIMVRYHGSLVT-----LCTATGTDGGDEIIMINKWREFISCNLNERTLEEIY 336
RL K D+MVRY G++ + A G DG D ++ +++ F S L+ + E+ Y
Sbjct: 846 RLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLV--EYQVFDSLRLSTKQFEKKY 903
Query: 337 R 337
R
Sbjct: 904 R 904
>pdb|4I78|A Chain A, Crystal Structure Of A Subtype H17 Hemagglutinin Homologue
From A/little Yellow-shouldered Bat/guatemala/060/2010
(h17n10)
pdb|4I78|B Chain B, Crystal Structure Of A Subtype H17 Hemagglutinin Homologue
From A/little Yellow-shouldered Bat/guatemala/060/2010
(h17n10)
Length = 328
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 21/89 (23%)
Query: 17 LPIKSLLRFKCVSKEWHCLISDPKFALYRQKKQGEIDNNNTIHQRVLVLAISPDRLQSLH 76
LP +S LR + LI+ P++ Y ++K+G+ + +L
Sbjct: 234 LPAQSTLRIESTGN----LIA-PEYGFYYKRKEGKG-------------GLMKSKLPISD 275
Query: 77 CLTRCIT---ELNFNFPFESIPNVIIGSC 102
C T+C T LN PF+++ IG+C
Sbjct: 276 CSTKCQTPLGALNSTLPFQNVHQQTIGNC 304
>pdb|3SZY|A Chain A, Crystal Structure Of Phosphonoacetate Hydrolase From
Sinorhizobium Meliloti 1021 In Apo Form
pdb|3SZZ|A Chain A, Crystal Structure Of Phosphonoacetate Hydrolase From
Sinorhizobium Meliloti 1021 In Complex With Acetate
pdb|3T00|A Chain A, Crystal Structure Of Phosphonoacetate Hydrolase From
Sinorhizobium Meliloti 1021 In Complex With Vanadate
pdb|3T01|A Chain A, Crystal Structure Of Phosphonoacetate Hydrolase From
Sinorhizobium Meliloti 1021 In Complex With
Phosphonoformate
Length = 427
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 109 ALHGCKDFFIYNPSTRAHKKLPDPDISLGSPYLYGFGYDSSTDDYKVLAVSCLRVLL 165
A+HG ++Y PST + DP L +P ++ YD+ V A LR LL
Sbjct: 85 AVHGICGNYLYEPSTGEEVMMNDPKF-LRAPTIFQAFYDAGARVAVVTAKDKLRALL 140
>pdb|3T02|A Chain A, Crystal Structure Of Phosphonoacetate Hydrolase From
Sinorhizobium Meliloti 1021 In Complex With
Phosphonoacetate
Length = 427
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 109 ALHGCKDFFIYNPSTRAHKKLPDPDISLGSPYLYGFGYDSSTDDYKVLAVSCLRVLL 165
A+HG ++Y PST + DP L +P ++ YD+ V A LR LL
Sbjct: 85 AVHGICGNYLYEPSTGEEVMMNDPKF-LRAPTIFQAFYDAGARVAVVTAKDKLRALL 140
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
0.324 0.140 0.459
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,838,920
Number of Sequences: 62578
Number of extensions: 503072
Number of successful extensions: 1097
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1096
Number of HSP's gapped (non-prelim): 7
length of query: 358
length of database: 14,973,337
effective HSP length: 100
effective length of query: 258
effective length of database: 8,715,537
effective search space: 2248608546
effective search space used: 2248608546
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: 52 (24.6 bits)