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= 032659
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MFQ|B Chain B, Crystal Structure Analysis Of A Ternary S-Domain Complex
Of Human Signal Recognition Particle
pdb|1RY1|B Chain B, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
pdb|2GO5|B Chain B, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
pdb|2J37|B Chain B, Model Of Mammalian Srp Bound To 80s Rncs
Length = 108
Score = 100 bits (250), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 51/107 (47%), Positives = 69/107 (64%), Gaps = 4/107 (3%)
Query: 10 KWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYP---- 65
+++ +YP Y+N+KKTIAEGRRI SKA ENPT EI D C + + +E +K Y
Sbjct: 2 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWN 61
Query: 66 RDFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAELVPRHPNRTK 112
RD RGRVRV LK+EDG+ SRK +ML+ AE++P+ RT+
Sbjct: 62 RDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ 108
>pdb|1JID|A Chain A, Human Srp19 In Complex With Helix 6 Of Human Srp Rna
pdb|3KTV|B Chain B, Crystal Structure Of The Human Srp19S-Domain Srp Rna
Complex
pdb|3KTV|D Chain D, Crystal Structure Of The Human Srp19S-Domain Srp Rna
Complex
Length = 128
Score = 100 bits (249), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 51/107 (47%), Positives = 69/107 (64%), Gaps = 4/107 (3%)
Query: 10 KWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYP---- 65
+++ +YP Y+N+KKTIAEGRRI SKA ENPT EI D C + + +E +K Y
Sbjct: 14 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWN 73
Query: 66 RDFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAELVPRHPNRTK 112
RD RGRVRV LK+EDG+ SRK +ML+ AE++P+ RT+
Sbjct: 74 RDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ 120
>pdb|1L9A|A Chain A, Crystal Structure Of Srp19 In Complex With The S Domain
Of Signal Recognition Particle Rna
Length = 87
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 12 VILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQ- 70
+I++P YI+ KK+ EGR++ A E P+ +I + L + I DK YPR +
Sbjct: 1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEI 60
Query: 71 RGRVRV 76
GRV V
Sbjct: 61 AGRVEV 66
>pdb|1LNG|A Chain A, Crystal Structure Of The Srp19-7s.S Srp Rna Complex Of
M. Jannaschii
pdb|2V3C|A Chain A, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna
Complex Of M. Jannaschii
pdb|2V3C|B Chain B, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna
Complex Of M. Jannaschii
pdb|3NDB|A Chain A, Crystal Structure Of A Signal Sequence Bound To The
Signal Recognition Particle
Length = 87
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 12 VILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQ 70
+I++P YI+ KK+ EGR++ A E P+ +I + L + I DK YPR +
Sbjct: 1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWE 59
>pdb|1KVN|A Chain A, Solution Structure Of Protein Srp19 Of The Arhaeoglobus
Fulgidus Signal Recognition Particle, 10 Structures
pdb|1KVV|A Chain A, Solution Structure Of Protein Srp19 Of The Archaeoglobus
Fulgidus Signal Recognition Particle, Minimized Average
Structure
Length = 104
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 11/89 (12%)
Query: 13 ILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRG 72
+++ V ++SKK+ AEGRRI A N E+ + + L + E +K YP+ + + G
Sbjct: 5 VVWTVNLDSKKSRAEGRRIPRRFAVPNVKLHELVEASKELGLKFRAE-EKKYPKSWWEEG 63
Query: 73 RVRVMLKREDGTFVNPAISSRKQLMLHVA 101
G V ++ +LM+ +A
Sbjct: 64 ----------GRVVVEKRGTKTKLMIELA 82
>pdb|2V50|A Chain A, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|B Chain B, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|C Chain C, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|D Chain D, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|E Chain E, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|F Chain F, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
Length = 1052
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 57 AIEIDKAYPRDFMQRGRV-RVMLKREDGTFVNPAISSRKQLMLHVAELVPRHPNRTKKQE 115
+I +Y DF+ RGRV RV L+ +NP S+ + E+VP + T K E
Sbjct: 750 SIAWGSSYVNDFIDRGRVKRVYLQGRPDARMNPDDLSKWYVRNDKGEMVPFNAFATGKWE 809
Query: 116 PAS 118
S
Sbjct: 810 YGS 812
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 0.134 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,262,935
Number of Sequences: 62578
Number of extensions: 107574
Number of successful extensions: 273
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 6
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
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: 46 (22.3 bits)