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= 043522
(84 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 28.9 bits (63), Expect = 0.74, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 25 LHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVR 74
HYN PP + TG + KRRE R KR + +++ + VR
Sbjct: 378 FHYN-FPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVR 426
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 28.9 bits (63), Expect = 0.74, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 25 LHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVR 74
HYN PP + TG + KRRE R KR + +++ + VR
Sbjct: 378 FHYN-FPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVR 426
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 28.9 bits (63), Expect = 0.74, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 25 LHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVR 74
HYN PP + TG + KRRE R KR + +++ + VR
Sbjct: 384 FHYN-FPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVR 432
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 28.9 bits (63), Expect = 0.74, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 25 LHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVR 74
HYN PP + TG + KRRE R KR + +++ + VR
Sbjct: 384 FHYN-FPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVR 432
>pdb|3A79|A Chain A, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
pdb|3A7B|A Chain A, Crystal Structure Of Tlr2-Streptococcus Pneumoniae
Lipoteichoic Acid Complex
pdb|3A7C|A Chain A, Crystal Structure Of Tlr2-Pe-Dtpa Complex
Length = 580
Score = 28.1 bits (61), Expect = 1.4, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 9 KHQYYPVPDESRWPPELHYNMLPPIIIRT--TGRPQTKKRREADEN 52
++ ++P+PD +WP ++ + L IR T PQT + + N
Sbjct: 422 RNTFHPMPDSCQWPEKMRFLNLSSTGIRVVKTCIPQTLEVLDVSNN 467
>pdb|2Z81|A Chain A, Crystal Structure Of The Tlr1-tlr2 Heterodimer Induced By
Binding Of A Tri-acylated Lipopeptide
pdb|2Z82|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 549
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 9 KHQYYPVPDESRWPPELHYNMLPPIIIRT--TGRPQTKKRREADEN 52
++ ++P+PD +WP ++ + L IR T PQT + + N
Sbjct: 396 RNTFHPMPDSCQWPEKMRFLNLSSTGIRVVKTCIPQTLEVLDVSNN 441
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
0.315 0.131 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,728,761
Number of Sequences: 62578
Number of extensions: 89457
Number of successful extensions: 103
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 103
Number of HSP's gapped (non-prelim): 6
length of query: 84
length of database: 14,973,337
effective HSP length: 52
effective length of query: 32
effective length of database: 11,719,281
effective search space: 375016992
effective search space used: 375016992
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)