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= psy6932
(150 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 129 bits (323), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 62/118 (52%), Positives = 83/118 (70%), Gaps = 1/118 (0%)
Query: 1 MATIDTKKHTDVERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKY 60
MA + D +R++CIYPAY+N KKT+AEGRRIP +KAV+NPT +I DV S GL
Sbjct: 1 MACAAARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNV 60
Query: 61 HIE-NKLYPREISKEHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSR 117
+E NK+Y RE +++ RGR RVQLK +DGS FP+R++VML+ +IPKLK+R
Sbjct: 61 FLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTR 118
>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 = 124 bits (311), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 59/105 (56%), Positives = 78/105 (74%), Gaps = 1/105 (0%)
Query: 14 RWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREIS 72
R++CIYPAY+N KKT+AEGRRIP +KAV+NPT +I DV S GL +E NK+Y RE +
Sbjct: 2 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWN 61
Query: 73 KEHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSR 117
++ RGR RVQLK +DGS FP+R++VML+ +IPKLK+R
Sbjct: 62 RDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTR 106
>pdb|1L9A|A Chain A, Crystal Structure Of Srp19 In Complex With The S Domain
Of Signal Recognition Particle Rna
Length = 87
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 47/75 (62%), Gaps = 6/75 (8%)
Query: 16 VCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHI-ENKLYPREISKE 74
+ I+P+YI++KK+ EGR++P+ A++ P+ KDI+ L GL+ I +K YPR +
Sbjct: 1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPR----Q 56
Query: 75 HF-VRGRARVQLKND 88
H+ + GR V K +
Sbjct: 57 HWEIAGRVEVDYKGN 71
>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 = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 18 IYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHI-ENKLYPRE 70
I+P+YI++KK+ EGR++P+ A++ P+ KDI+ L GL+ I +K YPR+
Sbjct: 3 IWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQ 56
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 17 CIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIENKLYPR 69
++ ++ KK+ AEGRRIP+ AV N ++ + GLK+ E K YP+
Sbjct: 5 VVWTVNLDSKKSRAEGRRIPRRFAVPNVKLHELVEASKELGLKFRAEEKKYPK 57
>pdb|1BFO|A Chain A, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|C Chain C, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|E Chain E, Campath-1g Igg2b Rat Monoclonal Fab
pdb|1BFO|G Chain G, Campath-1g Igg2b Rat Monoclonal Fab
Length = 214
Score = 33.1 bits (74), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 3 TIDTKKHTDVERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPT---YKDIDDVLSTTGLK 59
TI + + DV + C+ +I+R +T G ++ +A PT + + L+T G
Sbjct: 74 TISSLQPEDVATYFCL--QHISRPRTFGTGTKLELKRANAAPTVSIFPPSTEQLATGGAS 131
Query: 60 Y-HIENKLYPREISKEHFVRGRAR 82
+ NK YPR+IS + + G R
Sbjct: 132 VVCLMNKFYPRDISVKWKIDGTER 155
>pdb|3DLU|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus.
pdb|3DLU|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus.
pdb|3DLU|C Chain C, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus.
pdb|3DLU|D Chain D, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus.
pdb|3DLV|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus.
pdb|3DLV|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins
Assembling The Ribonucleic Core Of The Signal
Recognition Particle From The Archaeon Pyrococcus
Furiosus
Length = 106
Score = 29.3 bits (64), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 17 CIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHI----ENKLYPR 69
++P+ ++ + + GR +P++ AV++P ++I V + LK+ + E+KL PR
Sbjct: 5 VVWPSELDSRLSRKYGRIVPRSIAVESPRVEEI--VRAAEELKFKVIRVEEDKLNPR 59
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
0.317 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,089,350
Number of Sequences: 62578
Number of extensions: 157793
Number of successful extensions: 310
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 301
Number of HSP's gapped (non-prelim): 14
length of query: 150
length of database: 14,973,337
effective HSP length: 90
effective length of query: 60
effective length of database: 9,341,317
effective search space: 560479020
effective search space used: 560479020
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)