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= 030877
(170 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1KN9|A Chain A, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|B Chain B, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|C Chain C, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|D Chain D, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|3IIQ|A Chain A, Crystallographic Analysis Of Bacterial Signal Peptidase In
Ternary Complex With Arylomycin A2 And A Beta-Sultam
Inhibitor
pdb|3IIQ|B Chain B, Crystallographic Analysis Of Bacterial Signal Peptidase In
Ternary Complex With Arylomycin A2 And A Beta-Sultam
Inhibitor
Length = 249
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 109 KSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157
+ + T +VP G ++ GDN S DSR +G VP + GR IW
Sbjct: 179 QPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA-TAIW 226
>pdb|1T7D|A Chain A, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With A Lipopeptide Inhibitor
pdb|1T7D|B Chain B, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With A Lipopeptide Inhibitor
pdb|3S04|A Chain A, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With An Arylomycin Lipoglycopeptide
Antibiotic
pdb|3S04|B Chain B, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With An Arylomycin Lipoglycopeptide
Antibiotic
Length = 250
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 109 KSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157
+ + T +VP G ++ GDN S DSR +G VP + GR IW
Sbjct: 180 QPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA-TAIW 227
>pdb|1B12|A Chain A, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|B Chain B, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|C Chain C, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|D Chain D, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
Length = 248
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 109 KSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157
+ + T +VP G ++ GDN S DSR +G VP + GR IW
Sbjct: 178 QPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA-TAIW 225
>pdb|3DLB|A Chain A, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLB|B Chain B, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLH|A Chain A, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLH|B Chain B, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3F73|A Chain A, Alignment Of Guide-Target Seed Duplex Within An Argonaute
Silencing Complex
pdb|3F73|B Chain B, Alignment Of Guide-Target Seed Duplex Within An Argonaute
Silencing Complex
pdb|3HM9|A Chain A, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand
pdb|3HVR|A Chain A, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand With
Two Mg2+ At The Cleavage Site
pdb|3HVR|B Chain B, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand With
Two Mg2+ At The Cleavage Site
pdb|3HXM|A Chain A, Structure Of An Argonaute Complexed With Guide Dna And
Target Rna Duplex Containing Two Mismatches
Length = 685
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 93 RVIGMEGDRVSYVADPKSSDK 113
R+ G EG RV++VADPK K
Sbjct: 232 RLQGREGGRVAWVADPKDPRK 252
>pdb|3HO1|A Chain A, Crystal Structure Of T. Thermophilus Argonaute N546 Mutant
Protein Complexed With Dna Guide Strand And 12-Nt Rna
Target Strand
Length = 685
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 93 RVIGMEGDRVSYVADPKSSDK 113
R+ G EG RV++VADPK K
Sbjct: 232 RLQGREGGRVAWVADPKDPRK 252
>pdb|3HK2|A Chain A, Crystal Structure Of T. Thermophilus Argonaute N478 Mutant
Protein Complexed With Dna Guide Strand And 19-Nt Rna
Target Strand
pdb|3HK2|B Chain B, Crystal Structure Of T. Thermophilus Argonaute N478 Mutant
Protein Complexed With Dna Guide Strand And 19-Nt Rna
Target Strand
Length = 685
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 93 RVIGMEGDRVSYVADPKSSDK 113
R+ G EG RV++VADPK K
Sbjct: 232 RLQGREGGRVAWVADPKDPRK 252
>pdb|3HJF|A Chain A, Crystal Structure Of T. Thermophilus Argonaute E546 Mutant
Protein Complexed With Dna Guide Strand And 15-Nt Rna
Target Strand
Length = 685
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 93 RVIGMEGDRVSYVADPKSSDK 113
R+ G EG RV++VADPK K
Sbjct: 232 RLQGREGGRVAWVADPKDPRK 252
>pdb|3EU9|A Chain A, The Ankyrin Repeat Domain Of Huntingtin Interacting
Protein 14
pdb|3EU9|B Chain B, The Ankyrin Repeat Domain Of Huntingtin Interacting
Protein 14
pdb|3EU9|C Chain C, The Ankyrin Repeat Domain Of Huntingtin Interacting
Protein 14
Length = 240
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 4 RNQLSLFVTFAKEGFEKSLLVGKFFCCLHVVNTYVCTPALAY 45
+ LS+ V K G + SL+ G+ C+H+ + T +AY
Sbjct: 86 QGHLSMVVQLMKYGADPSLIDGEGCSCIHLAAQFGHTSIVAY 127
>pdb|1IRU|N Chain N, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
pdb|1IRU|2 Chain 2, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
Length = 219
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 101 RVSYVADPKSSDKFETVVVPQGHVWIEGDNIYESN 135
RV Y D +S ++F+T V + V IEG E+N
Sbjct: 174 RVLYYRDARSYNRFQTATVTEKGVEIEGPLSTETN 208
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 0.141 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,726,617
Number of Sequences: 62578
Number of extensions: 165193
Number of successful extensions: 268
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 255
Number of HSP's gapped (non-prelim): 13
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)